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Electrical properties of molecular crystals

International Nuclear Information System (INIS)

Barraud, A.

1968-01-01

This literature survey summarizes the electrical properties of molecular crystals: molecular crystal structure, transport and excitation mechanisms of charge-carriers, and differences compared to inorganic semi-conductors. The main results concerning the electrical conductivity of the most-studied molecular crystals are presented, together with the optical and photo-electrical properties of these crystals. Finally the different types of electrical measurements used are reviewed, as well as the limits of each method. (author) [fr
Molecular semiconductors photoelectrical properties and solar cells

CERN Document Server

Rees, Ch

1985-01-01

During the past thirty years considerable efforts have been made to design the synthesis and the study of molecular semiconductors. Molecular semiconductors - and more generally molecular materials - involve interactions between individual subunits which can be separately synthesized. Organic and metallo-organic derivatives are the basis of most of the molecular materials. A survey of the literature on molecular semiconductors leaves one rather confused. It does seem to be very difficult to correlate the molecular structure of these semiconductors with their experimental electrical properties. For inorganic materials a simple definition delimits a fairly homogeneous family. If an inorganic material has a conductivity intermediate between that of an 12 1 1 3 1 1 insulator « 10- n- cm- ) and that of a metal (> 10 n- cm- ), then it is a semiconductor and will exhibit the characteristic properties of this family, such as junction formation, photoconductivity, and the photovoltaic effect. For molecular compounds,...
Molecular Properties through Polarizable Embedding

DEFF Research Database (Denmark)

Olsen, Jógvan Magnus Haugaard; Kongsted, Jacob

2011-01-01

We review the theory related to the calculation of electric and magnetic molecular properties through polarizable embedding. In particular, we derive the expressions for the response functions up to the level of cubic response within the density functional theory-based polarizable embedding (PE......-DFT) formalism. In addition, we discuss some illustrative applications related to the calculation of nuclear magnetic resonance parameters, nonlinear optical properties, and electronic excited states in solution....
Fluctuation Solution Theory Properties from Molecular Simulation

DEFF Research Database (Denmark)

Abildskov, Jens; Wedberg, R.; O’Connell, John P.

2013-01-01

The thermodynamic properties obtained in the Fluctuation Solution Theory are based on spatial integrals of molecular TCFs between component pairs in the mixture. Molecular simulation, via either MD or MC calculations, can yield these correlation functions for model inter- and intramolecular...
Transport properties of molecular junctions

CERN Document Server

Zimbovskaya, Natalya A

2013-01-01

A comprehensive overview of the physical mechanisms that control electron transport and the characteristics of metal-molecule-metal (MMM) junctions is presented. As far as possible, methods and formalisms presented elsewhere to analyze electron transport through molecules are avoided. This title introduces basic concepts—a description of the electron transport through molecular junctions—and briefly describes relevant experimental methods. Theoretical methods commonly used to analyze the electron transport through molecules are presented. Various effects that manifest in the electron transport through MMMs, as well as the basics of density-functional theory and its applications to electronic structure calculations in molecules are presented. Nanoelectronic applications of molecular junctions and similar systems are discussed as well. Molecular electronics is a diverse and rapidly growing field. Transport Properties of Molecular Junctions presents an up-to-date survey of the field suitable for researchers ...
Molecular simulations of hydrocarbon lubricants: Impact of molecular architecture on performance properties

Science.gov (United States)

Kioupis, Loukas I.

2000-07-01

With the increased power of modern computers, molecular modeling has been used widely and proven to be a valuable tool for elucidating the physical processes important in many industrial and engineering problems. Of particular interest to us is the rheology and physical chemistry of complex fluids, such as hydrocarbon lubricants and polymers. The goal is to provide qualitative and quantitative molecular-level explanations for the behavior of such fluids, and provide guidance in the development of new improved materials. For example, during the production of poly-α-olefin (PAO) synthetic lubricants, the number of the isomer skeletal structures that can be obtained is staggering. Which of the countless PAO isomers produce a lubricant with superior performance properties? How does it behave under different operational conditions of temperature, pressure, and shear rate? A fundamental understanding of the effect that molecular structure has on the oil's rheological and lubricant performance is first needed, in order to answer these questions. To serve this purpose, we have developed efficient molecular dynamics (MD) simulation programs, which utilize multiple time step algorithms and parallel computational techniques. This enables us to conduct simulations of typical PAO isomers and compute the viscosity, as well as several other dynamic and static properties, as a function of temperature, pressure, and shear rate. The key molecular mechanisms that determine important macroscopic properties, such as viscosity index, viscosity-pressure coefficient, traction coefficient, and shear thinning behavior are discussed. Based on this analysis, lubricant and traction fluid structures that have a high likelihood of having desirable properties are proposed. In addition, studies on simple alkane mixtures are presented, in an attempt to understand the more complex polydisperse lubricant fluids, their blends, and their interaction with additives.
Collective properties of evolving molecular quasispecies

Directory of Open Access Journals (Sweden)

Manrubia Susanna C

2007-07-01

Full Text Available Abstract Background RNA molecules, through their dual appearance as sequence and structure, represent a suitable model to study evolutionary properties of quasispecies. The essential ingredient in this model is the differentiation between genotype (molecular sequences which are affected by mutation and phenotype (molecular structure, affected by selection. This framework allows a quantitative analysis of organizational properties of quasispecies as they adapt to different environments, such as their robustness, the effect of the degeneration of the sequence space, or the adaptation under different mutation rates and the error threshold associated. Results We describe and analyze the structural properties of molecular quasispecies adapting to different environments both during the transient time before adaptation takes place and in the asymptotic state, once optimization has occurred. We observe a minimum in the adaptation time at values of the mutation rate relatively far from the phenotypic error threshold. Through the definition of a consensus structure, it is shown that the quasispecies retains relevant structural information in a distributed fashion even above the error threshold. This structural robustness depends on the precise shape of the secondary structure used as target of selection. Experimental results available for natural RNA populations are in qualitative agreement with our observations. Conclusion Adaptation time of molecular quasispecies to a given environment is optimized at values of the mutation rate well below the phenotypic error threshold. The optimal value results from a trade-off between diversity generation and fixation of advantageous mutants. The critical value of the mutation rate is a function not only of the sequence length, but also of the specific properties of the environment, in this case the selection pressure and the shape of the secondary structure used as target phenotype. Certain functional motifs of RNA
Molecular simulation of the thermophysical properties of N-functionalized alkylimidazoles.

Science.gov (United States)

Turner, C Heath; Cooper, Alex; Zhang, Zhongtao; Shannon, Matthew S; Bara, Jason E

2012-06-07

Molecular simulations are used to probe the thermophysical properties of a series of N-functionalized alkylimidazoles, ranging from N-methylimidazole to N-heptylimidazole. These compounds have been previously synthesized, and their solvation properties have been shown to be potentially useful for CO(2) capture from industrial sources. In this work, we use first-principles calculations to fit electrostatic charges to the molecular models, which are then used to perform a series of molecular dynamics simulations. Over a range of different temperatures, we benchmark the simulated densities and heat capacities against experimental measurements. Also, we predict the Henry's constants for CO(2) absorption and probe the solvents' structures using molecular simulation techniques, such as fractional free volume analysis and void distributions. We find that our simulations are able to closely reproduce the experimental benchmarks and add additional insight into the molecular structure of these fluids, with respect to their observed solvent properties.
Statistical analysis of coding for molecular properties in the olfactory bulb

Directory of Open Access Journals (Sweden)

Benjamin eAuffarth

2011-07-01

Full Text Available The relationship between molecular properties of odorants and neural activities is arguably one of the most important issues in olfaction and the rules governing this relationship are still not clear. In the olfactory bulb (OB, glomeruli relay olfactory information to second-order neurons which in turn project to cortical areas. We investigate relevance of odorant properties, spatial localization of glomerular coding sites, and size of coding zones in a dataset of 2-deoxyglucose images of glomeruli over the entire OB of the rat. We relate molecular properties to activation of glomeruli in the OB using a nonparametric statistical test and a support-vector machine classification study. Our method permits to systematically map the topographic representation of various classes of odorants in the OB. Our results suggest many localized coding sites for particular molecular properties and some molecular properties that could form the basis for a spatial map of olfactory information. We found that alkynes, alkanes, alkenes, and amines affect activation maps very strongly as compared to other properties and that amines, sulfur-containing compounds, and alkynes have small zones and high relevance to activation changes, while aromatics, alkanes, and carboxylics acid recruit very big zones in the dataset. Results suggest a local spatial encoding for molecular properties.
Synthesis of one-dimensional metal-containing insulated molecular wire with versatile properties directed toward molecular electronics materials.

Science.gov (United States)

Masai, Hiroshi; Terao, Jun; Seki, Shu; Nakashima, Shigeto; Kiguchi, Manabu; Okoshi, Kento; Fujihara, Tetsuaki; Tsuji, Yasushi

2014-02-05

We report, herein, the design, synthesis, and properties of new materials directed toward molecular electronics. A transition metal-containing insulated molecular wire was synthesized through the coordination polymerization of a Ru(II) porphyrin with an insulated bridging ligand of well-defined structure. The wire displayed not only high linearity and rigidity, but also high intramolecular charge mobility. Owing to the unique properties of the coordination bond, the interconversion between the monomer and polymer states was realized under a carbon monoxide atmosphere or UV irradiation. The results demonstrated a high potential of the metal-containing insulated molecular wire for applications in molecular electronics.
Molecular modeling of polycarbonate materials: Glass transition and mechanical properties

Science.gov (United States)

Palczynski, Karol; Wilke, Andreas; Paeschke, Manfred; Dzubiella, Joachim

2017-09-01

Linking the experimentally accessible macroscopic properties of thermoplastic polymers to their microscopic static and dynamic properties is a key requirement for targeted material design. Classical molecular dynamics simulations enable us to study the structural and dynamic behavior of molecules on microscopic scales, and statistical physics provides a framework for relating these properties to the macroscopic properties. We take a first step toward creating an automated workflow for the theoretical prediction of thermoplastic material properties by developing an expeditious method for parameterizing a simple yet surprisingly powerful coarse-grained bisphenol-A polycarbonate model which goes beyond previous coarse-grained models and successfully reproduces the thermal expansion behavior, the glass transition temperature as a function of the molecular weight, and several elastic properties.
Amino acid properties conserved in molecular evolution.

Directory of Open Access Journals (Sweden)

Witold R Rudnicki

Full Text Available That amino acid properties are responsible for the way protein molecules evolve is natural and is also reasonably well supported both by the structure of the genetic code and, to a large extent, by the experimental measures of the amino acid similarity. Nevertheless, there remains a significant gap between observed similarity matrices and their reconstructions from amino acid properties. Therefore, we introduce a simple theoretical model of amino acid similarity matrices, which allows splitting the matrix into two parts - one that depends only on mutabilities of amino acids and another that depends on pairwise similarities between them. Then the new synthetic amino acid properties are derived from the pairwise similarities and used to reconstruct similarity matrices covering a wide range of information entropies. Our model allows us to explain up to 94% of the variability in the BLOSUM family of the amino acids similarity matrices in terms of amino acid properties. The new properties derived from amino acid similarity matrices correlate highly with properties known to be important for molecular evolution such as hydrophobicity, size, shape and charge of amino acids. This result closes the gap in our understanding of the influence of amino acids on evolution at the molecular level. The methods were applied to the single family of similarity matrices used often in general sequence homology searches, but it is general and can be used also for more specific matrices. The new synthetic properties can be used in analyzes of protein sequences in various biological applications.
MOlecular MAterials Property Prediction Package (MOMAP) 1.0: a software package for predicting the luminescent properties and mobility of organic functional materials

Science.gov (United States)

Niu, Yingli; Li, Wenqiang; Peng, Qian; Geng, Hua; Yi, Yuanping; Wang, Linjun; Nan, Guangjun; Wang, Dong; Shuai, Zhigang

2018-04-01

MOlecular MAterials Property Prediction Package (MOMAP) is a software toolkit for molecular materials property prediction. It focuses on luminescent properties and charge mobility properties. This article contains a brief descriptive introduction of key features, theoretical models and algorithms of the software, together with examples that illustrate the performance. First, we present the theoretical models and algorithms for molecular luminescent properties calculation, which includes the excited-state radiative/non-radiative decay rate constant and the optical spectra. Then, a multi-scale simulation approach and its algorithm for the molecular charge mobility are described. This approach is based on hopping model and combines with Kinetic Monte Carlo and molecular dynamics simulations, and it is especially applicable for describing a large category of organic semiconductors, whose inter-molecular electronic coupling is much smaller than intra-molecular charge reorganisation energy.
Molecular and solid-state properties of tris-(8-hydroxyquinolate)-aluminum

International Nuclear Information System (INIS)

Martin, Richard L.; Kress, Joel D.; Campbell, I. H.; Smith, D. L.

2000-01-01

We use a hybrid density-functional-theory approach to calculate ground-state electronic properties and a time-dependent density-functional-theory approach to investigate the excited state electronic properties of molecular tris-(8-hydroxyquinolate)-aluminum, Alq. The calculated molecular results are compared with measurements on dense solid-state films of Alq. We specifically consider: the optical absorption spectrum near the fundamental absorption threshold, the ionization potential, the single-particle energy gap, the static dielectric constant, and the electric-field dependence of the electron mobility. We find that the molecular calculations can describe the optical absorption spectrum near the fundamental absorption threshold without significant corrections for solid-state effects. The energies of the triplet excited states are computed and the lowest triplet is found to lie 0.64 eV below the lowest excited singlet state. In contrast, large dielectric corrections must be included for the molecular calculations to describe the ionization potential and single-particle energy gap. When these dielectric corrections are made, using the calculated molecular polarizability, which accurately gives the measured static dielectric constant, both the ionization potential and single-particle energy gap are well described. The calculated molecular dipole moment can be used to interpret the electric-field dependence of the electron mobility. The solid-state properties, determined from the molecular calculations, are then used in a device model to describe the measured current-voltage characteristics in Alq diodes. (c) 2000 The American Physical Society
Molecular simulation studies on thermophysical properties with application to working fluids

CERN Document Server

Raabe, Gabriele

2017-01-01

This book discusses the fundamentals of molecular simulation, starting with the basics of statistical mechanics and providing introductions to Monte Carlo and molecular dynamics simulation techniques. It also offers an overview of force-field models for molecular simulations and their parameterization, with a discussion of specific aspects. The book then summarizes the available know-how for analyzing molecular simulation outputs to derive information on thermophysical and structural properties. Both the force-field modeling and the analysis of simulation outputs are illustrated by various examples. Simulation studies on recently introduced HFO compounds as working fluids for different technical applications demonstrate the value of molecular simulations in providing predictions for poorly understood compounds and gaining a molecular-level understanding of their properties. This book will prove a valuable resource to researchers and students alike.
Molecular clips based on propanediurea : synthesis and physical properties

NARCIS (Netherlands)

Jansen, Robertus Johannes

2002-01-01

This thesis describes the synthesis and physical properties of a series of molecular clips derived from the concave molecule propanediurea. These molecular clips are cavity-containing receptors that can bind a variety of aromatic guests. This binding is a result of hydrogen bonding and pi-pi
Electronic transport properties of phenylacetylene molecular junctions

International Nuclear Information System (INIS)

Liu Wen; Cheng Jie; Yan Cui-Xia; Li Hai-Hong; Wang Yong-Juan; Liu De-Sheng

2011-01-01

Electronic transport properties of a kind of phenylacetylene compound— (4-mercaptophenyl)-phenylacetylene are calculated by the first-principles method in the framework of density functional theory and the nonequilibrium Green's function formalism. The molecular junction shows an obvious rectifying behaviour at a bias voltage larger than 1.0 V. The rectification effect is attributed to the asymmetry of the interface contacts. Moreover, at a bias voltage larger than 2.0 V, which is not referred to in a relevant experiment [Fang L, Park J Y, Ma H, Jen A K Y and Salmeron M 2007 Langmuir 23 11522], we find a negative differential resistance phenomenon. The negative differential resistance effect may originate from the change of the delocalization degree of the molecular orbitals induced by the bias. (condensed matter: electronic structure, electrical, magnetic, and optical properties)
Synthesis and properties of ionic polyurethane dispersions: influence of polyol molecular weight

International Nuclear Information System (INIS)

Valipour Ebrahimi, M.; Barikani, M.; Mohammad Seyed Mohaghegh, S.

2006-01-01

A series of water dispersible polyurethanes containing carboxylate anion as the hydrophilic pendant group were prepared from toluene diisocyanate (TDI), 1,4- butanediol (1,4-BDO), dimethylol propionic acid and different molecular weight of polytetramethylene glycol . IR Spectroscopy was used to check the end of polymerization reaction and characterization of polymer. The effect of polytetramethylene glycol molecular weight was studied on the particle size distribution, contact angle, and mechanical and thermal properties of the emulsion-cast films. Average particle size of prepared polyurethane emulsions decreases with increasing the polytetramethylene glycol molecular weight. Tensile strength and hardness decrease and elongation-at-break and contact angle increase with increase of the polytetramethylene glycol molecular weight. Thermal property and thermal stability are also effected by variation of polytetramethylene glycol molecular weight. The thermal stability increases with increasing polytetramethylene glycol molecular weight. Glass transition temperature (T g ) moved toward the lower temperatures by increasing molecular weight of the polyol. Decrease in T g and tensile properties are interpreted in terms of the decrease in hard segments and the increase in chain flexibility and phase separation in high molecular weight polytetramethylene glycol based polyurethane
Hydration effect on the electronic transport properties of oligomeric phenylene ethynylene molecular junctions

International Nuclear Information System (INIS)

Zong-Liang, Li; Huai-Zhi, Li; Yong, Ma; Guang-Ping, Zhang; Chuan-Kui, Wang

2010-01-01

A first-principles computational method based on the hybrid density functional theory is developed to simulate the electronic transport properties of oligomeric phenylene ethynylene molecular junctions with H 2 O molecules accumulated in the vicinity as recently reported by Na et al. [Nanotechnology 18 424001 (2007)]. The numerical results show that the hydrogen bonds between the oxygen atoms of the oligomeric phenylene ethynylene molecule and H 2 O molecules result in the localisation of the molecular orbitals and lead to the lower transition peaks. The H 2 O molecular chains accumulated in the vicinity of the molecular junction can not only change the electronic structure of the molecular junctions, but also open additional electronic transport pathways. The obvious influence of H 2 O molecules on the electronic structure of the molecular junction and its electronic transport properties is thus demonstrated. (condensed matter: electronic structure, electrical, magnetic, and optical properties)
Understanding the Synthesis and Properties of Molecular Silver Nanoparticles

Science.gov (United States)

Ashenfelter, Brian A.

Molecular nanoparticles have emerged as an interesting class of materials whose atomically precise structures and discrete properties set them apart from their larger counterparts. Molecular silver nanoparticles are of particular interest because they provide a host of advantages as optical materials for possible use in sensing and imaging applications. However, relatively little is known about molecular silver nanoparticles including the details of their formation and their optical and mechanical properties. Size control remains a longstanding challenge in the production of glutathionate (SG) protected silver nanoparticles. Singular Ag:SG nanoparticle products have been difficult to obtain directly, but size focusing of larger distributions through attrition has been found to lead to useful isolation of particular species. Here, we present a methodology for controlling the size of Ag:SG molecular nanoparticles that leverages the stability of the most robust species. These results were then used to develop a facile approach for achieving two of the most stable species in the Ag:SG system. Molecular metal nanoparticles are known to be much more fluorescent than larger plasmonic nanoparticles, however the nature and origin of this fluorescence are not fully understood. Fluorescence can originate from either the quantum states within the metal core or mixed ligand states at the inorganic-organic interface. We have presented compelling evidence that fluorescence from molecular silver glutathionate nanoparticles has its origin in interfacial electronic states. Fluorescence spectra were found to be independent of size, with very similar wavelength and bandwidth, although the quantum yield was not. Excitation spectra indicated that the strongest fluorescence had its origin in that part of the spectrum that is dominated by ligand-related states. Further, excitations to strictly core states and to higher lying d-band states had little to no contribution to the fluorescence

Machine learning for the structure-energy-property landscapes of molecular crystals.

Science.gov (United States)

Musil, Félix; De, Sandip; Yang, Jack; Campbell, Joshua E; Day, Graeme M; Ceriotti, Michele

2018-02-07

Molecular crystals play an important role in several fields of science and technology. They frequently crystallize in different polymorphs with substantially different physical properties. To help guide the synthesis of candidate materials, atomic-scale modelling can be used to enumerate the stable polymorphs and to predict their properties, as well as to propose heuristic rules to rationalize the correlations between crystal structure and materials properties. Here we show how a recently-developed machine-learning (ML) framework can be used to achieve inexpensive and accurate predictions of the stability and properties of polymorphs, and a data-driven classification that is less biased and more flexible than typical heuristic rules. We discuss, as examples, the lattice energy and property landscapes of pentacene and two azapentacene isomers that are of interest as organic semiconductor materials. We show that we can estimate force field or DFT lattice energies with sub-kJ mol -1 accuracy, using only a few hundred reference configurations, and reduce by a factor of ten the computational effort needed to predict charge mobility in the crystal structures. The automatic structural classification of the polymorphs reveals a more detailed picture of molecular packing than that provided by conventional heuristics, and helps disentangle the role of hydrogen bonded and π-stacking interactions in determining molecular self-assembly. This observation demonstrates that ML is not just a black-box scheme to interpolate between reference calculations, but can also be used as a tool to gain intuitive insights into structure-property relations in molecular crystal engineering.
Electronic properties of single-molecule junction: Effect of the molecular distortion

International Nuclear Information System (INIS)

Gao, W.; Zhao, M.; Jiang, Q.

2009-01-01

For a model system consisting of a benzenedithio (BDT) molecule sandwiched between two Au plates, the electronic properties as a function of different BDT geometry are investigated using density functional theory. The distorted BDT structures are got through stretching the electrode distance. The corresponding electronic properties, including the spatial distribution of the frontier orbits, the gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital levels and density of states at the Fermi energy are determined. It reveals that the molecular distortion essentially determines electronic structures. The result should be beneficial to understand the stress-dependent or structure-dependent transport mechanism of electrons of the BDT junction.
Physical Properties of Low-Molecular Weight Polydimethylsiloxane Fluids

Energy Technology Data Exchange (ETDEWEB)

Roberts, Christine Cardinal [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Graham, Alan [Univ. of Colorado, Denver, CO (United States); Nemer, Martin [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Phinney, Leslie M. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Garcia, Robert M. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Soehnel, Melissa Marie [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Stirrup, Emily Kate [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

2017-02-01

Physical property measurements including viscosity, density, thermal conductivity, and heat capacity of low-molecular weight polydimethylsiloxane (PDMS) fluids were measured over a wide temperature range (-50°C to 150°C when possible). Properties of blends of 1 cSt and 20 cSt PDMS fluids were also investigated. Uncertainties in the measurements are cited. These measurements will provide greater fidelity predictions of environmental sensing device behavior in hot and cold environments.
Ab initio study of structural and mechanical property of solid molecular hydrogens

Science.gov (United States)

Ye, Yingting; Yang, Li; Yang, Tianle; Nie, Jinlan; Peng, Shuming; Long, Xinggui; Zu, Xiaotao; Du, Jincheng

2015-06-01

Ab initio calculations based on density functional theory (DFT) were performed to investigate the structural and the elastic properties of solid molecular hydrogens (H2). The influence of molecular axes of H2 on structural relative stabilities of hexagonal close-packed (hcp) and face-centered cubic (fcc) structured hydrogen molecular crystals were systematically investigated. Our results indicate that for hcp structures, disordered hydrogen molecule structure is more stable, while for fcc structures, Pa3 hydrogen molecular crystal is most stable. The cohesive energy of fcc H2 crystal was found to be lower than hcp. The mechanical properties of fcc and hcp hydrogen molecular crystals were obtained, with results consistent with previous theoretical calculations. In addition, the effects of zero point energy (ZPE) and van der Waals (vdW) correction on the cohesive energy and the stability of hydrogen molecular crystals were systematically studied and discussed.
Effect of molecular weight distribution on e-beam exposure properties of polystyrene

International Nuclear Information System (INIS)

Dey, Ripon Kumar; Cui Bo

2013-01-01

Polystyrene is a negative electron beam resist whose exposure properties can be tuned simply by using different molecular weights (Mw). Most previous studies have used monodisperse polystyrene with a polydispersity index (PDI) of less than 1.1 in order to avoid any uncertainties. Here we show that despite the fact that polystyrene’s sensitivity is inversely proportional to its Mw, no noticeable effect of very broad molecular weight distribution on sensitivity, contrast and achievable resolution is observed. It is thus unnecessary to use the costly monodisperse polystyrene for electron beam lithography. Since the polydispersity is unknown for general purpose polystyrene, we simulated a high PDI polystyrene by mixing in a 1:1 weight ratio two polystyrene samples with Mw of 170 and 900 kg mol −1 for the high Mw range, and 2.5 and 13 kg mol −1 for the low Mw range. The exposure property of the mixture resembles that of a monodisperse polystyrene with similar number averaged molecular weight (Mn)-bar, which indicates that it is (Mn)-bar rather than (Mw)-bar (weight averaged molecular weight) that dominates the exposure properties of polystyrene resist. This also implies that polystyrene of a certain molecular weight can be simulated by a mixture of two polystyrenes having different molecular weights. (paper)
Influence of molecular weight on the fracture properties of aliphatic polyketone terpolymers

NARCIS (Netherlands)

Zuiderduin, W.C.J.; Homminga, D.S.; Homminga, D.S.; Huetink, Han; Gaymans, R.J.

2003-01-01

The influence of polymer molecular weight on the mechanical properties of aliphatic polyketones was investigated. The molecular weight varied from 100,000 to 300,000 g mol21. The crystallinity was found to be independent of polymer molecular weight, as was the glass transition temperature. The yield
Nonlinear and Nonsymmetric Single-Molecule Electronic Properties Towards Molecular Information Processing.

Science.gov (United States)

Tamaki, Takashi; Ogawa, Takuji

2017-09-05

This review highlights molecular design for nonlinear and nonsymmetric single-molecule electronic properties such as rectification, negative differential resistance, and switching, which are important components of future single-molecule information processing devices. Perspectives on integrated "molecular circuits" are also provided. Nonlinear and nonsymmetric single-molecule electronics can be designed by utilizing (1) asymmetric molecular cores, (2) asymmetric anchoring groups, (3) an asymmetric junction environment, and (4) asymmetric electrode materials. This review mainly focuses on the design of molecular cores.
Property Integration - A New Approach for Simultaneous Solution of Process and Molecular Design Problems

DEFF Research Database (Denmark)

The objective of this paper is to introduce the new concept of property integration. It is based on tracking and integrating properties throughout the process. This is made possible by exploiting the unique features at the interface of process and molecular design. Recently developed clustering...... concepts are employed to identify optimal properties without commitment to specific species. Subsequently, group contribution methods and molecular design techniques are employed to solve the reverse property prediction problem to design molecules possessing the optimal properties....
Electrical properties of molecular crystals; Proprietes electriques des cristaux moleculaires

Energy Technology Data Exchange (ETDEWEB)

Barraud, A [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

1968-07-01

This literature survey summarizes the electrical properties of molecular crystals: molecular crystal structure, transport and excitation mechanisms of charge-carriers, and differences compared to inorganic semi-conductors. The main results concerning the electrical conductivity of the most-studied molecular crystals are presented, together with the optical and photo-electrical properties of these crystals. Finally the different types of electrical measurements used are reviewed, as well as the limits of each method. (author) [French] Cette etude bibliographique resume les proprietes electriques des cristaux moleculaires: structure des cristaux moleculaires, mecanismes de transport et d'excitation des porteurs de charge et differences avec les semiconducteurs mineraux. Les principaux resultats sur la conductibilite electrique des cristaux moleculaires les plus etudies y sont exposes, ainsi que les proprietes optiques et photoelectriques de ces cristaux. Enfin les differents types de mesures electriques utilisees sont passees en revue ainsi que les limites de chaque methode. (auteur)
Electrical properties of molecular crystals; Proprietes electriques des cristaux moleculaires

Energy Technology Data Exchange (ETDEWEB)

Barraud, A. [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

1968-07-01

This literature survey summarizes the electrical properties of molecular crystals: molecular crystal structure, transport and excitation mechanisms of charge-carriers, and differences compared to inorganic semi-conductors. The main results concerning the electrical conductivity of the most-studied molecular crystals are presented, together with the optical and photo-electrical properties of these crystals. Finally the different types of electrical measurements used are reviewed, as well as the limits of each method. (author) [French] Cette etude bibliographique resume les proprietes electriques des cristaux moleculaires: structure des cristaux moleculaires, mecanismes de transport et d'excitation des porteurs de charge et differences avec les semiconducteurs mineraux. Les principaux resultats sur la conductibilite electrique des cristaux moleculaires les plus etudies y sont exposes, ainsi que les proprietes optiques et photoelectriques de ces cristaux. Enfin les differents types de mesures electriques utilisees sont passees en revue ainsi que les limites de chaque methode. (auteur)
Spin-polarized transport properties of a pyridinium-based molecular spintronics device

Science.gov (United States)

Zhang, J.; Xu, B.; Qin, Z.

2018-05-01

By applying a first-principles approach based on non-equilibrium Green's functions combined with density functional theory, the transport properties of a pyridinium-based "radical-π-radical" molecular spintronics device are investigated. The obvious negative differential resistance (NDR) and spin current polarization (SCP) effect, and abnormal magnetoresistance (MR) are obtained. Orbital reconstruction is responsible for novel transport properties such as that the MR increases with bias and then decreases and that the NDR being present for both parallel and antiparallel magnetization configurations, which may have future applications in the field of molecular spintronics.
Using molecular mechanics to predict bulk material properties of fibronectin fibers.

Directory of Open Access Journals (Sweden)

Mark J Bradshaw

Full Text Available The structural proteins of the extracellular matrix (ECM form fibers with finely tuned mechanical properties matched to the time scales of cell traction forces. Several proteins such as fibronectin (Fn and fibrin undergo molecular conformational changes that extend the proteins and are believed to be a major contributor to the extensibility of bulk fibers. The dynamics of these conformational changes have been thoroughly explored since the advent of single molecule force spectroscopy and molecular dynamics simulations but remarkably, these data have not been rigorously applied to the understanding of the time dependent mechanics of bulk ECM fibers. Using measurements of protein density within fibers, we have examined the influence of dynamic molecular conformational changes and the intermolecular arrangement of Fn within fibers on the bulk mechanical properties of Fn fibers. Fibers were simulated as molecular strands with architectures that promote either equal or disparate molecular loading under conditions of constant extension rate. Measurements of protein concentration within micron scale fibers using deep ultraviolet transmission microscopy allowed the simulations to be scaled appropriately for comparison to in vitro measurements of fiber mechanics as well as providing estimates of fiber porosity and water content, suggesting Fn fibers are approximately 75% solute. Comparing the properties predicted by single molecule measurements to in vitro measurements of Fn fibers showed that domain unfolding is sufficient to predict the high extensibility and nonlinear stiffness of Fn fibers with surprising accuracy, with disparately loaded fibers providing the best fit to experiment. This work shows the promise of this microstructural modeling approach for understanding Fn fiber properties, which is generally applicable to other ECM fibers, and could be further expanded to tissue scale by incorporating these simulated fibers into three dimensional
Molecular structure based property modeling: Development/ improvement of property models through a systematic property-data-model analysis

DEFF Research Database (Denmark)

Hukkerikar, Amol Shivajirao; Sarup, Bent; Sin, Gürkan

2013-01-01

models. To make the property-data-model analysis fast and efficient, an approach based on the “molecular structure similarity criteria” to identify molecules (mono-functional, bi-functional, etc.) containing specified set of structural parameters (that is, groups) is employed. The method has been applied...
Dynamical photo-induced electronic properties of molecular junctions

Science.gov (United States)

Beltako, K.; Michelini, F.; Cavassilas, N.; Raymond, L.

2018-03-01

Nanoscale molecular-electronic devices and machines are emerging as promising functional elements, naturally flexible and efficient, for next-generation technologies. A deeper understanding of carrier dynamics in molecular junctions is expected to benefit many fields of nanoelectronics and power devices. We determine time-resolved charge current flowing at the donor-acceptor interface in molecular junctions connected to metallic electrodes by means of quantum transport simulations. The current is induced by the interaction of the donor with a Gaussian-shape femtosecond laser pulse. Effects of the molecular internal coupling, metal-molecule tunneling, and light-donor coupling on photocurrent are discussed. We then define the time-resolved local density of states which is proposed as an efficient tool to describe the absorbing molecule in contact with metallic electrodes. Non-equilibrium reorganization of hybridized molecular orbitals through the light-donor interaction gives rise to two phenomena: the dynamical Rabi shift and the appearance of Floquet-like states. Such insights into the dynamical photoelectronic structure of molecules are of strong interest for ultrafast spectroscopy and open avenues toward the possibility of analyzing and controlling the internal properties of quantum nanodevices with pump-push photocurrent spectroscopy.
The Atom in a Molecule: Implications for Molecular Structure and Properties

Science.gov (United States)

2016-05-23

Briefing Charts 3. DATES COVERED (From - To) 01 February 2016 – 23 May 2016 4. TITLE AND SUBTITLE The atom in a molecule: Implications for molecular...For presentation at American Physical Society - Division of Atomic , Molecular, and Optical Physics (May 2016) PA Case Number: #16075; Clearance Date...10 Energy (eV) R C--H (au) R C--H(au) The Atom in a Molecule: Implications for Molecular Structures and Properties P. W. Langhoff, Chemistry
Molecular mechanisms in compatibility and mechanical properties of Polyacrylamide/Polyvinyl alcohol blends.

Science.gov (United States)

Wei, Qinghua; Wang, Yanen; Che, Yu; Yang, Mingming; Li, Xinpei; Zhang, Yingfeng

2017-01-01

The objectives of this study were to develop a computational model based on molecular dynamics technique to investigate the compatibility and mechanical properties of Polyacrylamide (PAM)/Polyvinyl alcohol (PVA) blends. Five simulation models of PAM/PVA with different composition ratios (4/0, 3/1, 2/2, 1/3, 0/4) were constructed and simulated by using molecular dynamics (MD) simulation. The interaction mechanisms of molecular chains in PAM/PVA blend system were elaborated from the aspects of the compatibility, mechanical properties, binding energy and pair correlation function, respectively. The computed values of solubility parameters for PAM and PVA indicate PAM has a good miscibility with PVA. The results of the static mechanical analysis, based on the equilibrium structures of blends with differing component ratios, shows us that the elastic coefficient, engineering modulus, and ductility are increased with the addition of PVA content, which is 4/0 PAM/PVAPVAPVAPVAPVA. Moreover, binding energy results indicate that a stronger interaction exists among PVA molecular chains comparing with PAM molecular chains, which is why the mechanical properties of blend system increasing with the addition of PVA content. Finally, the results of pair correlation functions (PCFs) between polar functional groups and its surrounding hydrogen atoms, indicated they interact with each other mainly by hydrogen bonds, and the strength of three types of polar functional groups has the order of O(-OH)>O(-C=O)>N(-NH 2 ). This further elaborates the root reason why the mechanical properties of blend system increase with the addition of PVA content. Copyright © 2016 Elsevier Ltd. All rights reserved.
Unexpected Molecular Sieving Properties of Zeolitic Imidazolate Framework-8

KAUST Repository

Zhang, Chen; Lively, Ryan P.; Zhang, Ke; Johnson, Justin R.; Karvan, Oguz; Koros, William J.

2012-01-01

We studied molecular sieving properties of zeolitic imidazolate framework-8 (ZIF-8) by estimating the thermodynamically corrected diffusivities of probe molecules at 35 °C. From helium (2.6 Å) to iso-C 4H 10 (5.0 Å), the corrected diffusivity drops 14 orders of magnitude. Our results further suggest that the effective aperture size of ZIF-8 for molecular sieving is in the range of 4.0 to 4.2 Å, which is significantly larger than the XRD-derived value (3.4 Å) and between the well-known aperture size of zeolite 4A (3.8 Å) and 5A (4.3 Å). Interestingly, because of aperture flexibility, the studied C 4 hydrocarbon molecules that are larger than this effective aperture size still adsorb in the micropores of ZIF-8 with kinetic selectivities for iso-C 4H 8/iso-C 4H 10 of 180 and n-C 4H 10/iso-C 4H 10 of 2.5 × 10 6. These unexpected molecular sieving properties open up new opportunities for ZIF materials for separations that cannot be economically achieved by traditional microporous adsorbents such as synthetic zeolites. © 2012 American Chemical Society.
Unexpected Molecular Sieving Properties of Zeolitic Imidazolate Framework-8

KAUST Repository

Zhang, Chen

2012-08-16

We studied molecular sieving properties of zeolitic imidazolate framework-8 (ZIF-8) by estimating the thermodynamically corrected diffusivities of probe molecules at 35 °C. From helium (2.6 Å) to iso-C 4H 10 (5.0 Å), the corrected diffusivity drops 14 orders of magnitude. Our results further suggest that the effective aperture size of ZIF-8 for molecular sieving is in the range of 4.0 to 4.2 Å, which is significantly larger than the XRD-derived value (3.4 Å) and between the well-known aperture size of zeolite 4A (3.8 Å) and 5A (4.3 Å). Interestingly, because of aperture flexibility, the studied C 4 hydrocarbon molecules that are larger than this effective aperture size still adsorb in the micropores of ZIF-8 with kinetic selectivities for iso-C 4H 8/iso-C 4H 10 of 180 and n-C 4H 10/iso-C 4H 10 of 2.5 × 10 6. These unexpected molecular sieving properties open up new opportunities for ZIF materials for separations that cannot be economically achieved by traditional microporous adsorbents such as synthetic zeolites. © 2012 American Chemical Society.
Effect of Molecular Weight on the Properties of Liquid Epoxidized Natural Rubber Acrylate (LENRA)/ Silica Hybrid Composites

International Nuclear Information System (INIS)

Eda Yuhana Ariffin; Azizan Ahmad; Dahlan Mohd; Mahathir Mohamed

2011-01-01

This paper reports on the effect of molecular weight on the morphological and mechanical properties of liquid epoxidized natural rubber acrylate (LENRA)/ silica hybrid composites prepared by sol-gel technique. The sol-gel reaction was conducted at different concentration of tetraethyl orthosilicate (TEOS), used as a precursor of silica. TEOS were introduced in 10, 20, 30, 40 and 50 parts per hundred rubber (phr) in the composites. Two different molecular weights of ENR were used to study the effect of molecular weight on the mechanical and morphological properties of the compounds. These compounds were cured by ultraviolet (UV) irradiation. The mechanical properties were studied through pendulum hardness and scratch tests. Higher molecular weight of ENR showed better mechanical properties than lower molecular weight. Transmission electron microscope was used to determine the silica size and to study the distribution and dispersion of the silica particles. High molecular weight showed greater distribution and dispersion of silica particles with diameter of 13 - 256 nm. Morphological and mechanical properties of LENRA/ silica hybrid composites were improved by using high molecular weight of ENR. (author)
Role of molecular properties of ulvans on their ability to elaborate antiadhesive surfaces.

Science.gov (United States)

Gadenne, Virginie; Lebrun, Laurent; Jouenne, Thierry; Thebault, Pascal

2015-03-01

Antiadhesive properties of polysaccharides (such ulvans) once immobilized on a surface are described in the literature but the parameters governing their antifouling properties are not yet well identified. In the present study, the relationship between molecular parameters of ulvans and the inhibition of bacterial adhesion was investigated. To this aim, various ulvans were grafted on silicon wafers under two different experimental immobilization conditions. Results showed that the experimental immobilization conditions and the polysaccharides molecular weight led to specific layer conformations which exhibited a key role in the surface antiadhesive properties. © 2014 Wiley Periodicals, Inc.

Prediction of mechanical properties for hexagonal boron nitride nanosheets using molecular mechanics model

Energy Technology Data Exchange (ETDEWEB)

Natsuki, Toshiaki [Shinshu University, Faculty of Textile Science and Technology, Ueda (Japan); Shinshu University, Institute of Carbon Science and Technology, Nagano (Japan); Natsuki, Jun [Shinshu University, Institute of Carbon Science and Technology, Nagano (Japan)

2017-04-15

Mechanical behaviors of nanomaterials are not easy to be evaluated in the laboratory because of their extremely small size and difficulty controlling. Thus, a suitable model for the estimation of the mechanical properties for nanomaterials becomes very important. In this study, the elastic properties of boron nitride (BN) nanosheets, including the elastic modulus, the shear modulus, and the Poisson's ratio, are predicted using a molecular mechanics model. The molecular mechanics force filed is established to directly incorporate the Morse potential function into the constitutive model of nanostructures. According to the molecular mechanics model, the chirality effect of hexagonal BN nanosheets on the elastic modulus is investigated through a closed-form solution. The simulated result shows that BN nanosheets exhibit an isotropic elastic property. The present analysis yields a set of very simple formulas and is able to be served as a good approximation on the mechanical properties for the BN nanosheets. (orig.)
Prediction of mechanical properties for hexagonal boron nitride nanosheets using molecular mechanics model

International Nuclear Information System (INIS)

Natsuki, Toshiaki; Natsuki, Jun

2017-01-01

Mechanical behaviors of nanomaterials are not easy to be evaluated in the laboratory because of their extremely small size and difficulty controlling. Thus, a suitable model for the estimation of the mechanical properties for nanomaterials becomes very important. In this study, the elastic properties of boron nitride (BN) nanosheets, including the elastic modulus, the shear modulus, and the Poisson's ratio, are predicted using a molecular mechanics model. The molecular mechanics force filed is established to directly incorporate the Morse potential function into the constitutive model of nanostructures. According to the molecular mechanics model, the chirality effect of hexagonal BN nanosheets on the elastic modulus is investigated through a closed-form solution. The simulated result shows that BN nanosheets exhibit an isotropic elastic property. The present analysis yields a set of very simple formulas and is able to be served as a good approximation on the mechanical properties for the BN nanosheets. (orig.)
Adsorption properties of the SAPO-5 molecular sieve

KAUST Repository

Hu, Enping; Lai, Zhiping; Wang, Kean

2010-01-01

The adsorption properties of an aluminophosphate molecular sieve, SAPO-5, were measured for a number of gases and vapors, including N2, water, isopropanol, and xylenes. The data showed that SAPO-5 is quite hydrophobic and has a strong selectivity of o-xylene over its isomers m- and p-xylene. © 2010 American Chemical Society.
Synthesis, molecular and crystalline architectures, and properties of ...

Indian Academy of Sciences (India)

The construction1 of coordination compounds of cobalt(II) of different nuclearities is the centre of attrac- tion due to interesting structural and physico-chemical properties.1–5 ... Design SQUID MPMS-XL magnetometer working in the 2–300 K range. ..... Complex 1 adopts a molecular architecture cor- responding to the gross ...
Adsorption properties of the SAPO-5 molecular sieve

KAUST Repository

Hu, Enping

2010-09-09

The adsorption properties of an aluminophosphate molecular sieve, SAPO-5, were measured for a number of gases and vapors, including N2, water, isopropanol, and xylenes. The data showed that SAPO-5 is quite hydrophobic and has a strong selectivity of o-xylene over its isomers m- and p-xylene. © 2010 American Chemical Society.
Estimating thermodynamic properties by molecular dynamics simulations: The properties of fluids at high pressures and temperatures

International Nuclear Information System (INIS)

Fraser, D.G.; Refson, K.

1992-01-01

The molecular dynamics calculations reported above give calculated P-V-T properties for H 2 O up to 1500 K and 100 GPa, which agree remarkably well with the available experimental data. We also observe the phase transition to a crystalline, orientationally disordered cubic ice structure. No account was taken of molecular flexibility in these calculations nor of potential dissociation at high pressures as suggested by Hamman (1981). However, we note that the closest next-nearest-neighbour O-H approach remains significantly greater than the TIP4P fixed O-H bond length within the water molecule for all pressures studied. The equation of state proposed here should be useful for estimating the properties of H 2 O at up to 1500 K and 100 G Pa (1 Mbar) and is much easier to use in practice than modified Redlich Kwong equations. Extension of these methods to the studies of other fluids and of fluid mixtures at high temperatures and pressures will require good potential models for the species involved, and this is likely to involve a combination of good ab initio work and semiempirical modelling. Once developed, these models should allow robust predictions of thermodynamic properties beyond the range of the experimental data on the basis of fundamental molecular information
MOLECULAR DISK PROPERTIES IN EARLY-TYPE GALAXIES

International Nuclear Information System (INIS)

Xu, X.; Walker, C.; Narayanan, D.

2010-01-01

We study the simulated CO emission from elliptical galaxies formed in the mergers of gas-rich disk galaxies. The cold gas not consumed in the merger-driven starburst quickly resettles into a disk-like configuration. By analyzing a variety of arbitrary merger orbits that produce a range of fast- to slow-rotating remnants, we find that molecular disk formation is a fairly common consequence of gas-rich galaxy mergers. Hence, if a molecular disk is observed in an early-type merger remnant, it is likely the result of a 'wet merger' rather than a 'dry merger'. We compare the physical properties from our simulated disks (e.g., size and mass) and find reasonably good agreement with recent observations. Finally, we discuss the detectability of these disks as an aid to future observations.
Physical properties of Cu nanoparticles: A molecular dynamics study

International Nuclear Information System (INIS)

Kart, H.H.; Yildirim, H.; Ozdemir Kart, S.; Çağin, T.

2014-01-01

Thermodynamical, structural and dynamical properties of Cu nanoparticles are investigated by using Molecular Dynamics (MD) simulations at various temperatures. In this work, MD simulations of the Cu-nanoparticles are performed by means of the MPiSiM codes by utilizing from Quantum Sutton-Chen (Q-SC) many-body force potential to define the interactions between the Cu atoms. The diameters of the copper nanoparticles are varied from 2 nm to 10 nm. MD simulations of Cu nanoparticles are carried out at low and high temperatures to study solid and liquid properties of Cu nanoparticles. Simulation results such as melting point, radial distribution function are compared with the available experimental bulk results. Radial distribution function, mean square displacement, diffusion coefficient, Lindemann index and Honeycutt–Andersen index are also calculated for estimating the melting point of the Copper nanoparticles. - Highlights: • Solid and liquid properties of Cu nanoparticles are studied. • Molecular dynamics utilizing the Quantum Sutton Chen potential is used in this work. • Melting temperatures of nanoparticles are strongly depended on nanoparticle sizes. • Heat capacity, radial distribution function and diffusion coefficients are studied. • Structures of nanoparticles are analyzed by Lindemann and Honeycutt–Andersen index
Modeling molecular acidity with electronic properties and Hammett constants for substituted benzoic acids.

Science.gov (United States)

Huang, Ying; Liu, Lianghong; Liu, Wanhui; Liu, Shaogang; Liu, Shubin

2011-12-29

Molecular acidity is an important physiochemical property essential in many fields of molecular studies, but an efficient and reliable computational approach to make accurate predictions is still missing. In this work, based on our previous studies to use gas phase electronic properties such as molecular electrostatic potential and valence natural atomic orbitals of the acidic atom and leaving proton, we demonstrate here that different approaches can be employed to tackle this problem. To that end, we employ 196 singly, doubly, and triply substituted benzoic acids for the study. We show that two different approaches are possible, one focusing on the carboxyl group through its localized electronic properties and the other on the substituting groups via Hammett constants and their additivity rule. Our present results clearly exhibit that with the linear models built from the singly substituted species, one can accurately predict the pK(a) values for the doubly and triply substituted species with both of these two approaches. The predictions from these approaches are consistent with each other and agree well with the experimental data. These intrinsically different approaches are the two manifestations of the same molecular acidity property, both valid and complementary to each other. © 2011 American Chemical Society
Characterization-Based Molecular Design of Biofuel Additives Using Chemometric and Property Clustering Techniques

Directory of Open Access Journals (Sweden)

Subin eHada

2014-06-01

Full Text Available In this work, multivariate characterization data such as infrared (IR spectroscopy was used as a source of descriptor data involving information on molecular architecture for designing structured molecules with tailored properties. Application of multivariate statistical techniques such as principal component analysis (PCA allowed capturing important features of the molecular architecture from complex data to build appropriate latent variable models. Combining the property clustering techniques and group contribution methods (GCM based on characterization data in a reverse problem formulation enabled identifying candidate components by combining or mixing molecular fragments until the resulting properties match the targets. The developed methodology is demonstrated using molecular design of biodiesel additive which when mixed with off-spec biodiesel produces biodiesel that meets the desired fuel specifications. The contribution of this work is that the complex structures and orientations of the molecule can be included in the design, thereby allowing enumeration of all feasible candidate molecules that matched the identified target but were not part of original training set of molecules.
Molecular Dynamics Simulation for the Mechanical Properties of CNT/Polymer Nanocomposites

International Nuclear Information System (INIS)

Yang, Seung Hwa; Cho, Maeg Hyo

2007-01-01

In order to obtain mechanical properties of CNT/Polymer nano-composites, molecular dynamics simulation is performed. Overall system was modeled as a flexible unit cell in which carbon nanotubes are embedded into a polyethylene matrix for N σ T ensemble simulation. COMPASS force field was chosen to describe inter and intra molecular potential and bulk effect was achieved via periodic boundary conditions. In CNT-polymer interface, only Lennard-Jones non-bond potential was considered. Using Parrinello-Rahman fluctuation method, mechanical properties of orthotropic nano-composites under various temperatures were successfully obtained. Also, we investigated thermal behavior of the short CNT reinforced nanocomposites system with predicting glass transition temperature
Molecular properties of steroids involved in their effects on the biophysical state of membranes.

Science.gov (United States)

Wenz, Jorge J

2015-10-01

The activity of steroids on membranes was studied in relation to their ordering, rigidifying, condensing and/or raft promoting ability. The structures of 82 steroids were modeled by a semi-empirical procedure (AM1) and 245 molecular descriptors were next computed on the optimized energy conformations. Principal component analysis, mean contrasting and logistic regression were used to correlate the molecular properties with 212 cases of documented activities. It was possible to group steroids based on their properties and activities, indicating that steroids having similar molecular properties have similar activities on membranes. Steroids having high values of area, partition coefficient, volume, number of rotatable bonds, molar refractivity, polarizability or mass displayed ordering, rigidifying, condensing and/or raft promoting activity on membranes higher than those steroids having low values in such molecular properties. After a variable selection procedure circumventing correlation problems among descriptors, area and log P were found as the most relevant properties in governing and predicting the activity of steroids on membranes. A logistic regression model as a function of the area and log P of the steroids is proposed, which is able to predict correctly 92.5% of the cases. A rationale of the findings is discussed. Copyright © 2015 Elsevier B.V. All rights reserved.
Exploring the Local Elastic Properties of Bilayer Membranes Using Molecular Dynamics Simulations

DEFF Research Database (Denmark)

Pieffet, Gilles; Botero, Alonso; Peters, Günther H.J.

2014-01-01

Membrane mechanical elastic properties regulate a variety of cellular processes involving local membrane deformation, such as ion channel function and vesicle fusion. In this work, we used molecular dynamics simulations to estimate the local elastic properties of a membrane. For this, we calculated...... the stretching process in molecular detail, allowing us to fit this profile to a previously proposed continuum elastic model. Through this approach, we calculated an effective membrane spring constant of 42 kJ-2.mol-1, which is in good agreement with the PMF calculation. Furthermore, the solvation energy we...
Molecular models of zinc phthalocyanines: semi-empirical molecular orbital computations and physicochemical properties studied by molecular mechanics simulations

International Nuclear Information System (INIS)

Gantchev, Tsvetan G.; van Lier, Johan E.; Hunting, Darel J.

2005-01-01

To build 3D-molecular models of Zinc-phthalocyanines (ZnPc) and to study their diverse chemical and photosensitization properties, we performed quantum mechanical molecular orbital (MO) semi-empirical (AM1) computations of the ground, excited singlet and triplet states as well as free radical (ionic) species. RHF and UHF (open shell) geometry optimizations led to near-perfect symmetrical ZnPc. Predicted ionization potentials (IP), electron affinities (EA) and lowest electronic transitions of ZnPc are in good agreement with the published experimental and theoretical data. The computation-derived D 4h /D 2h -symmetry 3D-structures of ground and excited states and free radicals of ZnPc, together with the frontier orbital energies and Mulliken electron population analysis enabled us to build robust molecular models. These models were used to predict important chemical-reactivity entities such as global electronegativity (χ), hardness (η) and local softness based on Fukui-functions analysis. Examples of molecular mechanics (MM) applications of the 3D-molecular models are presented as approaches to evaluate solvation free energy (ΔG 0 ) solv and to estimate ground- and excited- state oxidation/reduction potentials as well as intermolecular interactions and stability of ground and excited state dimers (exciplexes) and radical ion-pairs
Characterization-Based Molecular Design of Bio-Fuel Additives Using Chemometric and Property Clustering Techniques

International Nuclear Information System (INIS)

Hada, Subin; Solvason, Charles C.; Eden, Mario R.

2014-01-01

In this work, multivariate characterization data such as infrared spectroscopy was used as a source of descriptor data involving information on molecular architecture for designing structured molecules with tailored properties. Application of multivariate statistical techniques such as principal component analysis allowed capturing important features of the molecular architecture from enormous amount of complex data to build appropriate latent variable models. Combining the property clustering techniques and group contribution methods based on characterization (cGCM) data in a reverse problem formulation enabled identifying candidate components by combining or mixing molecular fragments until the resulting properties match the targets. The developed methodology is demonstrated using molecular design of biodiesel additive, which when mixed with off-spec biodiesel produces biodiesel that meets the desired fuel specifications. The contribution of this work is that the complex structures and orientations of the molecule can be included in the design, thereby allowing enumeration of all feasible candidate molecules that matched the identified target but were not part of original training set of molecules.
Characterization-Based Molecular Design of Bio-Fuel Additives Using Chemometric and Property Clustering Techniques

Energy Technology Data Exchange (ETDEWEB)

Hada, Subin; Solvason, Charles C.; Eden, Mario R., E-mail: edenmar@auburn.edu [Department of Chemical Engineering, Auburn University, Auburn, AL (United States)

2014-06-10

In this work, multivariate characterization data such as infrared spectroscopy was used as a source of descriptor data involving information on molecular architecture for designing structured molecules with tailored properties. Application of multivariate statistical techniques such as principal component analysis allowed capturing important features of the molecular architecture from enormous amount of complex data to build appropriate latent variable models. Combining the property clustering techniques and group contribution methods based on characterization (cGCM) data in a reverse problem formulation enabled identifying candidate components by combining or mixing molecular fragments until the resulting properties match the targets. The developed methodology is demonstrated using molecular design of biodiesel additive, which when mixed with off-spec biodiesel produces biodiesel that meets the desired fuel specifications. The contribution of this work is that the complex structures and orientations of the molecule can be included in the design, thereby allowing enumeration of all feasible candidate molecules that matched the identified target but were not part of original training set of molecules.
Efficient Syntheses of Novel Fluoro-Substituted Pentacenes and Azapentacenes: Molecular and Solid-State Properties.

Science.gov (United States)

Schwaben, Jonas; Münster, Niels; Klues, Michael; Breuer, Tobias; Hofmann, Philipp; Harms, Klaus; Witte, Gregor; Koert, Ulrich

2015-09-21

Non-symmetrical 6,13-disubstituted pentacenes bearing trifluoromethyl and aryl substituents have been synthesized starting from pentacenequinone. Diazapentacenes with a variety of fluorine substituents were prepared either via a Hartwig-Buchwald aryl amination route or by a SNAr strategy. As a result of a non-symmetric substitution pattern containing electron-donating substituents in combination with electron-accepting fluorine substituents, the synthesized compounds feature distinct molecular dipoles. All compounds are analyzed regarding their optoelectronic properties in solution with special focus on the frontier orbital energies as well as their molecular packing in the crystal structures. The analyses of isolated molecules are complemented by thin-film studies to examine their solid-state properties. A precise comparison between these and the molecular properties gave detailed insights into the exciton binding energies of these compounds, which are explained by means of a simple model considering the molecular packing and polarizabilities. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Molecular dynamics study on the relaxation properties of bilayered ...

Indian Academy of Sciences (India)

2017-08-31

Aug 31, 2017 ... Abstract. The influence of defects on the relaxation properties of bilayered graphene (BLG) has been studied by molecular dynamics simulation in nanometre sizes. Type and position of defects were taken into account in the calculated model. The results show that great changes begin to occur in the ...
Effects of surface proteins and lipids on molecular structure, thermal properties, and enzymatic hydrolysis of rice starch

Directory of Open Access Journals (Sweden)

Pan HU

Full Text Available Abstract Rice starches with different amylose contents were treated with sodium dodecyl sulfate (SDS to deplete surface proteins and lipids, and the changes in molecular structure, thermal properties, and enzymatic hydrolysis were evaluated. SDS treatment did not significantly change the molecular weight distribution, crystalline structure, short-range ordered degree, and gelatinization properties of starch, but significantly altered the pasting properties and increased the swelling power of starch. The removal of surface proteins and lipids increased the enzymatic hydrolysis and in vitro digestion of starch. The influences of removing surface proteins and lipids from starch on swelling power, pasting properties, and enzymatic hydrolysis were different among the various starches because of the differences in molecular structures of different starch styles. The aforementioned results indicated that removing the surface proteins and lipids from starch did not change the molecular structure but had significant effects on some functional properties.
Elastic properties of surfactant monolayers at liquid-liquid interfaces: A molecular dynamics study

DEFF Research Database (Denmark)

Laradji, Mohamed; Mouritsen, Ole G.

2000-01-01

Using a simple molecular model based on the Lennard-Jones potential, we systematically study the elastic properties of liquid-liquid interfaces containing surfactant molecules by means of extensive and large-scale molecular dynamics simulations. The main elastic constants of the interface, corres...

Vector properties in molecular photodissociation

International Nuclear Information System (INIS)

Underwood, J.

1999-12-01

The technique of resonance enhanced multi-photon ionization (REMPI) of atomic and molecular species produced from a photofragmentation event combined with time-of flight (TOF) detection is used to examine scalar and vector properties following photodissociation. This technique is applied to the study of methyl bromide dissociation in a product state specific manner. We report measurements of the angular distributions and kinetic energy releases of the resulting bromine atoms in the ground and first spin-orbit excited state. Additionally we report measurements of the angular distributions and kinetic energy releases of the methyl fragment in the ground vibrational state, and also the excited state with one quanta in the ν 2 vibrational modes. These studies were carried out in the red wing of the absorption band at several wavelengths. For these measurements we were able to resolve the spin orbit state of the partner bromine fragment. From our observations we find new evidence for enhanced nonadiabatic curve crossing active in methyl bromide dissociation in comparison with earlier studies of methyl iodide. The atomic polarization produced following photodissociation of a diatomic molecule was investigated both theoretically and experimentally. We develop theoretical expressions relating the lab frame and molecular frame atomic polarization to the photoexcitation and subsequent dissociation of a diatomic molecule. This treatment includes both incoherent, coherent and non-adiabatic processes which may be active in the photodissociation process. We treat the general case of a polarized diatomic molecule yielding two fragments with non zero angular momentum. Experimentally, an investigation of the polarization of atomic Cl( 2 P 3/2 ) photofragments from the ∼330 nm photolysis of molecular chlorine using the REMPI-TOF technique is reported. We present a theoretical framework in which to treat such experiments allowing the extraction of parameters with direct physical
Boron nitride ceramics from molecular precursors: synthesis, properties and applications.

Science.gov (United States)

Bernard, Samuel; Salameh, Chrystelle; Miele, Philippe

2016-01-21

Hexagonal boron nitride (h-BN) attracts considerable interest because its structure is similar to that of carbon graphite while it displays different properties which are of interest for environmental and green technologies. The polar nature of the B-N bond in sp(2)-bonded BN makes it a wide band gap insulator with different chemistry on its surface and particular physical and chemical properties such as a high thermal conductivity, a high temperature stability, a high resistance to corrosion and oxidation and a strong UV emission. It is chemically inert and nontoxic and has good environmental compatibility. h-BN also has enhanced physisorption properties due to the dipolar fields near its surface. Such properties are closely dependent on the processing method. Bottom-up approaches consist of transforming molecular precursors into non-oxide ceramics with retention of the structural units inherent to the precursor molecule. The purpose of the present review is to give an up-to-date overview on the most recent achievements in the preparation of h-BN from borazine-based molecular single-source precursors including borazine and 2,4,6-trichloroborazine through both vapor phase syntheses and methods in the liquid/solid state involving polymeric intermediates, called the Polymer-Derived Ceramics (PDCs) route. In particular, the effect of the chemistry, composition and architecture of the borazine-based precursors and derived polymers on the shaping ability as well as the properties of h-BN is particularly highlighted.
Synthesis and properties of aqueous polyurethane dispersions: Influence of molecular weight of polyethylene glycol

Energy Technology Data Exchange (ETDEWEB)

Mumtaz, Fatima; Zuber, Mohammad; Zia, Khalid Mahmood [Government College University, Faisalabad (Pakistan); Jamil, Tahir [University of the Punjab, Lahore (Pakistan); Hussain, Rizwan [National Engineering and Scientific Commission (NESCOM), Islamabad (Pakistan)

2013-12-15

Aqueous polyurethane dispersions (PUDs) have recently emerged as important alternatives to their solvent-based counterparts for various applications due to increasing health and environmental awareness. A series of aqueous polyurethane dispersions containing carboxylate anion as hydrophilic pendant groups were synthesized through step growth polymerization reaction using hexamethylene diisocyanate (HDI), 1,4-butanediol (1,4-BDO), dimethylol propionic acid (DMPA) and polyethylene glycol (PEG) of different molecular weight. Effect of PEG molecular weight was investigated on molecular structure, contact angle measurement, and physical and adhesive properties of PU emulsions. Fourier transform infrared spectroscopy (FT-IR) was used to check the completion of polymerization reaction. Contact angle measurement indicated that the hydrophilicity of polymer increases by increasing molecular weight of PEG with a corresponding decrease in contact angle. Results of T-peel test showed a decrease in peel strength by increasing molecular weight of PEG. Moreover, solid contents%, drying time and storage stability suggested fast drying properties and greater stability of aqueous PU dispersions.
Establishing whether the structural feature controlling the mechanical properties of starch films is molecular or crystalline.

Science.gov (United States)

Li, Ming; Xie, Fengwei; Hasjim, Jovin; Witt, Torsten; Halley, Peter J; Gilbert, Robert G

2015-03-06

The effects of molecular and crystalline structures on the tensile mechanical properties of thermoplastic starch (TPS) films from waxy, normal, and high-amylose maize were investigated. Starch structural variations were obtained through extrusion and hydrothermal treatment (HTT). The molecular and crystalline structures were characterized using size-exclusion chromatography and X-ray diffractometry, respectively. TPS from high-amylose maize showed higher elongation at break and tensile strength than those from normal maize and waxy maize starches when processed with 40% plasticizer. Within the same amylose content, the mechanical properties were not affected by amylopectin molecular size or the crystallinity of TPS prior to HTT. This lack of correlation between the molecular size, crystallinity and mechanical properties may be due to the dominant effect of the plasticizer on the mechanical properties. Further crystallization of normal maize TPS by HTT increased the tensile strength and Young's modulus, while decreasing the elongation at break. The results suggest that the crystallinity from the remaining ungelatinized starch granules has less significant effect on the mechanical properties than that resulting from starch recrystallization, possibly due to a stronger network from leached-out amylose surrounding the remaining starch granules. Copyright © 2014 Elsevier Ltd. All rights reserved.
PDMS Network Structure-Property Relationships: Influence of Molecular Architecture on Mechanical and Wetting Properties

Science.gov (United States)

Melillo, Matthew Joseph

Poly(dimethylsiloxane) (PDMS) is one of the most common elastomers, with applications ranging from sealants and marine-antifouling coatings to medical devices and absorbents for water treatment. Fundamental understanding of how liquids spread on the surface of and absorb into and leach out of PDMS networks is of critical importance for the design and use in another application - microfluidic devices. The growing use of PDMS in microfluidic devices raises the concern that some researchers may use this material without fully understanding all of its advantages, drawbacks, and intricacies. The primary goal of this Ph.D. dissertation is to elucidate PDMS network molecular structure to macroscopic property relationships and to demonstrate how molecular architecture can alter dynamic mechanical and wetting characteristics. We prepare PDMS materials by using vinyl/ tetrakis(dimethylsiloxy)silane (TDSS) and silanol/ tetraethylorthosilicate (TEOS) combinations of PDMS end-groups and crosslinkers as two model systems. Under constant curing conditions, we systematically study the effects of polymer molecular weight, loading of crosslinker, and end-group chemical functionality on the extent of gelation and the dynamic mechanical and water wetting properties of end-linked PDMS networks. The extent of the gelation reaction is determined using the Soxhlet extraction to quantify the amount of material that did and did not participate in the crosslinking reactions, termed the gel and sol fractions, respectively. We use the Miller-Macosko model in conjunction with the gel fraction and precise chemical composition (i.e., stoichiometric ratio and molecular weight) to determine the fractions of elastic and pendant material, the molecular weight between chemical crosslinks, and the average effective functionality of the crosslinker molecule. Based on dynamic mechanical testing, we find that the maximum storage moduli are achieved at optimal stoichiometric conditions in the vinyl
The influence of starch molecular mass on the properties of extruded thermoplastic starch

NARCIS (Netherlands)

Vliegenthart, J.F.G.; Soest, J.J.G. van; Benes, K.; Wit, D. de

1996-01-01

The mechanical properties of a low and a high molecular mass thermoplastic starch (TPS) were monitored at water contents in the range of 530% (w/w). The granular starches were plasticized by extrusion processing with glycerol and water. The low molecular mass starch was prepared by partial acid
Study of the Mechanical Properties and Vibration Isolation Performance of a Molecular Spring Isolator

Directory of Open Access Journals (Sweden)

Muchun Yu

2016-01-01

Full Text Available Molecular Spring Isolator (MSI is a novel passive vibration isolation technique, providing High-Static-Low-Dynamic (HSLD stiffness based on the use of molecular spring material. The molecular spring material is a solid-liquid mixture consisting of water and hydrophobic nanoporous materials. Under a certain level of external pressure, water molecules can intrude into the hydrophobic pores of nanoporous materials, developing an additional solid-liquid interface. Such interfaces are able to store, release, and transform mechanical energy, providing properties like mechanical spring. Having been only recently developed, the basic mechanic properties of a MSI have not been studied in depth. This paper focuses on the stiffness influence factors, the dynamic frequency response, and the vibration isolation performance of a MSI; these properties help engineers to design MSIs for different engineering applications. First, the working mechanism of a MSI is introduced from a three-dimensional general view of the water infiltration massive hydrophobic nanoporous pores. Next, a wide range of influence factors on the stiffness properties of MSI are studied. In addition, the frequency response functions (FRFs of the MSI vibration isolation system are studied utilizing the matching method based on equivalent piecewise linear (EPL system. Finally, the vibration isolation properties of MSI are evaluated by force transmissibility.
Thermophysical properties of liquid carbon dioxide under shock compressions: quantum molecular dynamic simulations.

Science.gov (United States)

Wang, Cong; Zhang, Ping

2010-10-07

Quantum molecular dynamics were used to calculate the equation of state, electrical, and optical properties of liquid carbon dioxide along the Hugoniot at shock pressures up to 74 GPa. The principal Hugoniot derived from the calculated equation of state is in good agreement with experimental results. Molecular dissociation and recombination are investigated through pair correlation functions and decomposition of carbon dioxide is found to be between 40 and 50 GPa along the Hugoniot, where nonmetal-metal transition is observed. In addition, the optical properties of shock compressed carbon dioxide are also theoretically predicted along the Hugoniot.
Assessing the Bonding Properties of Individual Molecular Orbitals

OpenAIRE

Robinson, PJ; Alexandrova, AN

2015-01-01

© 2015 American Chemical Society. Molecular orbitals (MOs), while one of the most widely used representations of the electronic structure of a system, are often too complex to intuit properties. Aside from the simplest of cases, it is not necessarily possible to visually tell which orbitals are bonding or antibonding along particular directions, especially in cases of highly delocalized and nontrivial bonding like metal clusters or solids. We propose a method for easily assessing and comparin...
Forcefields based molecular modeling on the mechanical and physical properties of emeraldine base polyaniline

NARCIS (Netherlands)

Chen, X.; Yuan, C.A.; Wong, K.Y.; Zhang, G.Q.

2010-01-01

Molecular dynamics (MD) and molecular mechanical (MM) analysis are carried out to provide reliable and accurate model for emeraldine base polyaniline. This study validate the forcefields and model with the physical and mechanical properties of the polyaniline. The temperature effects on non-bond
Molecular dynamics simulations of the dielectric properties of fructose aqueous solutions

International Nuclear Information System (INIS)

Sonoda, Milton T; Dolores Elola, M; Skaf, Munir S

2016-01-01

The static dielectric permittivity and dielectric relaxation properties of fructose aqueous solutions of different concentrations ranging from 1.0 to 4.0 mol l −1 are investigated by means of molecular dynamics simulations. The contributions from intra- and interspecies molecular correlations were computed individually for both the static and frequency-dependent dielectric properties, and the results were compared with the available experimental data. Simulation results in the time- and frequency-domains were analyzed and indicate that the presence of fructose has little effect on the position of the fast, high-frequency (>500 cm −1 ) components of the dielectric response spectrum. The low-frequency (<0.1 cm −1 ) components, however, are markedly influenced by sugar concentration. Our analysis indicates that fructose–fructose and fructose–water interactions strongly affect the rotational-diffusion regime of molecular motions in the solutions. Increasing fructose concentration not only enhances sugar–sugar and sugar-water low frequency contributions to the dielectric loss spectrum but also slows down the reorientational dynamics of water molecules. These results are consistent with previous computer simulations carried out for other disaccharide aqueous solutions. (paper)
Physical properties of CO-dark molecular gas with C+ and OH observations

Science.gov (United States)

Tang, Ningyu; Li, Di; Heiles, Carl E.; ISM Group in National Astronomical Observatories, CAS

2017-01-01

The lifecycle of interstellar medium (ISM) is critical for understanding galaxy evolution. The transition between atomic neutral medium and dense molecular gas, however, cannot be traced adequately by either HI or CO emission. Results from dust observations of Planck all-sky mission and gamma-ray observations of Energetic Gamma Ray Experiment Telescope (EGRET) have revealed the existence of “CO dark molecular gas” (DMG) - molecular gas without CO emission. The physical conditions of DMG including density, temperature, and molecular composition are basis of understanding the ISM evolution. We analyzed physical properties of DMG with HI-self absorption and C+ fine line emission at 158 um toward the lines of sight of Galactic Observations of Terahertz C+ (GOTC+). DMG clouds have a median excitation temperature of 56 K and median volume density of 230 cm2, showing intermediate physical properties between atomic and molecular gas. Sixteen DMG clouds with high visual extinction (AV>=2.7 mag) were found. CO abundance compared to H2 in these clouds is two orders magnitude smaller than the cannonical value in the Milky Way and cannot be explained by the chemical evolutionary model. They may be formed through the agglomeration of pre-existing molecular gas in the Milky Way. We have finished a follow up survey of OH 18 cm lines toward 51 sightlines of GOTC+ including sightlines with DMG clouds through Arecibo telescope. DMG may result in the absence of correlation between CO and OH column density. A possible correlation was found between C+ and OH column density in tracing DMG.
Study of effect of gamma radiation on molecular weight and mechanical properties of PHB and PHNV

International Nuclear Information System (INIS)

Fechine, Guilhermino J.M.; Terence, Mauro C.; Rabello, M.S.; Willen, Renate M.R.

2011-01-01

The effect of gamma radiation on molecular weight and mechanical properties (tensile and flexural) of PHB and PHBV samples was investigated. The values of stress and strain at the break point for both mechanical properties indicated that scission molecular reactions were predominant in PHB and PHBV samples submitted to gamma radiation. These results were confirmed by Size Exclusion Chromatography (SEC) analysis. (author)
The effect of chitosan molecular weight on the properties of alginate ...

African Journals Online (AJOL)

Purpose: The aim of the present study was to investigate the effect of chitosan molecular weight on size, size distribution, release rate, mucoadhesive properties and electrostatic bonding of alginate/chitosan microparticles containing prednisolone. Methods: Three mucoadhesive alginate/chitosan microparticle formulations, ...
Multi-scale calculation of the electric properties of organic-based devices from the molecular structure

KAUST Repository

Li, Haoyuan; Qiu, Yong; Duan, Lian

2016-01-01

A method is proposed to calculate the electric properties of organic-based devices from the molecular structure. The charge transfer rate is obtained using non-adiabatic molecular dynamics. The organic film in the device is modeled using
Toward Measuring Galactic Dense Molecular Gas Properties and 3D Distribution with Hi-GAL

Science.gov (United States)

Zetterlund, Erika; Glenn, Jason; Maloney, Phil

2016-01-01

The Herschel Space Observatory's submillimeter dust continuum survey Hi-GAL provides a powerful new dataset for characterizing the structure of the dense interstellar medium of the Milky Way. Hi-GAL observed a 2° wide strip covering the entire 360° of the Galactic plane in broad bands centered at 70, 160, 250, 350, and 500 μm, with angular resolution ranging from 10 to 40 arcseconds. We are adapting a molecular cloud clump-finding algorithm and a distance probability density function distance-determination method developed for the Bolocam Galactic Plane Survey (BGPS) to the Hi-GAL data. Using these methods we expect to generate a database of 105 cloud clumps, derive distance information for roughly half the clumps, and derive precise distances for approximately 20% of them. With five-color photometry and distances, we will measure the cloud clump properties, such as luminosities, physical sizes, and masses, and construct a three-dimensional map of the Milky Way's dense molecular gas distribution.The cloud clump properties and the dense gas distribution will provide critical ground truths for comparison to theoretical models of molecular cloud structure formation and galaxy evolution models that seek to emulate spiral galaxies. For example, such models cannot resolve star formation and use prescriptive recipes, such as converting a fixed fraction of interstellar gas to stars at a specified interstellar medium density threshold. The models should be compared to observed dense molecular gas properties and galactic distributions.As a pilot survey to refine the clump-finding and distance measurement algorithms developed for BGPS, we have identified molecular cloud clumps in six 2° × 2° patches of the Galactic plane, including one in the inner Galaxy along the line of sight through the Molecular Ring and the termination of the Galactic bar and one toward the outer Galaxy. Distances have been derived for the inner Galaxy clumps and compared to Bolocam Galactic Plane
Quantum molecular dynamics simulations of thermophysical properties of fluid ethane.

Science.gov (United States)

Zhang, Yujuan; Wang, Cong; Zheng, Fawei; Zhang, Ping

2012-12-01

We have performed first-principles molecular-dynamics simulations based on density-functional theory to study the thermophysical properties of ethane under extreme conditions. We present results for the equation of state of fluid ethane in the warm dense region. The optical conductivity is calculated via the Kubo-Greenwood formula from which the dc conductivity and optical reflectivity are derived. The close correlation between the nonmetal-metal transition of ethane and its decomposition, that ethane dissociates significantly into molecular and/or atomic hydrogen and some long alkane chains, has been systematically studied by analyzing the optical conductivity spectra, pair correlation functions, electronic density of states, and charge density distribution of fluid ethane.
The influence of extruded starch molecular mass on the properties of extruded thermoplastic starch

NARCIS (Netherlands)

Soest, van J.J.G.; Benes, K.; Wit, de D.; Vliegenthart, J.F.G.

1996-01-01

The mechanical properties of a low and a high molecular mass thermoplastic starch (TPS) were monitored at water contents in the range of 5-30% (w/w). The granular starches were plasticized by extrusion processing with glycerol and water. The low molecular mass starch was prepared by partial acid
Thermophysical properties of undercooled alloys: an overview of the molecular simulation approaches.

Science.gov (United States)

Lv, Yong J; Chen, Min

2011-01-10

We review the studies on the thermophysical properties of undercooled metals and alloys by molecular simulations in recent years. The simulation methods of melting temperature, enthalpy, specific heat, surface tension, diffusion coefficient and viscosity are introduced and the simulated results are summarized. By comparing the experimental results and various theoretical models, the temperature and the composition dependences of the thermophysical properties in undercooled regime are discussed.
High impact polystyrene (HIPS). Predicting its molecular, morphological and mechanical properties

International Nuclear Information System (INIS)

Luciani, C; Estenoz, D; Morales, G; Meira, G

2004-01-01

A mathematical model that is able to predict the molecular and morphological structure of high impact polystyrene (HIPS) and the Fluidity Index (MFI) is presented. The model is divided into two parts: a) the estimation of the material's molecular and morphological properties, simulating the polymerization process in discontinuous mass based on the recipe and the conditions of synthesis; and b) the prediction of rheological variables (viscosity at low deformation speeds and relaxation time), and of the MFI, based on average molecular and morphological variables. The model also combines with empirical correlations proposed in the literature [1] in order to estimate impact strength (IS). The predictions for a), b) and impact strength were co-validated by independent data and resulted in a good fit (CW)

p/n-Polarity of thiophene oligomers in photovoltaic cells: role of molecular vs. supramolecular properties.

Science.gov (United States)

Ghosh, Tanwistha; Gopal, Anesh; Saeki, Akinori; Seki, Shu; Nair, Vijayakumar C

2015-04-28

Molecular and supramolecular properties play key roles in the optoelectronic properties and photovoltaic performances of organic materials. In the present work, we show how small changes in the molecular structure affect such properties, which in turn control the intrinsic and fundamental properties such as the p/n-polarity of organic semiconductors in bulk-heterojunction solar cells. Herein, we designed and synthesized two acceptor-donor-acceptor type semiconducting thiophene oligomers end-functionalized with oxazolone/isoxazolone derivatives (OT1 and OT2 respectively). The HOMO-LUMO energy levels of both derivatives were found to be positioned in such a way that they can act as electron acceptors to P3HT and electron donors to PCBM. However, OT1 functions as a donor (with PCBM) and OT2 as an acceptor (with P3HT) in BHJ photovoltaic cells, and their reverse roles results in either no or poor performance of the cells. Detailed studies using UV-vis absorption and fluorescence spectroscopy, time-correlated single photon counting, UV-photoelectron spectroscopy, density functional theory calculations, X-ray diffraction, and thermal gravimetric analysis proved that both molecular and supramolecular properties contributed equally but in a contrasting manner to the abovementioned observation. The obtained results were further validated by flash-photolysis time-resolved microwave conductivity studies which showed an excellent correlation between the structure, property, and device performances of the materials.
The mechanical properties modeling of nano-scale materials by molecular dynamics

NARCIS (Netherlands)

Yuan, C.; Driel, W.D. van; Poelma, R.; Zhang, G.Q.

2012-01-01

We propose a molecular modeling strategy which is capable of mod-eling the mechanical properties on nano-scale low-dielectric (low-k) materials. Such modeling strategy has been also validated by the bulking force of carbon nano tube (CNT). This modeling framework consists of model generation method,
Thermophysical Properties of Undercooled Alloys: An Overview of the Molecular Simulation Approaches

Directory of Open Access Journals (Sweden)

Min Chen

2011-01-01

Full Text Available We review the studies on the thermophysical properties of undercooled metals and alloys by molecular simulations in recent years. The simulation methods of melting temperature, enthalpy, specific heat, surface tension, diffusion coefficient and viscosity are introduced and the simulated results are summarized. By comparing the experimental results and various theoretical models, the temperature and the composition dependences of the thermophysical properties in undercooled regime are discussed.
The Alexandria library, a quantum-chemical database of molecular properties for force field development.

Science.gov (United States)

Ghahremanpour, Mohammad M; van Maaren, Paul J; van der Spoel, David

2018-04-10

Data quality as well as library size are crucial issues for force field development. In order to predict molecular properties in a large chemical space, the foundation to build force fields on needs to encompass a large variety of chemical compounds. The tabulated molecular physicochemical properties also need to be accurate. Due to the limited transparency in data used for development of existing force fields it is hard to establish data quality and reusability is low. This paper presents the Alexandria library as an open and freely accessible database of optimized molecular geometries, frequencies, electrostatic moments up to the hexadecupole, electrostatic potential, polarizabilities, and thermochemistry, obtained from quantum chemistry calculations for 2704 compounds. Values are tabulated and where available compared to experimental data. This library can assist systematic development and training of empirical force fields for a broad range of molecules.
The Alexandria library, a quantum-chemical database of molecular properties for force field development

Science.gov (United States)

Ghahremanpour, Mohammad M.; van Maaren, Paul J.; van der Spoel, David

2018-04-01

Data quality as well as library size are crucial issues for force field development. In order to predict molecular properties in a large chemical space, the foundation to build force fields on needs to encompass a large variety of chemical compounds. The tabulated molecular physicochemical properties also need to be accurate. Due to the limited transparency in data used for development of existing force fields it is hard to establish data quality and reusability is low. This paper presents the Alexandria library as an open and freely accessible database of optimized molecular geometries, frequencies, electrostatic moments up to the hexadecupole, electrostatic potential, polarizabilities, and thermochemistry, obtained from quantum chemistry calculations for 2704 compounds. Values are tabulated and where available compared to experimental data. This library can assist systematic development and training of empirical force fields for a broad range of molecules.
Machine learning of molecular electronic properties in chemical compound space

International Nuclear Information System (INIS)

Montavon, Grégoire; Müller, Klaus-Robert; Rupp, Matthias; Gobre, Vivekanand; Hansen, Katja; Tkatchenko, Alexandre; Vazquez-Mayagoitia, Alvaro; Anatole von Lilienfeld, O

2013-01-01

The combination of modern scientific computing with electronic structure theory can lead to an unprecedented amount of data amenable to intelligent data analysis for the identification of meaningful, novel and predictive structure–property relationships. Such relationships enable high-throughput screening for relevant properties in an exponentially growing pool of virtual compounds that are synthetically accessible. Here, we present a machine learning model, trained on a database of ab initio calculation results for thousands of organic molecules, that simultaneously predicts multiple electronic ground- and excited-state properties. The properties include atomization energy, polarizability, frontier orbital eigenvalues, ionization potential, electron affinity and excitation energies. The machine learning model is based on a deep multi-task artificial neural network, exploiting the underlying correlations between various molecular properties. The input is identical to ab initio methods, i.e. nuclear charges and Cartesian coordinates of all atoms. For small organic molecules, the accuracy of such a ‘quantum machine’ is similar, and sometimes superior, to modern quantum-chemical methods—at negligible computational cost. (paper)
Machine learning of molecular electronic properties in chemical compound space

Science.gov (United States)

Montavon, Grégoire; Rupp, Matthias; Gobre, Vivekanand; Vazquez-Mayagoitia, Alvaro; Hansen, Katja; Tkatchenko, Alexandre; Müller, Klaus-Robert; Anatole von Lilienfeld, O.

2013-09-01

The combination of modern scientific computing with electronic structure theory can lead to an unprecedented amount of data amenable to intelligent data analysis for the identification of meaningful, novel and predictive structure-property relationships. Such relationships enable high-throughput screening for relevant properties in an exponentially growing pool of virtual compounds that are synthetically accessible. Here, we present a machine learning model, trained on a database of ab initio calculation results for thousands of organic molecules, that simultaneously predicts multiple electronic ground- and excited-state properties. The properties include atomization energy, polarizability, frontier orbital eigenvalues, ionization potential, electron affinity and excitation energies. The machine learning model is based on a deep multi-task artificial neural network, exploiting the underlying correlations between various molecular properties. The input is identical to ab initio methods, i.e. nuclear charges and Cartesian coordinates of all atoms. For small organic molecules, the accuracy of such a ‘quantum machine’ is similar, and sometimes superior, to modern quantum-chemical methods—at negligible computational cost.
Statistical properties of anti-symmetrized molecular dynamics

International Nuclear Information System (INIS)

Ohnishi, A.; Randrup, J.

1993-01-01

We study the statistical equilibrium properties of the recently developed anti-symmetrized molecular dynamics model for heavy-ion reactions. We consider A non-interacting fermions in one dimension, either bound in a common harmonic potential or moving freely within an interval, and perform a Metropolis sampling of the corresponding parameter space. Generally the average excitation and the specific heat, considered as functions of the imposed temperature, behave in a classical manner when the canonical weight is calculated in the mean-field approximation. However, it is possible to obtain results that are much closer to the quantal behavior by modifying the weight to take approximate account of the energy fluctuations within the individual wave packets. (orig.)
Mixed 2D molecular systems: Mechanic, thermodynamic and dielectric properties

Energy Technology Data Exchange (ETDEWEB)

Beno, Juraj [Department of Physics, Faculty of Electrical Engineering and Information Technology, Slovak University of Technology, Ilkovicova 3, 812 19-SK Bratislava (Slovakia); Weis, Martin [Department of Physics, Faculty of Electrical Engineering and Information Technology, Slovak University of Technology, Ilkovicova 3, 812 19-SK Bratislava (Slovakia)], E-mail: Martin.Weis@stuba.sk; Dobrocka, Edmund [Department of Physics, Faculty of Electrical Engineering and Information Technology, Slovak University of Technology, Ilkovicova 3, 812 19-SK Bratislava (Slovakia); Institute of Electrical Engineering, Slovak Academy of Sciences, Dubravska cesta 9, 841 04-SK Bratislava (Slovakia); Hasko, Daniel [International Laser Centre, Ilkovicova 3, 812 19-SK Bratislava (Slovakia)

2008-08-15

Study of Langmuir monolayers consisting of stearic acid (SA) and dipalmitoylphosphatidylcholine (DPPC) molecules was done by surface pressure-area isotherms ({pi}-A), the Maxwell displacement current (MDC) measurement, X-ray reflectivity (XRR) and atomic force microscopy (AFM) to investigate the selected mechanic, thermodynamic and dielectric properties based on orientational structure of monolayers. On the base of {pi}-A isotherms analysis we explain the creation of stable structures and found optimal monolayer composition. The dielectric properties represented by MDC generated monolayers were analyzed in terms of excess dipole moment, proposing the effect of dipole-dipole interaction. XRR and AFM results illustrate deposited film structure and molecular ordering.
Structures and physicochemical properties of molecular aggregates of lipids

International Nuclear Information System (INIS)

Iwahashi, Makio

2005-01-01

Structures and physicochemical properties of lipids such as fatty acids, alcohols, acylglycerols and steroids in their two- or three-dimensional states were studied through the measurements of surface pressure (π), surface-molecular area (A), vapor-pressure osmosis, radioactivity (R), self-diffusion coefficient (D), density, viscosity, near-infrared spectroscopy (NIR), 13 C-NMR spin-lattice relaxation time (T 1 ), ESR, SEM, DSC, X-ray diffraction and small-angle neutron scattering (SANS). Following results are obtained: (1) π-A and R-A relationships indicate that the explanation, being widely believed, of the reaction occurred in the oleic acid or the trioleylglycerol monolayer on the aqueous KMnO 4 solution is incorrect. (2) By using the LB film of 3 H-labelled fatty acid, the upper limit of the neutrino mass was determined. In addition, by using the LB film of 14 C-labelled fatty acid, a new type of crystal-transformation process was found, in which fatty-acid crystal transforms from its unstable state to its stable one by the transfer of the fatty acid molecules through the vapor phase. (3) Fatty acids always exist as their dimers in their liquid state and mostly in non-polar solvents; the dimers are the units of the molecular movements in the molten liquid and in solvents. T 1 results clearly showed the internal molecular movements of the dimers. In addition, D and SANS results indicated that two different kinds of fatty acids in their binary mixture make only each homodimers. (4) Furthermore, the study on the liquid structure of fatty acids such as cis-6-, cis-9-, cis-11-, trans-9-octadecenoic acids and stearic acid indicated that these fatty-acid dimers construct the clusters resemble to the smectic-liquid crystal in the liquid state. The clusters determine the physicochemical properties of the liquid of the fatty acid. (author)
Li-Carboxylate Anode Structure-Property Relationships from Molecular Modeling

KAUST Repository

Burkhardt, Stephen E.

2013-01-22

The full realization of a renewable energy strategy hinges upon electrical energy storage (EES). EES devices play a key role in storing energy from renewable sources (which are inherently intermittent), to efficient transmission (e.g., grid load-leveling), and finally into the electrification of transportation. Organic materials represent a promising class of electrode active materials for Li-ion and post-Li-ion batteries. Organics consist of low-cost, lightweight, widely available materials, and their properties can be rationally tuned using the well-established principles of organic chemistry. Within the class of organic EES materials, carboxylates distinguish themselves for Li-ion anode materials based on their observed thermal stability, rate capability, and high cyclability. Further, many of the carboxylates studied to date can be synthesized from renewable or waste feedstocks. This report begins with a preliminary molecular density-functional theory (DFT) study, in which the calculated molecular properties of a set of 12 known Li-ion electrode materials based on carboxylate and carbonyl redox couples are compared to literature data. Based on the agreement between theoretical and experimental data, an expanded study was undertaken to identify promising materials and establish design principles for anodes based on Li-carboxylate salts. Predictive computational studies represent an important step forward for the identification of organic anode materials. © 2012 American Chemical Society.
Confinement properties of 2D porous molecular networks on metal surfaces

International Nuclear Information System (INIS)

Müller, Kathrin; Enache, Mihaela; Stöhr, Meike

2016-01-01

Quantum effects that arise from confinement of electronic states have been extensively studied for the surface states of noble metals. Utilizing small artificial structures for confinement allows tailoring of the surface properties and offers unique opportunities for applications. So far, examples of surface state confinement include thin films, artificial nanoscale structures, vacancy and adatom islands, self-assembled 1D chains, vicinal surfaces, quantum dots and quantum corrals. In this review we summarize recent achievements in changing the electronic structure of surfaces by adsorption of nanoporous networks whose design principles are based on the concepts of supramolecular chemistry. Already in 1993, it was shown that quantum corrals made from Fe atoms on a Cu(1 1 1) surface using single atom manipulation with a scanning tunnelling microscope confine the Shockley surface state. However, since the atom manipulation technique for the construction of corral structures is a relatively time consuming process, the fabrication of periodic two-dimensional (2D) corral structures is practically impossible. On the other side, by using molecular self-assembly extended 2D porous structures can be achieved in a parallel process, i.e. all pores are formed at the same time. The molecular building blocks are usually held together by non-covalent interactions like hydrogen bonding, metal coordination or dipolar coupling. Due to the reversibility of the bond formation defect-free and long-range ordered networks can be achieved. However, recently also examples of porous networks formed by covalent coupling on the surface have been reported. By the choice of the molecular building blocks, the dimensions of the network (pore size and pore to pore distance) can be controlled. In this way, the confinement properties of the individual pores can be tuned. In addition, the effect of the confined state on the hosting properties of the pores will be discussed in this review article
Bending of conjugated molecular wires and its effect on electron conduction properties

International Nuclear Information System (INIS)

Das, Bidisa

2010-01-01

The electronic structure and electron transport properties of simple conjugated molecular wires like oligophenylene ethynylene (OPE) and oligophenylene vinylene (OPV) are studied under compression. If artificially confined to a given shorter length, the oligomers tend to bend and bending causes a loss in the overlap of the conjugated molecular orbitals. Theoretical modeling of electronic transport has been carried out for all undistorted and compressed OPE/OPV oligomers. OPV exists in step-like or V-like conformations and they have the same stability with very similar frontier molecular orbitals. The conductances of these molecular wires are calculated when inserted between two gold probes and the conductances for OPV are found to be comparable to OPE when the interfaces are same. The conductance decreases with bending due to the gradual loss in overlap of the molecular orbitals. It is also found that the conductances of the molecular wires decrease very strongly if the terminal sulfur atom is simultaneously bonded to hydrogen and a gold surface, thus reflecting the importance of the interface in determining the conductance in two-probe systems. From the conductance studies it may be concluded that if one or more benzene rings of OPE are rotated from coplanar conditions, the orthogonal molecular orbitals may completely block the electronic transport, rendering the molecule insulating.
Combined, solid-state molecular property and gamma spectrometers for CBRNE detection

Science.gov (United States)

Rogers, Ben; Grate, Jay; Pearson, Brett; Gallagher, Neal; Wise, Barry; Whitten, Ralph; Adams, Jesse

2013-05-01

Nevada Nanotech Systems, Inc. (Nevada Nano) has developed a multi-sensor solution to Chemical, Biological, Radiological, Nuclear and Explosives (CBRNE) detection that combines the Molecular Property Spectrometer™ (MPS™)—a micro-electro-mechanical chip-based technology capable of measuring a variety of thermodynamic and electrostatic molecular properties of sampled vapors and particles—and a compact, high-resolution, solid-state gamma spectrometer module for identifying radioactive materials, including isotopes used in dirty bombs and nuclear weapons. By conducting multiple measurements, the system can provide a more complete characterization of an unknown sample, leading to a more accurate identification. Positive identifications of threats are communicated using an integrated wireless module. Currently, system development is focused on detection of commercial, military and improvised explosives, radioactive materials, and chemical threats. The system can be configured for a variety of CBRNE applications, including handheld wands and swab-type threat detectors requiring short sample times, and ultra-high sensitivity detectors in which longer sampling times are used. Here we provide an overview of the system design and operation and present results from preliminary testing.
Methodology for predicting oily mixture properties in the mathematical modeling of molecular distillation

Directory of Open Access Journals (Sweden)

M. F. Gayol

2017-06-01

Full Text Available A methodology for predicting the thermodynamic and transport properties of a multi-component oily mixture, in which the different mixture components are grouped into a small number of pseudo components is shown. This prediction of properties is used in the mathematical modeling of molecular distillation, which consists of a system of differential equations in partial derivatives, according to the principles of the Transport Phenomena and is solved by an implicit finite difference method using a computer code. The mathematical model was validated with experimental data, specifically the molecular distillation of a deodorizer distillate (DD of sunflower oil. The results obtained were satisfactory, with errors less than 10% with respect to the experimental data in a temperature range in which it is possible to apply the proposed method.
Methodology for predicting oily mixture properties in the mathematical modeling of molecular distillation

International Nuclear Information System (INIS)

Gayol, M.F.; Pramparo, M.C.; Miró Erdmann, S.M.

2017-01-01

A methodology for predicting the thermodynamic and transport properties of a multi-component oily mixture, in which the different mixture components are grouped into a small number of pseudo components is shown. This prediction of properties is used in the mathematical modeling of molecular distillation, which consists of a system of differential equations in partial derivatives, according to the principles of the Transport Phenomena and is solved by an implicit finite difference method using a computer code. The mathematical model was validated with experimental data, specifically the molecular distillation of a deodorizer distillate (DD) of sunflower oil. The results obtained were satisfactory, with errors less than 10% with respect to the experimental data in a temperature range in which it is possible to apply the proposed method. [es
Non-linear optical techniques and optical properties of condensed molecular systems

Science.gov (United States)

Citroni, Margherita

2013-06-01

Structure, dynamics, and optical properties of molecular systems can be largely modified by the applied pressure, with remarkable consequences on their chemical stability. Several examples of selective reactions yielding technologically attractive products can be cited, which are particularly efficient when photochemical effects are exploited in conjunction with the structural conditions attained at high density. Non-linear optical techniques are a basic tool to unveil key aspects of the chemical reactivity and dynamic properties of molecules. Their application to high-pressure samples is experimentally challenging, mainly because of the small sample dimensions and of the non-linear effects generated in the anvil materials. In this talk I will present results on the electronic spectra of several aromatic crystals obtained through two-photon induced fluorescence and two-photon excitation profiles measured as a function of pressure (typically up to about 25 GPa), and discuss the relationship between the pressure-induced modifications of the electronic structure and the chemical reactivity at high pressure. I will also present the first successful pump-probe infrared measurement performed as a function of pressure on a condensed molecular system. The system under examination is liquid water, in a sapphire anvil cell, up to 1 GPa along isotherms at 298 and 363 K. These measurements give a new enlightening insight into the dynamical properties of low- and high-density water allowing a definition of the two structures.
Mechanical Properties of Nanostructured Materials Determined Through Molecular Modeling Techniques

Science.gov (United States)

Clancy, Thomas C.; Gates, Thomas S.

2005-01-01

The potential for gains in material properties over conventional materials has motivated an effort to develop novel nanostructured materials for aerospace applications. These novel materials typically consist of a polymer matrix reinforced with particles on the nanometer length scale. In this study, molecular modeling is used to construct fully atomistic models of a carbon nanotube embedded in an epoxy polymer matrix. Functionalization of the nanotube which consists of the introduction of direct chemical bonding between the polymer matrix and the nanotube, hence providing a load transfer mechanism, is systematically varied. The relative effectiveness of functionalization in a nanostructured material may depend on a variety of factors related to the details of the chemical bonding and the polymer structure at the nanotube-polymer interface. The objective of this modeling is to determine what influence the details of functionalization of the carbon nanotube with the polymer matrix has on the resulting mechanical properties. By considering a range of degree of functionalization, the structure-property relationships of these materials is examined and mechanical properties of these models are calculated using standard techniques.
rhf and dft study of the molecular properties of the malaria drug

African Journals Online (AJOL)

USER

The molecular geometries of the common malaria drug Proguanil in gas phase, water and Ethanol have been studied using ab- initio Quantum Chemical calculations at the Restricted Hartree-Fock ... In this research article; we provide a ..... through Emeritus Professor scheme (Grant ... “Synthesis and biological properties of.
Chapter 6 – Computer-Aided Molecular Design and Property Prediction

DEFF Research Database (Denmark)

Gani, Rafiqul; Zhang, L.; Kalakul, Sawitree

2017-01-01

for the initial stages of the design/development process. Therefore, computer-aided molecular design and property prediction techniques are two topics that play important roles in chemical product design, analysis, and application. In this chapter, an overview of the concepts, methods, and tools related......Today's society needs many chemical-based products for its survival, nutrition, health, transportation, agriculture, and the functioning of processes. Chemical-based products have to be designed/developed in order to meet these needs, while at the same time, they must be innovative and sustainable...... to these two topics are given. In addition, a generic computer-aided framework for the design of molecules, mixtures, and blends is presented. The application of the framework is highlighted for molecular products through two case studies involving the design of refrigerants and surfactants....

Properties of crosslinked ultra-high-molecular-weight polyethylene.

Science.gov (United States)

Lewis, G

2001-02-01

Substantially reducing the rate of generation of wear particles at the surfaces of ultra-high-molecular-weight polyethylene (UHMWPE) orthopedic implant bearing components, in vivo, is widely regarded as one of the most formidable challenges in modern arthroplasty. In the light of this, much research attention has been paid to the myriad of endogenous and exogenous factors that have been postulated to affect this wear rate, one such factor being the polymer itself. In recent years, there has been a resurgence of interest in crosslinking the polymer as a way of improving its properties that are considered relevant to its use for fabricating bearing components. Such properties include wear resistance, fatigue life, and fatigue crack propagation rate. Although a large volume of literature exists on the topic on the impact of crosslinking on the properties of UHMWPE, no critical appraisal of this literature has been published. This is one of the goals of the present article, which emphasizes three aspects. The first is the trade-off between improvement in wear resistance and depreciation in other mechanical and physical properties. The second aspect is the presentation of a method of estimating the optimal value of a crosslinking process variable (such as dose in radiation-induced crosslinking) that takes into account this trade-off. The third aspect is the description of a collection of under- and unexplored research areas in the field of crosslinked UHMWPE, such as the role of starting resin on the properties of the crosslinked polymer, and the in vitro evaluation of the wear rate of crosslinked tibial inserts and other bearing components that, in vivo, are subjected to nearly unidirectional motion.
Quantum molecular dynamics simulations of thermophysical properties of fluid ethane

OpenAIRE

Zhang, Yujuan; Wang, Cong; Zheng, Fawei; Zhang, Ping

2012-01-01

We have performed first-principles molecular-dynamics simulations based on density-functional theory to study the thermophysical properties of ethane under extreme conditions. We present new results for the equation of state of fluid ethane in the warm dense region. The optical conductivity is calculated via the Kubo-Greenwood formula from which the dc conductivity and optical reflectivity are derived. The close correlation between the nonmetal-metal transition of ethane and its decomposition...
Thermodynamic and Mechanical Properties of Epon 862 With Curing Agent Detda by Molecular Simulation

National Research Council Canada - National Science Library

Tack, Jeremy L

2006-01-01

Fully atomistic molecular dynamics (MD) simulations were used to predict the properties of EPON 862 cross-linked with curing agent DETDA, a potentially useful epoxy resin for future applications of nanocomposites...
Evaluating Molecular Properties Involved in Transport of Small Molecules in Stratum Corneum: A Quantitative Structure-Activity Relationship for Skin Permeability.

Science.gov (United States)

Chen, Chen-Peng; Chen, Chan-Cheng; Huang, Chia-Wen; Chang, Yen-Ching

2018-04-15

The skin permeability ( Kp ) defines the rate of a chemical penetrating across the stratum corneum. This value is widely used to quantitatively describe the transport of molecules in the outermost layer of epidermal skin and indicate the significance of skin absorption. This study defined a Kp quantitative structure-activity relationship (QSAR) based on 106 chemical substances of Kp measured using human skin and interpreted the molecular interactions underlying transport behavior of small molecules in the stratum corneum. The Kp QSAR developed in this study identified four molecular descriptors that described the molecular cyclicity in the molecule reflecting local geometrical environments, topological distances between pairs of oxygen and chlorine atoms, lipophilicity, and similarity to antineoplastics in molecular properties. This Kp QSAR considered the octanol-water partition coefficient to be a direct influence on transdermal movement of molecules. Moreover, the Kp QSAR identified a sub-domain of molecular properties initially defined to describe the antineoplastic resemblance of a compound as a significant factor in affecting transdermal permeation of solutes. This finding suggests that the influence of molecular size on the chemical's skin-permeating capability should be interpreted with other relevant physicochemical properties rather than being represented by molecular weight alone.
Molecular design chemical structure generation from the properties of pure organic compounds

CERN Document Server

Horvath, AL

1992-01-01

This book is a systematic presentation of the methods that have been developed for the interpretation of molecular modeling to the design of new chemicals. The main feature of the compilation is the co-ordination of the various scientific disciplines required for the generation of new compounds. The five chapters deal with such areas as structure and properties of organic compounds, relationships between structure and properties, and models for structure generation. The subject is covered in sufficient depth to provide readers with the necessary background to understand the modeling
Intellectual property considerations for molecular diagnostic development with emphasis on companion diagnostics.

Science.gov (United States)

Glorikian, Harry; Warburg, Richard Jeremy; Moore, Kelly; Malinowski, Jennifer

2018-02-01

The development of molecular diagnostics is a complex endeavor, with multiple regulatory pathways to consider and numerous approaches to development and commercialization. Companion diagnostics, devices which are "essential for the safe and effective use of a corresponding drug or diagnostic product" (see U.S. Food & Drug Administration, In Vitro Diagnostics - Companion Diagnostics, U.S. Dept. of Health & Human Services(2016), available at https://www.fda.gov/medicaldevices/productsandmedicalprocedures/invitrodiagnostics/ucm407297.htm ) and complementary diagnostics, which are more broadly associated with a class of drug, are becoming increasingly important as integral components of the implementation of precision medicine. Areas covered: The following article will highlight the intellectual property ('IP') considerations pertinent to molecular diagnostics development with special emphasis on companion diagnostics. Expert opinion/commentary Summary: For all molecular diagnostics, intellectual property (IP) concerns are of paramount concern, whether the device will be marketed only in the United States or abroad. Taking steps to protect IP at each stage of product development is critical to optimize profitability of a diagnostic product. Also the legal framework around IP protection of diagnostic technologies has been changing over the previous few years and can be expected to continue to change in the foreseeable near future, thus, a comprehensive IP strategy should take into account the fact that changes in the law can be expected.
Comparison of Molecular Iodine Spectral Properties at 514.7 and 532 nm Wavelengths

Directory of Open Access Journals (Sweden)

Hrabina J.

2014-08-01

Full Text Available We present results of investigation and comparison of spectral properties of molecular iodine transitions in the spectral region of 514.7 nm that are suitable for laser frequency stabilization and metrology of length. Eight Doppler-broadened transitions that were not studied in detail before were investigated with the help of frequency doubled Yb-doped fiber laser, and three of the most promising lines were studied in detail with prospect of using them in frequency stabilization of new laser standards. The spectral properties of hyperfine components (linewidths, signal-to-noise ratio were compared with transitions that are well known and traditionally used for stabilization of frequency doubled Nd:YAG laser at the 532 nm region with the same molecular iodine absorption. The external frequency doubling arrangement with waveguide crystal and the Yb-doped fiber laser is also briefly described together with the observed effect of laser aging.
Tailored Surfaces/Assemblies for Molecular Plasmonics and Plasmonic Molecular Electronics.

Science.gov (United States)

Lacroix, Jean-Christophe; Martin, Pascal; Lacaze, Pierre-Camille

2017-06-12

Molecular plasmonics uses and explores molecule-plasmon interactions on metal nanostructures for spectroscopic, nanophotonic, and nanoelectronic devices. This review focuses on tailored surfaces/assemblies for molecular plasmonics and describes active molecular plasmonic devices in which functional molecules and polymers change their structural, electrical, and/or optical properties in response to external stimuli and that can dynamically tune the plasmonic properties. We also explore an emerging research field combining molecular plasmonics and molecular electronics.
The importance of the biomimetic composites components for recreating the optical properties and molecular composition of intact dental tissues.

Science.gov (United States)

Seredin, P. V.; Goloshchapov, D. L.; Gushchin, M. S.; Ippolitov, Y. A.; Prutskij, T.

2017-11-01

The objective of this paper was to investigate whether it is possible to obtain biomimetic materials recreating the luminescent properties and molecular composition of intact dental tissues. Biomimetic materials were produced and their properties compared with native dental tissues. In addition, the overall contribution of the organic and non-organic components in the photoluminescence band was investigated. The results showed that it is possible to develop biomimetic materials with similar molecular composition and optical properties to native dental tissues for the early identification of dental caries.
Multi-scale calculation of the electric properties of organic-based devices from the molecular structure

KAUST Repository

Li, Haoyuan

2016-03-24

A method is proposed to calculate the electric properties of organic-based devices from the molecular structure. The charge transfer rate is obtained using non-adiabatic molecular dynamics. The organic film in the device is modeled using the snapshots from the dynamic trajectory of the simulated molecular system. Kinetic Monte Carlo simulations are carried out to calculate the current characteristics. A widely used hole-transporting material, N,N′-diphenyl-N,N′-bis(1-naphthyl)-1,1′-biphenyl-4,4′-diamine (NPB) is studied as an application of this method, and the properties of its hole-only device are investigated. The calculated current densities and dependence on the applied voltage without an injection barrier are close to those obtained by the Mott-Gurney equation. The results with injection barriers are also in good agreement with experiment. This method can be used to aid the design of molecules and guide the optimization of devices. © 2016 Elsevier B.V. All rights reserved.
Evaluating Molecular Properties Involved in Transport of Small Molecules in Stratum Corneum: A Quantitative Structure-Activity Relationship for Skin Permeability

Directory of Open Access Journals (Sweden)

Chen-Peng Chen

2018-04-01

Full Text Available The skin permeability (Kp defines the rate of a chemical penetrating across the stratum corneum. This value is widely used to quantitatively describe the transport of molecules in the outermost layer of epidermal skin and indicate the significance of skin absorption. This study defined a Kp quantitative structure-activity relationship (QSAR based on 106 chemical substances of Kp measured using human skin and interpreted the molecular interactions underlying transport behavior of small molecules in the stratum corneum. The Kp QSAR developed in this study identified four molecular descriptors that described the molecular cyclicity in the molecule reflecting local geometrical environments, topological distances between pairs of oxygen and chlorine atoms, lipophilicity, and similarity to antineoplastics in molecular properties. This Kp QSAR considered the octanol-water partition coefficient to be a direct influence on transdermal movement of molecules. Moreover, the Kp QSAR identified a sub-domain of molecular properties initially defined to describe the antineoplastic resemblance of a compound as a significant factor in affecting transdermal permeation of solutes. This finding suggests that the influence of molecular size on the chemical’s skin-permeating capability should be interpreted with other relevant physicochemical properties rather than being represented by molecular weight alone.
Molecular Properties of Red Wine Compounds and Cardiometabolic Benefits.

Science.gov (United States)

Markoski, Melissa M; Garavaglia, Juliano; Oliveira, Aline; Olivaes, Jessica; Marcadenti, Aline

2016-01-01

Wine has been used since the dawn of human civilization. Despite many health benefits, there is still a lot of discussion about the real properties of its components and its actions on cells and molecular interactions. A large part of these issues permeate the fine line between the amount of alcohol that causes problems to organic systems and the amount that could be beneficial for the health. However, even after the process of fermentation, wine conserves different organic compounds from grapes, such as polysaccharides, acids, and phenolic compounds, such as flavonoids and nonflavonoids. These substances have known anti-inflammatory and antioxidant capacities, and are considered as regulatory agents in cardiometabolic process. In this study, the main chemical components present in the wine, its interaction with molecules and biological mechanisms, and their interference with intra- and extracellular signaling are reviewed. Finally, the properties of wine that may benefit cardiovascular system are also revised.
Molecular Properties of Red Wine Compounds and Cardiometabolic Benefits

Science.gov (United States)

Markoski, Melissa M.; Garavaglia, Juliano; Oliveira, Aline; Olivaes, Jessica; Marcadenti, Aline

2016-01-01

Wine has been used since the dawn of human civilization. Despite many health benefits, there is still a lot of discussion about the real properties of its components and its actions on cells and molecular interactions. A large part of these issues permeate the fine line between the amount of alcohol that causes problems to organic systems and the amount that could be beneficial for the health. However, even after the process of fermentation, wine conserves different organic compounds from grapes, such as polysaccharides, acids, and phenolic compounds, such as flavonoids and nonflavonoids. These substances have known anti-inflammatory and antioxidant capacities, and are considered as regulatory agents in cardiometabolic process. In this study, the main chemical components present in the wine, its interaction with molecules and biological mechanisms, and their interference with intra- and extracellular signaling are reviewed. Finally, the properties of wine that may benefit cardiovascular system are also revised. PMID:27512338
Molecular Properties of Red Wine Compounds and Cardiometabolic Benefits

Directory of Open Access Journals (Sweden)

Melissa M. Markoski

2016-01-01

Full Text Available Wine has been used since the dawn of human civilization. Despite many health benefits, there is still a lot of discussion about the real properties of its components and its actions on cells and molecular interactions. A large part of these issues permeate the fine line between the amount of alcohol that causes problems to organic systems and the amount that could be beneficial for the health. However, even after the process of fermentation, wine conserves different organic compounds from grapes, such as polysaccharides, acids, and phenolic compounds, such as flavonoids and nonflavonoids. These substances have known anti-inflammatory and antioxidant capacities, and are considered as regulatory agents in cardiometabolic process. In this study, the main chemical components present in the wine, its interaction with molecules and biological mechanisms, and their interference with intra- and extracellular signaling are reviewed. Finally, the properties of wine that may benefit cardiovascular system are also revised.
Associations between the molecular and optical properties of dissolved organic matter in the Florida Everglades, a model coastal wetland system

Science.gov (United States)

Wagner, Sasha; Jaffe, Rudolf; Cawley, Kaelin; Dittmar, Thorsten; Stubbins, Aron

2015-11-01

Optical properties are easy-to-measure proxies for dissolved organic matter (DOM) composition, source and reactivity. However, the molecular signature of DOM associated with such optical parameters remains poorly defined. The Florida coastal Everglades is a subtropical wetland with diverse vegetation (e.g., sawgrass prairies, mangrove forests, seagrass meadows) and DOM sources (e.g., terrestrial, microbial and marine). As such, the Everglades is an excellent model system from which to draw samples of diverse origin and composition to allow classically-defined optical properties to be linked to molecular properties of the DOM pool. We characterized a suite of seasonally- and spatially-collected DOM samples using optical measurements (EEM-PARAFAC, SUVA254, S275-295, S350-400, SR, FI, freshness index and HIX) and ultrahigh resolution mass spectrometry (FTICR-MS). Spearman’s rank correlations between FTICR-MS signal intensities of individual molecular formulae and optical properties determined which molecular formulae were associated with each PARAFAC component and optical index. The molecular families that tracked with the optical indices were generally in agreement with conventional biogeochemical interpretations. Therefore, although they represent only a small portion of the bulk DOM pool, absorbance and fluorescence measurements appear to be appropriate proxies for the aquatic cycling of both optically-active and associated optically-inactive DOM in coastal wetlands.
The polysaccharide and low molecular weight components of Opuntia ficus indica cladodes: Structure and skin repairing properties.

Science.gov (United States)

Di Lorenzo, Flaviana; Silipo, Alba; Molinaro, Antonio; Parrilli, Michelangelo; Schiraldi, Chiara; D'Agostino, Antonella; Izzo, Elisabetta; Rizza, Luisa; Bonina, Andrea; Bonina, Francesco; Lanzetta, Rosa

2017-02-10

The Opuntia ficus-indica multiple properties are reflected in the increasing interest of chemists in the identification of its natural components having pharmaceutical and/or cosmetical applications. Here we report the structural elucidation of Opuntia ficus-indica mucilage that highlighted the presence of components differing for their chemical nature and the molecular weight distribution. The high molecular weight components were identified as a linear galactan polymer and a highly branched xyloarabinan. The low molecular weight components were identified as lactic acid, D-mannitol, piscidic, eucomic and 2-hydroxy-4-(4'-hydroxyphenyl)-butanoic acids. A wound healing assay was performed in order to test the cicatrizing properties of the various components, highlighting the ability of these latter to fasten dermal regeneration using a simplified in vitro cellular model based on a scratched keratinocytes monolayer. The results showed that the whole Opuntia mucilage and the low molecular weight components are active in the wound repair. Copyright © 2016 Elsevier Ltd. All rights reserved.
Influence of Molecular Conformations and Microstructure on the Optoelectronic Properties of Conjugated Polymers

KAUST Repository

Botiz, Ioan; Stingelin, Natalie

2014-01-01

It is increasingly obvious that the molecular conformations and the long-range arrangement that conjugated polymers can adopt under various experimental conditions in bulk, solutions or thin films, significantly impact their resulting optoelectronic properties. As a consequence, the functionalities and efficiencies of resulting organic devices, such as field-effect transistors, light-emitting diodes, or photovoltaic cells, also dramatically change due to the close structure/property relationship. A range of structure/optoelectronic properties relationships have been investigated over the last few years using various experimental and theoretical methods, and, further, interesting correlations are continuously revealed by the scientific community. In this review, we discuss the latest findings related to the structure/optoelectronic properties interrelationships that exist in organic devices fabricated with conjugated polymers in terms of charge mobility, absorption, photoluminescence, as well as photovoltaic properties. © 2014 by the authors.
Influence of Molecular Conformations and Microstructure on the Optoelectronic Properties of Conjugated Polymers

Directory of Open Access Journals (Sweden)

Ioan Botiz

2014-03-01

Full Text Available It is increasingly obvious that the molecular conformations and the long-range arrangement that conjugated polymers can adopt under various experimental conditions in bulk, solutions or thin films, significantly impact their resulting optoelectronic properties. As a consequence, the functionalities and efficiencies of resulting organic devices, such as field-effect transistors, light-emitting diodes, or photovoltaic cells, also dramatically change due to the close structure/property relationship. A range of structure/optoelectronic properties relationships have been investigated over the last few years using various experimental and theoretical methods, and, further, interesting correlations are continuously revealed by the scientific community. In this review, we discuss the latest findings related to the structure/optoelectronic properties interrelationships that exist in organic devices fabricated with conjugated polymers in terms of charge mobility, absorption, photoluminescence, as well as photovoltaic properties.
Influence of Molecular Conformations and Microstructure on the Optoelectronic Properties of Conjugated Polymers

KAUST Repository

Botiz, Ioan

2014-03-19

It is increasingly obvious that the molecular conformations and the long-range arrangement that conjugated polymers can adopt under various experimental conditions in bulk, solutions or thin films, significantly impact their resulting optoelectronic properties. As a consequence, the functionalities and efficiencies of resulting organic devices, such as field-effect transistors, light-emitting diodes, or photovoltaic cells, also dramatically change due to the close structure/property relationship. A range of structure/optoelectronic properties relationships have been investigated over the last few years using various experimental and theoretical methods, and, further, interesting correlations are continuously revealed by the scientific community. In this review, we discuss the latest findings related to the structure/optoelectronic properties interrelationships that exist in organic devices fabricated with conjugated polymers in terms of charge mobility, absorption, photoluminescence, as well as photovoltaic properties. © 2014 by the authors.
Synthesis and photophysical properties of a novel corrole–anthraquinone–corrole molecular system

International Nuclear Information System (INIS)

Sudhakar, Kolanu; Kanaparthi, Ravi Kumar; Kumar, Challa Kiran; Giribabu, Lingamallu

2014-01-01

A novel molecular triad (AQ-(H 3 ) 2 ) based on tritolylcorrole and anthraquinone having azomethine-bridge at the pyrrole-β position has been designed and synthesized by following a facile one step reaction. The molecular system, AQ-(H 3 ) 2 is characterized by elemental analysis, MALDI-MS, 1 H-NMR, UV–Visible and fluorescence spectroscopy (steady-state and time-resolved) as well as electrochemical methods. In absorption spectra, prominent changes such as red-shift (∼7 nm) and broadening of the both Soret and Q-bands with respect to their monomer units were observed. The present study supported by density functional theory calculations manifest that there exists a negligible electronic communication in the ground state between the donor tritolylcorrole and acceptor anthraquinone of the triad. However, interestingly, in the triad AQ-(H 3 ) 2 , fluorescence emission of the tritolylcorrole quenched significantly (17–80%) compared to their monomeric units. The emission quenching is attributed to the excited state intramolecular photoinduced electron transfer from donor tritolylcorrole to acceptor anthraquinone and the electron transfer rates (k ET ) are found in the range 4.1×10 8 to 2.4×10 9 s −1 and are found to be solvent dependent. - Highlights: • Molecular triad based on corrole and anthraquinone having azomethine-bridge at pyrrole-β position. • Ground state properties showed that there exist minimum π–π interactions. • Excited state properties showed intramolecular photoinduced electron transfer from corrole to anthraquinone

Equilibrium and Transport Properties of Primary, Secondary and Tertiary Amines by Molecular Simulation

International Nuclear Information System (INIS)

Orozco, Gustavo A.; Nieto-Draghi, Carlos; Lachet, Veronique; Mackie, Allan D.

2014-01-01

Using molecular simulation techniques such as Monte Carlo (MC) and molecular dynamics (MD), we present several simulation results of thermodynamic and transport properties for primary, secondary and tertiary amines. These calculations are based on a recently proposed force field for amines that follows the Anisotropic United Atom approach (AUA). Different amine molecules have been studied, including n-Butylamine, di-n-Butylamine, tri-n-Butylamine and 1,4-Butanediamine for primary, secondary, tertiary and multi-functional amines respectively. For the transport properties, we have calculated the viscosity coefficients as a function of temperature using the isothermal-isobaric (NPT) ensemble. In the case of the pure components, we have investigated different thermodynamic properties using NVT Gibbs ensemble simulations such as liquid-vapor phase equilibrium diagrams, vaporization enthalpies, vapor pressures, normal boiling points, critical temperatures and critical densities. We have also calculated the excess enthalpies for water-n-Butylamine and n-heptane-n-Butylamine mixtures using Monte Carlo simulations in the NPT ensemble. In addition, we present the calculation of liquid-vapor surface tensions of n-Butylamine using a two-phase NVT simulation as well as the radial distribution functions. Finally, we have investigated the physical Henry constants of nitrous oxide (N 2 O) and nitrogen (N 2 ) in an aqueous solutions of n-Butylamine. In general, we found a good agreement between the available experimental information and our simulation results for all the studied properties, ratifying the predictive capability of the AUA force field for amines. (authors)
High-pressure microscopy for tracking dynamic properties of molecular machines.

Science.gov (United States)

Nishiyama, Masayoshi

2017-12-01

High-pressure microscopy is one of the powerful techniques to visualize the effects of hydrostatic pressures on research targets. It could be used for monitoring the pressure-induced changes in the structure and function of molecular machines in vitro and in vivo. This review focuses on the dynamic properties of the assemblies and machines, analyzed by means of high-pressure microscopy measurement. We developed a high-pressure microscope that is optimized both for the best image formation and for the stability to hydrostatic pressure up to 150 MPa. Application of pressure could change polymerization and depolymerization processes of the microtubule cytoskeleton, suggesting a modulation of the intermolecular interaction between tubulin molecules. A novel motility assay demonstrated that high hydrostatic pressure induces counterclockwise (CCW) to clockwise (CW) reversals of the Escherichia coli flagellar motor. The present techniques could be extended to study how molecular machines in complicated systems respond to mechanical stimuli. Copyright © 2017 Elsevier B.V. All rights reserved.
Molecular markers of benzene polycarboxylic acids in describing biochar physiochemical properties and sorption characteristics.

Science.gov (United States)

Chang, Zhaofeng; Tian, Luping; Wu, Min; Dong, Xudong; Peng, Juan; Pan, Bo

2018-06-01

Biochar function in soil is based on properties such as sorption characteristics, and these are expected to change throughout the life cycle of the biochar. Because biochar particles cannot easily be separated from soil particles, this change is seldom investigated. Biochar-related molecular markers, such as benzene polycarboxylic acids (BPCAs) are promising tools for studying the properties of biochars in complex environmental matrices. In this study, biochars were derived from corn straw and pine wood sawdust at 200-500 °C, and their aging was simulated with NaClO. Biochar properties were characterized by elemental analysis, BET surface characterization and BPCA molecular marker analysis. Chemical oxidation decreased the surface area (SA) but increased the O content of biochars. The oxidation decreased the amount of biochars, with a mass loss in the range of 10-55%. A similar mass loss was also observed for BPCAs and was negatively related to both the pyrolysis temperature and the extent of the condensed structure (higher aromaticity). The biochar amounts were calculated quantitatively using the sum of BPCA contents, with a conversion factor (the ratio of biochar amount to BPCA content) in the range of 3.3-5.5, and were negatively related to the B5CA content. Three model pollutants, namely, bisphenol A (BPA), sulfamethoxazole (SMX), and phenanthrene (PHE), were chosen to study the sorption characteristics of biochar before and after oxidation. Chemical oxidation generally increased SMX sorption but decreased PHE sorption. The nonlinear factor n, based on Freundlich equation modeling, was negatively related to B6CA for all three chemicals. The BPCA molecular markers, especially B5CA and B6CA, were correlated to the biochar properties before and after oxidation and are thus a potentially useful technique for describing the characteristics of biochar in the environment. Copyright © 2018 Elsevier Ltd. All rights reserved.
Computational study of the human dystrophin repeats: interaction properties and molecular dynamics.

Directory of Open Access Journals (Sweden)

Baptiste Legrand

Full Text Available Dystrophin is a large protein involved in the rare genetic disease Duchenne muscular dystrophy (DMD. It functions as a mechanical linker between the cytoskeleton and the sarcolemma, and is able to resist shear stresses during muscle activity. In all, 75% of the dystrophin molecule consists of a large central rod domain made up of 24 repeat units that share high structural homology with spectrin-like repeats. However, in the absence of any high-resolution structure of these repeats, the molecular basis of dystrophin central domain's functions has not yet been deciphered. In this context, we have performed a computational study of the whole dystrophin central rod domain based on the rational homology modeling of successive and overlapping tandem repeats and the analysis of their surface properties. Each tandem repeat has very specific surface properties that make it unique. However, the repeats share enough electrostatic-surface similarities to be grouped into four separate clusters. Molecular dynamics simulations of four representative tandem repeats reveal specific flexibility or bending properties depending on the repeat sequence. We thus suggest that the dystrophin central rod domain is constituted of seven biologically relevant sub-domains. Our results provide evidence for the role of the dystrophin central rod domain as a scaffold platform with a wide range of surface features and biophysical properties allowing it to interact with its various known partners such as proteins and membrane lipids. This new integrative view is strongly supported by the previous experimental works that investigated the isolated domains and the observed heterogeneity of the severity of dystrophin related pathologies, especially Becker muscular dystrophy.
Associations between the molecular and optical properties of dissolved organic matter in the Florida Everglades, a model coastal wetland system

Directory of Open Access Journals (Sweden)

Sasha eWagner

2015-11-01

Full Text Available Optical properties are easy-to-measure proxies for dissolved organic matter (DOM composition, source and reactivity. However, the molecular signature of DOM associated with such optical parameters remains poorly defined. The Florida coastal Everglades is a subtropical wetland with diverse vegetation (e.g., sawgrass prairies, mangrove forests, seagrass meadows and DOM sources (e.g., terrestrial, microbial and marine. As such, the Everglades is an excellent model system from which to draw samples of diverse origin and composition to allow classically-defined optical properties to be linked to molecular properties of the DOM pool. We characterized a suite of seasonally- and spatially-collected DOM samples using optical measurements (EEM-PARAFAC, SUVA254, S275-295, S350-400, SR, FI, freshness index and HIX and ultrahigh resolution mass spectrometry (FTICR-MS. Spearman’s rank correlations between FTICR-MS signal intensities of individual molecular formulae and optical properties determined which molecular formulae were associated with each PARAFAC component and optical index. The molecular families that tracked with the optical indices were generally in agreement with conventional biogeochemical interpretations. Therefore, although they represent only a small portion of the bulk DOM pool, absorbance and fluorescence measurements appear to be appropriate proxies for the aquatic cycling of both optically-active and associated optically-inactive DOM in coastal wetlands.
New concepts for molecular magnets

Science.gov (United States)

Pilawa, Bernd

1999-03-01

Miller and Epstein (1994) define molecular magnets as magnetic materials which are prepared by the low-temperature methods of the preparative chemistry. This definition includes molecular crystals of neutral radicals, radical salts and charge transfer complexes as well as metal complexes and polymers with unpaired spins (Dormann 1995). The challenge of molecular magnets consists in tailoring magnetic properties by specific modifications of the molecular units. The combination of magnetism with mechanical or electrical properties of molecular compounds promise materials of high technical interest (Gatteschi 1994a and 1994b, Möhwald 1996) and both the chemical synthesis of new molecular materials with magnetic properties as well as the physical investigation and explanation of these properties is important, in order to achieve any progress. This work deals with the physical characterization of the magnetic properties of molecular materials. It is organized as follows. In the first part molecular crystals of neutral radicals are studied. After briefly discussing the general magnetic properties of these materials and after an overview over the physical principles of exchange interaction between organic radicals I focus on the interplay between the crystallographic structure and the magnetic properties of various derivatives of the verdazyl and nitronyl nitroxide radicals. The magnetic properties of metal complexes are the subject of the second part. After an overview over the experimental and theoretical tools which are used for the investigation of the magnetic properties I shortly discuss the exchange coupling of transition metal ions and the magnetic properties of complexes of two and three metal ions. Special emphasis is given to spin cluster compounds. Spin cluster denote complexes of many magnetic ions. They are attractive as building blocks of molecular magnets as well as magnetic model compounds for the study of spin frustration, molecular super
First-principles study of the electronic transport properties of the anthraquinone-based molecular switch

Energy Technology Data Exchange (ETDEWEB)

Zhao, P., E-mail: ss_zhaop@ujn.edu.c [School of Science, University of Jinan, Jinan 250022 (China); Liu, D.S. [School of Physics, State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100 (China); Department of Physics, Jining University, Qufu 273155 (China); Wang, P.J.; Zhang, Z. [School of Science, University of Jinan, Jinan 250022 (China); Fang, C.F.; Ji, G.M. [School of Physics, State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100 (China)

2011-02-15

By applying non-equilibrium Green's function (NEGF) formalism combined with first-principles density functional theory (DFT), we have investigated the electronic transport properties of the anthraquinone-based molecular switch. The molecule that comprises the switch can be converted between the hydroquinone (HQ) and anthraquinone (AQ) forms via redox reactions. The transmission spectra of these two forms are remarkably distinctive. Our results show that the current through the HQ form is significantly larger than that through the AQ form, which suggests that this system has attractive potential application in future molecular switch technology.
First-principles study of the electronic transport properties of the anthraquinone-based molecular switch

International Nuclear Information System (INIS)

Zhao, P.; Liu, D.S.; Wang, P.J.; Zhang, Z.; Fang, C.F.; Ji, G.M.

2011-01-01

By applying non-equilibrium Green's function (NEGF) formalism combined with first-principles density functional theory (DFT), we have investigated the electronic transport properties of the anthraquinone-based molecular switch. The molecule that comprises the switch can be converted between the hydroquinone (HQ) and anthraquinone (AQ) forms via redox reactions. The transmission spectra of these two forms are remarkably distinctive. Our results show that the current through the HQ form is significantly larger than that through the AQ form, which suggests that this system has attractive potential application in future molecular switch technology.
Beyond the Alphabet Soup: Molecular Properties of Aerosol Components Influence Optics. (Invited)

Science.gov (United States)

Thompson, J. E.

2013-12-01

Components within atmospheric aerosols exhibit almost every imaginable model of chemical bonding and physical diversity. The materials run the spectrum from crystalline to amorphous, covalent to ionic, and have varying viscosities, phase, and hygroscopicity. This seminar will focus on the molecular properties of materials that influence the optical behavior of aerosols. Special focus will be placed on the polarizability of materials, hygroscopic growth, and particle phase.
Synthesis and photophysical properties of a novel corrole–anthraquinone–corrole molecular system

Energy Technology Data Exchange (ETDEWEB)

Sudhakar, Kolanu [Inorganic and Physical Chemistry Division, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad-500007, Andhra Pradesh (India); Kanaparthi, Ravi Kumar [Inorganic and Physical Chemistry Division, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad-500007, Andhra Pradesh (India); Department of Chemistry, Central University of Kerala, Reverside Transit Campus, Padanakkad, Nileshwar Kasaragod District - 671 314 Kerala (India); Kumar, Challa Kiran [Inorganic and Physical Chemistry Division, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad-500007, Andhra Pradesh (India); Giribabu, Lingamallu, E-mail: giribabu@iict.res.in [Inorganic and Physical Chemistry Division, CSIR-Indian Institute of Chemical Technology, Tarnaka, Hyderabad-500007, Andhra Pradesh (India)

2014-09-15

A novel molecular triad (AQ-(H{sub 3}){sub 2}) based on tritolylcorrole and anthraquinone having azomethine-bridge at the pyrrole-β position has been designed and synthesized by following a facile one step reaction. The molecular system, AQ-(H{sub 3}){sub 2} is characterized by elemental analysis, MALDI-MS, {sup 1}H-NMR, UV–Visible and fluorescence spectroscopy (steady-state and time-resolved) as well as electrochemical methods. In absorption spectra, prominent changes such as red-shift (∼7 nm) and broadening of the both Soret and Q-bands with respect to their monomer units were observed. The present study supported by density functional theory calculations manifest that there exists a negligible electronic communication in the ground state between the donor tritolylcorrole and acceptor anthraquinone of the triad. However, interestingly, in the triad AQ-(H{sub 3}){sub 2}, fluorescence emission of the tritolylcorrole quenched significantly (17–80%) compared to their monomeric units. The emission quenching is attributed to the excited state intramolecular photoinduced electron transfer from donor tritolylcorrole to acceptor anthraquinone and the electron transfer rates (k{sub ET}) are found in the range 4.1×10{sup 8} to 2.4×10{sup 9} s{sup −1} and are found to be solvent dependent. - Highlights: • Molecular triad based on corrole and anthraquinone having azomethine-bridge at pyrrole-β position. • Ground state properties showed that there exist minimum π–π interactions. • Excited state properties showed intramolecular photoinduced electron transfer from corrole to anthraquinone.
CheckDen, a program to compute quantum molecular properties on spatial grids.

Science.gov (United States)

Pacios, Luis F; Fernandez, Alberto

2009-09-01

CheckDen, a program to compute quantum molecular properties on a variety of spatial grids is presented. The program reads as unique input wavefunction files written by standard quantum packages and calculates the electron density rho(r), promolecule and density difference function, gradient of rho(r), Laplacian of rho(r), information entropy, electrostatic potential, kinetic energy densities G(r) and K(r), electron localization function (ELF), and localized orbital locator (LOL) function. These properties can be calculated on a wide range of one-, two-, and three-dimensional grids that can be processed by widely used graphics programs to render high-resolution images. CheckDen offers also other options as extracting separate atom contributions to the property computed, converting grid output data into CUBE and OpenDX volumetric data formats, and perform arithmetic combinations with grid files in all the recognized formats.
The electronic and optical properties of warm dense nitrous oxide using quantum molecular dynamics simulations

International Nuclear Information System (INIS)

Zhang Yujuan; Wang Cong; Zhang Ping

2012-01-01

First-principles molecular-dynamics simulations based on density-functional theory have been used to study the electronic and optical properties of fluid nitrous oxide under extreme conditions. Systematic descriptions of pair-correlation function, atomic structure, and the charge density distribution are used to investigate the dissociation of fluid nitrous oxide. The electrical and optical properties are derived from the Kubo-Greenwood formula. It is found that the nonmetal-metal transition for fluid nitrous oxide can be directly associated to the dissociation and has significant influence on the optical properties of the fluid.
Structural, vibrational and theoretical studies of anilinium trichloroacetate: New hydrogen bonded molecular crystal with nonlinear optical properties

Science.gov (United States)

Tanak, H.; Pawlus, K.; Marchewka, M. K.; Pietraszko, A.

2014-01-01

In this work, we report a combined experimental and theoretical study on molecular structure, vibrational spectra and NBO analysis of the potential nonlinear optical (NLO) material anilinium trichloroacetate. The FT-IR and FT-Raman spectra of the compound have been recorded together between 4000-80 cm-1 and 3600-80 cm-1 regions, respectively. The compound crystallizes in the noncentrosymmetric space group of monoclinic system. The optimized molecular structure, vibrational wavenumbers, IR intensities and Raman activities have been calculated by using density functional method (B3LYP) with 6-311++G(d,p) as higher basis set. The obtained vibrational wavenumbers and optimized geometric parameters were seen to be in good agreement with the experimental data. DSC measurements on powder samples do not indicate clearly on the occurrence of phase transitions in the temperature 113-293 K. The Kurtz and Perry powder reflection technique appeared to be very effective in studies of second-order nonlinear optical properties of the molecule. The non-linear optical properties are also addressed theoretically. The predicted NLO properties of the title compound are much greater than ones of urea. In addition, DFT calculations of the title compound, molecular electrostatic potential, frontier orbitals and thermodynamic properties were also performed at 6-311++G(d,p) level of theory. For title crystal the SHG efficiency was estimated by Kurtz-Perry method to be deff = 0.70 deff (KDP).
Thermophysical properties of hydrogen-helium mixtures: re-examination of the mixing rules via quantum molecular dynamics simulations.

Science.gov (United States)

Wang, Cong; He, Xian-Tu; Zhang, Ping

2013-09-01

Thermophysical properties of hydrogen, helium, and hydrogen-helium mixtures have been investigated in the warm dense matter regime at electron number densities ranging from 6.02 × 10^{29} ∼ 2.41 × 10^{30} m^{-3} and temperatures from 4000 to 20000 K via quantum molecular dynamics simulations. We focus on the dynamical properties such as the equation of states, diffusion coefficients, and viscosity. Mixing rules (density matching, pressure matching, and binary ionic mixing rules) have been validated by checking composite properties of pure species against that of the fully interacting mixture derived from quantum molecular dynamics simulations. These mixing rules reproduce pressures within 10% accuracy, while it is 75% and 50% for the diffusion and viscosity, respectively. The binary ionic mixing rule moves the results into better agreement. Predictions from one component plasma model are also provided and discussed.
Adsorption properties of a molecular 5 A sieve for 85Kr

International Nuclear Information System (INIS)

Wardaszko, T.; Nidecka, J.

1978-01-01

The enrichment processes which are necessary at low-level 85 Kr determinations in the atmospheric air require the knowledge of adsorption properties of appropriate sorbing agents, such as a molecular 5A sieve. Following low-temperature adsorption, under specified conditions, of known amounts of 85 Kr diluted in the air, desorption was carried out and then the 85 Kr content in the temperature fraction as well as their total volume were determined. Distribution curves for the above quantities in fractions are presented. (author)
Rectifying Properties of a Nitrogen/Boron-Doped Capped-Carbon-Nanotube-Based Molecular Junction

International Nuclear Information System (INIS)

Zhao Peng; Zhang Ying; Wang Pei-Ji; Zhang Zhong; Liu De-Sheng

2011-01-01

Based on the non-equilibrium Green's function method and first-principles density functional theory calculations, we investigate the electronic transport properties of a nitrogen/boron-doped capped-single-walled carbon-nanotube-based molecular junction. Obvious rectifying behavior is observed and it is strongly dependent on the doping site. The best rectifying performance can be carried out when the nitrogen/boron atom dopes at a carbon site in the second layer. Moreover, the rectifying performance can be further improved by adjusting the distance between the C 60 nanotube caps. (condensed matter: electronic structure, electrical, magnetic, and optical properties)
Molecular simulation of the thermophysical properties and phase behaviour of impure CO2 relevant to CCS.

Science.gov (United States)

Cresswell, Alexander J; Wheatley, Richard J; Wilkinson, Richard D; Graham, Richard S

2016-10-20

Impurities from the CCS chain can greatly influence the physical properties of CO 2 . This has important design, safety and cost implications for the compression, transport and storage of CO 2 . There is an urgent need to understand and predict the properties of impure CO 2 to assist with CCS implementation. However, CCS presents demanding modelling requirements. A suitable model must both accurately and robustly predict CO 2 phase behaviour over a wide range of temperatures and pressures, and maintain that predictive power for CO 2 mixtures with numerous, mutually interacting chemical species. A promising technique to address this task is molecular simulation. It offers a molecular approach, with foundations in firmly established physical principles, along with the potential to predict the wide range of physical properties required for CCS. The quality of predictions from molecular simulation depends on accurate force-fields to describe the interactions between CO 2 and other molecules. Unfortunately, there is currently no universally applicable method to obtain force-fields suitable for molecular simulation. In this paper we present two methods of obtaining force-fields: the first being semi-empirical and the second using ab initio quantum-chemical calculations. In the first approach we optimise the impurity force-field against measurements of the phase and pressure-volume behaviour of CO 2 binary mixtures with N 2 , O 2 , Ar and H 2 . A gradient-free optimiser allows us to use the simulation itself as the underlying model. This leads to accurate and robust predictions under conditions relevant to CCS. In the second approach we use quantum-chemical calculations to produce ab initio evaluations of the interactions between CO 2 and relevant impurities, taking N 2 as an exemplar. We use a modest number of these calculations to train a machine-learning algorithm, known as a Gaussian process, to describe these data. The resulting model is then able to accurately
Gd doped Au nanoclusters: Molecular magnets with novel properties

KAUST Repository

Mokkath, Junais Habeeb

2014-01-01

The structural, magnetic, and optical properties of subnanometer Au N and AuN-1Gd1 gas phase clusters (N = 2 to 8) are systematically investigated in the framework of (time-dependent) density functional theory, using the B3LYP hybrid exchange correlation functional. The size dependent evolution of the gap between the highest occupied and lowest unoccupied molecular orbitals, the magnetism, and the absorption spectra are studied. The simultaneous appearance of large magnetic moments, significant band gaps, and plasmon resonances in the visible spectral region leads to novel multi-functional nanomaterials for applications in drug delivery, magnetic resonance imaging, and photo-responsive agents. © 2013 Elsevier B.V. All rights reserved.
pH-Induced Modulation of One- and Two-Photon Absorption Properties in a Naphthalene-Based Molecular Probe.

Science.gov (United States)

Murugan, N Arul; Kongsted, Jacob; Ågren, Hans

2013-08-13

Presently, there is a great demand for small probe molecules that can be used for two-photon excitation microscopy (TPM)-based monitoring of intracellular and intraorganelle activity and pH. The candidate molecules should ideally possess a large two-photon absorption cross section with optical properties sensitive to pH changes. In the present work, we investigate the potential of a methoxy napthalene (MONAP) derivative for its suitability to serve as a pH sensor using TPM. Using an integrated approach rooted in hybrid quantum mechanics/molecular mechanics, the structures, dynamics, and the one- and two-photon properties of the probe in dimethylformamide solvent are studied. It is found that the protonated form is responsible for the optical property of MONAP at moderately low pH, for which the calculated pH-induced red shift is in good agreement with experiments. A 2-fold increase in the two-photon absorption cross section in the IR region of the spectrum is predicted for the moderately low pH form of the probe, suggesting that this can be a potential probe for pH monitoring of living cells. We also propose some design principles aimed at obtaining control of the absorption spectral range of the probe by structural tuning. Our work indicates that the integrated approach employed is capable of capturing the pH-induced changes in structure and optical properties of organic molecular probes and that such in silico tools can be used to draw structure-property relationships to design novel molecular probes suitable for a specific application.
Machine learning predictions of molecular properties: Accurate many-body potentials and nonlocality in chemical space

International Nuclear Information System (INIS)

Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan; Pronobis, Wiktor; Lilienfeld, O. Anatole von; Müller, Klaus-Robert; Tkatchenko, Alexandre

2015-01-01

Simultaneously accurate and efficient prediction of molecular properties throughout chemical compound space is a critical ingredient toward rational compound design in chemical and pharmaceutical industries. Aiming toward this goal, we develop and apply a systematic hierarchy of efficient empirical methods to estimate atomization and total energies of molecules. These methods range from a simple sum over atoms, to addition of bond energies, to pairwise interatomic force fields, reaching to the more sophisticated machine learning approaches that are capable of describing collective interactions between many atoms or bonds. In the case of equilibrium molecular geometries, even simple pairwise force fields demonstrate prediction accuracy comparable to benchmark energies calculated using density functional theory with hybrid exchange-correlation functionals; however, accounting for the collective many-body interactions proves to be essential for approaching the 'holy grail' of chemical accuracy of 1 kcal/mol for both equilibrium and out-of-equilibrium geometries. This remarkable accuracy is achieved by a vectorized representation of molecules (so-called Bag of Bonds model) that exhibits strong nonlocality in chemical space. The same representation allows us to predict accurate electronic properties of molecules, such as their polarizability and molecular frontier orbital energies

Unique molecular properties of superoxide dismutase from teleost fish skin.

Science.gov (United States)

Nakano, T; Sato, M; Takeuchi, M

1995-02-27

A unique Cu,Zn-SOD was found and isolated from plaice Paralichthys olivaceus skin. Surprisingly, the properties of purified fish skin SOD were very different from those of SOD from other sources reported so far. The purified SOD was composed of four same subunits of 16 kDa and the molecular weight of the native SOD was found to be around 65 kDa. The dominant amino acids of the SOD were Ser, Thr, Pro and Glu. Above 70 degrees C, thermostability of the SOD was much lower than that of bovine erythrocyte Cu,Zn-SOD.
Effect of molecular properties on the performance of polymer light-emitting diodes

Energy Technology Data Exchange (ETDEWEB)

Ramos, Marta M.D.; Almeida, A.M.; Correia, Helena M.G.; Ribeiro, R. Mendes; Stoneham, A.M

2004-11-15

The performance of a single layer polymer light-emitting diode depends on several interdependent factors, although recombination between electrons and holes within the polymer layer is believed to play an important role. Our aim is to carry out computer experiments in which bipolar charge carriers are injected in polymer networks made of poly(p-phenylene vinylene) chains randomly oriented. In these simulations, we follow the charge evolution in time from some initial state to the steady state. The intra-molecular properties of the polymer molecules obtained from self-consistent quantum molecular dynamics calculations are used in the mesoscopic model. The purpose of the present work is to clarify the effects of intra-molecular charge mobility and energy disorder on recombination efficiency. In particular, we find that charge mobility along the polymer chains has a serious influence on recombination within the polymer layer. Our results also show that energy disorder due to differences in ionization potential and electron affinity of neighbouring molecules affects mainly recombinations that occur near the electrodes at polymer chains parallel to them.
Effect of molecular properties on the performance of polymer light-emitting diodes

International Nuclear Information System (INIS)

Ramos, Marta M.D.; Almeida, A.M.; Correia, Helena M.G.; Ribeiro, R. Mendes; Stoneham, A.M.

2004-01-01

The performance of a single layer polymer light-emitting diode depends on several interdependent factors, although recombination between electrons and holes within the polymer layer is believed to play an important role. Our aim is to carry out computer experiments in which bipolar charge carriers are injected in polymer networks made of poly(p-phenylene vinylene) chains randomly oriented. In these simulations, we follow the charge evolution in time from some initial state to the steady state. The intra-molecular properties of the polymer molecules obtained from self-consistent quantum molecular dynamics calculations are used in the mesoscopic model. The purpose of the present work is to clarify the effects of intra-molecular charge mobility and energy disorder on recombination efficiency. In particular, we find that charge mobility along the polymer chains has a serious influence on recombination within the polymer layer. Our results also show that energy disorder due to differences in ionization potential and electron affinity of neighbouring molecules affects mainly recombinations that occur near the electrodes at polymer chains parallel to them
Mechanical properties of pillared-graphene nanostructures using molecular dynamics simulations

International Nuclear Information System (INIS)

Wang, Chih-Hao; Fang, Te-Hua; Sun, Wei-Li

2014-01-01

The deformation behaviour and mechanical properties of three-dimensional (3D) pillared graphene are investigated using molecular dynamics simulations. The Tersoff–Brenner many-body potential model is employed to evaluate the interactions between 3D pillared-graphene carbon atoms and nanotube carbons. The Lennard-Jones potential model is used to compute the interactions between a conical indenter and 3D pillared-graphene carbon atoms. The effects of the size and geometric structure of 3D pillared-graphene are evaluated in terms of the indentation force and contact stiffness. The simulation results for an armchair nanotube of 3D pillared graphene show that the contact stiffness increases with increasing chiral vector of the 3D-pillared graphene. However, the adhesive force sharply decreases with increasing chiral vector of the 3D-pillared graphene. A zigzag nanotube of 3D-pillared graphene exhibits better mechanical properties compared with those of the armchair nanotube. (paper)
Effect of molecular topology on the transport properties of dendrimers in dilute solution at Θ temperature: A Brownian dynamics study

Science.gov (United States)

Bosko, Jaroslaw T.; Ravi Prakash, J.

2008-01-01

Structure and transport properties of dendrimers in dilute solution are studied with the aid of Brownian dynamics simulations. To investigate the effect of molecular topology on the properties, linear chain, star, and dendrimer molecules of comparable molecular weights are studied. A bead-spring chain model with finitely extensible springs and fluctuating hydrodynamic interactions is used to represent polymer molecules under Θ conditions. Structural properties as well as the diffusivity and zero-shear-rate intrinsic viscosity of polymers with varied degrees of branching are analyzed. Results for the free-draining case are compared to and found in very good agreement with the Rouse model predictions. Translational diffusivity is evaluated and the difference between the short-time and long-time behavior due to dynamic correlations is observed. Incorporation of hydrodynamic interactions is found to be sufficient to reproduce the maximum in the intrinsic viscosity versus molecular weight observed experimentally for dendrimers. Results of the nonequilibrium Brownian dynamics simulations of dendrimers and linear chain polymers subjected to a planar shear flow in a wide range of strain rates are also reported. The flow-induced molecular deformation of molecules is found to decrease hydrodynamic interactions and lead to the appearance of shear thickening. Further, branching is found to suppress flow-induced molecular alignment and deformation.
Characterization of the Structural, Mechanical, and Electronic Properties of Fullerene Mixtures: A Molecular Simulations Description

KAUST Repository

Tummala, Naga Rajesh

2017-10-06

We investigate mixtures of fullerenes and fullerene derivatives, the most commonly used electron accepting materials in organic solar cells, by using a combination of molecular dynamics and density functional theory methods. Our goal is to describe how mixing affects the molecular packing, mechanical properties, and electronic parameters (site energy disorder, electronic couplings) of interest for solar-cell applications. Specifically, we consider mixtures of: (i) C60 and C70; (ii) C60, C70, and C84, and (iii) PC61BM and PC71BM.
Recent research on inherent molecular structure, physiochemical properties, and bio-functions of food and feed-type Avena sativa oats and processing-induced changes revealed with molecular microspectroscopic techniques

Energy Technology Data Exchange (ETDEWEB)

Prates, Luciana Louzada [Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan, Canada; Yu, Peiqiang [Department of Animal and Poultry Science, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, Saskatchewan, Canada

2017-05-16

Avena sativa oat is a cereal widely used as human food and livestock feed. However, the low metabolized energy and the rapid rumen degradations of protein and starch have limited the use of A. sativa oat grains. To overcome this disadvantage, new A. sativa oat varieties have been developed. Additionally, heat-related processing has been performed to decrease the degradation rate and improve the absorption of amino acids in the small intestine. The nutritive value is reflected by both chemical composition and inherent molecular structure conformation. However, the traditional wet chemical analysis is not able to detect the inherent molecular structures within an intact tissue. The advanced synchrotron-radiation and globar-based molecular microspectroscopy have been developed recently and applied to study internal molecular structures and the processing induced structure changes in A. sativa oats and reveal how molecular structure changes in relation to nutrient availability. This review aimed to obtain the recent information regarding physiochemical properties, molecular structures, metabolic characteristics of protein, and the heat-induced changes in new A. sativa oat varieties. The use of the advanced vibrational molecular spectroscopy was emphasized, synchrotron- and globar-based (micro)spectroscopy, to reveal the inherent structure of A. sativa oats at cellular and molecular levels and to reveal the heat processing effect on the degradation characteristics and the protein molecular structure in A. sativa oats. The relationship between nutrient availability and protein molecular inherent structure was also presented. Information described in this review gives better insight in the physiochemical properties, molecular structure, and the heat-induced changes in A. sativa oat detected with advanced molecular spectroscopic techniques in combinination with conventional nutrition study techniques.
Mechanical properties of stanene under uniaxial and biaxial loading: A molecular dynamics study

Energy Technology Data Exchange (ETDEWEB)

Mojumder, Satyajit [Department of Mechanical Engineering, Bangladesh University of Engineering and Technology, Dhaka 1000 (Bangladesh); Amin, Abdullah Al [Department of Mechanical and Aerospace Engineering, Case western Reverse University, Cleveland, Ohio 44106 (United States); Islam, Md Mahbubul, E-mail: mmi122@psu.edu [Department of Mechanical and Nuclear Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802 (United States)

2015-09-28

Stanene, a graphene like two dimensional honeycomb structure of tin has attractive features in electronics application. In this study, we performed molecular dynamics simulations using modified embedded atom method potential to investigate mechanical properties of stanene. We studied the effect of temperature and strain rate on mechanical properties of α-stanene for both uniaxial and biaxial loading conditions. Our study suggests that with the increasing temperature, both the fracture strength and strain of the stanene decrease. Uniaxial loading in zigzag direction shows higher fracture strength and strain compared to the armchair direction, while no noticeable variation in the mechanical properties is observed for biaxial loading. We also found at a higher loading rate, material exhibits higher fracture strength and strain. These results will aid further investigation of stanene as a potential nano-electronics substitute.
Predicting the elastic properties of double-walled carbon nanotubes by molecular dynamics simulation

International Nuclear Information System (INIS)

Zhang Chenli; Shen Huishen

2008-01-01

Molecular dynamics simulation is performed on a double-walled carbon nanotube (DWCNT) to predict its elastic properties based on a double-walled shear deformable shell model. By direct buckling measurement, we present here a method for uniquely determining the effective wall thickness for the shell model. Accounting for two different kinds of DWCNTs by adding an inner or outer tube to a fiducial tube, the mechanical properties of DWCNTs are carefully investigated as compared with those of the fiducial tube. It is found that the predicted values of Young's and shear moduli depend strongly on the construction and helicity of DWCNTs, while the dependence on nanotube length is relatively small. The results also confirm that the temperature variation has a significant effect on the elastic properties of DWCNTs
The use of molecular dynamics for the thermodynamic properties of simple and transition metals

International Nuclear Information System (INIS)

Straub, G.K.

1987-04-01

The technique of computer simulation of the molecular dynamics in metallic systems to calculate thermodynamic properties is discussed. The nature of a metal as determined by its electronic structure is used to determine the total adiabatic potential. The effective screened ion-ion interaction can then be used in a molecular dynamics simulation. The method for the construction of a molecular dynamics ensemble, its relation to the canonical ensemble, and the definition of thermodynamic functions from the Helmholtz free energy is given. The method for the analysis of the molecular dynamics results from quasiharmonic lattice dynamics and the decomposition in terms of harmonic and anharmonic contributions is given for solids. For fluid phase metals, procedures for calculating the thermodynamics and determining the constant of entropy are presented. The solid-fluid phase boundary as a function of pressure and temperature is determined using the results of molecular dynamics. Throughout, examples and results for metallic sodium are used. The treatment of the transition metal electronic d-states in terms of an effective pair-wise interaction is also discussed and the phonon dispersion curves of Al, Ni, and Cu are calculated
Comparison of oxidation properties of Nb and Sn in mesoporous molecular sieves

Czech Academy of Sciences Publication Activity Database

Nowak, I.; Feliczak, A.; Nekoksová, Iveta; Čejka, Jiří

2007-01-01

Roč. 321, č. 1 (2007), s. 40-48 ISSN 0926-860X R&D Projects: GA MPO FT-TA/040; GA AV ČR 1ET400400413 Grant - others:Ministry of Scientific Research and Information Technology(PL) N204 084 31/1965 Institutional research plan: CEZ:AV0Z40400503 Keywords : mesoporous molecular sieves * niobium * tin * synthesis * oxidation properties Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.166, year: 2007
Computer aided molecular design with combined molecular modeling and group contribution

DEFF Research Database (Denmark)

Harper, Peter Mathias; Gani, Rafiqul; Kolar, Petr

1999-01-01

Computer-aided molecular design (CAMD) provides a means for determining molecules or mixtures of molecules (CAMMD) having a desirable set of physicochemical properties. The application range of CAMD is restricted due to limitations on the complexity of the generated molecular structures and on th......Computer-aided molecular design (CAMD) provides a means for determining molecules or mixtures of molecules (CAMMD) having a desirable set of physicochemical properties. The application range of CAMD is restricted due to limitations on the complexity of the generated molecular structures...
Thermophysical Properties of Homologous Tetracyanoborate-Based Ionic Liquids Using Experiments and Molecular Dynamics Simulations.

Science.gov (United States)

Koller, Thomas M; Ramos, Javier; Schulz, Peter S; Economou, Ioannis G; Rausch, Michael H; Fröba, Andreas P

2017-04-27

Thermophysical properties of low-viscosity ionic liquids (ILs) based on the tetracyanoborate ([B(CN) 4 ] - ) anion carrying a homologous series of 1-alkyl-3-methylimidazolium ([AMIM] + ) cations [EMIM] + (ethyl), [BMIM] + (butyl), [HMIM] + (hexyl), [OMIM] + (octyl), and [DMIM] + (decyl) were investigated by experimental methods and molecular dynamics (MD) simulations at atmospheric pressure and various temperatures. Spectroscopic methods based on nuclear magnetic resonance and surface light scattering were applied to measure the ion self-diffusion coefficients and dynamic viscosity, respectively. In terms of MD simulations, a nonpolarizable molecular model for [EMIM][B(CN) 4 ] developed by optimization to experimental data was transferred to the other homologous ILs. For the appropriate description of the inter- and intramolecular interactions, precise and approximate force fields (FFs) were tested regarding their transferability within the homologous IL series, aiming at reducing the computational effort in molecular simulations. It is shown that at comparable simulated and experimental densities, the calculated and measured data for viscosity and self-diffusion coefficients of the ILs agree well mostly within combined uncertainties, but deviate stronger for longer-chained ILs using an overly coarse FF model. For the [B(CN) 4 ] - -based ILs studied, a comparison with literature data, the influence of varying alkyl chain length in the cation on their structural and thermophysical properties, and a correlation between self-diffusivity and viscosity are discussed.
Molecular orbitals for properties and spectroscopies

Energy Technology Data Exchange (ETDEWEB)

Robert, Vincent [Laboratoire de Chimie Quantique, Institut de Chimie, Université de Strasbourg, 1 rue Blaise Pascal 67000 Strasbourg-France (France); Domingo, Alex [Quantum Chemistry and Physical Chemistry Celestijnenlaan 200f, 3001 Heverlee - Belgium (Belgium); Braunstein, Pierre; Danopoulos, Andreas; Monakhov, Kirill [Laboratoire de Chimie de Coordination, Institut de Chimie, Université de Strasbourg, 4 rue Blaise Pascal 67081 Strasbourg-France (France)

2015-12-31

The description and clarification of spectroscopies and properties goes through ab initio calculations. Wave function based calculations (CASSCF/CASPT2) are particularly appealing since they offer spectroscopic accuracy and means of interpretation. we performed such calculations to elucidate the origin of unusual structural changes and intramolecular electron transfer phenomenon. Based on optimized molecular orbitals and a reading of the multireference wave function, it is suggested that intimate interactions are likely to considerably modify the standard pictures. A so-called PIMA (polarization-induced metalâĹŠarene) interaction similar to the more familiar anion-π interaction is responsible for a significant deviation from sp{sup 3} geometry and an energetic stabilization of 50 kJ/mol in Cr(II) benzyl organometallic complexes. In a similar fashion, it is proposed that the energetic profile of the IVCT (inter valence charge transfer) exhibits strong similarities to the Marcus’ theory, suggesting a response behaviour of the ensemble of electrons as electron transfer occurs in Fe{sup 2+}/Fe{sup 3+} bimetallic compound. The electronic reorganization induced by the IVCT process accounts for 11.8 eV, a very large effect that reduces the transfer energy down to 0.89 eV, in very good agreement with experiments.
Correlation between the estimated molecular weight and the immunological properties of 125I-TSH

International Nuclear Information System (INIS)

Quiroga, S.E.; Ciscato, V.A.; Barmasch, M.; Kurcbart, H.; Veira de Giacomini, S.; Altschuler, N.; Caro, R.A.

1976-09-01

Thyrotropic Stimulating Hormone (TSH) was radioiodinated by the Chloramine T method in order to be used in radioimmu-noassay procedures. It was purified by gel filtration and each fraction of the eluate was analyzed in order to determine which one had the most suitable behaviour for that use. The molecular weight of each fraction was estimated, as well as its immunological reactivity and its non-specific binding. The 125 I-TSH fraction with better properties was the closest to the molecular weight of the native hormone, which is found at the posterior shoulder of the main proteic peak of the elution pattern. (author) [es
druGAN: An Advanced Generative Adversarial Autoencoder Model for de Novo Generation of New Molecules with Desired Molecular Properties in Silico.

Science.gov (United States)

Kadurin, Artur; Nikolenko, Sergey; Khrabrov, Kuzma; Aliper, Alex; Zhavoronkov, Alex

2017-09-05

Deep generative adversarial networks (GANs) are the emerging technology in drug discovery and biomarker development. In our recent work, we demonstrated a proof-of-concept of implementing deep generative adversarial autoencoder (AAE) to identify new molecular fingerprints with predefined anticancer properties. Another popular generative model is the variational autoencoder (VAE), which is based on deep neural architectures. In this work, we developed an advanced AAE model for molecular feature extraction problems, and demonstrated its advantages compared to VAE in terms of (a) adjustability in generating molecular fingerprints; (b) capacity of processing very large molecular data sets; and (c) efficiency in unsupervised pretraining for regression model. Our results suggest that the proposed AAE model significantly enhances the capacity and efficiency of development of the new molecules with specific anticancer properties using the deep generative models.
Effects of ionizing radiation on the properties of ultra-high molecular weight polyethylene (PE-UHMW)

International Nuclear Information System (INIS)

Kurth, M.

1990-01-01

Ultra high molecular weight polyethylene (PE-UHMW) is used in most artificial joint replacement devices. Prior to implantation in biological environment, radiatin sterilization by 60 Co or electron beam is common. It is well known that polyethylene exposed to ionizing radiation of any sort undergo physical changes due to chain scission and/or crosslinking. PE-UHMW sheets, 8 mm thick, were either 60 Co or electron beam irradiated, in the range of 10-150 kGy under air or nitrogen atmoshere. The crystallinity of the irradiated samples increases with the irradiation dose. The chain scission/crosslinking events ratio determine the network structure and the sol/gel ratio. The latter was found to depend on irradiation dose, radiation atmosphere and sample thickness. Moreover 60 Co-irradiation is about 5 times more effective in forming PE-UHMW gel than electron-irradiation. Besides the degree of crosslinking, the molecular weight distribution is the main determinant of the structural properties of PE-UHMW. Low molecular weight fractions were also found. Using a dose of 30 kGy ( 60 Co in air), the average molecular weight of the soluble part after extraction decreased from originally 2.3 million g/mol to 170.000 g/mol, corresponding to a factor of about 10. These changes in molecular weight have a strong influence on the mechanical properties of PE-UHMW. Crosslinking slightly increases the yield strength, while the elongation at break decreases. Long-term compressive creep is reduced if the material is irradiated. Obviously, increased crystallinity after oxidative chain scission affects a higher deformation resistance. Radiation crosslinked structures cause a significant increase in abrasion resistance. The above described structural changes occur even upon irradiation of very low doses as used during sterilization. This study will enable to reduce the radiation sterilization damage and thus to gain long term stability of PE-UHMW medical devices. (orig./BBR)
Molecular design, synthesis and physical properties of novel Cytisine-derivatives - Experimental and theoretical study

Science.gov (United States)

Ivanova, Bojidarka; Spiteller, Michael

2013-02-01

The paper presented a comprehensive theoretical and experimental study on the molecular drugs-design, synthesis, isolation, physical spectroscopic and mass spectrometric elucidation of novel functionalization derivatives of Cytisine (Cyt), using nucleosidic residues. Since these alkaloids have established biochemical profile, related the binding affinity of the nicotinic acetylcholine receptors (nAChRs), particularly α7 sub-type, the presented correlation between the molecular structure and properties allowed to evaluated the highlights of the biochemical hypothesises related the Schizophrenia. The anticancer activity of α7 subtype agonists and the crucial role of the nucleoside-based medications in the cancer therapy provided opportunity for further study on the biochemical relationship between Schizophrenia and few kinds of cancers, which has been hypothesized recently. The physical electronic absorptions (EAs), circular dichroic (CD) and Raman spectroscopic (RS) properties as well as mass spectrometric (MS) data, obtained using electrospray ionization (ESI) and atmospheric-pressure chemical ionization (APCI) methods under the positive single (MS) and tandem (MS/MS) modes of operation are discussed. Taking into account reports on a fatal intoxication of Cyt, the presented data would be of interest in the field of forensic chemistry, through development of highly selective and sensitive analytical protocols. Quantum chemical method is used to predict the physical properties of the isolated alkaloids, their affinity to the receptor loop and gas-phase stabilized species, observed mass spectrometrically.
Experiments for the Undergraduate Laboratory that Illustrate the Size-Exclusion Properties of Zeolite Molecular Sieves

Science.gov (United States)

Cooke, Jason; Henderson, Eric J.

2009-01-01

Experiments are presented that demonstrate the size-exclusion properties of zeolites and reveal the reason for naming zeolites "molecular sieves". If an IR spectrometer is available, the adsorption or exclusion of alcohols of varying sizes from dichloromethane or chloroform solutions can be readily demonstrated by monitoring changes in the…
Temperature-dependent mechanical properties of single-layer molybdenum disulphide: Molecular dynamics nanoindentation simulations

Energy Technology Data Exchange (ETDEWEB)

Zhao, Junhua, E-mail: junhua.zhao@uni-weimar.de [Jiangsu Province Key Laboratory of Advanced Manufacturing Equipment and Technology of Food, Jiangnan University, 214122 Wuxi (China); Institute of Structural Mechanics, Bauhaus-University Weimar, 99423 Weimar (Germany); Jiang, Jin-Wu, E-mail: jwjiang5918@hotmail.com [Institute of Structural Mechanics, Bauhaus-University Weimar, 99423 Weimar (Germany); Rabczuk, Timon, E-mail: timon.rabczuk@uni-weimar.de [Institute of Structural Mechanics, Bauhaus-University Weimar, 99423 Weimar (Germany); School of Civil, Environmental and Architectural Engineering, Korea University, 136-701 Seoul (Korea, Republic of)

2013-12-02

The temperature-dependent mechanical properties of single-layer molybdenum disulphide (MoS{sub 2}) are obtained using molecular dynamics (MD) nanoindentation simulations. The Young's moduli, maximum load stress, and maximum loading strain decrease with increasing temperature from 4.2 K to 500 K. The obtained Young's moduli are in good agreement with those using our MD uniaxial tension simulations and the available experimental results. The tendency of maximum loading strain with different temperature is opposite with that of metal materials due to the short range Stillinger-Weber potentials in MoS{sub 2}. Furthermore, the indenter tip radius and fitting strain effect on the mechanical properties are also discussed.

Noncovalent Intermolecular Interactions in Organic Electronic Materials: Implications for the Molecular Packing vs Electronic Properties of Acenes

KAUST Repository

Sutton, Christopher; Risko, Chad; Bredas, Jean-Luc

2015-01-01

Noncovalent intermolecular interactions, which can be tuned through the toolbox of synthetic chemistry, determine not only the molecular packing but also the resulting electronic, optical, and mechanical properties of materials derived from π
A Quantitative Structure-Property Relationship (QSPR Study of Aliphatic Alcohols by the Method of Dividing the Molecular Structure into Substructure

Directory of Open Access Journals (Sweden)

Bin Cheng

2011-04-01

Full Text Available A quantitative structure–property relationship (QSPR analysis of aliphatic alcohols is presented. Four physicochemical properties were studied: boiling point (BP, n-octanol–water partition coefficient (lg POW, water solubility (lg W and the chromatographic retention indices (RI on different polar stationary phases. In order to investigate the quantitative structure–property relationship of aliphatic alcohols, the molecular structure ROH is divided into two parts, R and OH to generate structural parameter. It was proposed that the property is affected by three main factors for aliphatic alcohols, alkyl group R, substituted group OH, and interaction between R and OH. On the basis of the polarizability effect index (PEI, previously developed by Cao, the novel molecular polarizability effect index (MPEI combined with odd-even index (OEI, the sum eigenvalues of bond-connecting matrix (SX1CH previously developed in our team, were used to predict the property of aliphatic alcohols. The sets of molecular descriptors were derived directly from the structure of the compounds based on graph theory. QSPR models were generated using only calculated descriptors and multiple linear regression techniques. These QSPR models showed high values of multiple correlation coefficient (R > 0.99 and Fisher-ratio statistics. The leave-one-out cross-validation demonstrated the final models to be statistically significant and reliable.
Molecular and Functional Properties of Regional Astrocytes in the Adult Brain.

Science.gov (United States)

Morel, Lydie; Chiang, Ming Sum R; Higashimori, Haruki; Shoneye, Temitope; Iyer, Lakshmanan K; Yelick, Julia; Tai, Albert; Yang, Yongjie

2017-09-06

The molecular signature and functional properties of astroglial subtypes in the adult CNS remain largely undefined. By using translational ribosome affinity purification followed by RNA-Seq, we profiled astroglial ribosome-associated (presumably translating) mRNAs in major cortical and subcortical brain regions (cortex, hippocampus, caudate-putamen, nucleus accumbens, thalamus, and hypothalamus) of BAC aldh1l1 -translational ribosome affinity purification (TRAP) mice (both sexes). We found that the expression of astroglial translating mRNAs closely follows the dorsoventral axis, especially from cortex/hippocampus to thalamus/hypothalamus posteriorly. This region-specific expression pattern of genes, such as synaptogenic modulator sparc and transcriptional factors ( emx2 , lhx2 , and hopx ), was validated by qRT-PCR and immunostaining in brain sections. Interestingly, cortical or subcortical astrocytes selectively promote neurite growth and synaptic activity of neurons only from the same region in mismatched cocultures, exhibiting region-matched astrocyte to neuron communication. Overall, these results generated new molecular signature of astrocyte types in the adult CNS, providing insights into their origin and functional diversity. SIGNIFICANCE STATEMENT We investigated the in vivo molecular and functional heterogeneity of astrocytes inter-regionally from adult brain. Our results showed that the expression pattern of ribosome-associated mRNA profiles in astrocytes closely follows the dorsoventral axis, especially posteriorly from cortex/hippocampus to thalamus/hypothalamus. In line with this, our functional results further demonstrated region-selective roles of cortical and subcortical astrocytes in regulating cortical or subcortical neuronal synaptogenesis and maturation. These in vivo studies provide a previously uncharacterized and important molecular atlas for exploring region-specific astroglial functions. Copyright © 2017 the authors 0270-6474/17/378706-12$15.00/0.
Proton transport properties of poly(aspartic acid) with different average molecular weights

Energy Technology Data Exchange (ETDEWEB)

Nagao, Yuki, E-mail: ynagao@kuchem.kyoto-u.ac.j [Department of Mechanical Systems and Design, Graduate School of Engineering, Tohoku University, 6-6-01 Aoba Aramaki, Aoba-ku, Sendai 980-8579 (Japan); Imai, Yuzuru [Institute of Development, Aging and Cancer (IDAC), Tohoku University, 4-1 Seiryo-cho, Aoba-ku, Sendai 980-8575 (Japan); Matsui, Jun [Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Sendai 980-8577 (Japan); Ogawa, Tomoyuki [Department of Electronic Engineering, Graduate School of Engineering, Tohoku University, 6-6-05 Aoba Aramaki, Aoba-ku, Sendai 980-8579 (Japan); Miyashita, Tokuji [Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Sendai 980-8577 (Japan)

2011-04-15

Research highlights: Seven polymers with different average molecular weights were synthesized. The proton conductivity depended on the number-average degree of polymerization. The difference of the proton conductivities was more than one order of magnitude. The number-average molecular weight contributed to the stability of the polymer. - Abstract: We synthesized seven partially protonated poly(aspartic acids)/sodium polyaspartates (P-Asp) with different average molecular weights to study their proton transport properties. The number-average degree of polymerization (DP) for each P-Asp was 30 (P-Asp30), 115 (P-Asp115), 140 (P-Asp140), 160 (P-Asp160), 185 (P-Asp185), 205 (P-Asp205), and 250 (P-Asp250). The proton conductivity depended on the number-average DP. The maximum and minimum proton conductivities under a relative humidity of 70% and 298 K were 1.7 . 10{sup -3} S cm{sup -1} (P-Asp140) and 4.6 . 10{sup -4} S cm{sup -1} (P-Asp250), respectively. Differential thermogravimetric analysis (TG-DTA) was carried out for each P-Asp. The results were classified into two categories. One exhibited two endothermic peaks between t = (270 and 300) {sup o}C, the other exhibited only one peak. The P-Asp group with two endothermic peaks exhibited high proton conductivity. The high proton conductivity is related to the stability of the polymer. The number-average molecular weight also contributed to the stability of the polymer.
Correlation Between Pyrolysis Atmosphere and Carbon Molecular Sieve Membrane Performance Properties

KAUST Repository

Kiyono, Mayumi; Koros, William J.; Williams, Paul J.

2011-01-01

Carbon molecular sieve (CMS) membranes have attractive separation performance properties, greatly exceeding an "upper bound" trade-off curve of polymeric membrane performance. CMS membranes are prepared by pyrolyzing polymers, well above their glass transition temperatures. Multiple factors, such as polymer precursor and pyrolysis protocol, are known to affect the separation performance. In this study, a correlation observed between pyrolysis atmosphere and CMS separation performance properties is discussed. Specifically, oxygen exposure during the pyrolysis process is the focus. The theory and details of the oxygen exposure and development of a new CMS preparation method using oxygen as a "dopant" will be described with a strong correlation observed with separation performance for CMS membranes prepared with various polymer precursors. In addition, study of possible mass transfer limitations on the oxygen "doping" process will be described to clarify the basis for the equilibrium-based interpretation of doping data. The method is also explored by changing the pyrolysis temperature. © 2011 Elsevier B.V.
Influence of molecular packing on the corrosion inhibition properties of self-assembled octadecyltrichlorosilane monolayers on silicon

International Nuclear Information System (INIS)

Hsieh, Shuchen; Chao, Wei-Jay; Lin, Pei-Ying; Hsieh, Chiung-Wen

2014-01-01

Highlights: •Molecular packing plays an important role in determining SAM film properties. •Loose-packed OTS monolayers on silicon were corroded by exposure to KMnO 4 . •Dense-packed OTS SAM films exhibited excellent corrosion protection efficacy. -- Abstract: The corrosion inhibition properties of octadecyltrichlorosilane (OTS) self-assembled monolayers (SAMs) on silicon were investigated. Atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), contact angle (CA), and lateral force microscopy (LFM) were used to determine the OTS film formation time, packing density, and corrosion protection efficacy. The OTS films reached adsorption saturation after 15 s; however, the molecular density continued to increase up to 24 h. The films were exposed to the strong oxidant KMnO 4 , and while 15-s film samples exhibited corrosion after a 1 min exposure, samples with films grown for 24 h were protected even after 24 h
Improved Prediction of Blood-Brain Barrier Permeability Through Machine Learning with Combined Use of Molecular Property-Based Descriptors and Fingerprints.

Science.gov (United States)

Yuan, Yaxia; Zheng, Fang; Zhan, Chang-Guo

2018-03-21

Blood-brain barrier (BBB) permeability of a compound determines whether the compound can effectively enter the brain. It is an essential property which must be accounted for in drug discovery with a target in the brain. Several computational methods have been used to predict the BBB permeability. In particular, support vector machine (SVM), which is a kernel-based machine learning method, has been used popularly in this field. For SVM training and prediction, the compounds are characterized by molecular descriptors. Some SVM models were based on the use of molecular property-based descriptors (including 1D, 2D, and 3D descriptors) or fragment-based descriptors (known as the fingerprints of a molecule). The selection of descriptors is critical for the performance of a SVM model. In this study, we aimed to develop a generally applicable new SVM model by combining all of the features of the molecular property-based descriptors and fingerprints to improve the accuracy for the BBB permeability prediction. The results indicate that our SVM model has improved accuracy compared to the currently available models of the BBB permeability prediction.
Electronic properties of liquid Hg-In alloys : Ab-initio molecular dynamics study

International Nuclear Information System (INIS)

Sharma, Nalini; Ahluwalia, P. K.; Thakur, Anil

2016-01-01

Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Three liquid Hg-In alloys (Hg_1_0In_9_0, Hg_3_0In_7_0_,_. Hg_5_0In_5_0, Hg_7_0In_3_0, and Hg_9_0Pb_1_0) at 299 K are considered. The calculated results for liquid Hg (l-Hg) and lead (l-In) are also drawn. Along with the calculated results of considered five liquid alloys of Hg-In alloy. The results obtained from electronic properties namely total density of state and partial density of states help to find the local arrangement of Hg and In atoms and the presence of liquid state in the considered five alloys.
Properties of Molecular organized assemblies at interfaces

Indian Academy of Sciences (India)

Dr.AURNA

Organized molecular assemblies. An organized molecular assembly is a group of atoms or ..... Simulations of the growth of clusters on a .... dynamics and function. ➢Actively ... Study of amphiphilic derivatives of YIGSR, mutated at hyper active ...
Noncovalent Intermolecular Interactions in Organic Electronic Materials: Implications for the Molecular Packing vs Electronic Properties of Acenes

KAUST Repository

Sutton, Christopher

2015-10-30

Noncovalent intermolecular interactions, which can be tuned through the toolbox of synthetic chemistry, determine not only the molecular packing but also the resulting electronic, optical, and mechanical properties of materials derived from π-conjugated molecules, oligomers, and polymers. Here, we provide an overview of the theoretical underpinnings of noncovalent intermolecular interactions and briefly discuss the computational chemistry approaches used to understand the magnitude of these interactions. These methodologies are then exploited to illustrate how noncovalent intermolecular interactions impact important electronic properties-such as the electronic coupling between adjacent molecules, a key parameter for charge-carrier transport-through a comparison between the prototype organic semiconductor pentacene with a series of N-substituted heteropentacenes. Incorporating an understanding of these interactions into the design of organic semiconductors can assist in developing novel materials systems from this fascinating molecular class. © 2015 American Chemical Society.
Molecular dynamics simulation of thermophysical properties of undercooled liquid cobalt

International Nuclear Information System (INIS)

Han, X J; Wang, J Z; Chen, M; Guo, Z Y

2004-01-01

Molecular dynamics simulations with two different embedded-atom-method (EAM) potentials are applied to calculate the density, specific heat and self-diffusion coefficient of liquid cobalt at temperatures above and below the melting temperature. Simulation shows that Pasianot's EAM model of cobalt constructed on the basis of a hcp structure is more successful than Stoop's EAM model in the framework of a fcc structure in predicting the thermophysical properties of liquid cobalt. Simulations with Pasianot's EAM model indicate that the density fits into ρ = 7.49-9.17 x 10 -4 (T- T m ) g cm -3 , and the self-diffusion coefficient is given by D = 1.291 x 10 -7 exp(-48 795.71/RT) m 2 s -1 . Dissimilar to the linear dependence of the density and the Arrhenius dependence of the self-diffusion coefficient on temperature, the specific heat shows almost a constant value of 38.595 ± 0.084 J mol -1 K -1 within the temperature range of simulation. The simulated properties of liquid cobalt are compared with experimental data available. Comparisons show reasonable agreements between the simulated results from Pasianot's EAM model and experimental data
Molecular modeling studies of structural properties of polyvinyl alcohol: a comparative study using INTERFACE force field.

Science.gov (United States)

Radosinski, Lukasz; Labus, Karolina

2017-10-05

Polyvinyl alcohol (PVA) is a material with a variety of applications in separation, biotechnology, and biomedicine. Using combined Monte Carlo and molecular dynamics techniques, we present an extensive comparative study of second- and third-generation force fields Universal, COMPASS, COMPASS II, PCFF, and the newly developed INTERFACE, as applied to this system. In particular, we show that an INTERFACE force field provides a possibility of composing a reliable atomistic model to reproduce density change of PVA matrix in a narrow temperature range (298-348 K) and calculate a thermal expansion coefficient with reasonable accuracy. Thus, the INTERFACE force field may be used to predict mechanical properties of the PVA system, being a scaffold for hydrogels, with much greater accuracy than latter approaches. Graphical abstract Molecular Dynamics and Monte Carlo studies indicate that it is possible to predict properties of the PVA in narrow temperature range by using the INTERFACE force field.
Molecular level computational studies of polyethylene and polyacrylonitrile composites containing single walled carbon nanotubes: effect of carboxylic acid functionalization on nanotube-polymer interfacial properties

Directory of Open Access Journals (Sweden)

Shayesteh eHaghighatpanah

2014-09-01

Full Text Available Molecular dynamics and molecular mechanics methods have been used to investigate additive-polymer interfacial properties in single walled carbon nanotube – polyethylene and single walled carbon nanotube – polyacrylonitrile composites. Properties such as the interfacial shear stress and bonding energy are similar for the two composites. In contrast, functionalizing the single walled carbon nanotubes with carboxylic acid groups leads to an increase in these properties, with a larger increase for the polar polyacrylonitrile composite. Increasing the percentage of carbon atoms that were functionalized from 1% to 5% also leads to an increase in the interfacial properties. In addition, the interfacial properties depend on the location of the functional groups on the single walled carbon nanotube wall.
Effect of the different chain transfer agents on molecular weight and optical properties of poly(methyl methacrylate)

Science.gov (United States)

Çetinkaya, Onur; Demirci, Gökhan; Mergo, Paweł

2017-08-01

Investigation of molecular weight and optical properties of poly(methyl metacrylate) (PMMA) polymerized in house with different chain transfer agents was studied. Isopropyl alcohol (IPA), n-butyl mercaptan (nBMC) and pentamethyl disilane (PMDS) were used as chain transfer agents. The molecular weight (Mw) of PMMA samples were measured by Ostwald viscometer. Mw of bulk polymer samples were decreased with increase the concentration of chain transfer agents (CTA). Since reactivity of used CTAs is not same, molecular weights of samples which were produced with different type of CTA but same concentration of CTA was varied. Higher concentration of n-BMC showed higher scattering. Transmission of samples could not be correlated with different concentration of CTA. Refractive index of samples was not affected by concentration of CTA nevertheless higher molecular weight of CTA showed higher refractive index.
Physical properties of CO-dark molecular gas traced by C+

Science.gov (United States)

Tang, Ningyu; Li, Di; Heiles, Carl; Wang, Shen; Pan, Zhichen; Wang, Jun-Jie

2016-09-01

Context. Neither Hi nor CO emission can reveal a significant quantity of so-called dark gas in the interstellar medium (ISM). It is considered that CO-dark molecular gas (DMG), the molecular gas with no or weak CO emission, dominates dark gas. Determination of physical properties of DMG is critical for understanding ISM evolution. Previous studies of DMG in the Galactic plane are based on assumptions of excitation temperature and volume density. Independent measurements of temperature and volume density are necessary. Aims: We intend to characterize physical properties of DMG in the Galactic plane based on C+ data from the Herschel open time key program, namely Galactic Observations of Terahertz C+ (GOT C+) and Hi narrow self-absorption (HINSA) data from international Hi 21 cm Galactic plane surveys. Methods: We identified DMG clouds with HINSA features by comparing Hi, C+, and CO spectra. We derived the Hi excitation temperature and Hi column density through spectral analysis of HINSA features. The Hi volume density was determined by utilizing the on-the-sky dimension of the cold foreground Hi cloud under the assumption of axial symmetry. The column and volume density of H2 were derived through excitation analysis of C+ emission. The derived parameters were then compared with a chemical evolutionary model. Results: We identified 36 DMG clouds with HINSA features. Based on uncertainty analysis, optical depth of HiτHi of 1 is a reasonable value for most clouds. With the assumption of τHi = 1, these clouds were characterized by excitation temperatures in a range of 20 K to 92 K with a median value of 55 K and volume densities in the range of 6.2 × 101 cm-3 to 1.2 × 103 cm-3 with a median value of 2.3 × 102 cm-3. The fraction of DMG column density in the cloud (fDMG) decreases with increasing excitation temperature following an empirical relation fDMG =-2.1 × 10-3Tex,(τHi = 1) + 1.0. The relation between fDMG and total hydrogen column density NH is given by f
A systematic investigation of the preparation and properties of composite carbon molecular sieves containing inorganic oxides

Science.gov (United States)

Foley, Henry C.

1990-01-01

The objective of this research is to define the methodology for the preparation and characterization of new carbon-based molecular sieves with composite structures. Carbon molecular sieves have found increasing application in the field of separation and purification of gases. These materials are relatively easy to prepare and their surfaces can be modified to some extent. It is expected that by combining inorganic oxides with the carbonaceous structure one can begin to design composite materials with a wider range of possible chemical and physical properties. In this way, the IOM-CMS materials may confer distinct advantages over pure carbon molecular sieves, not just for separation, but also for catalysis. The most recent results in the design and characterization of these IOM-CMS materials are reviewed and summarized. Directions for further research are also presented.
THE INFLUENCE OF FAR-ULTRAVIOLET RADIATION ON THE PROPERTIES OF MOLECULAR CLOUDS IN THE 30 DOR REGION OF THE LARGE MAGELLANIC CLOUD

International Nuclear Information System (INIS)

Pineda, Jorge L.; Klein, Ulrich; Ott, Juergen; Wong, Tony; Muller, Erik; Hughes, Annie

2009-01-01

We present a complete 12 CO J = 1 → 0 map of the prominent molecular ridge in the Large Magellanic Cloud (LMC) obtained with the 22 m ATNF Mopra Telescope. The region stretches southward by ∼2 deg. (or 1.7 kpc) from 30 Doradus, the most vigorous star-forming region in the Local Group. The location of this molecular ridge is unique insofar as it allows us to study the properties of molecular gas as a function of the ambient radiation field in a low-metallicity environment. We find that the physical properties of CO-emitting clumps within the molecular ridge do not vary with the strength of the far-ultraviolet radiation field. Since the peak CO brightness of the clumps shows no correlation with the radiation field strength, the observed constant value for CO-to-H 2 conversion factor along the ridge seems to require an increase in the kinetic temperature of the molecular gas that is offset by a decrease in the angular filling factor of the CO emission. We find that the difference between the CO-to-H 2 conversion factor in the molecular ridge and the outer Milky Way is smaller than has been reported by previous studies of the CO emission: applying the same cloud identification and analysis methods to our CO observations of the LMC molecular ridge and CO data from the outer Galaxy survey by Dame et al., we find that the average CO-to-H 2 conversion factor in the molecular ridge is X CO ≅ (3.9 ± 2.5) x 10 20 cm -2 (K km s -1 ) -1 , approximately twice the value that we determine for the outer Galaxy clouds. The mass spectrum and the scaling relations between the properties of the CO clumps in the molecular ridge are similar, but not identical, to those that have been established for Galactic molecular clouds.
Phase transition and mechanical properties of tungsten nanomaterials from molecular dynamic simulation

Energy Technology Data Exchange (ETDEWEB)

Chen, L.; Fan, J. L.; Gong, H. R., E-mail: gonghr@csu.edu.cn [Central South University, State Key Laboratory of Powder Metallurgy (China)

2017-03-15

Molecular dynamic simulation is used to systematically find out the effects of the size and shape of nanoparticles on phase transition and mechanical properties of W nanomaterials. It is revealed that the body-centered cubic (BCC) to face-centered cubic (FCC) phase transition could only happen in cubic nanoparticles of W, instead of the shapes of sphere, octahedron, and rhombic dodecahedron, and that the critical number to trigger the phase transition is 5374 atoms. Simulation also shows that the FCC nanocrystalline W should be prevented due to its much lower tensile strength than its BCC counterpart and that the octahedral and rhombic dodecahedral nanoparticles of W, rather than the cubic nanoparticles, should be preferred in terms of phase transition and mechanical properties. The derived results are discussed extensively through comparing with available observations in the literature to provide a deep understanding of W nanomaterials.
Size Effect on Transport Properties of Gaseous Argon: A Molecular Dynamics Simulation Study

International Nuclear Information System (INIS)

Lee, Songhi

2014-01-01

We have carried out a series of equilibrium molecular dynamics (EMD) simulations of gaseous argon at 273.15 K and 1.00 atm for the calculation of transport properties as a function of the number of argon molecules (N). While the diffusion coefficients (D) of gaseous argon approach to the experimental measure with increasing N, the viscosities (η) and thermal conductivities (λ) obtained for N = 432 are unreliable due to the high fluctuation of the time correlation functions and those for N = 1728 are rather acceptable. Increasing further to N = 6912 has improved the MD results a little closer to the experimental measures for η and λ. Both the EMD results for η and λ for N = 6912 underestimate the experimental measures and it is not expected that the more increasing N makes the closer results to the experimental measures. One possible explanation for the large disagreement between MD results and the experimental measures for η and λ may be due to the use of LJ parameters which were used for liquid argon. In a recent study, we have examined the Green-Kubo formula for the calculation of transport properties (diffusion coefficient, viscosity, and thermal conductivity) of noble gases (He, Ne, Ar, Kr, and Xe) by carrying out a series of equilibrium molecular dynamics (EMD) simulations for the system of N=1728 at 273.15 K and 1.00 atm.1 While the diffusion coefficients (D) of noble gases were obtained through the original Green-Kubo formula, the viscosities (η) and thermal conductivities (λ) were obtained by utilizing the revised Green-Kubo formulas. The structural and dynamic properties of gaseous argon are completely different from those of liquid argon at 94.4 K and 1.374 g/cm 3 . The results for transport properties (D, η, and λ) at 273.15 K and 1.00 atm obtained from our EMD simulations are in general agreement with the experimental data and superior to the rigorous results of the kinetic theory
Chemical structure and properties of low-molecular furin inhibitors

Directory of Open Access Journals (Sweden)

T. V. Osadchuk

2016-12-01

Full Text Available The review is devoted to the analysis of the relationship between a chemical structure and properties of low-molecular weight inhibitors of furin, the most studied proprotein convertase, which is involved in the development of some pathologies, such as oncologic diseases, viral and bacterial infections, etc. The latest data concerning the influence of peptides, pseudo-peptides, aromatic and heterocyclic compounds, some natural ones such as flavonoids, coumarins, and others on enzyme inactivation are considered. The power of furin inhibition is shown to rise with the increasing number of positively charged groups in the structure of these compounds. Peptidomimetics (Ki = 5-8 pM are shown to be the most effective furin inhibitors. The synthesized substances, however, have not been used in practical application yet. Nowadays it is very important to find more selective inhibitors, improve their stability, bioavailability and safety for the human organism.

Structure impact on the thermal and electronic properties of bismuth telluride by ab-initio and molecular dynamics calculations

International Nuclear Information System (INIS)

Termentzidis, K; Pokropivny, A; Xiong, S-Y; Chumakov, Y; Volz, S; Woda, M; Cortona, P

2012-01-01

We use molecular dynamics and ab-initio methods to predict the thermal and electronic properties of new materials with high figures of merit. The simulated systems are bulk bismuth tellurides with antisite and vacancy defects. Optimizations of the materials under investigation are performed by the SIESTA code for subsequent calculations of force constants, electronic properties, and Seebeck coefficients. The prediction of the thermal conductivity is made by Non-Equilibrium Molecular Dynamics (NEMD) using the LAMMPS code. The thermal conductivity of bulk bismuth telluride with different stoichiometry and with a number of substitution defects is calculated. We have found that the thermal conductivity can be decreased by 60% by introducing vacancy defects. The calculated thermal conductivities for the different structures are compared with the available experimental and theoretical results.
Computer modeling of properties of complex molecular systems

Energy Technology Data Exchange (ETDEWEB)

Kulkova, E.Yu. [Moscow State University of Technology “STANKIN”, Vadkovsky per., 1, Moscow 101472 (Russian Federation); Khrenova, M.G.; Polyakov, I.V. [Lomonosov Moscow State University, Chemistry Department, Leninskie Gory 1/3, Moscow 119991 (Russian Federation); Nemukhin, A.V. [Lomonosov Moscow State University, Chemistry Department, Leninskie Gory 1/3, Moscow 119991 (Russian Federation); N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina 4, Moscow 119334 (Russian Federation)

2015-03-10

Large molecular aggregates present important examples of strongly nonhomogeneous systems. We apply combined quantum mechanics / molecular mechanics approaches that assume treatment of a part of the system by quantum-based methods and the rest of the system with conventional force fields. Herein we illustrate these computational approaches by two different examples: (1) large-scale molecular systems mimicking natural photosynthetic centers, and (2) components of prospective solar cells containing titan dioxide and organic dye molecules. We demonstrate that modern computational tools are capable to predict structures and spectra of such complex molecular aggregates.
The interaction properties of the human Rab GTPase family--comparative analysis reveals determinants of molecular binding selectivity.

Directory of Open Access Journals (Sweden)

Matthias Stein

Full Text Available Rab GTPases constitute the largest subfamily of the Ras protein superfamily. Rab proteins regulate organelle biogenesis and transport, and display distinct binding preferences for effector and activator proteins, many of which have not been elucidated yet. The underlying molecular recognition motifs, binding partner preferences and selectivities are not well understood.Comparative analysis of the amino acid sequences and the three-dimensional electrostatic and hydrophobic molecular interaction fields of 62 human Rab proteins revealed a wide range of binding properties with large differences between some Rab proteins. This analysis assists the functional annotation of Rab proteins 12, 14, 26, 37 and 41 and provided an explanation for the shared function of Rab3 and 27. Rab7a and 7b have very different electrostatic potentials, indicating that they may bind to different effector proteins and thus, exert different functions. The subfamily V Rab GTPases which are associated with endosome differ subtly in the interaction properties of their switch regions, and this may explain exchange factor specificity and exchange kinetics.We have analysed conservation of sequence and of molecular interaction fields to cluster and annotate the human Rab proteins. The analysis of three dimensional molecular interaction fields provides detailed insight that is not available from a sequence-based approach alone. Based on our results, we predict novel functions for some Rab proteins and provide insights into their divergent functions and the determinants of their binding partner selectivity.
Property Analysis of Exfoliated Graphite Nanoplatelets Modified Asphalt Model Using Molecular Dynamics (MD Method

Directory of Open Access Journals (Sweden)

Hui Yao

2017-01-01

Full Text Available This Molecular Dynamics (MD simulation paper presents a physical property comparison study between exfoliated graphite nanoplatelets (xGNP modified and control asphalt models, including density, glass transition temperature, viscosity and thermal conductivity. The three-component control asphalt model consists of asphaltenes, aromatics, and saturates based on previous references. The xGNP asphalt model was built by incorporating an xGNP and control asphalt model and controlling mass ratios to represent the laboratory prepared samples. The Amber Cornell Extension Force Field (ACEFF was used with assigned molecular electro-static potential (ESP charge from NWChem analysis. After optimization and ensemble relaxation, the properties of the control and xGNP modified asphalt models were computed and analyzed using the MD method. The MD simulated results have a similar trend as the test results. The property analysis showed that: (1 the density of the xGNP modified model is higher than that of the control model; (2 the glass transition temperature of the xGNP modified model is closer to the laboratory data of the Strategic Highway Research Program (SHRP asphalt binders than that of the control model; (3 the viscosities of the xGNP modified model at different temperatures are higher than those of the control model, and it coincides with the trend in the laboratory data; (4 the thermal conductivities of the xGNP modified asphalt model are higher than those of the control asphalt model at different temperatures, and it is consistent with the trend in the laboratory data.
Small molecules make big differences: molecular doping effects on electronic and optical properties of phosphorene

International Nuclear Information System (INIS)

Jing, Yu; Tang, Qing; He, Peng; Zhou, Zhen; Shen, Panwen

2015-01-01

Systematical computations on the density functional theory were performed to investigate the adsorption of three typical organic molecules, tetracyanoquinodimethane (TCNQ), tetracyanoethylene (TCNE) and tetrathiafulvalene (TTF), on the surface of phosphorene monolayers and thicker layers. There exist considerable charge transfer and strong non-covalent interaction between these molecules and phosphorene. In particular, the band gap of phosphorene decreases dramatically due to the molecular modification and can be further tuned by applying an external electric field. Meanwhile, surface molecular modification has proven to be an effective way to enhance the light harvesting of phosphorene in different directions. Our results predict a flexible method toward modulating the electronic and optical properties of phosphorene and shed light on its experimental applications. (paper)
Synchrotron based mass spectrometry to investigate the molecular properties of mineral-organic associations

Energy Technology Data Exchange (ETDEWEB)

Liu, Suet Yi; Kleber, Markus; Takahashi, Lynelle K.; Nico, Peter; Keiluweit, Marco; Ahmed, Musahid

2013-04-01

Soil organic matter (OM) is important because its decay drives life processes in the biosphere. Analysis of organic compounds in geological systems is difficult because of their intimate association with mineral surfaces. To date there is no procedure capable of quantitatively separating organic from mineral phases without creating artifacts or mass loss. Therefore, analytical techniques that can (a) generate information about both organic and mineral phases simultaneously and (b) allow the examination of predetermined high-interest regions of the sample as opposed to conventional bulk analytical techniques are valuable. Laser Desorption Synchrotron Postionization (synchrotron-LDPI) mass spectrometry is introduced as a novel analytical tool to characterize the molecular properties of organic compounds in mineral-organic samples from terrestrial systems, and it is demonstrated that when combined with Secondary Ion Mass Spectrometry (SIMS), can provide complementary information on mineral composition. Mass spectrometry along a decomposition gradient in density fractions, verifies the consistency of our results with bulk analytical techniques. We further demonstrate that by changing laser and photoionization energies, variations in molecular stability of organic compounds associated with mineral surfaces can be determined. The combination of synchrotron-LDPI and SIMS shows that the energetic conditions involved in desorption and ionization of organic matter may be a greater determinant of mass spectral signatures than the inherent molecular structure of the organic compounds investigated. The latter has implications for molecular models of natural organic matter that are based on mass spectrometric information.
The relation between molecular properties of drugs and their transport across the intestinal membrane

Directory of Open Access Journals (Sweden)

Zakeri-Milani P.

2006-07-01

Full Text Available The aim of this study was to investigate the relationship between the intestinal absorption of structurally diverse model drugs across the rat intestinal mucosa and their molecular properties. Permeability coefficients for 13 compounds were determined in anaesthetized rats. Drug solution in phosphate buffered saline (PBS was perfused through the intestinal segment with flow rate of 0.21 ml/min and samples were taken from outlet tubing at different time points up to 90 min. The permeability values ranged from 1.6×10-5 to 2 ×10-4 cm/sec for atenolol and ibuprofen respectively. Molecular properties of drugs including the number of hydrogen bond donors and acceptors, log P, logD, topological polar surface area and number of rotatable bonds were considered. The results indicated that compounds which meet 10 or fewer number of rotatable bonds and topological surface area equal to or less than 140 A◦ have a high probability of good intestinal permeability and fraction of dose which is absorbed in human. Moreover the results indicated that lower number of hydrogen bond counts and higher logD and logP values are associated with higher permeability and bioavailabilty of drugs. Therefore the experimental and computational methods could be used for the prediction of intestinal drug permeability.
Effect of the molecular structure of phenolic novolac precursor resins on the properties of phenolic fibers

International Nuclear Information System (INIS)

Ying, Yong-Gang; Pan, Yan-Ping; Ren, Rui; Dang, Jiang-Min; Liu, Chun-Ling

2013-01-01

A series of phenolic resins with different weight-average molecular weights (M w ) and ortho/para (O/P) ratios were prepared. The effect of the phenolic precursor resin structure on the structure and properties of the resulting phenolic fibers was investigated. The structures of the resins and fibers were characterized by nuclear magnetic resonance spectroscopy, gel permeation chromatography, melt rheometry, dynamic mechanical analysis, and thermogravimetric analysis. The results show that the O/P ratio, unsubstituted ortho and para carbon ratio (O u /P u ), and M w of the phenolic resins play an important role in determining the properties of the phenolic fibers. The tensile strength of the phenolic fibers increases with increasing novolac precursor O u /P u ratios, corresponding to low O/P ratios, at comparable resin M w values. Also, the tensile strength of the phenolic fibers increases with increasing novolac M w values at comparable O/P ratios. Phenolic fibers with high tensile strength and good flame resistance characteristics were generated from a phenolic precursor resin, possessing a high weight-average molecular weight and a low O/P value. - Highlights: • Phenolic resins with different weight-average molecular weights and ortho/para ratios have been prepared. • The tensile strength of the phenolic fibers increases with reducing novolac O/P ratio. • The tensile strength of the phenolic fibers increases with increasing novolac M w
The anchoring effect on the spin transport properties and I-V characteristics of pentacene molecular devices suspended between nickel electrodes.

Science.gov (United States)

Caliskan, S; Laref, A

2014-07-14

Spin-polarized transport properties are determined for pentacene sandwiched between Ni surface electrodes with various anchoring ligands. These calculations are carried out using spin density functional theory in tandem with a non-equilibrium Green's function technique. The presence of a Se atom at the edge of the pentacene molecule significantly modifies the transport properties of the device because Se has a different electronegativity than S. Our theoretical results clearly show a larger current for spin-up electrons than for spin-down electrons in the molecular junction that is attached asymmetrically across the Se linker at one side of the Ni electrodes (in an APL magnetic orientation). Moreover, this molecular junction exhibits pronounced NDR as the bias voltage is increased from 0.8 to 1.0 V. However, this novel NDR behavior is only detected in this promising pentacene molecular device. The NDR in the current-voltage (I-V) curve results from the narrowness of the density of states for the molecular states. The feasibility of controlling the TMR is also predicted in these molecular device nanostructures. Spin-dependent transmission calculations show that the sign and strength of the current-bias voltage characteristics and the TMR could be tailored for the organic molecule devices. These molecular junctions are joined symmetrically and asymmetrically between Ni metallic probes across the S and Se atoms (at the ends of the edges of the pentacene molecule). Our theoretical findings show that spin-valve phenomena can occur in these prototypical molecular junctions. The TMR and NDR results show that nanoscale junctions with spin valves could play a vital role in the production of novel functional molecular devices.
Magnetic effects on the solvent properties investigated by molecular dynamics simulation

Energy Technology Data Exchange (ETDEWEB)

Moosavi, Fatemeh, E-mail: moosavibaigi@um.ac.ir; Gholizadeh, Mostafa

2014-03-15

This paper investigates how an external constant magnetic field in the Z-direction affects the performance of a solvent. The molecular dynamics simulation comprised common inorganic and organic solvents including water, acetone, acetonitrile, toluene, and n-hexane at the ambient temperature and pressure. A static magnetic field applied in the simulation process is able to reduce the solvent mobility in the solution in order to enhance the solvent–solute reaction. Simulation results show that the diffusivity decreases because of increasing the effective interactions. Besides, magnetic field reduces the volume of the solvent and increases the strength of the hydrogen bonds by maximizing attractive electrostatic and vdW interactions caused by changes in the radial distribution function of the solvents. Hydrogen-bonding characteristics of solvents investigated by molecular dynamics simulations were evidence for the hydrogen bonding strength of O···H that is a more efficient intermolecular hydrogen-bonding in comparison with N···H. - Highlights: • Molecular dynamics simulation technique investigates the effect of magnetic field on transport dynamics inside the solvent bulk. • External constant magnetic field influences on intermolecular interactions, thermophysics, and transport properties of the solvents. • Applying magnetic field strengthened hydrogen bond maximizes attractive electrostatic interactions, charge distribution becomes stronger, and the molecule mobility is demoted. • The low diffusivity of the solvents in the solutions increases the performance of the interactions and promotes the interactions. • On introducing a magnetic field of flux density parallel to the Z-direction, solvent acts as an obstacle to diffusion of solutes.
Controllable molecular aggregation and fluorescence properties of 1,3,4-oxadiazole derivative

KAUST Repository

Li, Min

2015-10-14

The molecular self-assembly behaviour of 2,2’-Bis-(4-hexyloxyphenyl)-bi-1,3,4-oxadiazole (BOXD-6) in solution, on surfaces and in bulk crystals, and its photo-physical properties were studied via a combination of experimental techniques and theoretical calculations. It is found that BOXD-6 molecules self-assemble into both H- and J-aggregates at moderate concentration (~10-4 M) and then transit to exclusive J-aggregates at higher concentration (~10-3 M) in tetrahydrofuran. In H-aggregation (α polymorph), BOXD-6 adopts a linear conformation and forms a one- dimensional layered structure; in J-aggregation (β polymorph), it adopts a Z-shaped conformation and form a more ordered two-dimensional layered structure. A π-stacking structure is observed in both cases, and adjacent molecules in the J-aggregation show larger displacement along the molecular long axis direction than that in H-aggregation. Although J-aggregates are almost the only component in concentrated solutions (10-3 M), both H- and J-aggregates can be obtained if concentrated solution is transformed onto substrates through a simple drop-casting method. Such a phase transition during film formation can be easily avoided by adding water as precipitator; a film with pure J-aggregates is then obtained. In order to get more information on molecular self-assembly, intermolecular interaction potential energy surfaces (PES) were evaluated via theoretical calculations at the DFT level (M062x/6-31G**). The PES not only confirm the molecular stacking structures found in crystals but also predict some other likely structures, which will be the target of future experiments.
Assessment of structural, thermal, and mechanical properties of portlandite through molecular dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Hajilar, Shahin, E-mail: shajilar@iastate.edu [Department of Civil, Construction and Environmental Engineering, Iowa State University, Ames, IA 50011-1066 (United States); Shafei, Behrouz, E-mail: shafei@iastate.edu [Department of Civil, Construction and Environmental Engineering, Department of Materials Science and Engineering, Iowa State University, Ames, IA 50011-1066 (United States)

2016-12-15

The structural, thermal, and mechanical properties of portlandite, the primary solid phase of ordinary hydrated cement paste, are investigated using the molecular dynamics method. To understand the effects of temperature on the structural properties of portlandite, the coefficients of thermal expansion of portlandite are determined in the current study and validated with what reported from the experimental tests. The atomic structure of portlandite equilibrated at various temperatures is then subjected to uniaxial tensile strains in the three orthogonal directions and the stress-strain curves are developed. Based on the obtained results, the effect of the direction of straining on the mechanical properties of portlandite is investigated in detail. Structural damage analysis is performed to reveal the failure mechanisms in different directions. The energies of the fractured surfaces are calculated in different directions and compared to those of the ideal surfaces available in the literature. The key mechanical properties, including tensile strength, Young's modulus, and fracture strain, are extracted from the stress-strain curves. The sensitivity of the obtained mechanical properties to temperature and strain rate is then explored in a systematic way. This leads to valuable information on how the structural and mechanical properties of portlandite are affected under various exposure conditions and loading rates. - Graphical abstract: Fracture mechanism of portlandite under uniaxial strain in the z-direction. - Highlights: • The structural, thermal, and mechanical properties of portlandite are investigated. • The coefficients of thermal expansion are determined. • The stress-strain relationships are studied in three orthogonal directions. • The effects of temperature and strain rate on mechanical properties are examined. • The plastic energy required for fracture in the crystalline structure is reported.
Influence of template/functional monomer/cross‐linking monomer ratio on particle size and binding properties of molecularly imprinted nanoparticles

DEFF Research Database (Denmark)

Yoshimatsu, Keiichi; Yamazaki, Tomohiko; Chronakis, Ioannis S.

2012-01-01

A series of molecularly imprinted polymer nanoparticles have been synthesized employing various template/functional monomer/crosslinking monomer ratio and characterized in detail to elucidate the correlation between the synthetic conditions used and the properties (e.g., particle size and templat...... tuning of particle size and binding properties are required to fit practical applications. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2012...
Thermophysical properties of liquid UO2, ZrO2 and corium by molecular dynamics and predictive models

International Nuclear Information System (INIS)

Kim, Woong Kee; Shim, Ji Hoon; Kaviany Massoud

2016-01-01

The analysis of such accidents (fate of the melt), requires accurate corium thermophysical properties data up to 5000 K. In addition, the initial corium melt superheat melt, determined from such properties, are key in predicting the fuel-coolant interactions (FCIs) and convection and retention of corium in accident scenarios, e.g., core-melt down corium discharge from reactor pressure vessels and spreading in external core-catcher. Due to the high temperatures, data on molten corium and its constituents are limited, so there are much data scatters and mostly extrapolations (even from solid state) have been used. Here we predict the thermophysical properties of molten UO 2 and ZrO 2 using classical molecular dynamics (MD) simulations (properties of corium are predicted using the mixture theories and UO 2 and ZrO 2 properties). The thermophysical properties (density, compressibility, heat capacity, viscosity and surface tension) of liquid UO 2 and ZrO 2 are predicted using classical molecular dynamics simulations, up to 5000 K. For atomic interactions, the CRG and the Teter potential models are found most appropriate. The liquid behavior is verified with the random motion of the constituent atoms and the pair-distribution functions, starting with the solid phase and raising the temperature to realize liquid phase. The viscosity and thermal conductivity are calculated with the Green-Kubo autocorrelation decay formulae and compared with the predictive models of Andrade and Bridgman. For liquid UO 2 , the CRG model gives satisfactory MD predictions. For ZrO 2 , the density is reliably predicted with the CRG potential model, while the compressibility and viscosity are more accurately predicted by the Teter model
Molecular and structural properties of polymer composites filled with activated charcoal particles

Energy Technology Data Exchange (ETDEWEB)

Tahir, Dahlang, E-mail: dtahir@fmipa.unhas.ac.id; Bakri, Fahrul [Department of Physics, Hasanuddin University, Makassar 90245 Indonesia (Indonesia); Liong, Syarifuddin [Department of Chemistry, Hasanuddin University, Makassar 90245 Indonesia (Indonesia)

2016-03-11

We have studied the molecular properties, structural properties, and chemical composition of composites by Fourier transform infrared (FTIR) spectroscopy, X-ray diffraction (XRD) spectroscopy, and X-ray fluorescence (XRF) spectroscopy, respectively. FTIR spectra shows absorption band of hydroxyl group (-OH), methyl group (-CH{sub 3}) and aromatic group (C-C). The absorption band for aromatic group (C-C) shows the formation of carbonaceous in composites. XRF shows chemical composition of composites, which the main chemicals are SO{sub 3}, Cl, and ZnO. The loss on ignition value (LOI) of activated charcoal indicates high carbonaceous matter. The crystallite size for diffraction pattern from hydrogel polymer is about 17 nm and for activated charcoal are about 19 nm. The crystallite size of the polymer is lower than that of activated charcoal, which make possible of the particle from filler in contact with each other to form continuous conducting polymer through polymer matrix.
Influence of alkyl chain length and temperature on thermophysical properties of ammonium-based ionic liquids with molecular solvent.

Science.gov (United States)

Kavitha, T; Attri, Pankaj; Venkatesu, Pannuru; Devi, R S Rama; Hofman, T

2012-04-19

Mixing of ionic liquids (ILs) with molecular solvent can expand the range of structural properties and the scope of molecular interactions between the molecules of the solvents. Exploiting of these phenomena essentially require a basic fundamental understanding of mixing behavior of ILs with molecular solvents. In this context, a series of protic ILs possessing tetra-alkyl ammonium cation [R(4)N](+) with commonly used anion hydroxide [OH](-) were synthesized and characterized by temperature dependent thermophysical properties. The ILs [R(4)N](+)[OH](-) are varying only in the length of alkyl chain (R is methyl, ethyl, propyl, or butyl) of tetra-alkyl ammonium on the cationic part. The ILs used for the present study included tetramethyl ammonium hydroxide [(CH(3))(4)N](+)[OH](-) (TMAH), tetraethyl ammonium hydroxide [(C(2)H(5))(4)N](+)[OH](-) (TEAH), tetrapropyl ammonium hydroxide [(C(3)H(7))(4)N](+)[OH](-) (TPAH) and tetrabutyl ammonium hydroxide [(C(4)H(9))(4)N](+)[OH](-) (TBAH). The alkyl chain length effect has been analyzed by precise measurements such as densities (ρ), ultrasonic sound velocity (u), and viscosity (η) of these ILs with polar solvent, N-methyl-2-pyrrolidone (NMP), over the full composition range as a function of temperature. The excess molar volume (V(E)), the deviation in isentropic compressibility (Δκ(s)) and deviation in viscosity (Δη) were predicted using these properties as a function of the concentration of ILs. Redlich-Kister polynomial was used to correlate the results. A qualitative analysis of the results is discussed in terms of the ion-dipole, ion-pair interactions, and hydrogen bonding between ILs and NMP molecules. Later, the hydrogen bonding features between ILs and NMP were also analyzed using a molecular modeling program with the help of HyperChem 7.
The spin-dependent electronic transport properties of M(dcdmp)2 (M = Cu, Au, Co, Ni) molecular devices based on zigzag graphene nanoribbon electrodes

Science.gov (United States)

Li, Dongde; Wu, Di; Zhang, Xiaojiao; Zeng, Bowen; Li, Mingjun; Duan, Haiming; Yang, Bingchu; Long, Mengqiu

2018-05-01

The spin-dependent electronic transport properties of M(dcdmp)2 (M = Cu, Au, Co, Ni; dcdmp = 2,3-dicyano-5,6-dimercaptopyrazyne) molecular devices based on zigzag graphene nanoribbon (ZGNR) electrodes were investigated by density functional theory combined nonequilibrium Green's function method (DFT-NEGF). Our results show that the spin-dependent transport properties of the M(dcdmp)2 molecular devices can be controlled by the spin configurations of the ZGNR electrodes, and the central 3d-transition metal atom can introduce a larger magnetism than that of the nonferrous metal one. Moreover, the perfect spin filtering effect, negative differential resistance, rectifying effect and magnetic resistance phenomena can be observed in our proposed M(dcdmp)2 molecular devices.
Magnetic properties of iron loaded MCM-48 molecular sieves

Energy Technology Data Exchange (ETDEWEB)

Elias, Veronica R. [Centro de Investigacion y Tecnologia Quimica, Universidad Tecnologica Nacional, Facultad Regional Cordoba. Cordoba (Argentina); CONICET (Argentina); Oliva, Marcos I. [Facultad de Matematica, Astronomia y Fisica, Universidad Nacional de Cordoba, Cordoba (Argentina); IFEG-CONICET (Argentina); Vaschetto, Eliana G. [Centro de Investigacion y Tecnologia Quimica, Universidad Tecnologica Nacional, Facultad Regional Cordoba. Cordoba (Argentina); Urreta, Silvia E., E-mail: urreta@famaf.unc.edu.a [Facultad de Matematica, Astronomia y Fisica, Universidad Nacional de Cordoba, Cordoba (Argentina); Eimer, Griselda A. [Centro de Investigacion y Tecnologia Quimica, Universidad Tecnologica Nacional, Facultad Regional Cordoba. Cordoba (Argentina); CONICET (Argentina); Silvetti, Silvia P. [Facultad de Matematica, Astronomia y Fisica, Universidad Nacional de Cordoba, Cordoba (Argentina)

2010-11-15

Mesoporous molecular sieves of MCM-48 type were loaded with iron by the wet impregnation method, using Fe(III) nitrate or Fe(II) sulfate aqueous solutions as Fe sources, to obtain a magnetic porous composite. The iron loaded materials were characterized by XRD, N{sub 2} adsorption and DRUV-vis and compared with the Si-MCM-48 host. Their magnetic properties were studied by measuring the hysteresis loops up to 1.5 T at different temperatures (5-300 K) and by magnetization vs. temperature curves following the conventional zero field cooling (ZFC) and field cooling (FC) protocols. Materials with high structure regularity and surface area are obtained, which exhibit a mixed paramagnetic and superparamagnetic behavior, arising in isolated iron ions inserted in the host framework, and in small iron oxide clusters or nanoparticles forming inside the pores, respectively. Larger hematite particles (8-13 nm) grown on the external surface provide a quite small ferromagnetic contribution to the hysteresis loop.
Magnetic properties of iron loaded MCM-48 molecular sieves

International Nuclear Information System (INIS)

Elias, Veronica R.; Oliva, Marcos I.; Vaschetto, Eliana G.; Urreta, Silvia E.; Eimer, Griselda A.; Silvetti, Silvia P.

2010-01-01

Mesoporous molecular sieves of MCM-48 type were loaded with iron by the wet impregnation method, using Fe(III) nitrate or Fe(II) sulfate aqueous solutions as Fe sources, to obtain a magnetic porous composite. The iron loaded materials were characterized by XRD, N 2 adsorption and DRUV-vis and compared with the Si-MCM-48 host. Their magnetic properties were studied by measuring the hysteresis loops up to 1.5 T at different temperatures (5-300 K) and by magnetization vs. temperature curves following the conventional zero field cooling (ZFC) and field cooling (FC) protocols. Materials with high structure regularity and surface area are obtained, which exhibit a mixed paramagnetic and superparamagnetic behavior, arising in isolated iron ions inserted in the host framework, and in small iron oxide clusters or nanoparticles forming inside the pores, respectively. Larger hematite particles (8-13 nm) grown on the external surface provide a quite small ferromagnetic contribution to the hysteresis loop.
Thermophysical properties of liquid Ni around the melting temperature from molecular dynamics simulation

Energy Technology Data Exchange (ETDEWEB)

Rozas, R. E. [Institut für Theoretische Physik II: Soft Matter, Heinrich Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf (Germany); Department of Physics, University of Bío-Bío, Av. Collao 1202, P.O. Box 5C, Concepción (Chile); Demiraǧ, A. D.; Horbach, J. [Institut für Theoretische Physik II: Soft Matter, Heinrich Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf (Germany); Toledo, P. G. [Chemical Engineering Department and Surface Analysis Laboratory (ASIF), University of Concepción, P.O. Box 160-C, Correo 3, Concepción (Chile)

2016-08-14

Thermophysical properties of liquid nickel (Ni) around the melting temperature are investigated by means of classical molecular dynamics (MD) simulation, using three different embedded atom method potentials to model the interactions between the Ni atoms. Melting temperature, enthalpy, static structure factor, self-diffusion coefficient, shear viscosity, and thermal diffusivity are compared to recent experimental results. Using ab initio MD simulation, we also determine the static structure factor and the mean-squared displacement at the experimental melting point. For most of the properties, excellent agreement is found between experiment and simulation, provided the comparison relative to the corresponding melting temperature. We discuss the validity of the Hansen-Verlet criterion for the static structure factor as well as the Stokes-Einstein relation between self-diffusion coefficient and shear viscosity. The thermal diffusivity is extracted from the autocorrelation function of a wavenumber-dependent temperature fluctuation variable.

Microscopic properties of ionic liquid/organic semiconductor interfaces revealed by molecular dynamics simulations.

Science.gov (United States)

Yokota, Yasuyuki; Miyamoto, Hiroo; Imanishi, Akihito; Takeya, Jun; Inagaki, Kouji; Morikawa, Yoshitada; Fukui, Ken-Ichi

2018-05-09

Electric double-layer transistors based on ionic liquid/organic semiconductor interfaces have been extensively studied during the past decade because of their high carrier densities at low operation voltages. Microscopic structures and the dynamics of ionic liquids likely determine the device performance; however, knowledge of these is limited by a lack of appropriate experimental tools. In this study, we investigated ionic liquid/organic semiconductor interfaces using molecular dynamics to reveal the microscopic properties of ionic liquids. The organic semiconductors include pentacene, rubrene, fullerene, and 7,7,8,8-tetracyanoquinodimethane (TCNQ). While ionic liquids close to the substrate always form the specific layered structures, the surface properties of organic semiconductors drastically alter the ionic dynamics. Ionic liquids at the fullerene interface behave as a two-dimensional ionic crystal because of the energy gain derived from the favorable electrostatic interaction on the corrugated periodic substrate.
Molecular outflows driven by low-mass protostars. I. Correcting for underestimates when measuring outflow masses and dynamical properties

Energy Technology Data Exchange (ETDEWEB)

Dunham, Michael M. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, MS 78, Cambridge, MA 02138 (United States); Arce, Héctor G. [Department of Astronomy, Yale University, P.O. Box 208101, New Haven, CT 06520 (United States); Mardones, Diego [Departamento de Astronomía, Universidad de Chile, Casilla 36-D, Santiago (Chile); Lee, Jeong-Eun [Department of Astronomy and Space Science, Kyung Hee University, Yongin, Gyeonggi 446-701 (Korea, Republic of); Matthews, Brenda C. [National Research Council of Canada, Herzberg Astronomy and Astrophysics, 5071 W. Saanich Road, Victoria, BC V9E 2E7 (Canada); Stutz, Amelia M. [Max-Planck-Institut für Astronomie, Königstuhl 17, D-69117, Heidelberg (Germany); Williams, Jonathan P., E-mail: mdunham@cfa.harvard.edu [Institute for Astronomy, University of Hawaii, Honolulu, HI 96822 (United States)

2014-03-01

We present a survey of 28 molecular outflows driven by low-mass protostars, all of which are sufficiently isolated spatially and/or kinematically to fully separate into individual outflows. Using a combination of new and archival data from several single-dish telescopes, 17 outflows are mapped in {sup 12}CO (2-1) and 17 are mapped in {sup 12}CO (3-2), with 6 mapped in both transitions. For each outflow, we calculate and tabulate the mass (M {sub flow}), momentum (P {sub flow}), kinetic energy (E {sub flow}), mechanical luminosity (L {sub flow}), and force (F {sub flow}) assuming optically thin emission in LTE at an excitation temperature, T {sub ex}, of 50 K. We show that all of the calculated properties are underestimated when calculated under these assumptions. Taken together, the effects of opacity, outflow emission at low velocities confused with ambient cloud emission, and emission below the sensitivities of the observations increase outflow masses and dynamical properties by an order of magnitude, on average, and factors of 50-90 in the most extreme cases. Different (and non-uniform) excitation temperatures, inclination effects, and dissociation of molecular gas will all work to further increase outflow properties. Molecular outflows are thus almost certainly more massive and energetic than commonly reported. Additionally, outflow properties are lower, on average, by almost an order of magnitude when calculated from the {sup 12}CO (3-2) maps compared to the {sup 12}CO (2-1) maps, even after accounting for different opacities, map sensitivities, and possible excitation temperature variations. It has recently been argued in the literature that the {sup 12}CO (3-2) line is subthermally excited in outflows, and our results support this finding.
Molecular dynamics simulation of the ionic liquid N-octylpyridinium tetrafluoroborate and acetonitrile: Thermodynamic and structural properties

Science.gov (United States)

Zhou, Siwen; Zhu, Guanglai; Kang, Xianqu; Li, Qiang; Sha, Maolin; Cui, Zhifeng; Xu, Xinsheng

2018-06-01

Using molecular dynamics simulation, the research obtained the thermodynamic properties and microstructures of the mixture of N-octylpyridinium tetrafluoroborate and acetonitrile, including density, self-diffusion coefficients, excess properties, radial distribution functions (RDFs) and spatial distribution functions (SDFs). Both RDFs and SDFs indicate that the local microstructure of the polar region is different from the nonpolar region with different mole fraction of ionic liquids. Acetonitrile could increase the order of the polar regions. While with acetonitrile increasing, the orderliness of the nonpolar region increases firstly and then decreases. In relatively dilute solution, ionic liquids were dispersed to form small aggregates wrapped by acetonitrile.
A Molecular Dynamics Study of Crosslinked Phthalonitrile Polymers: The Effect of Crosslink Density on Thermomechanical and Dielectric Properties

Directory of Open Access Journals (Sweden)

Janel Chua

2018-01-01

Full Text Available In this work, molecular dynamics (MD and molecular mechanics (MM simulations are used to study well-equilibrated models of 4,4′-bis(3,4-dicyanophenoxybiphenyl (BPh–1,3-bis(3-aminophenoxybenzene (m-APB phthalonitrile (PN system with a range of crosslink densities. A cross-linking technique is introduced to build a series of systems with different crosslink densities; several key properties of this material, including thermal expansion, mechanical properties and dielectric properties are studied and compared with experimental results. It is found that the coefficient of linear thermal expansion predicted by the model is in good agreement with experimental results and indicative of the good thermal stability of the PN polymeric system. The simulation also shows that this polymer has excellent mechanical property, whose strength increases with increasing crosslink density. Lastly and most importantly, the calculated dielectric constant—which shows that this polymer is an excellent insulating material—indicates that there is an inverse relation between cross-linking density and dielectric constant. The trend gave rise to an empirical quadratic function which can be used to predict the limits of attainable dielectric constant for highly crosslinked polymer systems. The current computational work provides strong evidence that this polymer is a promising material for aerospace applications and offers guidance for experimental studies of the effect of cross-linking density on the thermal, mechanical and dielectric properties of the material.
Effects of Electrode Distances on Geometric Structure and Electronic Transport Properties of Molecular 4,4'-Bipyridine Junction

International Nuclear Information System (INIS)

Li Zongliang; Zou Bin; Wang Chuankui; Luo Yi

2006-01-01

Influences of electrode distances on geometric structure of molecule and on electronic transport properties of molecular junctions have been investigated by means of a generalized quantum chemical approach based on the elastic scattering Green's function method. Numerical results show that, for organic molecule 4,4'-bipyridine, the geometric structure of the molecule especially the dihedral angle between the two pyridine rings is sensitive to the distances between the two electrodes. The currents of the molecular junction are taken nonlinearly increase with the increase of the bias. Shortening the distance of the metallic electrodes will result in stronger coupling and larger conductance
Seeing the Forest Through the Trees: The Distribution and Properties of Dense Molecular Gas in the Milky Way Galaxy

Science.gov (United States)

Ellsworth-Bowers, Timothy P.

The Milky Way Galaxy serves as a vast laboratory for studying the dynamics and evolution of the dense interstellar medium and the processes of and surrounding massive star formation. From our vantage point within the Galactic plane, however, it has been extremely difficult to construct a coherent picture of Galactic structure; we cannot see the forest for the trees. The principal difficulties in studying the structure of the Galactic disk have been obscuration by the ubiquitous dust and molecular gas and confusion between objects along a line of sight. Recent technological advances have led to large-scale blind surveys of the Galactic plane at (sub-)millimeter wavelengths, where Galactic dust is generally optically thin, and have opened a new avenue for studying the forest. The Bolocam Galactic Plane Survey (BGPS) observed over 190 deg 2 of the Galactic plane in dust continuum emission near lambda = 1.1 mm, producing a catalog of over 8,000 dense molecular cloud structures across a wide swath of the Galactic disk. Deriving the spatial distribution and physical properties of these objects requires knowledge of distance, a component lacking in the data themselves. This thesis presents a generalized Bayesian probabilistic distance estimation method for dense molecular cloud structures, and demonstrates it with the BGPS data set. Distance probability density functions (DPDFs) are computed from kinematic distance likelihoods (which may be double- peaked for objects in the inner Galaxy) and an expandable suite of prior information to produce a comprehensive tally of our knowledge (and ignorance) of the distances to dense molecular cloud structures. As part of the DPDF formalism, this thesis derives several prior DPDFs for resolving the kinematic distance ambiguity in the inner Galaxy. From the collection of posterior DPDFs, a set of objects with well-constrained distance estimates is produced for deriving Galactic structure and the physical properties of dense molecular
Charge Transport Processes in Molecular Junctions

Science.gov (United States)

Smith, Christopher Eugene

Molecular electronics (ME) has evolved into a rich area of exploration that combines the fields of chemistry, materials, electronic engineering and computational modeling to explore the physics behind electronic conduction at the molecular level. Through studying charge transport properties of single molecules and nanoscale molecular materials the field has gained the potential to bring about new avenues for the miniaturization of electrical components where quantum phenomena are utilized to achieve solid state molecular device functionality. Molecular junctions are platforms that enable these studies and consist of a single molecule or a small group of molecules directly connected to electrodes. The work presented in this thesis has built upon the current understanding of the mechanisms of charge transport in ordered junctions using self-assembled monolayer (SAM) molecular thin films. Donor and acceptor compounds were synthesized and incorporated into SAMs grown on metal substrates then the transport properties were measured with conducting probe atomic force microscopy (CP-AFM). In addition to experimentally measured current-voltage (I-V) curves, the transport properties were addressed computationally and modeled theoretically. The key objectives of this project were to 1) investigate the impact of molecular structure on hole and electron charge transport, 2) understand the nature of the charge carriers and their structure-transport properties through long (chemically gated to modulate the transport. These results help advance our understanding of transport behavior in semiconducting molecular thin films, and open opportunities to engineer improved electronic functionality into molecular devices.
Investigation of the Physical and Molecular Properties of Asphalt Binders Processed with Used Motor Oils

Directory of Open Access Journals (Sweden)

Mohyeldin Ragab

2015-01-01

Full Text Available In this work we investigated the performance aspects of addition of used motor oils (UMO to neat and crumb rubber modified asphalts (CRMA and related that to the change of molecular size distribution of modified asphalt’s fractions; asphaltenes, saturates, naphthene aromatics, and polar aromatics. Based on the results of temperature sweep viscoelastic tests, addition of crumb rubber modifier (CRM alone or with UMO results in the formation of internal network within the modified asphalt. Based on the results of short and long term aged asphalts, the utilization of combination of UMO and CRM enhanced the aging behavior of asphalt. Bending beam rheometer was utilized to investigate the low temperature behavior of UMO modified asphalts. Based on those tests, the utilization of the UMO and CRM enhanced the low temperature properties of asphalts. Based on the results of the asphalt separation tests and the Gel Permeation Chromatography (GPC analysis, it was found that saturates and naphthene aromatics are the two asphalt fractions that have similar molecular size fractions as those of UMO. However, UMO only shifts the molecular sizes of saturates after interaction with asphalt. Results also show that polar aromatics pose higher molecular size structures than UMO.
Investigations of transport properties of molten sodium fluoride using molecular dynamics simulations

International Nuclear Information System (INIS)

Chattaraj, D.; Dash, Smruti

2013-01-01

The thermal conductivity and coefficient of shear viscosity of molten sodium fluoride were calculated using Green-Kubo equilibrium molecular dynamics (EMD) simulation. The Green-Kubo method is an equilibrium technique based on the fluctuation-dissipation theorem of statistical thermodynamics. The canonical ensemble (N, V, T) was used in the MD simulation to obtain the transport properties of molten NaF. In this simulation, several state points were investigated using the Born-Meyer-Huggins-Tosi-Fumi interionic potential model. The electrostatic interactions present in this ionic fluid were calculated through the Ewald method. The results obtained in this study were found to be in good agreement with the reported experimental data. (author)
Properties of liquid clusters in large-scale molecular dynamics nucleation simulations

International Nuclear Information System (INIS)

Angélil, Raymond; Diemand, Jürg; Tanaka, Kyoko K.; Tanaka, Hidekazu

2014-01-01

We have performed large-scale Lennard-Jones molecular dynamics simulations of homogeneous vapor-to-liquid nucleation, with 10 9 atoms. This large number allows us to resolve extremely low nucleation rates, and also provides excellent statistics for cluster properties over a wide range of cluster sizes. The nucleation rates, cluster growth rates, and size distributions are presented in Diemand et al. [J. Chem. Phys. 139, 74309 (2013)], while this paper analyses the properties of the clusters. We explore the cluster temperatures, density profiles, potential energies, and shapes. A thorough understanding of the properties of the clusters is crucial to the formulation of nucleation models. Significant latent heat is retained by stable clusters, by as much as ΔkT = 0.1ε for clusters with size i = 100. We find that the clusters deviate remarkably from spherical—with ellipsoidal axis ratios for critical cluster sizes typically within b/c = 0.7 ± 0.05 and a/c = 0.5 ± 0.05. We examine cluster spin angular momentum, and find that it plays a negligible role in the cluster dynamics. The interfaces of large, stable clusters are thinner than planar equilibrium interfaces by 10%−30%. At the critical cluster size, the cluster central densities are between 5% and 30% lower than the bulk liquid expectations. These lower densities imply larger-than-expected surface areas, which increase the energy cost to form a surface, which lowers nucleation rates
Magnetismo Molecular (Molecular Magentism)

Energy Technology Data Exchange (ETDEWEB)

Reis, Mario S [Universidade Federal Fluminense, Brasil; Moreira Dos Santos, Antonio F [ORNL

2010-07-01

The new synthesis processes in chemistry open a new world of research, new and surprising materials never before found in nature can now be synthesized and, as a wonderful result, observed a series of physical phenomena never before imagined. Among these are many new materials the molecular magnets, the subject of this book and magnetic properties that are often reflections of the quantum behavior of these materials. Aside from the wonderful experience of exploring something new, the theoretical models that describe the behavior these magnetic materials are, in most cases, soluble analytically, which allows us to know in detail the physical mechanisms governing these materials. Still, the academic interest in parallel this subject, these materials have a number of properties that are promising to be used in technological devices, such as in computers quantum magnetic recording, magnetocaloric effect, spintronics and many other devices. This volume will journey through the world of molecular magnets, from the structural description of these materials to state of the art research.
NATO Advanced Research Workshop on Geometrical Derivatives of Energy Surfaces and Molecular Properties

CERN Document Server

Simons, Jack

1986-01-01

The development and computational implementation of analytical expres sions for the low-order derivatives of electronic energy surfaces and other molecular properties has undergone rapid growth in recent years. It is now fairly routine for chemists to make use of energy gradient information in locating and identifying stable geometries and transition states. The use of second analytical derivative (Hessian or curvature) expressions is not yet routine, and third and higher energy derivatives as well as property (e.g., dipole moment, polarizability) derivatives are just beginning to be applied to chemical problems. This NATO Advanced Research Workshop focused on analyzing the re lative merits of various strategies for deriving the requisite analyti cal expressions, for computing necessary integral derivatives and wave function parameter derivatives, and for efficiently coding these expres sions on conventional scalar machines and vector-oriented computers. The participant list contained many scientist...
Prediction of the mechanical properties of zeolite pellets for aerospace molecular decontamination applications

Directory of Open Access Journals (Sweden)

Guillaume Rioland

2016-11-01

Full Text Available Zeolite pellets containing 5 wt % of binder (methylcellulose or sodium metasilicate were formed with a hydraulic press. This paper describes a mathematical model to predict the mechanical properties (uniaxial and diametric compression of these pellets for arbitrary dimensions (height and diameter using a design of experiments (DOE methodology. A second-degree polynomial equation including interactions was used to approximate the experimental results. This leads to an empirical model for the estimation of the mechanical properties of zeolite pellets with 5 wt % of binder. The model was verified by additional experimental tests including pellets of different dimensions created with different applied pressures. The optimum dimensions were found to be a diameter of 10–23 mm, a height of 1–3.5 mm and an applied pressure higher than 200 MPa. These pellets are promising for technological uses in molecular decontamination for aerospace-based applications.
Molecular and excited state properties of isomeric scarlet disperse dyes

Science.gov (United States)

Lim, Jihye; Szymczyk, Malgorzata; Mehraban, Nahid; Ding, Yi; Parrillo-Chapman, Lisa; El-Shafei, Ahmed; Freeman, Harold S.

2018-06-01

This work was part of an investigation aimed at characterizing the molecular and excited state properties of currently available disperse dyes developed to provide stability to extensive sunlight exposures when adsorbed on poly(ethylene terephthalate) (PET) fibers. Having completed the characterization of yellow, magenta, and cyan disperse dyes for PET-based fabrics used outdoors, our attention turned to the colors designed to enhance the color gamut of a standard 4-member (cyan/yellow/magenta/black) color set. The present study pertained specifically to the characterization of commercially available scarlet dyes. In this regard, HPLC analysis showed that a scarlet product used for PET coloration was mainly a 70/30 mixture of dyes, and the use of HRMS and single crystal X-ray diffraction analyses indicated that these two dyes were azo compounds derived from isomeric pyridine-based couplers which differed in the location of the primary amino (sbnd NH2) and anilino (sbnd NHPh) groups attached to the pyridine ring. One dye structure has the sbnd NHPh group para to the azo group (Sc2), while the other has that group in the ortho position (Sc3). The presence of either ortho substituent provides photostabilization through intramolecular H-bonding with the azo moiety. Further, results from molecular modeling studies showed that the lower excited state oxidation potential of Sc3 relative to that of Sc2 allows Sc3 to function as an energy quencher for the excited state of Sc2 - through thermodynamically favorable electron transfer.
Structural properties of iron nitride on Cu(100): An ab-initio molecular dynamics study

KAUST Repository

Heryadi, Dodi

2011-01-01

Due to their potential applications in magnetic storage devices, iron nitrides have been a subject of numerous experimental and theoretical investigations. Thin films of iron nitride have been successfully grown on different substrates. To study the structural properties of a single monolayer film of FeN we have performed an ab-initio molecular dynamics simulation of its formation on a Cu(100) substrate. The iron nitride layer formed in our simulation shows a p4gm(2x2) reconstructed surface, in agreement with experimental results. In addition to its structural properties, we are also able to determine the magnetization of this thin film. Our results show that one monolayer of iron nitride on Cu(100) is ferromagnetic with a magnetic moment of 1.67 μ B. © 2011 Materials Research Society.
Computational Study of Geometry, Solvation Free Energy, Dipole Moment, Polarizability, Hyperpolarizability and Molecular Properties of 2-Methylimidazole

Directory of Open Access Journals (Sweden)

Mohammad Firoz Khan

2016-12-01

Full Text Available Ab initio calculations were carried out to study the geometry, solvation free energy, dipole moment, molecular electrostatic potential (MESP, Mulliken and Natural charge distribution, polarizability, hyperpolarizability, Natural Bond Orbital (NBO energetic and different molecular properties like global reactivity descriptors (chemical hardness, softness, chemical potential, electronegativity, electrophilicity index of 2-methylimidazole. B3LYP/6-31G(d,p level of theory was used to optimize the structure both in the gas phase and in solution. The solvation free energy, dipole moment and molecular properties were calculated by applying the Solvation Model on Density (SMD in four solvent systems, namely water, dimethylsulfoxide (DMSO, n-octanol and chloroform. The computed bond distances, bond angles and dihedral angles of 2-methylimidazole agreed reasonably well with the experimental data except for C(2-N(1, C(4-C(5 and N(1-H(7 bond lengths and N(1-C(5-C(4 bond angle. The solvation free energy, dipole moment, polarizability, first order hyperpolarizability, chemical potential, electronegativity and electrophilicity index of 2-methylimidazole increased on going from non-polar to polar solvents. Chemical hardness also increased with increasing polarity of the solvent and the opposite relation was found in the case of softness. These results provide better understanding of the stability and reactivity of 2-methylimidazole in different solvent systems.
Prediction of the Fate of Organic Compounds in the Environment From Their Molecular Properties: A Review.

Science.gov (United States)

Mamy, Laure; Patureau, Dominique; Barriuso, Enrique; Bedos, Carole; Bessac, Fabienne; Louchart, Xavier; Martin-Laurent, Fabrice; Miege, Cecile; Benoit, Pierre

2015-06-18

A comprehensive review of quantitative structure-activity relationships (QSAR) allowing the prediction of the fate of organic compounds in the environment from their molecular properties was done. The considered processes were water dissolution, dissociation, volatilization, retention on soils and sediments (mainly adsorption and desorption), degradation (biotic and abiotic), and absorption by plants. A total of 790 equations involving 686 structural molecular descriptors are reported to estimate 90 environmental parameters related to these processes. A significant number of equations was found for dissociation process (pK a ), water dissolution or hydrophobic behavior (especially through the K OW parameter), adsorption to soils and biodegradation. A lack of QSAR was observed to estimate desorption or potential of transfer to water. Among the 686 molecular descriptors, five were found to be dominant in the 790 collected equations and the most generic ones: four quantum-chemical descriptors, the energy of the highest occupied molecular orbital (E HOMO ) and the energy of the lowest unoccupied molecular orbital (E LUMO ), polarizability (α) and dipole moment (μ), and one constitutional descriptor, the molecular weight. Keeping in mind that the combination of descriptors belonging to different categories (constitutional, topological, quantum-chemical) led to improve QSAR performances, these descriptors should be considered for the development of new QSAR, for further predictions of environmental parameters. This review also allows finding of the relevant QSAR equations to predict the fate of a wide diversity of compounds in the environment.
Adhesion properties of Cu(111)/α-quartz (0001) interfaces: A molecular dynamics study

Energy Technology Data Exchange (ETDEWEB)

Yu, Wenshan, E-mail: wenshan@mail.xjtu.edu.cn; Wu, Lianping; Shen, Shengping, E-mail: sshen@mail.xjtu.edu.cn

2017-05-17

The fundamental properties of Cu/SiO{sub 2} interface are worth studying because they impact the quality and performance of silicon-based microelectronics and related devices. Using the charge-optimized many-body (COMB) potential in this study, we present a molecular dynamics simulation study of the structural, adhesive and electronic properties of Cu(111)/α-quartz SiO{sub 2} (0001) interfaces with two different crystalline orientations and various terminations by double-oxygens (OO), single-oxygen(O) and silicon(Si). For the equilibrated interfaces, the largest adhesion energies correspond to the oxygen richest OO-terminated interface in which the oxidation level of Cu is highest due to the largest charge transfer across the interface. In particular, we also investigate the properties of a series of nonequilibrated OO-, O- and Si-terminated interfaces that are created from their equilibrated counterparts by introducing vacancies of different numbers and different types. It is found that the adhesion energies of interfaces mostly decrease upon vacancy introductions only except for Si vacancies added in the Si-terminated interface. For all nonequilibrated interfaces of different terminations, we found a linear correlation between adhesive energy and area average excess charge transfer in Cu.
Facilitating Students' Interaction with Real Gas Properties Using a Discovery-Based Approach and Molecular Dynamics Simulations

Science.gov (United States)

Sweet, Chelsea; Akinfenwa, Oyewumi; Foley, Jonathan J., IV

2018-01-01

We present an interactive discovery-based approach to studying the properties of real gases using simple, yet realistic, molecular dynamics software. Use of this approach opens up a variety of opportunities for students to interact with the behaviors and underlying theories of real gases. Students can visualize gas behavior under a variety of…
Time-dependent motor properties of multipedal molecular spiders.

Science.gov (United States)

Samii, Laleh; Blab, Gerhard A; Bromley, Elizabeth H C; Linke, Heiner; Curmi, Paul M G; Zuckermann, Martin J; Forde, Nancy R

2011-09-01

Molecular spiders are synthetic biomolecular walkers that use the asymmetry resulting from cleavage of their tracks to bias the direction of their stepping motion. Using Monte Carlo simulations that implement the Gillespie algorithm, we investigate the dependence of the biased motion of molecular spiders, along with binding time and processivity, on tunable experimental parameters, such as number of legs, span between the legs, and unbinding rate of a leg from a substrate site. We find that an increase in the number of legs increases the spiders' processivity and binding time but not their mean velocity. However, we can increase the mean velocity of spiders with simultaneous tuning of the span and the unbinding rate of a spider leg from a substrate site. To study the efficiency of molecular spiders, we introduce a time-dependent expression for the thermodynamic efficiency of a molecular motor, allowing us to account for the behavior of spider populations as a function of time. Based on this definition, we find that spiders exhibit transient motor function over time scales of many hours and have a maximum efficiency on the order of 1%, weak compared to other types of molecular motors.

Molecular dynamics investigation of the elastic and fracture properties of the R-graphyne under uniaxial tension

Energy Technology Data Exchange (ETDEWEB)

Rouhi, Saeed, E-mail: s_rouhi@iaul.ac.ir

2017-05-15

In this paper, the mechanical properties of the R-graphynes are investigated by using molecular dynamics simulations. For this purpose, the uniaxial strain is applied on the nanosheets. The effects of R-graphyne chirality and dimension on their fracture and elastic properties are investigated. It is shown that the fracture properties of the armchair R-graphyne are approximately independent from the nanosheet sizes. However, a clear dependence is observed in the fracture properties of the zigzag R-graphyne on the nanosheet dimensions. Comparing the elastic modulus of the armchair and zigzag R-graphynes, it is shown that for the same sizes, the elastic modulus of armchair R-graphyne is approximately equal to 2.5 times of the elastic modulus of the zigzag ones. Pursuing the fracture process of R-graphynes with different chiralities, it is represented that the fracture propagates in the zigzag nanosheet with a higher velocity than the armchair ones.
Surface properties of poly(acrylonitrile) (PAN) precipitation polymerized in supercritical CO2 and the influence of the molecular weight.

Science.gov (United States)

Shen, Qing; Gu, Qing-Feng; Hu, Jian-Feng; Teng, Xin-Rong; Zhu, Yun-Feng

2003-11-15

In this paper, the surface properties, e.g., the total surface free energy and the related Lifshitz-van der Waals and Lewis acid-base components, of polyacrylonitrile (PAN) precipitation polymerized in supercritical CO(2) have been characterized. Moreover, the influence of molecular weight varying has been also investigated. Results show that the surface properties of PAN resulting from supercritical CO(2) are different from those obtained by the conventional method. Of these data, one important finding is that the supercritical CO(2) PAN seems to decrease the surface free energy with the increased molecular weight. Based on previous recorded NMR spectra of this PAN and especially compared to commercial PAN, such phenomena are discussed and ascribed to an increase of the H-bonds and a reduction of the isotacticity in the supercritical CO(2) condition for PAN.
Tailoring the mechanical properties by molecular integration of flexible and stiff polymer networks.

Science.gov (United States)

Wan, Haixiao; Shen, Jianxiang; Gao, Naishen; Liu, Jun; Gao, Yangyang; Zhang, Liqun

2018-03-28

Designing a multiple-network structure at the molecular level to tailor the mechanical properties of polymeric materials is of great scientific and technological importance. Through the coarse-grained molecular dynamics simulation, we successfully construct an interpenetrating polymer network (IPN) composed of a flexible polymer network and a stiff polymer network. First, we find that there is an optimal chain stiffness for a single network (SN) to achieve the best stress-strain behavior. Then we turn to study the mechanical behaviors of IPNs. The result shows that the stress-strain behaviors of the IPNs appreciably exceed the sum of that of the corresponding single flexible and stiff network, which highlights the advantage of the IPN structure. By systematically varying the stiffness of the stiff polymer network of the IPNs, optimal stiffness also exists to achieve the best performance. We attribute this to a much larger contribution of the non-bonded interaction energy. Last, the effect of the component concentration ratio is probed. With the increase of the concentration of the flexible network, the stress-strain behavior of the IPNs is gradually enhanced, while an optimized concentration (around 60% molar ration) of the stiff network occurs, which could result from the dominant role of the enthalpy rather than the entropy. In general, our work is expected to provide some guidelines to better tailor the mechanical properties of the IPNs made of a flexible network and a stiff network, by manipulating the stiffness of the stiff polymer network and the component concentration ratio.
Thermal characterization of static and dynamical properties of the confined molecular systems interacting through dispersion force.

Science.gov (United States)

Ramos, Sergio Luis L M; Ogino, Michihiko; Oguni, Masaharu

2015-01-28

We investigated the thermal properties of liquid methylcyclohexane and racemic sec-butylcyclohexane, as representatives of a molecular system with only dispersion-force intermolecular interactions, confined in the pores (thickness/diameter d = 12, 6, 1.1 nm) of silica gels by adiabatic calorimetry. The results imply a heterogeneous picture for molecular aggregate under confinement consisting of an interfacial region and an inner pore one. In the vicinity of a glass-transition temperature T(g,bulk) of bulk liquid, two distinguishable relaxation phenomena were observed for the confined systems and their origins were attributed to the devitrification, namely glass transition, processes of (1) a layer of interfacial molecules adjacent to the pore walls and (2) the molecules located in the middle of the pore. A third glass-transition phenomenon was observed at lower temperatures and ascribed to a secondary relaxation process. The glass transition of the interfacial-layer molecules was found to proceed at temperatures rather above T(g,bulk), whereas that of the molecules located in the inner pore region occurred at temperatures below T(g,bulk). We discuss the reason why the molecules located in different places in the pores reveal the respectively different dynamical properties.
Controllable Molecular Packing Motif and Overlap Type in Organic Nanomaterials for Advanced Optical Properties

Directory of Open Access Journals (Sweden)

Taoyu Zou

2018-01-01

Full Text Available The optical properties of organic materials are very sensitive to subtle structural modification, and a proper understanding of the structure-property relationship is essential to improve the performance of organic electronic devices. The phase transitions of the η-CuPc to the α-CuPc, then to the β-CuPc were investigated using In situ X-ray diffraction and the differential scanning calorimetry (DSC. The five stages in the phase-transition process from low to high-temperature were observed, which consisted of (1 the η-CuPc; (2 a mixture of the η- and α-CuPc; (3 a mixture of the η-, α- and β-CuPc; (4 a mixture of the α- and β-CuPc; and (5 the β-CuPc. The vibrational and optical properties at different phase-transition stages were correlated to molecular packing motif and molecule overlap type through systematic analyses of the Fourier–transform infrared, Raman and UV-VIS spectra. Moreover, the mechanism for the morphology evolution was also discussed in detail.
a Moessbauer Effect and Fenske-Hall Molecular Orbital Study of the Electronic Properties of Organoiron Clusters.

Science.gov (United States)

Buhl, Margaret Linn

The electronic properties of trinuclear iron, tetranuclear iron butterfly, iron-cobalt, and iron-copper clusters have been studied experimentally at 78K by the Mossbauer effect and theoretically by Fenske-Hall molecular orbital calculations. The Mossbauer effect isomer shift is very sensitive to the differences in the iron s-electron densities in these clusters and, as expected, decreases as the sum of the iron 4s Mulliken population and the Clementi and Raimondi effective nuclear charge increases. The molecular orbital wave functions and the Mulliken atomic charges are used to calculate the electric field gradient at the metal nuclei and the iron Mossbauer effect quadrupole splittings. The valence contribution was found to be the major component of the electric field gradient in all the clusters studied. In general the calculated value of Delta E_ {Q} is larger than the observed value, as a result of neglect of the valence Sternheimer factor, R. The metal charge depends upon its electronegativity and upon the nature of its Lewis base ligands. The carbonyl ligand carbon charge becomes more positive as the metal electronegativity increases. The oxygen charge becomes more negative as the anionic cluster charge increases, and in so doing, yields the maximum anionic charge separation. The electronic properties of the terminal carbonyl ligands are similar to those of carbon monoxide, whereas the electronic properties of the bridging carbonyl ligands are similar to those of the carbonyl group found in aldehydes and ketones.
Machine learning of molecular properties: Locality and active learning

Science.gov (United States)

Gubaev, Konstantin; Podryabinkin, Evgeny V.; Shapeev, Alexander V.

2018-06-01

In recent years, the machine learning techniques have shown great potent1ial in various problems from a multitude of disciplines, including materials design and drug discovery. The high computational speed on the one hand and the accuracy comparable to that of density functional theory on another hand make machine learning algorithms efficient for high-throughput screening through chemical and configurational space. However, the machine learning algorithms available in the literature require large training datasets to reach the chemical accuracy and also show large errors for the so-called outliers—the out-of-sample molecules, not well-represented in the training set. In the present paper, we propose a new machine learning algorithm for predicting molecular properties that addresses these two issues: it is based on a local model of interatomic interactions providing high accuracy when trained on relatively small training sets and an active learning algorithm of optimally choosing the training set that significantly reduces the errors for the outliers. We compare our model to the other state-of-the-art algorithms from the literature on the widely used benchmark tests.
Thermodynamic properties by equation of state and from Ab initio molecular dynamics of liquid potassium under pressure

Science.gov (United States)

Li, Huaming; Tian, Yanting; Sun, Yongli; Li, Mo; Nonequilibrium materials; physics Team; Computational materials science Team

In this work, we apply a general equation of state of liquid and Ab initio molecular-dynamics method to study thermodynamic properties in liquid potassium under high pressure. Isothermal bulk modulus and molar volume of molten sodium are calculated within good precision as compared with the experimental data. The calculated internal energy data and the calculated values of isobaric heat capacity of molten potassium show the minimum along the isothermal lines as the previous result obtained in liquid sodium. The expressions for acoustical parameter and nonlinearity parameter are obtained based on thermodynamic relations from the equation of state. Both parameters for liquid potassium are calculated under high pressure along the isothermal lines by using the available thermodynamic data and numeric derivations. Furthermore, Ab initio molecular-dynamics simulations are used to calculate some thermodynamic properties of liquid potassium along the isothermal lines. Scientific Research Starting Foundation from Taiyuan university of Technology, Shanxi Provincial government (``100-talents program''), China Scholarship Council and National Natural Science Foundation of China (NSFC) under Grant No. 51602213.
Structural, dynamical, and electronic properties of amorphous silicon: An ab initio molecular dynamics study

Energy Technology Data Exchange (ETDEWEB)

Car, R.; Parrinello, M.

1988-01-18

An amorphous silicon structure is obtained with a computer simulation based on a new molecular-dynamics technique in which the interatomic potential is derived from a parameter-free quantum mechanical method. Our results for the atomic structure, the phonon spectrum, and the electronic properties are in excellent agreement with experiment. In addition we study details of the microscopic dynamics which are not directly accessible to experiment. We find in particular that structural defects are associated with weak bonds. These may give rise to low-frequency vibrational modes.
Gas-Transport-Property Performance of Hybrid Carbon Molecular Sieve−Polymer Materials

KAUST Repository

Das, Mita

2010-10-06

High-performance hybrid materials using carbon molecular sieve materials and 6FDA-6FpDA were produced. A detailed analysis of the effects of casting processes and the annealing temperature is reported. Two existing major obstacles, sieve agglomeration and residual stress, were addressed in this work, and subsequently a new membrane formation technique was developed to produce high-performing membranes. The successfully improved interfacial region of the hybrid membranes allows the sieves to increase the selectivity of the membranes above the neat polymer properties. Furthermore, an additional performance enhancement was seen with increased sieve loading in the hybrid membranes, leading to an actual performance above the upper bound for pure polymer membranes. The membranes were also tested under a mixed-gas environment, which further demonstrated promising results. © 2010 American Chemical Society.
Effect of structure and molecular weight on properties of pressure sensitive adhesives (PSA) formulated from palm oil based urethane acrylate (POBUA)

International Nuclear Information System (INIS)

Mohd Hilmi Mahmood; Shahrol Najmin Baharom; Rida Tajau; Mek Zah Salleh; Khairul Zaman Mohd Dahlan; Rosley Che Ismail

2004-01-01

Various palm oil (RBD Palm Olein) based urethane acrylate prepolymers (UPs) having different structures and molecular weight were synthesized from palm oil based polyols, diisocyanate compounds and hydroxyl terminated acrylate monomers by following established synthesis procedures described elsewhere. The products (UPs) were compared with each other in term of their molecular weight (MW), viscosities and UV curing performances of pressure sensitive adhesives (PSA) UP based formulations. The molecular structure of diisocyanate compounds and hydroxyl acrylate monomers tend to determine the molecular weight and hence viscosities of the final products of urethane acrylate prepolymers (UP), whereas, the MW of the UP has no direct effects on the coatings and adhesive properties of UV curable UP based PSA. (Author)
Molecular dynamics simulation on the elastoplastic properties of copper nanowire under torsion

Science.gov (United States)

Yang, Yong; Li, Ying; Yang, Zailin; Zhang, Guowei; Wang, Xizhi; Liu, Jin

2018-02-01

Influences of different factors on the torsion properties of single crystal copper nanowire are studied by molecular dynamics method. The length, torsional rate, and temperature of the nanowire are discussed at the elastic-plastic critical point. According to the average potential energy curve and shear stress curve, the elastic-plastic critical angle is determined. Also, the dislocation at elastoplastic critical points is analyzed. The simulation results show that the single crystal copper nanowire can be strengthened by lengthening the model, decreasing the torsional rate, and lowering the temperature. Moreover, atoms move violently and dislocation is more likely to occur with a higher temperature. This work mainly describes the mechanical behavior of the model under different states.
First-principles study of the electronic transport properties in (GaAs)n (n=2–4) nanocluster-based molecular junctions

International Nuclear Information System (INIS)

Zhang, Daoli; Xu, Yuanlan; Zhang, Jianbing; Miao, Xiangshui

2012-01-01

In this program the geometric structures and electronic transport properties of a series of (GaAs) n (n=2,3,4) clusters are comparatively studied using non-equilibrium Green's function (NEGF) combined with density functional theory (DFT). It is find that all the GaAs nanocluster-based molecular junctions show metallic behavior at low biases ([−2 V,2 V]) while negative differential resistance (NDR) appears at a certain high bias range. Our calculation shows that the current of (GaAs) 3 nanocluster-based molecular junction is almost the smallest at any bias. The mechanisms of the current–voltage characteristics of all the three molecular junctions are proposed.
Relationships between Molecular Composition and Optical Properties of Dissolved Organic Matter

Science.gov (United States)

Cooper, W. T.; Tfaily, M.; Osborne, D.; Paul, A.; Podgorski, D. C.; Corbett, J.; Chanton, J.

2009-12-01

Our focus is on the relationships between the optical properties of dissolved organic matter (DOM) and its molecular composition. For example, we demonstrated that changes in the absorption and fluorescence characteristics of DOM in outwelling from Brazilian mangrove forests correlated with decreases in highly unsaturated organic compounds as DOM was transported from mangrove porewaters to the continental shelf. In that work we combined ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) that provided detailed compositional information with absorption and Excitation/Emission Matrix (EEM) spectroscopy This presentation will highlight new results utilizing the combination of optical spectroscopy and FT-ICR mass spectrometry to illuminate the processes which control DOM cycling. Our focus will be on the contributions of the heteroatom components of DOM (i.e. organic sulfur and organic nitrogen) to its optical properties and how changes in optical properties correlate with important environmental processes like humification and bioavailability. Figure 1 below includes a narrow 0.20 Dalton window from a mass spectrum which demonstrates the ability of ultrahigh resolution mass spectrometry to resolve and identify nitrogen heteroatom compounds in DOM. Our study sites include the Glacial Lake Agassiz Peatlands (GLAP) in northern Minnesota and wetlands in the Caloosahatchee River basin in South Florida. Figure 1. Isolated 0.20 Da window of an ESI-FT-ICR mass spectrum of DOM from a GLAP bog. Labels identify N1 (d,e,f) and N3 classes of nitrogen heteroatoms. The 0.0031 Da mass spacing is used to confirm the N3 class.
Electronic properties of organic monolayers and molecular devices

Indian Academy of Sciences (India)

These devices exhibit a marked current–voltage rectification behavior due to resonant transport between the Si conduction band and the molecule highest occupied molecular orbital of the molecule. We discuss the role of metal Fermi level pinning in the current–voltage behavior of these molecular junctions. We also ...
Effect of electron beam radiation on the structure and mechanical properties of ultra high molecular weight polyethylene fibers

International Nuclear Information System (INIS)

Li Shujun; Sun Weijun; Liu Xiuju; Gao Yongzhong; Li Huisheng

1998-01-01

Ultra high molecular weight polyethylene fibers have been crosslinked by electron beam. The structure and mechanical properties of them have been investigated in different irradiation atmospheres. The obtained results show that the gel content and crosslinking density increase with the increase of dose, the swelling ratio and average molecular weight of crosslinked net decrease with the increase of dose, the tensile strength and failure elongation decrease with the increase of dose, the tensile modulus increases with the increase of dose. When the samples are irradiated in air, vacuum and acetylene atmospheres, the effect of irradiation in acetylene atmosphere is best
Galaxy pairs in the SDSS - XIII. The connection between enhanced star formation and molecular gas properties in galaxy mergers

Science.gov (United States)

Violino, Giulio; Ellison, Sara L.; Sargent, Mark; Coppin, Kristen E. K.; Scudder, Jillian M.; Mendel, Trevor J.; Saintonge, Amelie

2018-05-01

We investigate the connection between star formation and molecular gas properties in galaxy mergers at low redshift (z ≤ 0.06). The study we present is based on IRAM 30-m CO(1-0) observations of 11 galaxies with a close companion selected from the Sloan Digital Sky Survey (SDSS). The pairs have mass ratios ≤4, projected separations rp ≤ 30 kpc and velocity separations ΔV ≤ 300 km s-1, and have been selected to exhibit enhanced specific star formation rates (sSFRs). We calculate molecular gas (H2) masses, assigning to each galaxy a physically motivated conversion factor αCO, and we derive molecular gas fractions and depletion times. We compare these quantities with those of isolated galaxies from the extended CO Legacy Data base for the GALEX Arecibo SDSS Survey sample (xCOLDGASS; Saintonge et al.) with gas quantities computed in an identical way. Ours is the first study which directly compares the gas properties of galaxy pairs and those of a control sample of normal galaxies with rigorous control procedures and for which SFR and H2 masses have been estimated using the same method. We find that the galaxy pairs have shorter depletion times and an average molecular gas fraction enhancement of 0.4 dex compared to the mass matched control sample drawn from xCOLDGASS. However, the gas masses (and fractions) in galaxy pairs and their depletion times are consistent with those of non-mergers whose SFRs are similarly elevated. We conclude that both external interactions and internal processes may lead to molecular gas enhancement and decreased depletion times.
Effect of protonation on the electronic properties of DNA base pairs: applications for molecular electronics.

Science.gov (United States)

Mallajosyula, Sairam S; Pati, Swapan K

2007-10-11

Protonation of DNA basepairs is a reversible phenomenon that can be controlled by tuning the pH of the system. Under mild acidic conditions, the hydrogen-bonding pattern of the DNA basepairs undergoes a change. We study the effect of protonation on the electronic properties of the DNA basepairs to probe for possible molecular electronics applications. We find that, under mild acidic pH conditions, the A:T basepair shows excellent rectification behavior that is, however, absent in the G:C basepair. The mechanism of rectification has been discussed using a simple chemical potential model. We also consider the noncanonical A:A basepair and find that it can be used as efficient pH dependent molecular switch. The switching action in the A:A basepair is explained in the light of pi-pi interactions, which lead to efficient delocalization over the entire basepair.
Molecular dynamics calculation of thermophysical properties for a highly reactive liquid.

Science.gov (United States)

Wang, H P; Luo, B C; Wei, B

2008-10-01

In order to further understand the physical characteristics of liquid silicon, the thermophysical properties are required over a broad temperature range. However, its high reactivity brings about great difficulties in the experimental measurement. Here we report the thermophysical properties by molecular dynamics calculation, including density, specific heat, diffusion coefficient, and surface tension. The calculation is performed with a system consisting of 64,000 atoms, and employing the Stillinger-Weber (SW) potential model and the modified embedded atom method (MEAM) potential model. The results show that the density increases as a quadratic function of undercooling, and the value calculated by SW potential model is only 2-4 % smaller than the reported experimental data. The specific heat is obtained to be 30.95 J mol;{-1}K;{-1} by SW potential model and 32.50 J mol;{-1}K;{-1} by MEAM potential model, both of which are constants in the corresponding ranges of temperature. The self-diffusion coefficient is exponentially dependent on the temperature and consistent with the Arrhenius equation. The surface tension increases linearly with the rise of undercooling and agrees well with the reported experimental results. This work provides reasonable data in much wider temperature range, especially for the undercooled metastable state.
Molecular and optical properties of tree-derived dissolved organic matter in throughfall and stemflow from live oaks and eastern red cedar

Science.gov (United States)

Stubbins, Aron; Silva, Leticia M.; Dittmar, Thorsten; Van Stan, John T.

2017-03-01

Studies of dissolved organic matter (DOM) transport through terrestrial aquatic systems usually start at the stream. However, the interception of rainwater by vegetation marks the beginning of the terrestrial hydrological cycle making trees the headwaters of aquatic carbon cycling. Rainwater interacts with trees picking up tree-DOM, which is then exported from the tree in stemflow and throughfall. Stemflow denotes water flowing down the tree trunk, while throughfall is the water that drips through the leaves of the canopy. We report the concentrations, optical properties (light absorbance) and molecular signatures (ultrahigh resolution mass spectrometry) of tree-DOM in throughfall and stemflow from two tree species (live oak and eastern red cedar) with varying epiphyte cover on Skidaway Island, Savannah, Georgia, USA. Both stemflow and throughfall were enriched in DOM compared to rainwater, indicating trees were a significant source of DOM. The optical and molecular properties of tree-DOM were broadly consistent with those of DOM in other aquatic ecosystems. Stemflow was enriched in highly colored DOM compared to throughfall. Elemental formulas identified clustered the samples into three groups: oak stemflow, oak throughfall and cedar. The molecular properties of each cluster are consistent with an autochthonous aromatic-rich source associated with the trees, their epiphytes and the microhabitats they support. Elemental formulas enriched in oak stemflow were more diverse, enriched in aromatic formulas, and of higher molecular mass than for other tree-DOM classes, suggesting greater contributions from fresh and partially modified plant-derived organics. Oak throughfall was enriched in lower molecular weight, aliphatic and sugar formulas, suggesting greater contributions from foliar surfaces. While the optical properties and the majority of the elemental formulas within tree-DOM were consistent with vascular plant-derived organics, condensed aromatic formulas were

Molecular, biophysical, and pharmacological properties of calcium-activated chloride channels.

Science.gov (United States)

Kamaleddin, Mohammad Amin

2018-02-01

Calcium-activated chloride channels (CaCCs) are a family of anionic transmembrane ion channels. They are mainly responsible for the movement of Cl - and other anions across the biological membranes, and they are widely expressed in different tissues. Since the Cl - flow into or out of the cell plays a crucial role in hyperpolarizing or depolarizing the cells, respectively, the impact of intracellular Ca 2+ concentration on these channels is attracting a lot of attentions. After summarizing the molecular, biophysical, and pharmacological properties of CaCCs, the role of CaCCs in normal cellular functions will be discussed, and I will emphasize how dysregulation of CaCCs in pathological conditions can account for different diseases. A better understanding of CaCCs and a pivotal regulatory role of Ca 2+ can shed more light on the therapeutic strategies for different neurological disorders that arise from chloride dysregulation, such as asthma, cystic fibrosis, and neuropathic pain. © 2017 Wiley Periodicals, Inc.
Effects of styrene unit on molecular conformation and spectral properties of CNsbnd PhCHdbnd NPhCHdbnd CHPhsbnd CN

Science.gov (United States)

Fang, Zhengjun; Wu, Feng; Jiao, Yingchun; Wang, Nanfang; Au, Chaktong; Cao, Chenzhong; Yi, Bing

2018-05-01

Compound CN-PhCH=NPhCH=CHPh-CN with both stilbene and benzylidene aniline units was synthesized, and studied from the viewpoint of molecular conformation and spectroscopic property by a combined use of experimental and computational methods. The maximum UV absorption wavelength (λmax) of the compound in ethanol, acetonitrile, chloroform and cyclohexane solvents were measured, and the 13C NMR chemical shift value δC(Cdbnd N) in chloroform-d was determined. The crystal structure of the compound was determined by X-ray diffraction. The frontier molecular orbital was calculated by density functional theory method. The results show that the UV absorption spectrum of the titled compound is similar to those of Schiff bases, while there is a larger red shift of λmax comparing to that of CN-PhCH=NPh-CN. Moreover, the molecular configuration of the titled compound relative to Cdbnd N is anti-form, having a more obvious twisted structure. The spectral and structural behaviors are further supported by the results of frontier molecular orbital analyses, NBO, electrostatic potentials and TD-DFT calculations. The study provides deeper insights into the molecular conformation of Schiff bases.
Investigation of the Influence of PLA Molecular Structure on the Crystalline Forms (α’ and α and Mechanical Properties of Wet Spinning Fibres

Directory of Open Access Journals (Sweden)

Michał Puchalski

2017-01-01

Full Text Available In this paper, the influence of the molecular structure of polylactide (PLA—characterised by its molar mass and content of d-lactide isomer—on the molecular ordering and α’–α form transition during fibre manufacturing by the wet spinning method is described. Fibres were studied by wide-angle X-ray diffraction (WAXD and differential scanning calorimetry (DSC. Additionally, the physical and mechanical properties of the fibres were determined. This study also examines the preliminary molecular ordering and crystallisation of PLA fibres at various draw ratios. The performed experiments clearly show the dependence of the molecular ordering of PLA on the molar mass and d-lactide content during the wet spinning process. The fibres manufactured from PLA with the lowest content of d-lactide and the lowest molar mass were characterised by a higher tendency for crystallisation and a higher possibility to undergo the disorder-to-order phase transition (α’ to α form. The structural changes in PLA explain the observed changes in the physical and mechanical properties of the obtained fibres.
Thermophysical properties of liquid UO{sub 2}, ZrO{sub 2} and corium by molecular dynamics and predictive models

Energy Technology Data Exchange (ETDEWEB)

Kim, Woong Kee; Shim, Ji Hoon [Pohang University of Science and Technology, Pohang (Korea, Republic of); Kaviany Massoud [University of Michigan, Ann Arbor (United States)

2016-10-15

The analysis of such accidents (fate of the melt), requires accurate corium thermophysical properties data up to 5000 K. In addition, the initial corium melt superheat melt, determined from such properties, are key in predicting the fuel-coolant interactions (FCIs) and convection and retention of corium in accident scenarios, e.g., core-melt down corium discharge from reactor pressure vessels and spreading in external core-catcher. Due to the high temperatures, data on molten corium and its constituents are limited, so there are much data scatters and mostly extrapolations (even from solid state) have been used. Here we predict the thermophysical properties of molten UO{sub 2} and ZrO{sub 2} using classical molecular dynamics (MD) simulations (properties of corium are predicted using the mixture theories and UO{sub 2} and ZrO{sub 2} properties). The thermophysical properties (density, compressibility, heat capacity, viscosity and surface tension) of liquid UO{sub 2} and ZrO{sub 2} are predicted using classical molecular dynamics simulations, up to 5000 K. For atomic interactions, the CRG and the Teter potential models are found most appropriate. The liquid behavior is verified with the random motion of the constituent atoms and the pair-distribution functions, starting with the solid phase and raising the temperature to realize liquid phase. The viscosity and thermal conductivity are calculated with the Green-Kubo autocorrelation decay formulae and compared with the predictive models of Andrade and Bridgman. For liquid UO{sub 2}, the CRG model gives satisfactory MD predictions. For ZrO{sub 2}, the density is reliably predicted with the CRG potential model, while the compressibility and viscosity are more accurately predicted by the Teter model.
Molecular structure of sodium lignosulfonate from different sources and their properties as dispersant of TiO2 slurry

Science.gov (United States)

Haifeng Zhou; Dongjie Yang; Junyong Zhu

2016-01-01

The molecular structure and properties of four sodium lignosulfates (LSs) derived from pulping or bioethanol production were evaluated and compared. SXP and SAL were produced by sulfite pulping and sulfonation reaction of lignin from alkali pulping of poplar, respectively. LS-180 and LS-150 were from sulfite pretreatment to overcome recalcitrance of lignocelluloses (...
Luminescence studies of molecular materials

International Nuclear Information System (INIS)

Miller, P.F.

2000-01-01

Molecular materials have been widely studied for their potential uses in novel semiconductor devices. They occupy the intellectually interesting area between molecular and bulk descriptions of matter, and as such often have unique and useful characteristics. The design and engineering of these structures is inter-disciplinary in its nature, embracing the fields of physics, electrical engineering and both synthetic and physical chemistry. In this thesis luminescence studies of molecular materials will be presented that probe the nature of the excited states in two promising semiconductor systems. Luminescence techniques provide a powerful and sensitive tool in the investigation of kinetic pathways of radiative and non-radiative emission from these samples. This is particularly appropriate here, as the materials being studied are of potential use in electroluminescent devices. The suitability of photoluminescence techniques comes from both the electroluminescence and photoluminescence sharing the same emitting state. The first class of material studied here is an organic semiconducting polymer, cyano-substituted polyphenylenevinylene (CN-PPV). Conjugated polymers combine semiconducting electronic properties with favourable processing properties and offer the possibility of tuning their optical and electronic properties chemically. The cyanosubstitution increases the electron affinity of the polymer backbone, facilitating electron injection in light-emitting diodes. The polymers are soluble in solvents such as toluene and chloroform due the presence of alkoxy sidegroups. CdSe semiconductor nanocrystals are the other class of material characterised in this work. Semiconductor nanocrystals exhibit interesting size-tunable optical properties due to the confinement of the electronic wave functions. Characterisation of samples produced by different synthetic routes has been carried out to demonstrate the advantages of a novel synthetic method in terms of physical and
Bayesian screening for active compounds in high-dimensional chemical spaces combining property descriptors and molecular fingerprints.

Science.gov (United States)

Vogt, Martin; Bajorath, Jürgen

2008-01-01

Bayesian classifiers are increasingly being used to distinguish active from inactive compounds and search large databases for novel active molecules. We introduce an approach to directly combine the contributions of property descriptors and molecular fingerprints in the search for active compounds that is based on a Bayesian framework. Conventionally, property descriptors and fingerprints are used as alternative features for virtual screening methods. Following the approach introduced here, probability distributions of descriptor values and fingerprint bit settings are calculated for active and database molecules and the divergence between the resulting combined distributions is determined as a measure of biological activity. In test calculations on a large number of compound activity classes, this methodology was found to consistently perform better than similarity searching using fingerprints and multiple reference compounds or Bayesian screening calculations using probability distributions calculated only from property descriptors. These findings demonstrate that there is considerable synergy between different types of property descriptors and fingerprints in recognizing diverse structure-activity relationships, at least in the context of Bayesian modeling.
Dynamic properties of sensory stimulation evoked responses in mouse cerebellar granule cell layer and molecular layer.

Science.gov (United States)

Bing, Yan-Hua; Zhang, Guang-Jian; Sun, Lei; Chu, Chun-Ping; Qiu, De-Lai

2015-01-12

Sensory information coming from climbing fiber and mossy fiber-granule cell pathways, generates motor-related outputs according to internal rules of integration and computation in the cerebellar cortex. However, the dynamic properties of sensory information processing in mouse cerebellar cortex are less understood. Here, we studied the dynamic properties of sensory stimulation-evoked responses in the cerebellar granule cell layer (GCL) and molecular layer (ML) by electrophysiological recordings method. Our data showed that air-puff stimulation (5-10 ms in duration) of the ipsilateral whisker pad evoked single-peak responses in the GCL and ML; whereas a duration of stimulation ≥30 ms in GCL and ≥60 ms in ML, evoked double-peak responses that corresponded with stimulation-on and -off responses via mossy fiber pathway. The highest frequency of stimulation train for evoking GCL responses was 33 Hz. In contrast, the highest frequency of stimulation train for evoking ML responses was 4 Hz. These results indicate that the cerebellar granule cells transfer the high-fidelity sensory information from mossy fibers, which is cut-off by molecular layer interneurons (MLIs). Our results suggest that the MLIs network acts as a low-pass filter during the processing of high-frequency sensory information. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.
Molecular and Thermodynamic Properties of Zwitterions versus Ionic Liquids: A Comprehensive Computational Analysis to Develop Advanced Separation Processes.

Science.gov (United States)

Moreno, Daniel; Gonzalez-Miquel, Maria; Ferro, Victor R; Palomar, Jose

2018-04-05

Zwitterion ionic liquids (ZIs) are compounds in which both counterions are covalently tethered, conferring them with unique characteristics; however, most of their properties are still unknown, representing a bottleneck to exploit their practical applications. Herein, the molecular and fluid properties of ZIs and their mixtures were explored by means of quantum chemical analysis based on the density functional theory (DFT) and COSMO-RS method, and compared against homologous ionic liquids (ILs) to provide a comprehensive overview of the effect of the distinct structures on their physicochemical and thermodynamic behavior. Overall, ZIs were revealed as compounds with higher polarity and stronger hydrogen-bonding capacity, implying higher density, viscosity, melting point, and even lower volatility than structurally similar ILs. The phase equilibrium of binary and ternary systems supports stronger attractive interactions between ZIs and polar compounds, whereas higher liquid-liquid immiscibility with nonpolar compounds may be expected. Ultimately, the performance of ZIs in the wider context of separation processes is illustrated, while providing molecular insights to allow their selection and design for relevant applications. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Spectroscopic analysis of 8-hydroxyquinoline derivatives and investigation of its reactive properties by DFT and molecular dynamics simulations

Science.gov (United States)

Sureshkumar, B.; Mary, Y. Sheena; Resmi, K. S.; Panicker, C. Yohannan; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, C.; Narayana, B.; Suma, S.

2018-03-01

Two 8-hydroxyquinoline derivatives, 5,7-dichloro-8-hydroxyquinoline (57DC8HQ) and 5-chloro-7-iodo-8-hydroxy quinoline (5CL7I8HQ) have been investigated in details by means of spectroscopic characterization and computational molecular modelling techniques. FT-IR and FT-Raman experimental spectroscopic approaches have been utilized in order to obtain detailed spectroscopic signatures of title compounds, while DFT calculations have been used in order to visualize and assign vibrations. The computed values of dipole moment, polarizability and hyperpolarizability indicate that the title molecules exhibit NLO properties. The evaluated HOMO and LUMO energies demonstrate the chemical stability of the molecules. NBO analysis is made to study the stability of the molecules arising from hyperconjugative interactions and charge delocalization. DFT calculations have been also used jointly with MD simulations in order to investigate in details global and local reactivity properties of title compounds. Also, molecular docking has been also used in order to investigate affinity of title compounds against decarboxylase inhibitor and quinoline derivatives can be a lead compounds for developing new antiparkinsonian drug.
Density scaling of the transport properties of molecular and ionic liquids.

Science.gov (United States)

López, Enriqueta R; Pensado, Alfonso S; Comuñas, María J P; Pádua, Agílio A H; Fernández, Josefa; Harris, Kenneth R

2011-04-14

Casalini and Roland [Phys. Rev. E 69, 062501 (2004); J. Non-Cryst. Solids 353, 3936 (2007)] and other authors have found that both the dielectric relaxation times and the viscosity, η, of liquids can be expressed solely as functions of the group (TV (γ)), where T is the temperature, V is the molar volume, and γ a state-independent scaling exponent. Here we report scaling exponents γ, for the viscosities of 46 compounds, including 11 ionic liquids. A generalization of this thermodynamic scaling to other transport properties, namely, the self-diffusion coefficients for ionic and molecular liquids and the electrical conductivity for ionic liquids is examined. Scaling exponents, γ, for the electrical conductivities of six ionic liquids for which viscosity data are available, are found to be quite close to those obtained from viscosities. Using the scaling exponents obtained from viscosities it was possible to correlate molar conductivity over broad ranges of temperature and pressure. However, application of the same procedures to the self-diffusion coefficients, D, of six ionic and 13 molecular liquids leads to superpositioning of poorer quality, as the scaling yields different exponents from those obtained with viscosities and, in the case of the ionic liquids, slightly different values for the anion and the cation. This situation can be improved by using the ratio (D∕T), consistent with the Stokes-Einstein relation, yielding γ values closer to those of viscosity.
Using non-invasive molecular spectroscopic techniques to detect unique aspects of protein Amide functional groups and chemical properties of modeled forage from different sourced-origins.

Science.gov (United States)

Ji, Cuiying; Zhang, Xuewei; Yu, Peiqiang

2016-03-05

The non-invasive molecular spectroscopic technique-FT/IR is capable to detect the molecular structure spectral features that are associated with biological, nutritional and biodegradation functions. However, to date, few researches have been conducted to use these non-invasive molecular spectroscopic techniques to study forage internal protein structures associated with biodegradation and biological functions. The objectives of this study were to detect unique aspects and association of protein Amide functional groups in terms of protein Amide I and II spectral profiles and chemical properties in the alfalfa forage (Medicago sativa L.) from different sourced-origins. In this study, alfalfa hay with two different origins was used as modeled forage for molecular structure and chemical property study. In each forage origin, five to seven sources were analyzed. The molecular spectral profiles were determined using FT/IR non-invasive molecular spectroscopy. The parameters of protein spectral profiles included functional groups of Amide I, Amide II and Amide I to II ratio. The results show that the modeled forage Amide I and Amide II were centered at 1653 cm(-1) and 1545 cm(-1), respectively. The Amide I spectral height and area intensities were from 0.02 to 0.03 and 2.67 to 3.36 AI, respectively. The Amide II spectral height and area intensities were from 0.01 to 0.02 and 0.71 to 0.93 AI, respectively. The Amide I to II spectral peak height and area ratios were from 1.86 to 1.88 and 3.68 to 3.79, respectively. Our results show that the non-invasive molecular spectroscopic techniques are capable to detect forage internal protein structure features which are associated with forage chemical properties. Copyright © 2015 Elsevier B.V. All rights reserved.
Effect of molecular weight and testing rate on adhesion property of pressure-sensitive adhesives prepared from epoxidized natural rubber

International Nuclear Information System (INIS)

Khan, Imran; Poh, B.T.

2011-01-01

Research highlights: → Elucidation of adhesion property of epoxidized natural rubber (ENR 25). → Correlation of peel and shear strength with molecular weight and rate of testing. → Confirmation of miscibility of tackifier and ENR 25 by DSC and FTIR study. → Applicability of Fox equation in ENR 25/coumarone-indene resin system. -- Abstract: The dependence of peel strength and shear strength of epoxidized natural rubber (ENR 25)-based pressure-sensitive adhesive on molecular weight and rate of testing was investigated using coumarone-indene as the tackifying resin. Toluene and polyethylene terephthalate (PET) were used as the solvent and substrate respectively throughout the study. A SHEEN hand coater was used to coat the adhesive on the substrate at a coating thickness of 120 μm. All the adhesion properties were determined by a Llyod Adhesion Tester operating at different rates of testing. Result shows that peel strength and shear strength increases up to an optimum molecular weight of 6.5 x 10 4 of ENR 25. For peel strength, the observation is attributed to the combined effects of wettability and mechanical strength of rubber at the optimum molecular weight, whereas for the shear strength, it is ascribed to the increasing amount of adhesive present in the coating layer which enhances the shear resistance of the adhesive. Peel strength and shear strength also increases with increase in rate of testing, an observation which is associated to the viscoeslastic response of the adhesive. Differential scanning calorimetry (DSC) and Fourier transform infrared spectroscopy (FTIR) study confirms the miscibility of tackifier and the ENR 25.
Hybrid method coupling molecular dynamics and Monte Carlo simulations to study the properties of gases in microchannels and nanochannels

NARCIS (Netherlands)

Nedea, S.V.; Frijns, A.J.H.; Steenhoven, van A.A.; Markvoort, Albert. J.; Hilbers, P.A.J.

2005-01-01

We combine molecular dynamics (MD) and Monte Carlo (MC) simulations to study the properties of gas molecules confined between two hard walls of a microchannel or nanochannel. The coupling between MD and MC simulations is introduced by performing MD near the boundaries for accuracy and MC in the bulk
Tuning electronic properties of graphene nanoflake polyaromatic hydrocarbon through molecular charge-transfer interactions

Science.gov (United States)

Sharma, Vaishali; Dabhi, Shweta D.; Shinde, Satyam; Jha, Prafulla K.

2018-05-01

By means of first principles calculation we have tuned the electronic properties of graphene nanoflake polyaromatic hydrocarbon via molecular charge transfer. Acceptor/donor Tetracyanoquinodimethane (TCNQ) and Tetrathiafulvalene (TTF) organic molecules are adsorbed on polyaromatic hydrocarbons (PAH) in order to introduce the charge transfer. The substrate's n- or p- type nature depends on the accepting/donating behavior of dopant molecules. Two different classes of PAH (extended form of triangulene) namely Bow-tie graphene nanoflake (BTGNF) and triangular zigzag graphene nanoflake (TZGNF). It is revealed that all the TCNQ and TTF modified graphene nanoflakes exhibit significant changes in HOMO-LUMO gap in range from 0.58 eV to 0.64 eV and 0.01 eV to 0.05 eV respectively. The adsorption energies are in the range of -0.05 kcal/mol to -2.6 kcal/mol. The change in work function is also calculated and discussed, the maximum charge transfer is for TCNQ adsorbed BTGNF. These alluring findings in the tuning of electronic properties will be advantageous for promoting graphene nanoflake polyaromatic hydrocarbon for their applications in electronic devices.
Tensile mechanical properties of Ni-based superalloy of nanophases using molecular dynamics simulation

Energy Technology Data Exchange (ETDEWEB)

Ma, Lei; Hu, Wangyu [College of Materials Science and Engineering, Hunan University, Changsha (China); Department of Applied Physics, Hunan University, Changsha (China); Xiao, Shifang; Deng, Huiqiu [Department of Applied Physics, Hunan University, Changsha (China)

2016-04-15

The mechanical properties of Ni/Ni{sub 3}Al monocrystal of nanophases with varying temperatures, strain rates, and phase sizes have been studied using molecular dynamics simulation. The simulation results show that the primary deformation mechanisms in Ni/Ni{sub 3}Al monocrystal of nanophases were slip bands and antiphase boundaries at room temperature. The studies on the effects of temperature showed that the yield strain, yield strength, and elastic module decreased as temperature increased. However, the influences of strain rate and phase size on the mechanical properties of Ni/Ni{sub 3}Al monocrystal of nanophases showed that the high strain rate led to the increase of yield stress, and the phase sizes had no significant influence on the maximum yield stress. In addition, the behavior of crack propagation in the model of Ni/Ni{sub 3}Al interface was investigated under cyclic loading, and it was found that the interface of Ni/Ni{sub 3}Al was resistance to the fatigue crack propagation. (copyright 2015 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)
Biochemical and Molecular Study of Carpobrotus edulis Bioactive Properties and Their Effects on Dugesia sicula (Turbellaria, Tricladida) Regeneration.

Science.gov (United States)

Meddeb, Emna; Charni, Mohamed; Ghazouani, Tesnime; Cozzolino, Autilia; Fratianni, Florinda; Raboudi, Faten; Nazzaro, Filomena; Fattouch, Sami

2017-07-01

The traditional medicinal properties of Carpobrotus edulis are well recognized, particularly in Tunisia where it is used for wound healing. Thus, in this study, biochemical and molecular properties of its leaves' bioactive aqueous-acetone extract were investigated. The total phenolic content (TPC) of the extract was estimated to be 184 ± 5 mg/100 g of fresh matter (FM). The qualitative and quantitative polyphenolic profile was determined by ultra performance liquid chromatography with diode array detection (UPLC-DAD) and showed that chlorogenic acid was the major compound (43.7%). The extract exhibits potent antioxidant capacities with IC50 = 56.19 and 58.91 μg/ml, as accessed via the anionic DPPH and cationic ABTS radical scavenging assays, respectively. The extract has high antibacterial properties, especially against the Gram+ Staphylococcus aureus and Bacillus cereus strains. To investigate the extract effect on regeneration, the flatworm Dugesia sicula Lepori, 1948, was used as a model. The macroscopic analysis of planarian cultures in ordinary medium containing phenolic extract at non-toxic concentrations illustrated that the extract caused morphological changes. Additionally, the molecular study through the fluorescence-activated cell sorting (FACS) technique showed that C. edulis polyphenols can harm the stem cells' development. These results emphasize the ecotoxicological impact of phenolic rejections in the environment on flatworms' physiology.
Communication: Electronic and transport properties of molecular junctions under a finite bias: A dual mean field approach

International Nuclear Information System (INIS)

Liu, Shuanglong; Feng, Yuan Ping; Zhang, Chun

2013-01-01

We show that when a molecular junction is under an external bias, its properties cannot be uniquely determined by the total electron density in the same manner as the density functional theory for ground state properties. In order to correctly incorporate bias-induced nonequilibrium effects, we present a dual mean field (DMF) approach. The key idea is that the total electron density together with the density of current-carrying electrons are sufficient to determine the properties of the system. Two mean fields, one for current-carrying electrons and the other one for equilibrium electrons can then be derived. Calculations for a graphene nanoribbon junction show that compared with the commonly used ab initio transport theory, the DMF approach could significantly reduce the electric current at low biases due to the non-equilibrium corrections to the mean field potential in the scattering region
Computation of Ground-State Properties in Molecular Systems: Back-Propagation with Auxiliary-Field Quantum Monte Carlo.

Science.gov (United States)

Motta, Mario; Zhang, Shiwei

2017-11-14

We address the computation of ground-state properties of chemical systems and realistic materials within the auxiliary-field quantum Monte Carlo method. The phase constraint to control the Fermion phase problem requires the random walks in Slater determinant space to be open-ended with branching. This in turn makes it necessary to use back-propagation (BP) to compute averages and correlation functions of operators that do not commute with the Hamiltonian. Several BP schemes are investigated, and their optimization with respect to the phaseless constraint is considered. We propose a modified BP method for the computation of observables in electronic systems, discuss its numerical stability and computational complexity, and assess its performance by computing ground-state properties in several molecular systems, including small organic molecules.
Orbital free ab initio molecular dynamics simulation study of some static and dynamic properties of liquid noble metals

Directory of Open Access Journals (Sweden)

G.M. Bhuiyan

2012-10-01

Full Text Available Several static and dynamic properties of liquid Cu, Ag and Au at thermodynamic states near their respective melting points, have been evaluated by means of the orbital free ab-initio molecular dynamics simulation method. The calculated static structure shows good agreement with the available X-ray and neutron diffraction data. As for the dynamic properties, the calculated dynamic structure factors point to the existence of collective density excitations along with a positive dispersion for l-Cu and l-Ag. Several transport coefficients have been obtained which show a reasonable agreement with the available experimental data.

Topology in Molecular Biology

CERN Document Server

Monastyrsky, Michail Ilych

2007-01-01

The book presents a class of new results in molecular biology for which topological methods and ideas are important. These include: the large-scale conformation properties of DNA; computational methods (Monte Carlo) allowing the simulation of large-scale properties of DNA; the tangle model of DNA recombination and other applications of Knot theory; dynamics of supercoiled DNA and biocatalitic properties of DNA; the structure of proteins; and other very recent problems in molecular biology. The text also provides a short course of modern topology intended for the broad audience of biologists and physicists. The authors are renowned specialists in their fields and some of the new results presented here are documented for the first time in monographic form.
Identifying the molecular functions of electron transport proteins using radial basis function networks and biochemical properties.

Science.gov (United States)

Le, Nguyen-Quoc-Khanh; Nguyen, Trinh-Trung-Duong; Ou, Yu-Yen

2017-05-01

The electron transport proteins have an important role in storing and transferring electrons in cellular respiration, which is the most proficient process through which cells gather energy from consumed food. According to the molecular functions, the electron transport chain components could be formed with five complexes with several different electron carriers and functions. Therefore, identifying the molecular functions in the electron transport chain is vital for helping biologists understand the electron transport chain process and energy production in cells. This work includes two phases for discriminating electron transport proteins from transport proteins and classifying categories of five complexes in electron transport proteins. In the first phase, the performances from PSSM with AAIndex feature set were successful in identifying electron transport proteins in transport proteins with achieved sensitivity of 73.2%, specificity of 94.1%, and accuracy of 91.3%, with MCC of 0.64 for independent data set. With the second phase, our method can approach a precise model for identifying of five complexes with different molecular functions in electron transport proteins. The PSSM with AAIndex properties in five complexes achieved MCC of 0.51, 0.47, 0.42, 0.74, and 1.00 for independent data set, respectively. We suggest that our study could be a power model for determining new proteins that belongs into which molecular function of electron transport proteins. Copyright © 2017 Elsevier Inc. All rights reserved.
A test of systematic coarse-graining of molecular dynamics simulations: Thermodynamic properties

Science.gov (United States)

Fu, Chia-Chun; Kulkarni, Pandurang M.; Scott Shell, M.; Gary Leal, L.

2012-10-01

Coarse-graining (CG) techniques have recently attracted great interest for providing descriptions at a mesoscopic level of resolution that preserve fluid thermodynamic and transport behaviors with a reduced number of degrees of freedom and hence less computational effort. One fundamental question arises: how well and to what extent can a "bottom-up" developed mesoscale model recover the physical properties of a molecular scale system? To answer this question, we explore systematically the properties of a CG model that is developed to represent an intermediate mesoscale model between the atomistic and continuum scales. This CG model aims to reduce the computational cost relative to a full atomistic simulation, and we assess to what extent it is possible to preserve both the thermodynamic and transport properties of an underlying reference all-atom Lennard-Jones (LJ) system. In this paper, only the thermodynamic properties are considered in detail. The transport properties will be examined in subsequent work. To coarse-grain, we first use the iterative Boltzmann inversion (IBI) to determine a CG potential for a (1-ϕ)N mesoscale particle system, where ϕ is the degree of coarse-graining, so as to reproduce the radial distribution function (RDF) of an N atomic particle system. Even though the uniqueness theorem guarantees a one to one relationship between the RDF and an effective pairwise potential, we find that RDFs are insensitive to the long-range part of the IBI-determined potentials, which provides some significant flexibility in further matching other properties. We then propose a reformulation of IBI as a robust minimization procedure that enables simultaneous matching of the RDF and the fluid pressure. We find that this new method mainly changes the attractive tail region of the CG potentials, and it improves the isothermal compressibility relative to pure IBI. We also find that there are optimal interaction cutoff lengths for the CG system, as a function of �
Determination of structure and properties of molecular crystals from first principles.

Science.gov (United States)

Szalewicz, Krzysztof

2014-11-18

CONSPECTUS: Until recently, it had been impossible to predict structures of molecular crystals just from the knowledge of the chemical formula for the constituent molecule(s). A solution of this problem has been achieved using intermolecular force fields computed from first principles. These fields were developed by calculating interaction energies of molecular dimers and trimers using an ab initio method called symmetry-adapted perturbation theory (SAPT) based on density-functional theory (DFT) description of monomers [SAPT(DFT)]. For clusters containing up to a dozen or so atoms, interaction energies computed using SAPT(DFT) are comparable in accuracy to the results of the best wave function-based methods, whereas the former approach can be applied to systems an order of magnitude larger than the latter. In fact, for monomers with a couple dozen atoms, SAPT(DFT) is about equally time-consuming as the supermolecular DFT approach. To develop a force field, SAPT(DFT) calculations are performed for a large number of dimer and possibly also trimer configurations (grid points in intermolecular coordinates), and the interaction energies are then fitted by analytic functions. The resulting force fields can be used to determine crystal structures and properties by applying them in molecular packing, lattice energy minimization, and molecular dynamics calculations. In this way, some of the first successful determinations of crystal structures were achieved from first principles, with crystal densities and lattice parameters agreeing with experimental values to within about 1%. Crystal properties obtained using similar procedures but empirical force fields fitted to crystal data have typical errors of several percent due to low sensitivity of empirical fits to interactions beyond those of the nearest neighbors. The first-principles approach has additional advantages over the empirical approach for notional crystals and cocrystals since empirical force fields can only be
Oxyhydroxide of metallic nanowires in a molecular H2O and H2O2 environment and their effects on mechanical properties.

Science.gov (United States)

Aral, Gurcan; Islam, Md Mahbubul; Wang, Yun-Jiang; Ogata, Shigenobu; Duin, Adri C T van

2018-06-14

To avoid unexpected environmental mechanical failure, there is a strong need to fully understand the details of the oxidation process and intrinsic mechanical properties of reactive metallic iron (Fe) nanowires (NWs) under various aqueous reactive environmental conditions. Herein, we employed ReaxFF reactive molecular dynamics (MD) simulations to elucidate the oxidation of Fe NWs exposed to molecular water (H2O) and hydrogen peroxide (H2O2) environment, and the influence of the oxide shell layer on the tensile mechanical deformation properties of Fe NWs. Our structural analysis shows that oxidation of Fe NWs occurs with the formation of different iron oxide and hydroxide phases in the aqueous molecular H2O and H2O2 oxidizing environments. We observe that the resulting microstructure due to pre-oxide shell layer formation reduces the mechanical stress via increasing the initial defect sites in the vicinity of the oxide region to facilitate the onset of plastic deformation during tensile loading. Specifically, the oxide layer of Fe NWs formed in the H2O2 environment has a relatively significant effect on the deterioration of the mechanical properties of Fe NWs. The weakening of the yield stress and Young modulus of H2O2 oxidized Fe NWs indicates the important role of local oxide microstructures on mechanical deformation properties of individual Fe NWs. Notably, deformation twinning is found as the primary mechanical plastic deformation mechanism of all Fe NWs, but it is initially observed at low strain and stress level for the oxidized Fe NWs.
Anomalous behaviour of thermophysical properties of stoichiometric uranium dioxide by molecular dynamics simulation

International Nuclear Information System (INIS)

Lunev, A.V.; Tarasov, B.A.; Nazarov, A.V.

2011-01-01

We present a classical molecular dynamics simulation of uranium dioxide in the temperature range of 300-3000 K. Temperature dependences of thermal conductivity, heat capacity and ionic conductivity are investigated. Our study shows the rise of thermal conductivity of uranium dioxide at very high temperatures (above 2500 K), which is not predicted by the former anharmonic theories. Several pair potentials are used in the simulation, and they depict similar effects. Long range forces are accounted by Ewald sums. Static thermal properties are evaluated in NPT ensemble. It is shown that a high-temperature peak on heat capacity is present and is more legible in large systems. To ensure the best reliability, transport properties are evaluated using the theory of autocorrelation functions in NVE ensemble. In order to properly define thermal conductivity in ionic systems with charge fluxes, an expression which accounts the thermoelectric effect is derived from Onsager reciprocal relations. The rise on temperature dependence of thermal conductivity is accompanied by the peak on heat capacity and an anomalous rise of ionic conductivity. However, it is shown that there is no partial melting of the oxygen sublattice, which suggests that the system does not necessarily exhibit a superionic transition. Instead, kick-out diffusion in oxygen sublattice is proposed to be the origin of such anomalous behavior of thermophysical properties. (author)
Effect of molecular weight reduction by gamma irradiation on chitosan film properties

Energy Technology Data Exchange (ETDEWEB)

García, Mario A., E-mail: marioifal@gmail.com [Pharmacy and Food Institute, University of Havana, St. 222 No. 2317, ZC 13600 Havana (Cuba); Pérez, Liliam [Pharmacy and Food Institute, University of Havana, St. 222 No. 2317, ZC 13600 Havana (Cuba); Paz, Nilia de la [Drugs Research and Development Center, Ave. 26 No. 1605, Havana (Cuba); González, Juan [Food Industry Research Institute, Carretera al Guatao km 3 1/2, Havana, CP 19200 (Cuba); Rapado, Manuel [Radiobiology Department, Center for Technological Applications and Nuclear Development, St. 30 No. 502, Playa, Havana (Cuba); Casariego, Alicia [Pharmacy and Food Institute, University of Havana, St. 222 No. 2317, ZC 13600 Havana (Cuba)

2015-10-01

The present work aimed the influence of molecular weight (MW) reduction by irradiation with {sup 60}Co and polymer concentration on some physical properties of chitosan films. Irradiation of chitosan with a MW of 275.221 kDa and 74.74% of deacetylation degree was performed using a {sup 60}Co source to provide doses of 5, 10, 20 and 50 kGy to obtain chitosans with molecular weights of 247.847, 221.563, 126.469 and 77.063 kDa, respectively. Films were prepared via the solution casting method. Film-forming solutions (FFS) of chitosan irradiated or not, were prepared at 1.5 and 2% (w/v) in a solution of lactic acid at 1% (v/v) and 0.1% (v/v) of Tween 80. The FFS were poured into glass plates of 400 cm{sup 2} and dried at 60 °C during 10 h without airflow. The decrease of MW and increase of chitosan concentration increased the tensil strength and water vapor permeability while decreased the elongation at break of the films. The chitosan MW did not significantly influence (p > 0.05) the water solubility of films within a same polymer concentration. There was a decrease in the films' brightness with the increase of concentration and a decrease of the MW of irradiated chitosan, while the b* values of films increased and there was an increasing tendency of their apparent opacity. - Highlights: • MW reduction by {sup 60}Co irradiation increased the tensil strength of chitosan films. • MW reduction increased the water vapor permeability of chitosan films. • MW did not affect the films' water solubility within a same chitosan concentration. • Films' brightness decreased with the chitosan molecular weight reduction.
Effect of molecular weight reduction by gamma irradiation on chitosan film properties

International Nuclear Information System (INIS)

García, Mario A.; Pérez, Liliam; Paz, Nilia de la; González, Juan; Rapado, Manuel; Casariego, Alicia

2015-01-01

The present work aimed the influence of molecular weight (MW) reduction by irradiation with 60 Co and polymer concentration on some physical properties of chitosan films. Irradiation of chitosan with a MW of 275.221 kDa and 74.74% of deacetylation degree was performed using a 60 Co source to provide doses of 5, 10, 20 and 50 kGy to obtain chitosans with molecular weights of 247.847, 221.563, 126.469 and 77.063 kDa, respectively. Films were prepared via the solution casting method. Film-forming solutions (FFS) of chitosan irradiated or not, were prepared at 1.5 and 2% (w/v) in a solution of lactic acid at 1% (v/v) and 0.1% (v/v) of Tween 80. The FFS were poured into glass plates of 400 cm 2 and dried at 60 °C during 10 h without airflow. The decrease of MW and increase of chitosan concentration increased the tensil strength and water vapor permeability while decreased the elongation at break of the films. The chitosan MW did not significantly influence (p > 0.05) the water solubility of films within a same polymer concentration. There was a decrease in the films' brightness with the increase of concentration and a decrease of the MW of irradiated chitosan, while the b* values of films increased and there was an increasing tendency of their apparent opacity. - Highlights: • MW reduction by 60 Co irradiation increased the tensil strength of chitosan films. • MW reduction increased the water vapor permeability of chitosan films. • MW did not affect the films' water solubility within a same chitosan concentration. • Films' brightness decreased with the chitosan molecular weight reduction
Structure-dependent tuning of electro-optic and thermoplastic properties in triphenyl groups containing molecular glasses

Energy Technology Data Exchange (ETDEWEB)

Traskovskis, Kaspars, E-mail: kaspars.traskovskis@rtu.lv [Riga Technical University, Faculty of Materials Science and Applied Chemistry, 3/7 Paula Valdena Street, Riga LV-1048 (Latvia); Zarins, Elmars; Laipniece, Lauma [Riga Technical University, Faculty of Materials Science and Applied Chemistry, 3/7 Paula Valdena Street, Riga LV-1048 (Latvia); Tokmakovs, Andrejs [Institute of Solid State Physics, University of Latvia, 8 Kengaraga Street, Riga LV-1063 (Latvia); Kokars, Valdis [Riga Technical University, Faculty of Materials Science and Applied Chemistry, 3/7 Paula Valdena Street, Riga LV-1048 (Latvia); Rutkis, Martins [Institute of Solid State Physics, University of Latvia, 8 Kengaraga Street, Riga LV-1063 (Latvia)

2015-04-01

The series of seven molecular compounds composed of D–π–A chromophores and triphenylmethyl auxiliary groups were characterized by UV–Vis spectroscopy, differential scanning calorimetry and quantum chemical calculations. Nonlinear optical (NLO) properties of compounds were determined by second harmonic generation measurements in corona poled thin glassy films. The results show that triphenylmethyl auxiliary groups are effective at shielding undesirable dipole interactions in solid phase thus increasing NLO efficiency of materials. Thermal stability up to 108 °C was achieved for a polar order in poled samples. - Highlights: • Triphenylmethyl groups can be used to reduce solid phase dipole interactions in organic molecular materials. • NLO efficiency of a poled material is higher, if a number of present triphenyl groups increases. • NLO efficiency of materials decreases, if polarity of used chromophores increases. • Thermal stability of polar order up to 108 °C can be achieved in poled organic glasses.
Mechanical and charge transport properties of alkanethiol self-assembled monolayers on Au (111) surface: The Role of Molecular Tilt

Energy Technology Data Exchange (ETDEWEB)

Mulleregan, Alice; Qi, Yabing; Ratera, Imma; Park, Jeong Y.; Ashby, Paul D.; Quek, Su Ying; Neaton, J. B.; Salmeron, Miquel

2007-11-12

The relationship between charge transport and mechanical properties of alkanethiol self-assembled monolayers (SAM) on Au(111) films has been investigated using an atomic force microscope with a conductive tip. Molecular tilts induced by the pressure applied by the tip cause stepwise increases in film conductivity. A decay constant {beta} = 0.57 {+-} 0.03 {angstrom}{sup -1} was found for the current passing through the film as a function of tip-substrate separation due to this molecular tilt. This is significantly smaller than the value of {approx} 1 {angstrom}{sup -1} found when the separation is changed by changing the length of the alkanethiol molecules. Calculations indicate that for isolated dithiol molecules S-bonded to hollow sites, the junction conductance does not vary significantly as a function of molecular tilt. The impact of S-Au bonding on SAM conductance is discussed.
Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

Energy Technology Data Exchange (ETDEWEB)

Ji, Pengfei; Zhang, Yuwen, E-mail: zhangyu@missouri.edu [Department of Mechanical and Aerospace Engineering, University of Missouri, Columbia, Missouri 65211 (United States); Yang, Mo [College of Energy and Power Engineering, University of Shanghai for Science and Technology, Shanghai 200093 (China)

2013-12-21

The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.
Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

International Nuclear Information System (INIS)

Ji, Pengfei; Zhang, Yuwen; Yang, Mo

2013-01-01

The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective
Structural, dynamic, and vibrational properties during heat transfer in Si/Ge superlattices: A Car-Parrinello molecular dynamics study

Science.gov (United States)

Ji, Pengfei; Zhang, Yuwen; Yang, Mo

2013-12-01

The structural, dynamic, and vibrational properties during heat transfer process in Si/Ge superlattices are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) are computed and plotted to analyze the contributions of phonons with different frequencies to the heat conduction. Coherent heat conduction of the low frequency phonons is found and their contributions to facilitate heat transfer are confirmed. The Car-Parrinello molecular dynamics simulation outputs in the work show reasonable thermophysical results of the thermal energy transport process and shed light on the potential applications of treating the heat transfer in the superlattices of semiconductor materials from a quantum mechanical molecular dynamics simulation perspective.
Constant size descriptors for accurate machine learning models of molecular properties

Science.gov (United States)

Collins, Christopher R.; Gordon, Geoffrey J.; von Lilienfeld, O. Anatole; Yaron, David J.

2018-06-01

Two different classes of molecular representations for use in machine learning of thermodynamic and electronic properties are studied. The representations are evaluated by monitoring the performance of linear and kernel ridge regression models on well-studied data sets of small organic molecules. One class of representations studied here counts the occurrence of bonding patterns in the molecule. These require only the connectivity of atoms in the molecule as may be obtained from a line diagram or a SMILES string. The second class utilizes the three-dimensional structure of the molecule. These include the Coulomb matrix and Bag of Bonds, which list the inter-atomic distances present in the molecule, and Encoded Bonds, which encode such lists into a feature vector whose length is independent of molecular size. Encoded Bonds' features introduced here have the advantage of leading to models that may be trained on smaller molecules and then used successfully on larger molecules. A wide range of feature sets are constructed by selecting, at each rank, either a graph or geometry-based feature. Here, rank refers to the number of atoms involved in the feature, e.g., atom counts are rank 1, while Encoded Bonds are rank 2. For atomization energies in the QM7 data set, the best graph-based feature set gives a mean absolute error of 3.4 kcal/mol. Inclusion of 3D geometry substantially enhances the performance, with Encoded Bonds giving 2.4 kcal/mol, when used alone, and 1.19 kcal/mol, when combined with graph features.
Current Progress of Nanomaterials in Molecularly Imprinted Electrochemical Sensing.

Science.gov (United States)

Zhong, Chunju; Yang, Bin; Jiang, Xinxin; Li, Jianping

2018-01-02

Nanomaterials have received much attention during the past decade because of their excellent optical, electronic, and catalytic properties. Nanomaterials possess high chemical reactivity, also high surface energy. Thus, provide a stable immobilization platform for biomolecules, while preserving their reactivity. Due to the conductive and catalytic properties, nanomaterials can also enhance the sensitivity of molecularly imprinted electrochemical sensors by amplifying the electrode surface, increasing the electron transfer, and catalyzing the electrochemical reactions. Molecularly imprinted polymers that contain specific molecular recognition sites can be designed for a particular target analyte. Incorporating nanomaterials into molecularly imprinted polymers is important because nanomaterials can improve the response signal, increase the sensitivity, and decrease the detection limit of the sensors. This study describes the classification of nanomaterials in molecularly imprinted polymers, their analytical properties, and their applications in the electrochemical sensors. The progress of the research on nanomaterials in molecularly imprinted polymers and the application of nanomaterials in molecularly imprinted polymers is also reviewed.
A Hybrid Density Functional Theory/Molecular Mechanics Approach for Linear Response Properties in Heterogeneous Environments.

Science.gov (United States)

Rinkevicius, Zilvinas; Li, Xin; Sandberg, Jaime A R; Mikkelsen, Kurt V; Ågren, Hans

2014-03-11

We introduce a density functional theory/molecular mechanical approach for computation of linear response properties of molecules in heterogeneous environments, such as metal surfaces or nanoparticles embedded in solvents. The heterogeneous embedding environment, consisting from metallic and nonmetallic parts, is described by combined force fields, where conventional force fields are used for the nonmetallic part and capacitance-polarization-based force fields are used for the metallic part. The presented approach enables studies of properties and spectra of systems embedded in or placed at arbitrary shaped metallic surfaces, clusters, or nanoparticles. The capability and performance of the proposed approach is illustrated by sample calculations of optical absorption spectra of thymidine absorbed on gold surfaces in an aqueous environment, where we study how different organizations of the gold surface and how the combined, nonadditive effect of the two environments is reflected in the optical absorption spectrum.
Transport Properties of the Nuclear Pasta Phase with Quantum Molecular Dynamics

Science.gov (United States)

Nandi, Rana; Schramm, Stefan

2018-01-01

We study the transport properties of nuclear pasta for a wide range of density, temperature, and proton fractions, relevant for different astrophysical scenarios adopting a quantum molecular dynamics model. In particular, we estimate the values of shear viscosity as well as electrical and thermal conductivities by calculating the static structure factor S(q) using simulation data. In the density and temperature range where the pasta phase appears, the static structure factor shows irregular behavior. The presence of a slab phase greatly enhances the peak in S(q). However, the effect of irregularities in S(q) on the transport coefficients is not very dramatic. The values of all three transport coefficients are found to have the same orders of magnitude as found in theoretical calculations for the inner crust matter of neutron stars without the pasta phase; therefore, the values are in contrast to earlier speculations that a pasta layer might be highly resistive, both thermally and electrically.
Cooling of molecular ion beams

International Nuclear Information System (INIS)

Wolf, A.; Krohn, S.; Kreckel, H.; Lammich, L.; Lange, M.; Strasser, D.; Grieser, M.; Schwalm, D.; Zajfman, D.

2004-01-01

An overview of the use of stored ion beams and phase space cooling (electron cooling) is given for the field of molecular physics. Emphasis is given to interactions between molecular ions and electrons studied in the electron cooler: dissociative recombination and, for internally excited molecular ions, electron-induced ro-vibrational cooling. Diagnostic methods for the transverse ion beam properties and for the internal excitation of the molecular ions are discussed, and results for phase space cooling and internal (vibrational) cooling are presented for hydrogen molecular ions
EDITORIAL: Molecular switches at surfaces Molecular switches at surfaces

Science.gov (United States)

Weinelt, Martin; von Oppen, Felix

2012-10-01

In nature, molecules exploit interaction with their environment to realize complex functionalities on the nanometer length scale. Physical, chemical and/or biological specificity is frequently achieved by the switching of molecules between microscopically different states. Paradigmatic examples are the energy production in proton pumps of bacteria or the signal conversion in human vision, which rely on switching molecules between different configurations or conformations by external stimuli. The remarkable reproducibility and unparalleled fatigue resistance of these natural processes makes it highly desirable to emulate nature and develop artificial systems with molecular functionalities. A promising avenue towards this goal is to anchor the molecular switches at surfaces, offering new pathways to control their functional properties, to apply electrical contacts, or to integrate switches into larger systems. Anchoring at surfaces allows one to access the full range from individual molecular switches to self-assembled monolayers of well-defined geometry and to customize the coupling between molecules and substrate or between adsorbed molecules. Progress in this field requires both synthesis and preparation of appropriate molecular systems and control over suitable external stimuli, such as light, heat, or electrical currents. To optimize switching and generate function, it is essential to unravel the geometric structure, the electronic properties and the dynamic interactions of the molecular switches on surfaces. This special section, Molecular Switches at Surfaces, collects 17 contributions describing different aspects of this research field. They analyze elementary processes, both in single molecules and in ensembles of molecules, which involve molecular switching and concomitant changes of optical, electronic, or magnetic properties. Two topical reviews summarize the current status, including both challenges and achievements in the field of molecular switches on
Characterization of the mechanical properties of polyphenylene polymer using molecular dynamics simulations

International Nuclear Information System (INIS)

Ansari, R.; Ajori, S.; Rouhi, S.

2016-01-01

Synthesizing polyphenylene polymer, a two-dimensional hydrocarbon known as porous graphene, has led to the initiation of a new age in nanoscience. In this investigation, molecular dynamics (MD) simulations are carried out to study the mechanical properties of porous graphene such as Young's modulus, Poisson's ratio, bulk modulus and ultimate strength and strain. The fracture initiation and propagation pattern of porous graphene are also considered in this study. The results show that Young's and bulk moduli of porous graphene are lower than those of graphene, graphene and graphyne. Unlikely, it is also observed that its Poisson's ratio is considerably more than that of graphene, graphene and graphyne. Furthermore, it is found out that Young's and bulk moduli as well as fracture strain and ultimate stress are extremely size-dependent and also the porous graphene can be considered as an isotropic material.

Structural and dynamical properties of the porins OmpF and OmpC: insights from molecular simulations

International Nuclear Information System (INIS)

Kumar, Amit; Hajjar, Eric; Ruggerone, Paolo; Ceccarelli, Matteo

2010-01-01

In this paper we investigate the structural and dynamical properties of the two major porins (OmpF and OmpC) in Escherichia coli, using molecular dynamics (MD) simulations. In particular we characterized the atomic fluctuations, correlated motions, temperature dependence, solvent-accessible cross-sectional area and water dynamics in the key regions of the two channels. Our in-depth analysis allows us to highlight the importance of both the key conserved and substituted residues between OmpF and OmpC. The latter is characterized by a narrower and longer constriction region with respect to OmpF. OmpC also showed a higher stability upon increasing temperature. We then present the results of transport properties by using accelerated MD simulations to probe the diffusion of norfloxacin (a fluoroquinolone antibiotic) through the two porins OmpF/OmpC. Our study constitutes a step forward towards understanding the structure-function relationship of the two porins' channels. This will benefit the research of antibacterials with improved permeation properties and nanopores that aim to use these porins as sensing systems.
Light and redox switchable molecular components for molecular electronics.

Science.gov (United States)

Browne, Wesley R; Feringa, Ben L

2010-01-01

The field of molecular and organic electronics has seen rapid progress in recent years, developing from concept and design to actual demonstration devices in which both single molecules and self-assembled monolayers are employed as light-responsive components. Research in this field has seen numerous unexpected challenges that have slowed progress and the initial promise of complex molecular-based computers has not yet been realised. Primarily this has been due to the realisation at an early stage that molecular-based nano-electronics brings with it the interface between the hard (semiconductor) and soft (molecular) worlds and the challenges which accompany working in such an environment. Issues such as addressability, cross-talk, molecular stability and perturbation of molecular properties (e.g., inhibition of photochemistry) have nevertheless driven development in molecular design and synthesis as well as our ability to interface molecular components with bulk metal contacts to a very high level of sophistication. Numerous groups have played key roles in progressing this field not least teams such as those led by Whitesides, Aviram, Ratner, Stoddart and Heath. In this short review we will however focus on the contributions from our own group and those of our collaborators, in employing diarylethene based molecular components.
Molecular sensors and molecular logic gates

International Nuclear Information System (INIS)

Georgiev, N.; Bojinov, V.

2013-01-01

Full text: The rapid grow of nanotechnology field extended the concept of a macroscopic device to the molecular level. Because of this reason the design and synthesis of (supra)-molecular species capable of mimicking the functions of macroscopic devices are currently of great interest. Molecular devices operate via electronic and/or nuclear rearrangements and, like macroscopic devices, need energy to operate and communicate between their elements. The energy needed to make a device work can be supplied as chemical energy, electrical energy, or light. Luminescence is one of the most useful techniques to monitor the operation of molecular-level devices. This fact determinates the synthesis of novel fluorescence compounds as a considerable and inseparable part of nanoscience development. Further miniaturization of semiconductors in electronic field reaches their limit. Therefore the design and construction of molecular systems capable of performing complex logic functions is of great scientific interest now. In semiconductor devices the logic gates work using binary logic, where the signals are encoded as 0 and 1 (low and high current). This process is executable on molecular level by several ways, but the most common are based on the optical properties of the molecule switches encoding the low and high concentrations of the input guest molecules and the output fluorescent intensities with binary 0 and 1 respectively. The first proposal to execute logic operations at the molecular level was made in 1988, but the field developed only five years later when the analogy between molecular switches and logic gates was experimentally demonstrated by de Silva. There are seven basic logic gates: AND, OR, XOR, NOT, NAND, NOR and XNOR and all of them were achieved by molecules, the fluorescence switching as well. key words: fluorescence, molecular sensors, molecular logic gates
New molecular descriptors based on local properties at the molecular surface and a boiling-point model derived from them.

Science.gov (United States)

Ehresmann, Bernd; de Groot, Marcel J; Alex, Alexander; Clark, Timothy

2004-01-01

New molecular descriptors based on statistical descriptions of the local ionization potential, local electron affinity, and the local polarizability at the surface of the molecule are proposed. The significance of these descriptors has been tested by calculating them for the Maybridge database in addition to our set of 26 descriptors reported previously. The new descriptors show little correlation with those already in use. Furthermore, the principal components of the extended set of descriptors for the Maybridge data show that especially the descriptors based on the local electron affinity extend the variance in our set of descriptors, which we have previously shown to be relevant to physical properties. The first nine principal components are shown to be most significant. As an example of the usefulness of the new descriptors, we have set up a QSPR model for boiling points using both the old and new descriptors.
Reactive molecular dynamics simulations of the mechanical properties of various phosphorene allotropes

Science.gov (United States)

Le, Minh-Quy

2018-05-01

Although various phosphorene allotropes have been theoretically predicted to be stable at 0 K, the mechanical properties and fracture mechanism at room temperature remain unclear for many of them. We investigate through reactive molecular dynamics simulations at room temperature the mechanical properties of phosphorene allotropes including: five sheets with hexagonal structures (β-, γ-, δ-, θ-, and α-phosphorene), one sheet with 4-8 membered rings (4-8-P), and two sheets with 5-7 membered rings. High, moderate and slight anisotropies in their mechanical properties are observed, depending on their crystal structures. Their Young’s moduli and tensile strength are approximately in the range from 7.3% through 25%, and from 8.6% through 22% of those of graphene, respectively. At the early stage of fracture, eye-shaped cracks are formed by local bond breaking and perpendicular to the tensile direction in hexagonal and 4-8-P sheets. Complete fractures take place with straight cracks in these hexagonal sheets under tension along the zigzag direction and under tension along the square edge direction in the 4-8-P sheet. Crack meandering and branching are observed during the tension of α-, β-, and γ-phosphorene along the armchair direction; and along the square diagonal direction in the 4-8-P sheet. Under uniaxial tension of two phosphorene sheets with 5-7 atom rings, 12 and 10 membered rings are formed by merging two neighbor heptagons, and a heptagon and its neighbor pentagon, respectively. These 12 and 10 membered rings coalesce subsequently, causing the failure of these two sheets. The results are of great importance in the design of these novel phosphorene allotropes.
Organic-based molecular switches for molecular electronics.

Science.gov (United States)

Fuentes, Noelia; Martín-Lasanta, Ana; Alvarez de Cienfuegos, Luis; Ribagorda, Maria; Parra, Andres; Cuerva, Juan M

2011-10-05

In a general sense, molecular electronics (ME) is the branch of nanotechnology which studies the application of molecular building blocks for the fabrication of electronic components. Among the different types of molecules, organic compounds have been revealed as promising candidates for ME, due to the easy access, great structural diversity and suitable electronic and mechanical properties. Thanks to these useful capabilities, organic molecules have been used to emulate electronic devices at the nanoscopic scale. In this feature article, we present the diverse strategies used to develop organic switches towards ME with special attention to non-volatile systems.
Molecular dynamics calculations of the thermal expansion properties and melting points of Si and Ge

International Nuclear Information System (INIS)

Timon, V; Brand, S; Clark, S J; Abram, R A

2006-01-01

The thermal expansion properties and melting points of silicon and germanium are calculated using molecular dynamics simulations within the density functional theory framework. An isothermal-isobaric (NPT) ensemble is considered in a periodic system with a relatively small number of particles per unit cell to obtain the thermal expansion data over a range of temperatures, and it is found that the calculated thermal expansion coefficients and bond lengths agree well with experimental data. Also, the positions of discontinuities in the potential energy as a function of temperature are in good agreement with the experimental melting points
Sporulation environment influences spore properties in Bacillus: evidence and insights on underlying molecular and physiological mechanisms.

Science.gov (United States)

Bressuire-Isoard, Christelle; Broussolle, Véronique; Carlin, Frédéric

2018-05-17

Bacterial spores are resistant to physical and chemical insults, which make them a major concern for public health and for industry. Spores help bacteria to survive extreme environmental conditions that vegetative cells cannot tolerate. Spore resistance and dormancy are important properties for applications in medicine, veterinary health, food safety, crop protection, and other domains. The resistance of bacterial spores results from a protective multilayered structure and from the unique composition of the spore core. The mechanisms of sporulation and germination, the first stage after breaking of dormancy, and organization of spore structure have been extensively studied in Bacillus species. This review aims to illustrate how far the structure, composition and properties of spores are shaped by the environmental conditions in which spores form. We look at the physiological and molecular mechanisms underpinning how sporulation media and environment deeply affect spore yield, spore properties like resistance to wet heat and physical and chemical agents, germination, and further growth. For example, spore core water content decreases as sporulation temperature increases, and resistance to wet heat increases. Controlling the fate of Bacillus spores is pivotal to controlling bacterial risks and process efficiencies in, for example, the food industry, and better control hinges on better understanding how sporulation conditions influence spore properties.
Effect of Terminal Modification on the Molecular Assembly and Mechanical Properties of Protein-Based Block Copolymers.

Science.gov (United States)

Jacobsen, Matthew M; Tokareva, Olena S; Ebrahimi, Davoud; Huang, Wenwen; Ling, Shengjie; Dinjaski, Nina; Li, David; Simon, Marc; Staii, Cristian; Buehler, Markus J; Kaplan, David L; Wong, Joyce Y

2017-09-01

Accurate prediction and validation of the assembly of bioinspired peptide sequences into fibers with defined mechanical characteristics would aid significantly in designing and creating materials with desired properties. This process may also be utilized to provide insight into how the molecular architecture of many natural protein fibers is assembled. In this work, computational modeling and experimentation are used in tandem to determine how peptide terminal modification affects a fiber-forming core domain. Modeling shows that increased terminal molecular weight and hydrophilicity improve peptide chain alignment under shearing conditions and promote consolidation of semicrystalline domains. Mechanical analysis shows acute improvements to strength and elasticity, but significantly reduced extensibility and overall toughness. These results highlight an important entropic function that terminal domains of fiber-forming peptides exhibit as chain alignment promoters, which ultimately has notable consequences on the mechanical behavior of the final fiber products. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Molecular packing and magnetic properties of lithium naphthalocyanine crystals: hollow channels enabling permeability and paramagnetic sensitivity to molecular oxygen

Science.gov (United States)

Pandian, Ramasamy P.; Dolgos, Michelle; Marginean, Camelia; Woodward, Patrick M.; Hammel, P. Chris; Manoharan, Periakaruppan T.; Kuppusamy, Periannan

2009-01-01

The synthesis, structural framework, magnetic and oxygen-sensing properties of a lithium naphthalocyanine (LiNc) radical probe are presented. LiNc was synthesized in the form of a microcrystalline powder using a chemical method and characterized by electron paramagnetic resonance (EPR) spectroscopy, magnetic susceptibility, powder X-ray diffraction analysis, and mass spectrometry. X-Ray powder diffraction studies revealed a structural framework that possesses long, hollow channels running parallel to the packing direction. The channels measured approximately 5.0 × 5.4 Å2 in the two-dimensional plane perpendicular to the length of the channel, enabling diffusion of oxygen molecules (2.9 × 3.9 Å2) through the channel. The powdered LiNc exhibited a single, sharp EPR line under anoxic conditions, with a peak-to-peak linewidth of 630 mG at room temperature. The linewidth was sensitive to surrounding molecular oxygen, showing a linear increase in pO2 with an oxygen sensitivity of 31.2 mG per mmHg. The LiNc microcrystals can be further prepared as nano-sized crystals without the loss of its high oxygen-sensing properties. The thermal variation of the magnetic properties of LiNc, such as the EPR linewidth, EPR intensity and magnetic susceptibility revealed the existence of two different temperature regimes of magnetic coupling and hence differing columnar packing, both being one-dimensional antiferromagnetic chains but with differing magnitudes of exchange coupling constants. At a temperature of ∼50 K, LiNc crystals undergo a reversible phase transition. The high degree of oxygen-sensitivity of micro- and nano-sized crystals of LiNc, combined with excellent stability, should enable precise and accurate measurements of oxygen concentration in biological systems using EPR spectroscopy. PMID:19809598
Relation between photochromic properties and molecular structures in salicylideneaniline crystals.

Science.gov (United States)

Johmoto, Kohei; Ishida, Takashi; Sekine, Akiko; Uekusa, Hidehiro; Ohashi, Yuji

2012-06-01

The crystal structures of the salicylideneaniline derivatives N-salicylidene-4-tert-butyl-aniline (1), N-3,5-di-tert-butyl-salicylidene-3-methoxyaniline (2), N-3,5-di-tert-butyl-salicylidene-3-bromoaniline (3), N-3,5-di-tert-butyl-salicylidene-3-chloroaniline (4), N-3,5-di-tert-butyl-salicylidene-4-bromoaniline (5), N-3,5-di-tert-butyl-salicylidene-aniline (6), N-3,5-di-tert-butyl-salicylidene-4-carboxyaniline (7) and N-salicylidene-2-chloroaniline (8) were analyzed by X-ray diffraction analysis at ambient temperature to investigate the relationship between their photochromic properties and molecular structures. A clear correlation between photochromism and the dihedral angle of the two benzene rings in the salicylideneaniline derivatives was observed. Crystals with dihedral angles less than 20° were non-photochromic, whereas those with dihedral angles greater than 30° were photochromic. Crystals with dihedral angles between 20 and 30° could be either photochromic or non-photochromic. Inhibition of the pedal motion by intra- or intermolecular steric hindrance, however, can result in non-photochromic behaviour even if the dihedral angle is larger than 30°.
Bronchial Mucus as a Complex Fluid: Molecular Interactions and Influence of Nanostructured Particles on Rheological and Transport Properties

Directory of Open Access Journals (Sweden)

Odziomek Marcin

2017-06-01

Full Text Available Transport properties of bronchial mucus are investigated by two-stage experimental approach focused on: (a rheological properties and (b mass transfer rate through the stagnant layer of solutions of mucus components (mucine, DNA, proteins and simulated multi-component mucus. Studies were done using thermostated horizontal diffusion cells with sodium cromoglycate and carminic acid as transferred solutes. Rheological properties of tested liquids was studied by a rotational viscometer and a cone-plate rheometer (dynamic method. First part of the studies demonstrated that inter-molecular interactions in these complex liquids influence both rheological and permeability characteristics. Transfer rate is governed not only by mucus composition and concentration but also by hydrophobic/hydrophilic properties of transported molecules. Second part was focused on the properties of such a layer in presence of selected nanostructured particles (different nanoclays and graphene oxide which may be present in lungs after inhalation. It was shown that most of such particles increase visco-elasticity of the mucus and reduce the rate of mass transfer of model drugs. Measured effects may have adverse impact on health, since they will reduce mucociliary clearance in vivo and slow down drug penetration to the bronchial epithelium during inhalation therapy.
Molecularly Imprinted Membranes

Science.gov (United States)

Trotta, Francesco; Biasizzo, Miriam; Caldera, Fabrizio

2012-01-01

Although the roots of molecularly imprinted polymers lie in the beginning of 1930s in the past century, they have had an exponential growth only 40–50 years later by the works of Wulff and especially by Mosbach. More recently, it was also proved that molecular imprinted membranes (i.e., polymer thin films) that show recognition properties at molecular level of the template molecule are used in their formation. Different procedures and potential application in separation processes and catalysis are reported. The influences of different parameters on the discrimination abilities are also discussed. PMID:24958291
Pathways to Structure-Property Relationships of Peptide-Materials Interfaces: Challenges in Predicting Molecular Structures.

Science.gov (United States)

Walsh, Tiffany R

2017-07-18

An in-depth appreciation of how to manipulate the molecular-level recognition between peptides and aqueous materials interfaces, including nanoparticles, will advance technologies based on self-organized metamaterials for photonics and plasmonics, biosensing, catalysis, energy generation and harvesting, and nanomedicine. Exploitation of the materials-selective binding of biomolecules is pivotal to success in these areas and may be particularly key to producing new hierarchically structured biobased materials. These applications could be accomplished by realizing preferential adsorption of a given biomolecule onto one materials composition over another, one surface facet over another, or one crystalline polymorph over another. Deeper knowledge of the aqueous abiotic-biotic interface, to establish clear structure-property relationships in these systems, is needed to meet this goal. In particular, a thorough structural characterization of the surface-adsorbed peptides is essential for establishing these relationships but can often be challenging to accomplish via experimental approaches alone. In addition to myriad existing challenges associated with determining the detailed molecular structure of any molecule adsorbed at an aqueous interface, experimental characterization of materials-binding peptides brings new, complex challenges because many materials-binding peptides are thought to be intrinsically disordered. This means that these peptides are not amenable to experimental techniques that rely on the presence of well-defined secondary structure in the peptide when in the adsorbed state. To address this challenge, and in partnership with experiment, molecular simulations at the atomistic level can bring complementary and critical insights into the origins of this abiotic/biotic recognition and suggest routes for manipulating this phenomenon to realize new types of hybrid materials. For the reasons outlined above, molecular simulation approaches also face
The appropriateness of density-functional theory for the calculation of molecular electronics properties.

Science.gov (United States)

Reimers, Jeffrey R; Cai, Zheng-Li; Bilić, Ante; Hush, Noel S

2003-12-01

As molecular electronics advances, efficient and reliable computation procedures are required for the simulation of the atomic structures of actual devices, as well as for the prediction of their electronic properties. Density-functional theory (DFT) has had widespread success throughout chemistry and solid-state physics, and it offers the possibility of fulfilling these roles. In its modern form it is an empirically parameterized approach that cannot be extended toward exact solutions in a prescribed way, ab initio. Thus, it is essential that the weaknesses of the method be identified and likely shortcomings anticipated in advance. We consider four known systematic failures of modern DFT: dispersion, charge transfer, extended pi conjugation, and bond cleavage. Their ramifications for molecular electronics applications are outlined and we suggest that great care is required when using modern DFT to partition charge flow across electrode-molecule junctions, screen applied electric fields, position molecular orbitals with respect to electrode Fermi energies, and in evaluating the distance dependence of through-molecule conductivity. The causes of these difficulties are traced to errors inherent in the types of density functionals in common use, associated with their inability to treat very long-range electron correlation effects. Heuristic enhancements of modern DFT designed to eliminate individual problems are outlined, as are three new schemes that each represent significant departures from modern DFT implementations designed to provide a priori improvements in at least one and possible all problem areas. Finally, fully semiempirical schemes based on both Hartree-Fock and Kohn-Sham theory are described that, in the short term, offer the means to avoid the inherent problems of modern DFT and, in the long term, offer competitive accuracy at dramatically reduced computational costs.
Tip-Enhanced Raman Scattering Microscopy: A Step toward Nanoscale Control of Intrinsic Molecular Properties

Science.gov (United States)

Yano, Taka-aki; Hara, Masahiko

2018-06-01

Tip-enhanced Raman scattering microscopy, a family of scanning probe microscopy techniques, has been recognized as a powerful surface analytical technique with both single-molecule sensitivity and angstrom-scale spatial resolution. This review covers the current status of tip-enhanced Raman scattering microscopy in surface and material nanosciences, including a brief history, the basic principles, and applications for the nanoscale characterization of a variety of nanomaterials. The focus is on the recent trend of combining tip-enhanced Raman scattering microscopy with various external stimuli such as pressure, voltage, light, and temperature, which enables the local control of the molecular properties and functions and also enables chemical reactions to be induced on a nanometer scale.
Characterization of the mechanical properties of polyphenylene polymer using molecular dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Ansari, R.; Ajori, S. [Department of Mechanical Engineering, University of Guilan, P.O. Box 3756, Rasht (Iran, Islamic Republic of); Rouhi, S., E-mail: s_rouhi@iaul.ac.ir [Young Researchers and Elite Club, Langroud Branch, Islamic Azad University, Langroud, Guilan (Iran, Islamic Republic of)

2016-01-15

Synthesizing polyphenylene polymer, a two-dimensional hydrocarbon known as porous graphene, has led to the initiation of a new age in nanoscience. In this investigation, molecular dynamics (MD) simulations are carried out to study the mechanical properties of porous graphene such as Young's modulus, Poisson's ratio, bulk modulus and ultimate strength and strain. The fracture initiation and propagation pattern of porous graphene are also considered in this study. The results show that Young's and bulk moduli of porous graphene are lower than those of graphene, graphene and graphyne. Unlikely, it is also observed that its Poisson's ratio is considerably more than that of graphene, graphene and graphyne. Furthermore, it is found out that Young's and bulk moduli as well as fracture strain and ultimate stress are extremely size-dependent and also the porous graphene can be considered as an isotropic material.
Quantum molecular dynamics simulations of the thermophysical properties of shocked liquid ammonia for pressures up to 1.3 TPa.

Science.gov (United States)

Li, Dafang; Zhang, Ping; Yan, Jun

2013-10-07

We investigate via quantum molecular-dynamics simulations the thermophysical properties of shocked liquid ammonia up to the pressure 1.3 TPa and temperature 120,000 K. The principal Hugoniot is predicted from the wide-range equation of state, which agrees well with the available experimental measurements up to 64 GPa. Our systematic study of the structural properties demonstrates that the liquid ammonia undergoes a gradual phase transition along the Hugoniot. At about 4800 K, the system transforms into a metallic, complex mixture state consisting of NH3, N2, H2, N, and H. Furthermore, we discuss the implications for the interiors of Uranus and Neptune.
Spiers Memorial Lecture. Molecular mechanics and molecular electronics.

Science.gov (United States)

Beckman, Robert; Beverly, Kris; Boukai, Akram; Bunimovich, Yuri; Choi, Jang Wook; DeIonno, Erica; Green, Johnny; Johnston-Halperin, Ezekiel; Luo, Yi; Sheriff, Bonnie; Stoddart, Fraser; Heath, James R

2006-01-01

We describe our research into building integrated molecular electronics circuitry for a diverse set of functions, and with a focus on the fundamental scientific issues that surround this project. In particular, we discuss experiments aimed at understanding the function of bistable rotaxane molecular electronic switches by correlating the switching kinetics and ground state thermodynamic properties of those switches in various environments, ranging from the solution phase to a Langmuir monolayer of the switching molecules sandwiched between two electrodes. We discuss various devices, low bit-density memory circuits, and ultra-high density memory circuits that utilize the electrochemical switching characteristics of these molecules in conjunction with novel patterning methods. We also discuss interconnect schemes that are capable of bridging the micrometre to submicrometre length scales of conventional patterning approaches to the near-molecular length scales of the ultra-dense memory circuits. Finally, we discuss some of the challenges associated with fabricated ultra-dense molecular electronic integrated circuits.
Thermophysical properties of imidazolium tricyanomethanide ionic liquids: experiments and molecular simulation.

Science.gov (United States)

Zubeir, Lawien F; Rocha, Marisa A A; Vergadou, Niki; Weggemans, Wilko M A; Peristeras, Loukas D; Schulz, Peter S; Economou, Ioannis G; Kroon, Maaike C

2016-08-17

The low-viscous tricyanomethanide ([TCM](-))-based ionic liquids (ILs) are gaining increasing interest as attractive fluids for a variety of industrial applications. The thermophysical properties (density, viscosity, surface tension, electrical conductivity and self-diffusion coefficient) of the 1-alkyl-3-methylimidazolium tricyanomethanide [Cnmim][TCM] (n = 2, 4 and 6-8) IL series were experimentally measured over the temperature range from 288 to 363 K. Moreover, a classical force field optimized for the imidazolium-based [TCM](-) ILs was used to calculate their thermodynamic, structural and transport properties (density, surface tension, self-diffusion coefficients, viscosity) in the temperature range from 300 to 366 K. The predictions were directly compared against the experimental measurements. The effects of anion and alkyl chain length on the structure and thermophysical properties have been evaluated. In cyano-based ILs, the density decreases with increasing molar mass, in contrast to the behavior of the fluorinated anions, being in agreement with the literature. The contribution per -CH2- group to the increase of the viscosity presents the following sequence: [PF6](-) > [BF4](-) > [Tf2N](-) > [DCA](-) > [TCB](-) > [TCM](-). [TCM](-)-based ILs show lower viscosity than dicyanamide ([DCA](-))- and tetracyanoborate ([TCB](-))-based ILs, while the latter two exhibit a crossover which depends both on temperature and the alkyl chain length of the cation. The surface tension of the investigated ILs decreases with increasing alkyl chain length. [C2mim][TCM] shows an outlier behavior compared to other members of the homologous series. The surface enthalpies and surface entropies for all the studied systems have been calculated based on the experimentally determined surface tensions. The relationship between molar conductivity and viscosity was analyzed using the Walden rule. The experimentally determined self-diffusion coefficients of the cations are in good

Measuring the mechanical properties of molecular conformers

Science.gov (United States)

Jarvis, S. P.; Taylor, S.; Baran, J. D.; Champness, N. R.; Larsson, J. A.; Moriarty, P.

2015-09-01

Scanning probe-actuated single molecule manipulation has proven to be an exceptionally powerful tool for the systematic atomic-scale interrogation of molecular adsorbates. To date, however, the extent to which molecular conformation affects the force required to push or pull a single molecule has not been explored. Here we probe the mechanochemical response of two tetra(4-bromophenyl)porphyrin conformers using non-contact atomic force microscopy where we find a large difference between the lateral forces required for manipulation. Remarkably, despite sharing very similar adsorption characteristics, variations in the potential energy surface are capable of prohibiting probe-induced positioning of one conformer, while simultaneously permitting manipulation of the alternative conformational form. Our results are interpreted in the context of dispersion-corrected density functional theory calculations which reveal significant differences in the diffusion barriers for each conformer. These results demonstrate that conformational variation significantly modifies the mechanical response of even simple porpyhrins, potentially affecting many other flexible molecules.
Mechanical Properties of Boehmite Evaluated by Atomic Force Microscopy Experiments and Molecular Dynamic Finite Element Simulations

International Nuclear Information System (INIS)

Fankhanel, J.; Daum, B.; Kempe, A.; Rolfes, R.; Silbernagl, D.; Khorasani, M.Gh.Z.; Sturm, H.; Sturm, H.

2016-01-01

Boehmite nanoparticles show great potential in improving mechanical properties of fiber reinforced polymers. In order to predict the properties of nanocomposites, knowledge about the material parameters of the constituent phases, including the boehmite particles, is crucial. In this study, the mechanical behavior of boehmite is investigated using Atomic Force Microscopy (AFM) experiments and Molecular Dynamic Finite Element Method (MDFEM) simulations. Young’s modulus of the perfect crystalline boehmite nanoparticles is derived from numerical AFM simulations. Results of AFM experiments on boehmite nanoparticles deviate significantly. Possible causes are identified by experiments on complementary types of boehmite, that is, geological and hydrothermally synthesized samples, and further simulations of imperfect crystals and combined boehmite/epoxy models. Under certain circumstances, the mechanical behavior of boehmite was found to be dominated by inelastic effects that are discussed in detail in the present work. The studies are substantiated with accompanying X-ray diffraction and Raman experiments.
Structural, Dynamic, and Vibrational Properties during Heat Transfer in Si/Ge Superlattices: A Car-Parrinello Molecular Dynamics Study

OpenAIRE

Ji, Pengfei; Zhang, Yuwen; Yang, Mo

2016-01-01

The structural, dynamic, and vibrational properties during the heat transfer process in Si/Ge superlattices, are studied by analyzing the trajectories generated by the ab initio Car-Parrinello molecular dynamics simulation. The radial distribution functions and mean square displacements are calculated and further discussions are made to explain and probe the structural changes relating to the heat transfer phenomenon. Furthermore, the vibrational density of states of the two layers (Si/Ge) ar...
Molecular recognition by gold, silver and copper nanoparticles

Science.gov (United States)

Tauran, Yannick; Brioude, Arnaud; Coleman, Anthony W; Rhimi, Moez; Kim, Beonjoom

2013-01-01

The intrinsic physical properties of the noble metal nanoparticles, which are highly sensitive to the nature of their local molecular environment, make such systems ideal for the detection of molecular recognition events. The current review describes the state of the art concerning molecular recognition of Noble metal nanoparticles. In the first part the preparation of such nanoparticles is discussed along with methods of capping and stabilization. A brief discussion of the three common methods of functionalization: Electrostatic adsorption; Chemisorption; Affinity-based coordination is given. In the second section a discussion of the optical and electrical properties of nanoparticles is given to aid the reader in understanding the use of such properties in molecular recognition. In the main section the various types of capping agents for molecular recognition; nucleic acid coatings, protein coatings and molecules from the family of supramolecular chemistry are described along with their numerous applications. Emphasis for the nucleic acids is on complementary oligonucleotide and aptamer recognition. For the proteins the recognition properties of antibodies form the core of the section. With respect to the supramolecular systems the cyclodextrins, calix[n]arenes, dendrimers, crown ethers and the cucurbitales are treated in depth. Finally a short section deals with the possible toxicity of the nanoparticles, a concern in public health. PMID:23977421
Molecular dynamics simulation of nanotribology properties of CuZr metallic glasses

Energy Technology Data Exchange (ETDEWEB)

Wu, Cheng-Da [Chung Yuan Christian University, Department of Mechanical Engineering, Taoyuan City (China)

2016-04-15

The effects of scratch depth, scratch speed, and alloy composition on the mechanical deformation and nanotribology properties of CuZr metallic glasses are studied using molecular dynamics simulations based on the second-moment approximation of the many-body tight-binding potential. These effects are investigated in terms of atomic trajectories, slip vectors, friction force, normal force, and friction coefficient. The simulation results show that a few shear transformation zones independently develop at the contact area between the probe tip and the film. Pileup occurs in the nanoscratch process but not during nanoindentation at a depth of 2.4 nm. There are two areas on the surface where the atoms have high slip vector values during nanoscratching. These areas form due to the removal of atoms that piled up around the probe tip and those behind the probe tip, respectively. Both the friction force and the normal force increase with increasing scratch depth and scratch speed. Friction coefficients decrease with increasing scratch depth, scratch speed, and Zr content in films. (orig.)
Investigation of multi-state charge-storage properties of redox-active organic molecules in silicon-molecular hybrid devices for DRAM and Flash applications

Science.gov (United States)

Gowda, Srivardhan Shivappa

Molecular electronics has recently spawned a considerable amount of interest with several molecules possessing charge-conduction and charge-storage properties proposed for use in electronic devices. Hybrid silicon-molecular technology has the promise of augmenting the current silicon technology and provide for a transitional path to future molecule-only technology. The focus of this dissertation work has been on developing a class of hybrid silicon-molecular electronic devices for DRAM and Flash memory applications utilizing redox-active molecules. This work exploits the ability of molecules to store charges with single-electron precision at room temperature. The hybrid devices are fabricated by forming self-assembled monolayers of redox-active molecules on Si and oxide (SiO2 and HfO2) surfaces via formation of covalent linkages. The molecules possess discrete quantum states from which electrons can tunnel to the Si substrate at discrete applied voltages (oxidation process, cell write), leaving behind a positively charged layer of molecules. The reduction (erase) process, which is the process of electrons tunneling back from Si to the molecules, neutralizes the positively charged molecular monolayer. Hybrid silicon-molecular capacitor test structures were electrically characterized with an electrolyte gate using cyclic voltammetry (CyV) and impedance spectroscopy (CV) techniques. The redox voltages, kinetics (write/erase speeds) and charge-retention characteristics were found to be strongly dependent on the Si doping type and densities, and ambient light. It was also determined that the redox energy states in the molecules communicate with the valence band of the Si substrate. This allows tuning of write and read states by modulating minority carriers in n- and p-Si substrates. Ultra-thin dielectric tunnel barriers (SiO2, HfO2) were placed between the molecules and the Si substrate to augment charge-retention for Flash memory applications. The redox response was
Active molecular plasmonics: tuning surface plasmon resonances by exploiting molecular dimensions

Science.gov (United States)

Chen, Kai; Leong, Eunice Sok Ping; Rukavina, Michael; Nagao, Tadaaki; Liu, Yan Jun; Zheng, Yuebing

2015-06-01

Molecular plasmonics explores and exploits the molecule-plasmon interactions on metal nanostructures to harness light at the nanoscale for nanophotonic spectroscopy and devices. With the functional molecules and polymers that change their structural, electrical, and/or optical properties in response to external stimuli such as electric fields and light, one can dynamically tune the plasmonic properties for enhanced or new applications, leading to a new research area known as active molecular plasmonics (AMP). Recent progress in molecular design, tailored synthesis, and self-assembly has enabled a variety of scenarios of plasmonic tuning for a broad range of AMP applications. Dimension (i.e., zero-, two-, and threedimensional) of the molecules on metal nanostructures has proved to be an effective indicator for defining the specific scenarios. In this review article, we focus on structuring the field of AMP based on the dimension of molecules and discussing the state of the art of AMP. Our perspective on the upcoming challenges and opportunities in the emerging field of AMP is also included.
Active molecular plasmonics: tuning surface plasmon resonances by exploiting molecular dimensions

Directory of Open Access Journals (Sweden)

Chen Kai

2015-06-01

Full Text Available Molecular plasmonics explores and exploits the molecule–plasmon interactions on metal nanostructures to harness light at the nanoscale for nanophotonic spectroscopy and devices. With the functional molecules and polymers that change their structural, electrical, and/or optical properties in response to external stimuli such as electric fields and light, one can dynamically tune the plasmonic properties for enhanced or new applications, leading to a new research area known as active molecular plasmonics (AMP. Recent progress in molecular design, tailored synthesis, and self-assembly has enabled a variety of scenarios of plasmonic tuning for a broad range of AMP applications. Dimension (i.e., zero-, two-, and threedimensional of the molecules on metal nanostructures has proved to be an effective indicator for defining the specific scenarios. In this review article, we focus on structuring the field of AMP based on the dimension of molecules and discussing the state of the art of AMP. Our perspective on the upcoming challenges and opportunities in the emerging field of AMP is also included.
Influence of thermal annealing-induced molecular aggregation on film properties and photovoltaic performance of bulk heterojunction solar cells based on a squaraine dye

Science.gov (United States)

Zhang, Pengpeng; Ling, Zhitian; Chen, Guo; Wei, Bin

2018-04-01

Squaraine (SQ) dyes have been considered as efficient photoactive materials for organic solar cells. In this work, we purposely controlled the molecular aggregation of an SQ dye, 2,4-bis[4-(N,N-dibutylamino)-2-dihydroxyphenyl] SQ (DBSQ-(OH)2) in the DBSQ(OH)2:[6,6]-phenyl-C61-butyric acid methyl ester (PCBM) blend film by using the thermal annealing method, to study the influence of the molecular aggregation on film properties as well as the photovoltaic performance of DBSQ(OH)2:PCBM-based bulk heterojunction (BHJ) solar cells. Our results demonstrate that thermal annealing may change the aggregation behavior of DBSQ(OH)2 in the DBSQ(OH)2:PCBM film, and thus significantly influence the surface morphology, optical and electrical properties of the blend film, as well as the photovoltaic performance of DBSQ(OH)2:PCBM BHJ cells.
Using molecular dynamics simulations and finite element method to study the mechanical properties of nanotube reinforced polyethylene and polyketone

Science.gov (United States)

Rouhi, S.; Alizadeh, Y.; Ansari, R.; Aryayi, M.

2015-09-01

Molecular dynamics simulations are used to study the mechanical behavior of single-walled carbon nanotube reinforced composites. Polyethylene and polyketone are selected as the polymer matrices. The effects of nanotube atomic structure and diameter on the mechanical properties of polymer matrix nanocomposites are investigated. It is shown that although adding nanotube to the polymer matrix raises the longitudinal elastic modulus significantly, the transverse tensile and shear moduli do not experience important change. As the previous finite element models could not be used for polymer matrices with the atom types other than carbon, molecular dynamics simulations are used to propose a finite element model which can be used for any polymer matrices. It is shown that this model can predict Young’s modulus with an acceptable accuracy.
Transitional grain boundary structures and the influence on thermal, mechanical and energy properties from molecular dynamics simulations

International Nuclear Information System (INIS)

Burbery, N.J.; Das, R.; Ferguson, W.G.

2016-01-01

The thermo-kinetic characteristics that dictate the activation of atomistic crystal defects significantly influence the mechanical properties of crystalline materials. Grain boundaries (GBs) primarily influence the plastic deformation of FCC metals through their interaction with mobile dislocation defects. The activation thresholds and atomic mechanisms that dictate the thermo-kinetic properties of grain boundaries have been difficult to study due to complex and highly variable GB structure. This paper presents a new approach for modelling GBs which is based on a systematic structural analysis of metastable and stable GBs. GB structural transformation accommodates defect interactions at the interface. The activation energy for such structural transformations was evaluated with nudged elastic band analysis of bi-crystals with several metastable 0 K grain boundary structures in pure FCC Aluminium (Al). The resultant activation energy was used to evaluate the thermal stability of the metastable grain boundary structures, with predictions of transition time based on transition state theory. The predictions are in very good agreement with the minimum time for irreversible structure transformation at 300 K obtained with molecular dynamics simulations. Analytical methods were used to evaluate the activation volume, which in turn was used to predict and explain the influence of stress and strain rate on the thermal and mechanical properties. Results of molecular dynamics simulations show that the GB structure is more closely related to the elastic strength at 0 K than the GB energy. Furthermore, the thermal instability of the GB structure directly influences the relationship between bi-crystal strength, temperature and strain rate. Hence, theoretically consistent models are established on the basis of activation criteria, and used to make predictions of temperature-dependent yield stress at a low strain rate, in agreement with experimental results.
Theoretical molecular biophysics

CERN Document Server

Scherer, Philipp O J

2017-01-01

This book gives an introduction to molecular biophysics. It starts from material properties at equilibrium related to polymers, dielectrics and membranes. Electronic spectra are developed for the understanding of elementary dynamic processes in photosynthesis including proton transfer and dynamics of molecular motors. Since the molecular structures of functional groups of bio-systems were resolved, it has become feasible to develop a theory based on the quantum theory and statistical physics with emphasis on the specifics of the high complexity of bio-systems. This introduction to molecular aspects of the field focuses on solvable models. Elementary biological processes provide as special challenge the presence of partial disorder in the structure which does not destroy the basic reproducibility of the processes. Apparently the elementary molecular processes are organized in a way to optimize the efficiency. Learning from nature by means exploring the relation between structure and function may even help to b...
Mass Transport Properties of LiD-U Mixtures from Orbital FreeMolecular Dynamics Simulations and a Pressure-Matching Mixing Rule

International Nuclear Information System (INIS)

Burakovsky, Leonid; Kress, Joel D.; Collins, Lee A.

2012-01-01

Mass transport properties for LiD-U mixtures were calculated using a pressure matching mixture rule for the mixing of LiD and of U properties simulated with Orbital Free Molecular Dynamics (OFMD). The mixing rule was checked against benchmark OFMD simulations for the fully interacting three-component (Li, D, U) system. To obtain transport coefficients for LiD-U mixtures of different (LiD) x U (1-x) compositions as functions of temperature and mixture density is a tedious task. Quantum molecular dynamics (MD) simulations can be employed, as in the case LiD or U. However, due to the presence of the heavy constituent U, such simulations proceed so slowly that only a limited number of numerical data points in the (x, ρ, T) phase space can be obtained. To finesse this difficulty, transport coefficients for a mixture can be obtained using a pressure-matching mixing rule discussed. For both LiD and U, the corresponding transport coefficients were obtained earlier from quantum molecular dynamics simulations. In these simulations, the quantum behavior of the electrons was represented using an orbital free (OF) version of density functional theory, and ions were advanced in time using classical molecular dynamics. The total pressure of the system, P = nk B T/V + P e , is the sum of the ideal gas pressure of the ions plus the electron pressure. The mass self-diffusion coefficient for species α, D α , the mutual diffusion coefficient for species α and β, Dαβ, and the shear viscosity, η, are computed from the appropriate autocorrelation function. The details of similar QMD calculations on LiH are described in Ref. [1] for 0.5 eV < T < 3 eV, and in Ref. [2] for 2 eV < T < 6 eV.
Optical properties of helical cylindrical molecular aggregates : the homogeneous limit

NARCIS (Netherlands)

Didraga, C.; Klugkist, J.A.; Knoester, J.

2002-01-01

Using a Frenkel exciton model, we study the optical absorption spectrum and linear and circular dichroism (CD) spectra of cylindrical molecular aggregates. We demonstrate that such aggregates can always be described as a stack of molecular rings with nearest-neighbor rings rotated relative to each
Optical Properties of Helical Cylindrical Molecular Aggregates : The Homogeneous Limit

NARCIS (Netherlands)

Didraga, Cătălin; Klugkist, Joost A.; Knoester, Jasper

2002-01-01

Using a Frenkel exciton model, we study the optical absorption spectrum and linear and circular dichroism (CD) spectra of cylindrical molecular aggregates. We demonstrate that such aggregates can always be described as a stack of molecular rings with nearest-neighbor rings rotated relative to each
Quantifying and Visualizing Uncertainties in Molecular Models

OpenAIRE

Rasheed, Muhibur; Clement, Nathan; Bhowmick, Abhishek; Bajaj, Chandrajit

2015-01-01

Computational molecular modeling and visualization has seen significant progress in recent years with sev- eral molecular modeling and visualization software systems in use today. Nevertheless the molecular biology community lacks techniques and tools for the rigorous analysis, quantification and visualization of the associated errors in molecular structure and its associated properties. This paper attempts at filling this vacuum with the introduction of a systematic statistical framework whe...
Photocatalytic Properties of Nb/MCM-41 Molecular Sieves: Effect of the Synthesis Conditions

Directory of Open Access Journals (Sweden)

Caterine Daza Gomez

2015-08-01

Full Text Available The effect of synthesis conditions and niobium incorporation levels on the photocatalytic properties of Nb/MCM-41 molecular sieves was assessed. Niobium pentoxide supported on MCM-41 mesoporous silica was obtained using two methods: sol-gel and incipient impregnation, in each case also varying the percentage of niobium incorporation. The synthesized Nb-MCM-41 ceramic powders were characterized using the spectroscopic techniques of infrared spectroscopy (IR, Raman spectroscopy, X-ray diffraction (XRD, and transmission electron microscopy (TEM. The photodegradation capacity of the powders was studied using the organic molecule, methylene blue. The effect of both the method of synthesis and the percentage of niobium present in the sample on the photodegradation action of the solids was determined. The mesoporous Nb-MCM-41 that produced the greatest photodegradation response was obtained using the sol-gel method and 20% niobium incorporation.
Thermal transport property of Ge34 and d-Ge investigated by molecular dynamics and the Slack's equation

International Nuclear Information System (INIS)

Han-Fu, Wang; Wei-Guo, Chu; Yan-Jun, Guo; Hao, Jin

2010-01-01

In this study, we evaluate the values of lattice thermal conductivity κ L of type II Ge clathrate (Ge 34 ) and diamond phase Ge crystal (d-Ge) with the equilibrium molecular dynamics (EMD) method and the Slack's equation. The key parameters of the Slack's equation are derived from the thermodynamic properties obtained from the lattice dynamics (LD) calculations. The empirical Tersoff's potential is used in both EMD and LD simulations. The thermal conductivities of d-Ge calculated by both methods are in accordance with the experimental values. The predictions of the Slack's equation are consistent with the EMD results above 250 K for both Ge 34 and d-Ge. In a temperature range of 200–1000 K, the κ L value of d-Ge is about several times larger than that of Ge 34 . (condensed matter: structure, thermal and mechanical properties)
Influence of grain size on the mechanical properties of nano-crystalline copper; insights from molecular dynamics simulation

Science.gov (United States)

Rida, A.; Makke, A.; Rouhaud, E.; Micoulaut, M.

2017-10-01

We use molecular dynamics simulations to study the mechanical properties of a columnar nanocrystalline copper with a mean grain size between 8.91 nm and 24 nm. The used samples were generated by using a melting cooling method. These samples were submitted to uniaxial tensile test. The results reveal the presence of a critical mean grain size between 16 and 20 nm, where there is an inversion in the conventional Hall-Petch tendency. This inversion is illustrated by the increase of flow stress with the increase of the mean grain size. This transition is caused by shifting of the deformation mechanism from dislocations to a combination of grain boundaries sliding and dislocations. Moreover, the effect of temperature on the mechanical properties of nanocrystalline copper has been investigated. The results show a decrease of the flow stress and Young's modulus when the temperature increases.
Syntheses, spectroscopic properties and molecular structure of silver phytate complexes - IR, UV-VIS studies and DFT calculations

Science.gov (United States)

Zając, A.; Dymińska, L.; Lorenc, J.; Ptak, M.; Hanuza, J.

2018-03-01

Silver phytate IP6, IP6Ag, IP6Ag2 and IP6Ag3 complexes in the solid state have been synthesized changing the phosphate to metal mole ratio. The obtained products have been characterized by means of chemical and spectroscopic studies. Attenuated total reflection Fourier transform infrared technique and Raman microscope were used in the measurements. These results were discussed in terms of DFT (Density Functional Theory) quantum chemical calculations using the B3LYP/6-31G(d,p) approach. The molecular structures of these compounds have been proposed on the basis of group theory and geometry optimization taking into account the shape and the number of the observed bands corresponding to the stretching and bending vibrations of the phosphate group and metal-oxygen polyhedron. The role of inter- and intra-hydrogen bonds in stabilization of the structure has been discussed. It was found that three types of hydrogen bonds appear in the studied compounds: terminal, and those engaged in the inter- and intra-molecular interactions. The Fermi resonance as a result of the strong intra-molecular Osbnd H⋯O hydrogen bonds was discovered. Electron absorption spectra have been measured to characterize the electron properties of the studied complexes and their local symmetry.

Deep Generative Models for Molecular Science

DEFF Research Database (Denmark)

Jørgensen, Peter Bjørn; Schmidt, Mikkel Nørgaard; Winther, Ole

2018-01-01

Generative deep machine learning models now rival traditional quantum-mechanical computations in predicting properties of new structures, and they come with a significantly lower computational cost, opening new avenues in computational molecular science. In the last few years, a variety of deep...... generative models have been proposed for modeling molecules, which differ in both their model structure and choice of input features. We review these recent advances within deep generative models for predicting molecular properties, with particular focus on models based on the probabilistic autoencoder (or...
Influence of substrate quality on structural properties of AlGaN/GaN superlattices grown by molecular beam epitaxy

Energy Technology Data Exchange (ETDEWEB)

Schubert, F. [NaMLab gGmbH, Nöthnitzer Straße 64, 01187 Dresden (Germany); Merkel, U.; Schmult, S. [TU Dresden, Institute of Semiconductors and Microsystems, Nöthnitzer Straße 64, 01187 Dresden (Germany); Mikolajick, T. [NaMLab gGmbH, Nöthnitzer Straße 64, 01187 Dresden (Germany); TU Dresden, Institute of Semiconductors and Microsystems, Nöthnitzer Straße 64, 01187 Dresden (Germany)

2014-02-28

Short-period AlGaN/GaN superlattices were established as versatile test structures to investigate the structural properties of molecular beam epitaxy (MBE)-grown GaN and AlGaN layers and their dependence on the GaN substrate quality. X-ray diffractometry data of the investigated superlattices allow access to relevant structural parameters such as aluminum mole fraction and layer thicknesses. The occurrence of theoretically predicted intense high-order satellite peaks and pronounced interface fringes in the diffraction pattern reflects abrupt interfaces and perfect 2-dimensional growth resulting in smooth surfaces. The data unambiguously demonstrate that the structural quality of the MBE grown layers is limited by the structural properties of the GaN substrate.
Molecular dynamics simulation study of thermodynamic and mechanical properties of the Cu-Pd random alloy

International Nuclear Information System (INIS)

Davoodi, J.; Ahmadi, M.; Rafii-Tabar, H.

2010-01-01

Molecular dynamics (MD) simulations have been performed to investigate the thermodynamic and mechanical properties of Cu-x% Pd (at%) random alloy, as well as those of the Cu 3 Pd and CuPd 3 ordered alloys, in the temperature range from 200 K up to the melting point. The quantum Sutton-Chen (Q-SC) many-body interatomic potentials have been used to describe the energetics of the Cu and Pd pure metals, and a standard mixing rule has been employed to obtain the potential parameters for the mixed (alloy) states. We have computed the variation of the melting temperature with the concentration of Pd. Furthermore, the variation of the cohesive energy, the order parameter, the thermal expansion coefficient, the density, the isobaric heat capacity, the bulk modulus, and the elastic stiffness constants were also calculated at different temperatures and concentrations for these materials. The computed variations of the thermodynamic and mechanical properties with temperature are fitted to a polynomial function. Our computed results show good agreement with other computational simulations, as well as with the experimental results where they have been available.
Spectroscopic analysis of 8-hydroxyquinoline-5-sulphonic acid and investigation of its reactive properties by DFT and molecular dynamics simulations

Science.gov (United States)

Sureshkumar, B.; Sheena Mary, Y.; Panicker, C. Yohannan; Resmi, K. S.; Suma, S.; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, C.

2017-12-01

A detailed interpretation of the FT-IR and FT-Raman spectra has been performed on the basis of the observed and calculated infrared and Raman spectra as well as calculated potential energy distribution values. Comparison of Raman and SERS spectra suggests a tilted orientation of the rings on the metal surface. The dipole moment, polarizability and first and second order hyperpolarizability values of the molecule were calculated. Global reactivity parameters were predicted. The relative reactivities towards electrophilic and nucleophilic attack are predicted using molecular electrostatic potential map. Average local ionization energy (ALIE) and Fukui functions have been inspected in order to investigate local reactivity properties of title molecule. The importance of autoxidation and hydrolysis mechanisms for the title molecule has been assessed by DFT calculations of bond dissociation energies (BDE) and by calculations of radial distribution functions (RDFs) after molecular dynamics (MD) simulations. Molecular docking studies suggest that the title compound can be a lead compound for developing new anti-cancerous drug.
The effect of hot multistage drawing on molecular structure and optical properties of polyethylene terephthalate fibers

Directory of Open Access Journals (Sweden)

Aminoddin Haji

2012-08-01

Full Text Available In this work, mechanical and structural parameters related to the optical properties of polyethylene terephthalate (PET fibers drawn at hot multistage have been investigated. The changes in optical parameters upon changing draw ratio are used to obtain the mechanical orientation factors and , various orientation functions f2(θ, f4(θ and f6(θ, and amorphous and crystalline orientation functions (f a and f c. Also, the numbers of random links between the network junction points (N1, the average optical orientation (Fav, and the distribution function of segment ω(cos θ were calculated. In addition, an empirical formula was suggested to correlate changes in the birefringence with the draw ratio and its constants were determined. The study demonstrated change on the molecular orientation functions and structural parameters upon hot multistage drawing. Significant variations in the characteristic properties of the drawn PET fibers were due to reorientation of the molecules caused by applied heat and external tension.
Introducing Stable Radicals into Molecular Machines.

Science.gov (United States)

Wang, Yuping; Frasconi, Marco; Stoddart, J Fraser

2017-09-27

Ever since their discovery, stable organic radicals have received considerable attention from chemists because of their unique optical, electronic, and magnetic properties. Currently, one of the most appealing challenges for the chemical community is to develop sophisticated artificial molecular machines that can do work by consuming external energy, after the manner of motor proteins. In this context, radical-pairing interactions are important in addressing the challenge: they not only provide supramolecular assistance in the synthesis of molecular machines but also open the door to developing multifunctional systems relying on the various properties of the radical species. In this Outlook, by taking the radical cationic state of 1,1'-dialkyl-4,4'-bipyridinium (BIPY •+ ) as an example, we highlight our research on the art and science of introducing radical-pairing interactions into functional systems, from prototypical molecular switches to complex molecular machines, followed by a discussion of the (i) limitations of the current systems and (ii) future research directions for designing BIPY •+ -based molecular machines with useful functions.
Identification of unprecedented anticancer properties of high molecular weight biomacromolecular complex containing bovine lactoferrin (HMW-bLf.

Directory of Open Access Journals (Sweden)

Fawzi Ebrahim

Full Text Available With the successful clinical trials, multifunctional glycoprotein bovine lactoferrin is gaining attention as a safe nutraceutical and biologic drug targeting cancer, chronic-inflammatory, viral and microbial diseases. Interestingly, recent findings that human lactoferrin oligomerizes under simulated physiological conditions signify the possible role of oligomerization in the multifunctional activities of lactoferrin molecule during infections and in disease targeting signaling pathways. Here we report the purification and physicochemical characterization of high molecular weight biomacromolecular complex containing bovine lactoferrin (≥250 kDa, from bovine colostrum, a naturally enriched source of lactoferrin. It showed structural similarities to native monomeric iron free (Apo lactoferrin (∼78-80 kDa, retained anti-bovine lactoferrin antibody specific binding and displayed potential receptor binding properties when tested for cellular internalization. It further displayed higher thermal stability and better resistance to gut enzyme digestion than native bLf monomer. High molecular weight bovine lactoferrin was functionally bioactive and inhibited significantly the cell proliferation (p<0.01 of human breast and colon carcinoma derived cells. It induced significantly higher cancer cell death (apoptosis and cytotoxicity in a dose-dependent manner in cancer cells than the normal intestinal cells. Upon cellular internalization, it led to the up-regulation of caspase-3 expression and degradation of actin. In order to identify the cutting edge future potential of this bio-macromolecule in medicine over the monomer, its in-depth structural and functional properties need to be investigated further.
Effect of Solar Radiation on the Optical Properties and Molecular Composition of Laboratory Proxies of Atmospheric Brown Carbon

Energy Technology Data Exchange (ETDEWEB)

Lee, Hyun Ji; Aiona, Paige K.; Laskin, Alexander; Laskin, Julia; Nizkorodov, Sergey

2014-09-02

Sources, optical properties, and chemical composition of atmospheric brown carbon (BrC) aerosol are uncertain, making it challenging to estimate its contribution to radiative forcing. Furthermore, optical properties of BrC may change significantly during its atmospheric aging. We examined the effect of solar photolysis on the molecular composition, mass absorption coefficient, and fluorescence of secondary organic aerosol prepared by high-NO_x photooxidation of naphthalene (NAP SOA). The aqueous solutions of NAP SOA was observed to photobleach with an effective half-time of ~15 hours (with sun in its zenith) for the loss of the near-UV (300 -400 nm) absorbance. The molecular composition of NAP SOA was significantly modified by photolysis, with the average SOA formula changing from C_14.1H_14.5O_5.1N_0.08 to C_11.8H_14.9O_4.5N_0.02 after 4 hours of irradiation. The average O/C ratio did not change significantly, however, suggesting that it is not a good metric for assessing the extent of photolysis-driven aging in NAP SOA (and in BrC in general). In contrast to NAP SOA, the photolysis of BrC material produced by aqueous reaction of limonene+O₃ SOA (LIM/O₃ SOA) with ammonium sulfate was much faster, but it did not result in a significant change in the molecular level composition. The characteristic absorbance of the aged LIM/O₃ SOA in the 450-600 nm range decayed with an effective half-time of <0.5 hour. This result emphasizes the highly variable and dynamic nature of different types of atmospheric BrC.
Resilient Amorphous Networks Prepared by Photo-Crosslinking High-Molecular-Weight D,L-Lactide and Trimethylene Carbonate Macromers: Mechanical Properties and Shape-Memory Behavior

NARCIS (Netherlands)

Sharifi, Shahriar; Grijpma, Dirk W.

2012-01-01

Tough networks are prepared by photo-crosslinking high-molecular-weight DLLA and TMC macromers. These amorphous networks exhibit tunable thermal and mechanical properties and have excellent shape-memory features. Variation of the monomer ratio allows adjustment of Tg between approximately −13 and
Synthesis of Polyimides in Molecular-Scale Confinement for Low-Density Hybrid Nanocomposites.

Science.gov (United States)

Isaacson, Scott G; Fostvedt, Jade I; Koerner, Hilmar; Baur, Jeffery W; Lionti, Krystelle; Volksen, Willi; Dubois, Geraud; Dauskardt, Reinhold H

2017-11-08

In this work, we exploit a confinement-induced molecular synthesis and a resulting bridging mechanism to create confined polyimide thermoset nanocomposites that couple molecular confinement-enhanced toughening with an unprecedented combination of high-temperature properties at low density. We describe a synthesis strategy that involves the infiltration of individual polymer chains through a nanoscale porous network while simultaneous imidization reactions increase the molecular backbone stiffness. In the extreme limit where the confinement length scale is much smaller than the polymer's molecular size, confinement-induced molecular mechanisms give rise to exceptional mechanical properties. We find that polyimide oligomers can undergo cross-linking reactions even in such molecular-scale confinement, increasing the molecular weight of the organic phase and toughening the nanocomposite through a confinement-induced energy dissipation mechanism. This work demonstrates that the confinement-induced molecular bridging mechanism can be extended to thermoset polymers with multifunctional properties, such as excellent thermo-oxidative stability and high service temperatures (>350 °C).
The interstellar medium and star formation of galactic disks. I. Interstellar medium and giant molecular cloud properties with diffuse far-ultraviolet and cosmic-ray backgrounds

Science.gov (United States)

Li, Qi; Tan, Jonathan C.; Christie, Duncan; Bisbas, Thomas G.; Wu, Benjamin

2018-01-01

We present a series of adaptive mesh refinement hydrodynamic simulations of flat rotation curve galactic gas disks, with a detailed treatment of the interstellar medium (ISM) physics of the atomic to molecular phase transition under the influence of diffuse far-ultraviolet (FUV) radiation fields and cosmic-ray backgrounds. We explore the effects of different FUV intensities, including a model with a radial gradient designed to mimic the Milky Way. The effects of cosmic rays, including radial gradients in their heating and ionization rates, are also explored. The final simulations in this series achieve 4 pc resolution across the ˜20 kpc global disk diameter, with heating and cooling followed down to temperatures of ˜10 K. The disks are evolved for 300 Myr, which is enough time for the ISM to achieve a quasi-statistical equilibrium. In particular, the mass fraction of molecular gas is stabilized by ˜200 Myr. Additional global ISM properties are analyzed. Giant molecular clouds (GMCs) are also identified and the statistical properties of their populations are examined. GMCs are tracked as the disks evolve. GMC collisions, which may be a means of triggering star cluster formation, are counted and their rates are compared with analytic models. Relatively frequent GMC collision rates are seen in these simulations, and their implications for understanding GMC properties, including the driving of internal turbulence, are discussed.
The interstellar medium and star formation of galactic disks. I. Interstellar medium and giant molecular cloud properties with diffuse far-ultraviolet and cosmic-ray backgrounds

Science.gov (United States)

Li, Qi; Tan, Jonathan C.; Christie, Duncan; Bisbas, Thomas G.; Wu, Benjamin

2018-05-01

We present a series of adaptive mesh refinement hydrodynamic simulations of flat rotation curve galactic gas disks, with a detailed treatment of the interstellar medium (ISM) physics of the atomic to molecular phase transition under the influence of diffuse far-ultraviolet (FUV) radiation fields and cosmic-ray backgrounds. We explore the effects of different FUV intensities, including a model with a radial gradient designed to mimic the Milky Way. The effects of cosmic rays, including radial gradients in their heating and ionization rates, are also explored. The final simulations in this series achieve 4 pc resolution across the ˜20 kpc global disk diameter, with heating and cooling followed down to temperatures of ˜10 K. The disks are evolved for 300 Myr, which is enough time for the ISM to achieve a quasi-statistical equilibrium. In particular, the mass fraction of molecular gas is stabilized by ˜200 Myr. Additional global ISM properties are analyzed. Giant molecular clouds (GMCs) are also identified and the statistical properties of their populations are examined. GMCs are tracked as the disks evolve. GMC collisions, which may be a means of triggering star cluster formation, are counted and their rates are compared with analytic models. Relatively frequent GMC collision rates are seen in these simulations, and their implications for understanding GMC properties, including the driving of internal turbulence, are discussed.
PHYSICOCHEMICAL PROPERTY CALCULATIONS

Science.gov (United States)

Computer models have been developed to estimate a wide range of physical-chemical properties from molecular structure. The SPARC modeling system approaches calculations as site specific reactions (pKa, hydrolysis, hydration) and `whole molecule' properties (vapor pressure, boilin...
Attractive mechanical properties of a lightweight highly sensitive bi layer thermistor: polycarbonate/organic molecular conductor

International Nuclear Information System (INIS)

Laukhina, E; Lebedev, V; Rovira, C; Laukhin, V; Veciana, J

2016-01-01

The paper covers some of the basic mechanical characteristics of a recently developed bi layer thermistor: polycarbonate/(001) oriented layer of organic molecular conductor α’-(BEDT-TTF) 2 I x Br 3-x , were BEDT-TTF=bis(ethylenedithio)tetrathiafulvalen. The nano and macro mechanical properties have been studied in order to use this flexible, low cost thermistor in sensing applications by proper way. The nano-mechanical properties of the temperature sensitive semiconducting layer of α’-(BEDT-TTF) 2 I x Br 3-x were tested using nanoindentation method. The value of Young's modulus in direction being perpendicular to the layer plan was found as 9.0 ±1.4 GPa. The macro mechanical properties of the thermistor were studied using a 5848 MicroTester. The tensile tests showed that basic mechanical characteristics of the thermistor are close to those of polycarbonate films. This indicates a good mechanical strength of the developed sensor. Therefore, the thermistor can be used in technologies that need to be instrumented with highly robustness lightweight low cost temperature sensors. The paper also reports synthetic details on fabricating temperature sensing e-textile. As the temperature control is becoming more and more important in biomedical technologies like healthcare monitoring, this work strongly contributes on the ongoing research on engineering sensitive conducting materials for biomedical applications. (paper)
Application of the finite-field coupled-cluster method to calculate molecular properties relevant to electron electric-dipole-moment searches

Science.gov (United States)

Abe, M.; Prasannaa, V. S.; Das, B. P.

2018-03-01

Heavy polar diatomic molecules are currently among the most promising probes of fundamental physics. Constraining the electric dipole moment of the electron (e EDM ), in order to explore physics beyond the standard model, requires a synergy of molecular experiment and theory. Recent advances in experiment in this field have motivated us to implement a finite-field coupled-cluster (FFCC) approach. This work has distinct advantages over the theoretical methods that we had used earlier in the analysis of e EDM searches. We used relativistic FFCC to calculate molecular properties of interest to e EDM experiments, that is, the effective electric field (Eeff) and the permanent electric dipole moment (PDM). We theoretically determine these quantities for the alkaline-earth monofluorides (AEMs), the mercury monohalides (Hg X ), and PbF. The latter two systems, as well as BaF from the AEMs, are of interest to e EDM searches. We also report the calculation of the properties using a relativistic finite-field coupled-cluster approach with single, double, and partial triples' excitations, which is considered to be the gold standard of electronic structure calculations. We also present a detailed error estimate, including errors that stem from our choice of basis sets, and higher-order correlation effects.
Molecular Dynamic Modeling and Simulation for Polymers

National Research Council Canada - National Science Library

Harrell, Anthony

2003-01-01

... the mechanical properties of polymers. In particular, the goal was to develop insights as to how a molecular level structure is connected to the bulk properties of materials assuming homogeneity...
Synthetic CO, H2 and H I surveys of the second galactic quadrant, and the properties of molecular gas

Science.gov (United States)

Duarte-Cabral, A.; Acreman, D. M.; Dobbs, C. L.; Mottram, J. C.; Gibson, S. J.; Brunt, C. M.; Douglas, K. A.

2015-03-01

We present CO, H2, H I and HISA (H I self-absorption) distributions from a set of simulations of grand design spirals including stellar feedback, self-gravity, heating and cooling. We replicate the emission of the second galactic quadrant by placing the observer inside the modelled galaxies and post-process the simulations using a radiative transfer code, so as to create synthetic observations. We compare the synthetic data cubes to observations of the second quadrant of the Milky Way to test the ability of the current models to reproduce the basic chemistry of the Galactic interstellar medium (ISM), as well as to test how sensitive such galaxy models are to different recipes of chemistry and/or feedback. We find that models which include feedback and self-gravity can reproduce the production of CO with respect to H2 as observed in our Galaxy, as well as the distribution of the material perpendicular to the Galactic plane. While changes in the chemistry/feedback recipes do not have a huge impact on the statistical properties of the chemistry in the simulated galaxies, we find that the inclusion of both feedback and self-gravity are crucial ingredients, as our test without feedback failed to reproduce all of the observables. Finally, even though the transition from H2 to CO seems to be robust, we find that all models seem to underproduce molecular gas, and have a lower molecular to atomic gas fraction than is observed. Nevertheless, our fiducial model with feedback and self-gravity has shown to be robust in reproducing the statistical properties of the basic molecular gas components of the ISM in our Galaxy.
Modeling of molecular weight and molecular weight distribution in slurry polymerization of propylene by Ziegler-Natta catalysts

International Nuclear Information System (INIS)

Khorasani, R.; Pourmahdian, S.

2007-01-01

The Precise prediction of polypropylene synthesized by heterogeneous Ziegler-Natta catalysts needs good knowledge of parameters affecting on polymerization. molecular weight and molecular weight distribution are among important characteristics of a polymer determining physical-mechanical properties. broadening of molecular weight distribution is an important and well known characteristic of polypropylene synthesized by heterogeneous Ziegler-Natta catalysts, So it is important to understand the origin of broad molecular weight. Two main factors in broadening molecular weight, namely mass transfer resistances and multiplicity of active sites, are discussed in this paper and a model including these factors is presented. Then we calculate molecular weight and molecular weight distribution by the model and compare our results with
Molecular Dynamics Simulations of Poly(dimethylsiloxane) Properties

Czech Academy of Sciences Publication Activity Database

Fojtíková, J.; Kalvoda, L.; Sedlák, Petr

2015-01-01

Roč. 128, č. 4 (2015), s. 637-639 ISSN 0587-4246 R&D Projects: GA ČR GB14-36566G Institutional support: RVO:61388998 Keywords : molecular dynamics * poly(dimethylsiloxane) * dissipative particle dynamics Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.525, year: 2015 http://przyrbwn.icm.edu.pl/APP/PDF/128/a128z4p40.pdf
CONSTRAINING DUST AND MOLECULAR GAS PROPERTIES IN Lyα BLOBS AT z ∼ 3

International Nuclear Information System (INIS)

Yang Yujin; Decarli, Roberto; Walter, Fabian; Leipski, Christian; Dannerbauer, Helmut; Le Floc'h, Emeric; Weiss, Axel; Menten, Karl M.; Dey, Arjun; Chapman, Scott C.; Prescott, Moire K. M.; Neri, Roberto; Borys, Colin; Matsuda, Yuichi; Yamada, Toru; Hayashino, Tomoki; Tapken, Christian

2012-01-01

In order to constrain the bolometric luminosities, dust properties, and molecular gas content of giant Lyα nebulae, the so-called Lyα blobs, we have carried out a study of dust continuum and CO line emission in two well-studied representatives of this population at z ∼ 3: an Lyα blob discovered by its strong Spitzer Multiband Infrared Photometer 24 μm detection (LABd05) and the Steidel blob 1 (SSA22-LAB01). We find that the spectral energy distribution of LABd05 is well described by an active-galactic-nucleus-starburst composite template with L FIR = (4.0 ± 0.5) × 10 12 L ☉ , comparable to high-z submillimeter galaxies and ultraluminous infrared galaxies. New Large APEX Bolometer Camera 870 μm measurements rule out the reported Submillimeter Common-User Bolometer Array detection of the SSA22-LAB01 (S 850μm = 16.8 mJy) at the >4σ level. Consistent with this, ultradeep Plateau de Bure Interferometer observations with ∼2'' spatial resolution also fail to detect any 1.2 mm continuum source down to ≈0.45 mJy beam –1 (3σ). Combined with the existing (sub)millimeter observations in the literature, we conclude that the FIR luminosity of SSA22-LAB01 remains uncertain. No CO line is detected in either case down to integrated flux limits of S ν ΔV ∼ –1 , indicating a modest molecular gas reservoir, M(H 2 ) 10 M ☉ . The non-detections exclude, with high significance (12σ), the previous tentative detection of a CO J = 4-3 line in the SSA22-LAB01. The increased sensitivity afforded by the Atacama Large Millimeter/submillimeter Array will be critical in studying molecular gas and dust in these interesting systems.

Vibrational Spectra of β″-Type BEDT-TTF Salts: Relationship between Conducting Property, Time-Averaged Site Charge and Inter-Molecular Distance

Directory of Open Access Journals (Sweden)

Takashi Yamamoto

2012-07-01

Full Text Available The relationship between the conducting behavior and the degree of charge fluctuation in the β″-type BEDT-TTF salts is reviewed from the standpoints of vibrational spectroscopy and crystal structure. A group of β″-type ET salts demonstrates the best model compounds for achieving the above relationship because the two-dimensional structure is simple and great diversity in conducting behavior is realized under ambient pressure. After describing the requirement for the model compound, the methodology for analyzing the results of the vibrational spectra is presented. Vibrational spectroscopy provides the time-averaged molecular charge, the charge distribution in the two-dimensional layer, and the inter-molecular interactions, etc. The experimental results applied to 2/3-filled and 3/4-filled β″-type ET salts are reported. These experimental results suggest that the conducting property, the difference in the time-averaged molecular charges between the ionic and neutral-like sites, the alternation in the inter-molecular distances and the energy levels in the charge distributions are relevant to one another. The difference in the time-averaged molecular charges, ∆ρ, is a useful criterion for indicating conducting behavior. All superconductors presented in this review are characterized as small but finite ∆ρ.
Molecular heterojunctions of oligo(phenylene ethynylene)s with linear to cruciform framework

DEFF Research Database (Denmark)

Wei, Zhongming; Hansen, Tim; Santella, Marco

2015-01-01

Electrical transport properties of molecular junctions are fundamentally affected by the energy alignment between molecular frontier orbitals (highest occupied molecular orbital (HOMO) or lowest unoccupied molecular orbital (LUMO)) and Fermi level (or work function) of electrode metals. Dithiaful......Electrical transport properties of molecular junctions are fundamentally affected by the energy alignment between molecular frontier orbitals (highest occupied molecular orbital (HOMO) or lowest unoccupied molecular orbital (LUMO)) and Fermi level (or work function) of electrode metals......-tetrathiafulvalene (TTF) can form good self-assembled monolayers (SAMs) on Au substrates. Molecular heterojunctions based on these SAMs are investigated using conducting probe-atomic force microscopy with different tips (Ag, Au, and Pt) and Fermi levels. The calibrated conductance values follow the sequence OPE3-TTF...... > OPE3-DTF > OPE3 irrespective of the tip metal. Rectification properties (or diode behavior) are observed in case of the Ag tip for which the work function is furthest from the HOMO levels of the OPE3s. Quantum chemical calculations of the transmission qualitatively agree with the experimental data...
Activating the molecular spinterface

Science.gov (United States)

Cinchetti, Mirko; Dediu, V. Alek; Hueso, Luis E.

2017-05-01

The miniaturization trend in the semiconductor industry has led to the understanding that interfacial properties are crucial for device behaviour. Spintronics has not been alien to this trend, and phenomena such as preferential spin tunnelling, the spin-to-charge conversion due to the Rashba-Edelstein effect and the spin-momentum locking at the surface of topological insulators have arisen mainly from emergent interfacial properties, rather than the bulk of the constituent materials. In this Perspective we explore inorganic/molecular interfaces by looking closely at both sides of the interface. We describe recent developments and discuss the interface as an ideal platform for creating new spin effects. Finally, we outline possible technologies that can be generated thanks to the unique active tunability of molecular spinterfaces.
Molecular characterization of composite interfaces

International Nuclear Information System (INIS)

Ishida, H.

1982-01-01

The Fourier Transform Infrared Spectroscopy was applied to elucidate the molecular structures of the glass/matrix interface. The various interfaces and interphases were studied. It is found that the structure of the silane in a treating solution is important in determining the structure of the silane on glass fibers, influences the macroscopic properties of composites. The amount of silane on glass fibers, the state of hydrogen bonding, orientation, copolymerization of the organicfunctionality with the matrix, curing of the silane, and effect of water on the interface were investigated. It is shown that the molecular approach is useful to interpret and predict physicomechanical properties of composites
Gaussian basis sets for use in correlated molecular calculations. IV. Calculation of static electrical response properties

International Nuclear Information System (INIS)

Woon, D.E.; Dunning, T.H. Jr.

1994-01-01

An accurate description of the electrical properties of atoms and molecules is critical for quantitative predictions of the nonlinear properties of molecules and of long-range atomic and molecular interactions between both neutral and charged species. We report a systematic study of the basis sets required to obtain accurate correlated values for the static dipole (α 1 ), quadrupole (α 2 ), and octopole (α 3 ) polarizabilities and the hyperpolarizability (γ) of the rare gas atoms He, Ne, and Ar. Several methods of correlation treatment were examined, including various orders of Moller--Plesset perturbation theory (MP2, MP3, MP4), coupled-cluster theory with and without perturbative treatment of triple excitations [CCSD, CCSD(T)], and singles and doubles configuration interaction (CISD). All of the basis sets considered here were constructed by adding even-tempered sets of diffuse functions to the correlation consistent basis sets of Dunning and co-workers. With multiply-augmented sets we find that the electrical properties of the rare gas atoms converge smoothly to values that are in excellent agreement with the available experimental data and/or previously computed results. As a further test of the basis sets presented here, the dipole polarizabilities of the F - and Cl - anions and of the HCl and N 2 molecules are also reported
Molecular properties and prebiotic effect of inulin obtained from artichoke (Cynara scolymus L.).

Science.gov (United States)

López-Molina, Dorotea; Navarro-Martínez, María Dolores; Rojas Melgarejo, Francisco; Hiner, Alexander N P; Chazarra, Soledad; Rodríguez-López, José Neptuno

2005-06-01

A high molecular weight inulin has been prepared from artichoke (Cynara scolymus L.) agroindustrial wastes using environmentally benign aqueous extraction procedures. Physico-chemical analysis of the properties of artichoke inulin was carried out. Its average degree of polymerization was 46, which is higher than for Jerusalem artichoke, chicory, and dahlia inulins. GC-MS confirmed that the main constituent monosaccharide in artichoke inulin was fructose and its degradation by inulinase indicated that it contained the expected beta-2,1-fructan bonds. The FT-IR spectrum was identical to that of chicory inulin. These data indicate that artichoke inulin will be suitable for use in a wide range of food applications. The health-promoting prebiotic effects of artichoke inulin were demonstrated in an extensive microbiological study showing a long lasting bifidogenic effect on Bifidobacterium bifidum ATCC 29521 cultures and also in mixed cultures of colonic bacteria.
Properties of molecular solids and fluids at high pressures and temperatures. [Final report

International Nuclear Information System (INIS)

Etters, R.D.

1985-01-01

Equilibrium structures and orientations, lattice vibrational and librational model frequencies, intramolecular vibron mode frequencies, sound velocities, equations of state, compressibilities, and structural and orientational phase transitions in molecular solids are determined over a wide range of pressures and temperatures. In the high temperature fluid phase the equations of state, vibron frequencies, the melting transition, specific heats, compressibilities, second virial coefficients, viscosities and other transport properties, and the nature of orientational and magnetic correlations are determined. The techniques used include several strategies to optimize multi-dimensional functions as a means to determine equilibrium structures and orientations, self consistent phonon lattice dynamics methods, constant pressure and constant volume Monte-Carlo strategies with continuously deformable boundary conditions, mean field approximations, and classical perturbation methods. Systems studied include N 2 , O 2 , CO, CO 2 , F 2 , N 2 O, benzine, nitromethane, HCL, HBr, and H 2 . 50 refs., 4 figs
Preparation and Property Recognition of Nimodipine Molecularly Imprinted Polymer

Directory of Open Access Journals (Sweden)

Fei-fei CHEN

2015-09-01

Full Text Available Objective: To explore the application of molecular imprinting technique in the separation and detection of nimodipine. Methods: Methacrylic acid as functional monomer, pentaerythritol triacrylate as cross-linking agent were used to prepare molecularly imprinted polymer (MIP with the feature of specific recognition performance on imprinting molecule nimodipine under condition of template molecule nimodipine. The preparation conditions, recognition performance of MIP on nimodipine, different proportions of template molecule and functional monomer, the selectivity to other substrate, and the relationship between adsorption quantity (Q and time were observed. Results: MIP was prepared successfully bynimodipine as template and pentaerythritol triacrylate as cross-linking agent, with the feature of specific recognition performance on nimodipine. The static adsorption distribution coefficient (KD was 0.2264. The equation of Q and the concentration of substrate of template MIP was y = -0.21x+0.2204. Combining capacity of template molecule at the same concentration enhanced with the increasing proportion of functional monomer.Conclusion: Nimodipine MIP based on molecular imprinting technique may become a new approach to chiral separation for nimodipine.
Practical Photoemission Characterization Of Molecular Films And Related Interfaces

International Nuclear Information System (INIS)

Ivanco, J.

2013-01-01

Even though the term ‘organic electronics’ evokes rather organic devices, a significant part of its scope deals with physical properties of ‘active elements’ such as organic films and interfaces. Examination of the film growth and the evolution of the interface formation are particularly needful for the understanding a mechanism controlling their final properties. Performing such experiments in an ultra-high vacuum allows both to ‘stretch’ the time scale for pseudo real-time observations and to control properties of the probed systems on the atomic level. Photoemission technique probes directly electronic and chemical structure and it has thereby established among major tools employed in the field.This review primarily focuses to electronic properties of oligomeric molecular films and their interfaces examined by photoemission. Yet, it does not aspire after a complete overview on the topic; it rather aims to otherwise standard issues encountered at the photoemission characterization and analysis of the organic materials, though requiring to consider particularities of molecular films in terms of the growth, electronic properties, and their characterization and analysis. In particular, the fundamental electronic parameters of molecular films such as the work function, the ionization energy, and the interfacial energy level alignment, and their interplay, will be pursued with considering often neglected influence of the molecular orientation. Further, the implication on the band bending in molecular films based on photoemission characterization, and a model on the driving mechanism for the interfacial energy level alignment will be addressed. (author)
Semiquantum molecular dynamics simulation of thermal properties and heat transport in low-dimensional nanostructures

Science.gov (United States)

Savin, Alexander V.; Kosevich, Yuriy A.; Cantarero, Andres

2012-08-01

We present a detailed description of semiquantum molecular dynamics simulation of stochastic dynamics of a system of interacting particles. Within this approach, the dynamics of the system is described with the use of classical Newtonian equations of motion in which the effects of phonon quantum statistics are introduced through random Langevin-like forces with a specific power spectral density (the color noise). The color noise describes the interaction of the molecular system with the thermostat. We apply this technique to the simulation of thermal properties and heat transport in different low-dimensional nanostructures. We describe the determination of temperature in quantum lattice systems, to which the equipartition limit is not applied. We show that one can determine the temperature of such a system from the measured power spectrum and temperature- and relaxation-rate-independent density of vibrational (phonon) states. We simulate the specific heat and heat transport in carbon nanotubes, as well as the heat transport in molecular nanoribbons with perfect (atomically smooth) and rough (porous) edges, and in nanoribbons with strongly anharmonic periodic interatomic potentials. We show that the effects of quantum statistics of phonons are essential for the carbon nanotube in the whole temperature range T<500K, in which the values of the specific heat and thermal conductivity of the nanotube are considerably less than that obtained within the description based on classical statistics of phonons. This conclusion is also applicable to other carbon-based materials and systems with high Debye temperature like graphene, graphene nanoribbons, fullerene, diamond, diamond nanowires, etc. We show that the existence of rough edges and quantum statistics of phonons change drastically the low-temperature thermal conductivity of the nanoribbon in comparison with that of the nanoribbon with perfect edges and classical phonon dynamics and statistics. The semiquantum molecular
Ultra-High Molecular Weight Polyethylene: Influence of the Chemical, Physical and Mechanical Properties on the Wear Behavior. A Review

Directory of Open Access Journals (Sweden)

Pierangiola Bracco

2017-07-01

Full Text Available Ultra-high molecular weight polyethylene (UHMWPE is the most common bearing material in total joint arthroplasty due to its unique combination of superior mechanical properties and wear resistance over other polymers. A great deal of research in recent decades has focused on further improving its performances, in order to provide durable implants in young and active patients. From “historical”, gamma-air sterilized polyethylenes, to the so-called first and second generation of highly crosslinked materials, a variety of different formulations have progressively appeared in the market. This paper reviews the structure–properties relationship of these materials, with a particular emphasis on the in vitro and in vivo wear performances, through an analysis of the existing literature.
Molecular Dynamics Modeling of the Effect of Axial and Transverse Compression on the Residual Tensile Properties of Ballistic Fiber

Directory of Open Access Journals (Sweden)

Sanjib C. Chowdhury

2017-02-01

Full Text Available Ballistic impact induces multiaxial loading on Kevlar® and polyethylene fibers used in protective armor systems. The influence of multiaxial loading on fiber failure is not well understood. Experiments show reduction in the tensile strength of these fibers after axial and transverse compression. In this paper, we use molecular dynamics (MD simulations to explain and develop a fundamental understanding of this experimental observation since the property reduction mechanism evolves from the atomistic level. An all-atom MD method is used where bonded and non-bonded atomic interactions are described through a state-of-the-art reactive force field. Monotonic tension simulations in three principal directions of the models are conducted to determine the anisotropic elastic and strength properties. Then the models are subjected to multi-axial loads—axial compression, followed by axial tension and transverse compression, followed by axial tension. MD simulation results indicate that pre-compression distorts the crystal structure, inducing preloading of the covalent bonds and resulting in lower tensile properties.
Sintering, structure, and mechanical properties of nanophase SiC: A molecular-dynamics and neutron scattering study

International Nuclear Information System (INIS)

Chatterjee, Alok; Kalia, Rajiv K.; Nakano, Aiichiro; Omeltchenko, Andrey; Tsuruta, Kenji; Vashishta, Priya; Loong, Chun-Keung; Winterer, Markus; Klein, Sylke

2000-01-01

Structure, mechanical properties, and sintering of nanostructured SiC (n-SiC) are investigated with neutron scattering and molecular-dynamics (MD) techniques. Both MD and the experiment indicate the onset of sintering around 1500 K. During sintering, the pores shrink while maintaining their morphology: the fractal dimension is ∼2 and the surface roughness exponent is ∼0.45. Structural analyses reveal that interfacial regions in n-SiC are disordered with nearly the same number of three- and fourfold coordinated Si atoms. The elastic moduli scale with the density as ∼ρ μ , where μ=3.4±0.1. (c) 2000 American Institute of Physics
Applicability of effective fragment potential version 2 - Molecular dynamics (EFP2-MD) simulations for predicting excess properties of mixed solvents

Science.gov (United States)

Kuroki, Nahoko; Mori, Hirotoshi

2018-02-01

Effective fragment potential version 2 - molecular dynamics (EFP2-MD) simulations, where the EFP2 is a polarizable force field based on ab initio electronic structure calculations were applied to water-methanol binary mixture. Comparing EFP2s defined with (aug-)cc-pVXZ (X = D,T) basis sets, it was found that large sets are necessary to generate sufficiently accurate EFP2 for predicting mixture properties. It was shown that EFP2-MD could predict the excess molar volume. Since the computational cost of EFP2-MD are far less than ab initio MD, the results presented herein demonstrate that EFP2-MD is promising for predicting physicochemical properties of novel mixed solvents.
Mechanical properties of irradiated nanowires – A molecular dynamics study

Energy Technology Data Exchange (ETDEWEB)

Figueroa, Emilio [Grupo de NanoMateriales, Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla, 653 Santiago (Chile); Departamento de Física, Facultad de Ciencias Naturales, Matemática y del Medio Ambiente, Universidad Tecnológica Metropolitana, Santiago 7800002 (Chile); Tramontina, Diego [Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, 5500 Mendoza (Argentina); Instituto de Bioingeniería, Universidad de Mendoza, 5500 Mendoza (Argentina); Gutiérrez, Gonzalo, E-mail: gonzalo@fisica.ciencias.uchile.cl [Grupo de NanoMateriales, Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla, 653 Santiago (Chile); Bringa, Eduardo [Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, 5500 Mendoza (Argentina)

2015-12-15

In this work we study, by means of molecular dynamics simulation, the change in the mechanical properties of a gold nanowire with pre-existing radiation damage. The gold nanowire is used as a simple model for a nanofoam, made of connected nanowires. Radiation damage by keV ions leads to the formation of a stacking fault tetrahedron (SFT), and this defect leads to a reduced plastic threshold, as expected, when the nanowire is subjected to tension. We quantify dislocation and twin density during the deformation, and find that the early activation of the SFT as a dislocation source leads to reduced dislocation densities compared to the case without radiation damage. In addition, we observed a total destruction of the SFT, as opposed to a recent simulation study where it was postulated that SFTs might act as self-generating dislocation sources. The flow stress at large deformation is also found to be slightly larger for the irradiated case, in agreement with recent experiments. - Highlights: • Stacking Fault Tetrahedra (SFT) formation proceeds by cascades, containing typically a vacancy cluster and interstitials. • Applied tension leads to the destruction of the SFT, in contrast to a recently reported case of a SFT which soften the NW. • After the initial dislocation activity, strength is controlled by a few surviving dislocations.
Photon Upconversion and Molecular Solar Energy Storage by Maximizing the Potential of Molecular Self-Assembly.

Science.gov (United States)

Kimizuka, Nobuo; Yanai, Nobuhiro; Morikawa, Masa-Aki

2016-11-29

The self-assembly of functional molecules into ordered molecular assemblies and the fulfillment of potentials unique to their nanotomesoscopic structures have been one of the central challenges in chemistry. This Feature Article provides an overview of recent progress in the field of molecular self-assembly with the focus on the triplet-triplet annihilation-based photon upconversion (TTA-UC) and supramolecular storage of photon energy. On the basis of the integration of molecular self-assembly and photon energy harvesting, triplet energy migration-based TTA-UC has been achieved in varied molecular systems. Interestingly, some molecular self-assemblies dispersed in solution or organogels revealed oxygen barrier properties, which allowed TTA-UC even under aerated conditions. The elements of molecular self-assembly were also introduced to the field of molecular solar thermal fuel, where reversible photoliquefaction of ionic crystals to ionic liquids was found to double the molecular storage capacity with the simultaneous pursuit of switching ionic conductivity. A future prospect in terms of innovating molecular self-assembly toward molecular systems chemistry is also discussed.
Dynamic adsorption property of xenon on activated carbon and carbon molecular sieves

International Nuclear Information System (INIS)

Feng Shujuan; Zhou Guoqing; Jin Yuren; Zhou Chongyang

2010-01-01

In order to select well adsorptive xenon adsorbent, the dynamic adsorption property of xenon on activated carbon and carbon molecular sieves (CMS) was studied by measuring the xenon dynamic adsorption coefficient as a function velocity of gas, temperature, carrier gas, pressure and concentration of CO 2 . The results show that the highest value of xenon dynamic adsorption coefficient is on CMS1, and the second highest value is on CMS2; when the xenon concentration is less than 10 -5 mol/L or concentration of CO 2 is less than 5 x 10 -5 mol/L, the xenon dynamic adsorption coefficient nearly keeps constant at the specific experimental flow rate. Then the xenon dynamic adsorption coefficient would vary when it was mixed with different kind of carrier gas and become less at more than 5 x 10 -5 mol/L concentration of CO 2 . And the maximal effect factors are temperature and pressure. Therefore, the feasible measures to improve the xenon capability are to cool the adsorbent and increase adsorption pressure. (authors)
Surface properties of heat-induced soluble soy protein aggregates of different molecular masses.

Science.gov (United States)

Guo, Fengxian; Xiong, Youling L; Qin, Fang; Jian, Huajun; Huang, Xiaolin; Chen, Jie

2015-02-01

Suspensions (2% and 5%, w/v) of soy protein isolate (SPI) were heated at 80, 90, or 100 °C for different time periods to produce soluble aggregates of different molecular sizes to investigate the relationship between particle size and surface properties (emulsions and foams). Soluble aggregates generated in these model systems were characterized by gel permeation chromatography and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Heat treatment increased surface hydrophobicity, induced SPI aggregation via hydrophobic interaction and disulfide bonds, and formed soluble aggregates of different sizes. Heating of 5% SPI always promoted large-size aggregate (LA; >1000 kDa) formation irrespective of temperature, whereas the aggregate size distribution in 2% SPI was temperature dependent: the LA fraction progressively rose with temperature (80→90→100 °C), corresponding to the attenuation of medium-size aggregates (MA; 670 to 1000 kDa) initially abundant at 80 °C. Heated SPI with abundant LA (>50%) promoted foam stability. LA also exhibited excellent emulsifying activity and stabilized emulsions by promoting the formation of small oil droplets covered with a thick interfacial protein layer. However, despite a similar influence on emulsion stability, MA enhanced foaming capacity but were less capable of stabilizing emulsions than LA. The functionality variation between heated SPI samples is clearly related to the distribution of aggregates that differ in molecular size and surface activity. The findings may encourage further research to develop functional SPI aggregates for various commercial applications. © 2015 Institute of Food Technologists®
Molecular dynamics simulation study of thermodynamic and mechanical properties of the Cu-Pd random alloy

Energy Technology Data Exchange (ETDEWEB)

Davoodi, J., E-mail: jdavoodi@znu.ac.ir [Departmant of Physics, University of Zanjan, P.O. Box 45371-38111, Zanjan (Iran, Islamic Republic of); Ahmadi, M. [Departmant of Physics, University of Zanjan, P.O. Box 45371-38111, Zanjan (Iran, Islamic Republic of); Rafii-Tabar, H. [Department of Medical Physics and Biomedical Engineering and Research Center for Medical Nanotechnology and Tissue Engineering, Shahid Beheshti University of Medical Sciences, Evin, Tehran (Iran, Islamic Republic of); Computational Physical Sciences Research Laboratory, Department of Nano-Science, Institute for Research in Fundamental Sciences (IPM), P.O. Box 19395-5531, Tehran (Iran, Islamic Republic of)

2010-06-25

Molecular dynamics (MD) simulations have been performed to investigate the thermodynamic and mechanical properties of Cu-x% Pd (at%) random alloy, as well as those of the Cu{sub 3}Pd and CuPd{sub 3} ordered alloys, in the temperature range from 200 K up to the melting point. The quantum Sutton-Chen (Q-SC) many-body interatomic potentials have been used to describe the energetics of the Cu and Pd pure metals, and a standard mixing rule has been employed to obtain the potential parameters for the mixed (alloy) states. We have computed the variation of the melting temperature with the concentration of Pd. Furthermore, the variation of the cohesive energy, the order parameter, the thermal expansion coefficient, the density, the isobaric heat capacity, the bulk modulus, and the elastic stiffness constants were also calculated at different temperatures and concentrations for these materials. The computed variations of the thermodynamic and mechanical properties with temperature are fitted to a polynomial function. Our computed results show good agreement with other computational simulations, as well as with the experimental results where they have been available.
Nanomaterials under extreme environments: A study of structural and dynamic properties using reactive molecular dynamics simulations

Science.gov (United States)

Shekhar, Adarsh

nanoporous silica are different from that of bulk water, and insight into the properties of confined water is important for our understanding of many geological and biological processes. Nanoporous silica has a wide range of technological applications because it is easy to tune the size of pores and their morphologies and to functionalize pore surfaces with a variety of molecular moieties. Nanoporous silica is used in catalysis, chromatography, anticorrosion coatings, desalination membranes, and as drug delivery vehicles. We use reactive molecular dynamics to study the structure and dynamics of nanoconfined water between 100 and 300 K

Assessment of Molecular Modeling & Simulation

Energy Technology Data Exchange (ETDEWEB)

None

2002-01-03

This report reviews the development and applications of molecular and materials modeling in Europe and Japan in comparison to those in the United States. Topics covered include computational quantum chemistry, molecular simulations by molecular dynamics and Monte Carlo methods, mesoscale modeling of material domains, molecular-structure/macroscale property correlations like QSARs and QSPRs, and related information technologies like informatics and special-purpose molecular-modeling computers. The panel's findings include the following: The United States leads this field in many scientific areas. However, Canada has particular strengths in DFT methods and homogeneous catalysis; Europe in heterogeneous catalysis, mesoscale, and materials modeling; and Japan in materials modeling and special-purpose computing. Major government-industry initiatives are underway in Europe and Japan, notably in multi-scale materials modeling and in development of chemistry-capable ab-initio molecular dynamics codes.
Molecular thermodynamics of nonideal fluids

CERN Document Server

Lee, Lloyd L

2013-01-01

Molecular Thermodynamics of Nonideal Fluids serves as an introductory presentation for engineers to the concepts and principles behind and the advances in molecular thermodynamics of nonideal fluids. The book covers related topics such as the laws of thermodynamics; entropy; its ensembles; the different properties of the ideal gas; and the structure of liquids. Also covered in the book are topics such as integral equation theories; theories for polar fluids; solution thermodynamics; and molecular dynamics. The text is recommended for engineers who would like to be familiarized with the concept
Molecular property diagnostic suite (MPDS): Development of disease-specific open source web portals for drug discovery.

Science.gov (United States)

Nagamani, S; Gaur, A S; Tanneeru, K; Muneeswaran, G; Madugula, S S; Consortium, Mpds; Druzhilovskiy, D; Poroikov, V V; Sastry, G N

2017-11-01

Molecular property diagnostic suite (MPDS) is a Galaxy-based open source drug discovery and development platform. MPDS web portals are designed for several diseases, such as tuberculosis, diabetes mellitus, and other metabolic disorders, specifically aimed to evaluate and estimate the drug-likeness of a given molecule. MPDS consists of three modules, namely data libraries, data processing, and data analysis tools which are configured and interconnected to assist drug discovery for specific diseases. The data library module encompasses vast information on chemical space, wherein the MPDS compound library comprises 110.31 million unique molecules generated from public domain databases. Every molecule is assigned with a unique ID and card, which provides complete information for the molecule. Some of the modules in the MPDS are specific to the diseases, while others are non-specific. Importantly, a suitably altered protocol can be effectively generated for another disease-specific MPDS web portal by modifying some of the modules. Thus, the MPDS suite of web portals shows great promise to emerge as disease-specific portals of great value, integrating chemoinformatics, bioinformatics, molecular modelling, and structure- and analogue-based drug discovery approaches.
Advances in visual representation of molecular potentials.

Science.gov (United States)

Du, Qi-Shi; Huang, Ri-Bo; Chou, Kuo-Chen

2010-06-01

The recent advances in visual representations of molecular properties in 3D space are summarized, and their applications in molecular modeling study and rational drug design are introduced. The visual representation methods provide us with detailed insights into protein-ligand interactions, and hence can play a major role in elucidating the structure or reactivity of a biomolecular system. Three newly developed computation and visualization methods for studying the physical and chemical properties of molecules are introduced, including their electrostatic potential, lipophilicity potential and excess chemical potential. The newest application examples of visual representations in structure-based rational drug are presented. The 3D electrostatic potentials, calculated using the empirical method (EM-ESP), in which the classical Coulomb equation and traditional atomic partial changes are discarded, are highly consistent with the results by the higher level quantum chemical method. The 3D lipophilicity potentials, computed by the heuristic molecular lipophilicity potential method based on the principles of quantum mechanics and statistical mechanics, are more accurate and reliable than those by using the traditional empirical methods. The 3D excess chemical potentials, derived by the reference interaction site model-hypernetted chain theory, provide a new tool for computational chemistry and molecular modeling. For structure-based drug design, the visual representations of molecular properties will play a significant role in practical applications. It is anticipated that the new advances in computational chemistry will stimulate the development of molecular modeling methods, further enriching the visual representation techniques for rational drug design, as well as other relevant fields in life science.
Density functional theory based molecular dynamics study of hydration and electronic properties of aqueous La(3+).

Science.gov (United States)

Terrier, Cyril; Vitorge, Pierre; Gaigeot, Marie-Pierre; Spezia, Riccardo; Vuilleumier, Rodolphe

2010-07-28

Structural and electronic properties of La(3+) immersed in bulk water have been assessed by means of density functional theory (DFT)-based Car-Parrinello molecular dynamics (CPMD) simulations. Correct structural properties, i.e., La(III)-water distances and La(III) coordination number, can be obtained within the framework of Car-Parrinello simulations providing that both the La pseudopotential and conditions of the dynamics (fictitious mass and time step) are carefully set up. DFT-MD explicitly treats electronic densities and is shown here to provide a theoretical justification to the necessity of including polarization when studying highly charged cations such as lanthanoids(III) with classical MD. La(3+) was found to strongly polarize the water molecules located in the first shell, giving rise to dipole moments about 0.5 D larger than those of bulk water molecules. Finally, analyzing Kohn-Sham orbitals, we found La(3+) empty 4f orbitals extremely compact and to a great extent uncoupled from the water conduction band, while the 5d empty orbitals exhibit mixing with unoccupied states of water.
Molecular characterization of dissolved organic matter from subtropical wetlands: a comparative study through the analysis of optical properties, NMR and FTICR/MS

Science.gov (United States)

Hertkorn, Norbert; Harir, Mourad; Cawley, Kaelin M.; Schmitt-Kopplin, Philippe; Jaffé, Rudolf

2016-04-01

Wetlands provide quintessential ecosystem services such as maintenance of water quality, water supply and biodiversity, among others; however, wetlands are also among the most threatened ecosystems worldwide. Natural dissolved organic matter (DOM) is an abundant and critical component in wetland biogeochemistry. This study describes the first detailed, comparative, molecular characterization of DOM in subtropical, pulsed, wetlands, namely the Everglades (USA), the Pantanal (Brazil) and the Okavango Delta (Botswana), using optical properties, high-field nuclear magnetic resonance (NMR) and ultrahigh-resolution mass spectrometry (FT-ICRMS), and compares compositional features to variations in organic matter sources and flooding characteristics (i.e., differences in hydroperiod). While optical properties showed a high degree of variability within and between the three wetlands, analogies in DOM fluorescence properties were such that an established excitation emission matrix fluorescence parallel factor analysis (EEM-PARAFAC) model for the Everglades was perfectly applicable to the other two wetlands. Area-normalized 1H NMR spectra of selected samples revealed clear distinctions of samples while a pronounced congruence within the three pairs of wetland DOM readily suggested the presence of an individual wetland-specific molecular signature. Within sample pairs (long- vs. short-hydroperiod sites), internal differences mainly referred to intensity variations (denoting variable abundance) rather than to alterations of NMR resonances positioning (denoting diversity of molecules). The relative disparity was largest between the Everglades long- and short-hydroperiod samples, whereas Pantanal and Okavango samples were more alike among themselves. Otherwise, molecular divergence was most obvious in the case of unsaturated protons (δH > 5 ppm). 2-D NMR spectroscopy for a particular sample revealed a large richness of aliphatic and unsaturated substructures, likely derived from
The Influence of Molecular Weight and Tacticity on Thermal, Morphological and Mechanical Properties of Ziegler–Natta Catalyzed Isotactic and Syndiotactic Polypropylene Blends

Directory of Open Access Journals (Sweden)

Ismael AMER

2016-09-01

Full Text Available The thermal, morphological and mechanical properties of polypropylene blends as influenced by the molecular weight and tacticity were investigated. Polypropylene sample blends (50/50 wt.% were injection moulded into standard disks for morphological and mechanical tests. The thermal properties of the polypropylene blends were measured by differential scanning calorimetry (DSC, while the morphological and mechanical properties of specimens were investigated by means of optical microscope (OM, scanning electron microscopy (SEM, microhardness (MH and dynamic mechanical analysis (DMA. DSC results of the bulk crystallization of the various isotactic polypropylene blends showed one melting peak, which indicates that cocrystallization of the blends occurred. However, the crystallization behavior of the polymer blends was strongly affected by the configuration (tacticity and molecular weight of the polypropylene polymers. In addition, the MH and DMA measurements showed that blends of two different isotactic polypropylenes presented MH and storage modulus values between the values of the respective two MH and storage modulus values of the homopolymer samples, which in turn, depended on the type and degree of the crystallinity of the blends. However, the presence of syndiotactic polypropylene in a blend with isotactic polypropylene leads to a decrease in the MH value of the isotactic polypropylene samples. Normal 0 19 false false false LT X-NONE X-NONE
Chiroptical Molecular Switches 1; Principles and Syntheses.

NARCIS (Netherlands)

Lange, Ben de; Jager, Wolter F.; Feringa, Bernard

1992-01-01

The concept and the synthesis of the basic molecules for a chiroptical molecular switch are described. This molecular switch is based on photochemical interconversion of two bistable forms of chiral sterically overcrowded olefins. A large variety of these alkenes with different properties have been
Biological and molecular properties of yellow venom of the Amazonian coral snake Micrurus surinamensis.

Science.gov (United States)

Oliveira, Fabiana da Rocha; Noronha, Maria das Dores Nogueira; Lozano, Jorge Luis Lopez

2017-01-01

The coral snake Micrurus surinamensis, which is widely distributed throughout Amazonia, has a neurotoxic venom. It is important to characterize the biological and molecular properties of this venom in order to develop effective antitoxins. Toxins from the venom of M. surinamensis were analyzed by two-dimensional polyacrylamide gel electrophoresis and their neurotoxic effects in vivo were evaluated. Most proteins in the venom had masses < 14kDa, low phospholipase A2 activity, and no proteolytic activity. The toxins inhibited the coagulation cascade. The venom had neurotoxic effects in mice, with a median lethal dose upon intravenous administration of 700 µg/kg. Immunogenic studies revealed abundant cross-reactivity of antielapidic serum with 14kDa toxins and limited cross-reactivity with toxins < 10kDa. These results indicate that antielapidic serum against M. surinamensis venom has weak potency (0.35mg/ml) in mice.
The role of molecular architecture and layer composition on the properties and performance of CuPc-C6 photovoltaic devices

International Nuclear Information System (INIS)

Schultes, S.M.; Sullivan, P.; Heutz, S.; Sanderson, B.M.; Jones, T.S.

2005-01-01

We have studied the effects of molecular architecture, co-deposition and annealing on the properties and performance of photovoltaic cells based on copper phthalocyanine (CuPc)-fullerene (C 6 ) heterojunctions. Significant improvements in performance are achieved when mixed CuPc:C 6 layers are incorporated into the device structure due to the creation of an intermolecularly mixed donor (D)-acceptor (A) blend that favours efficient exciton dissociation. We utilise the control afforded by organic molecular beam deposition to show that the mixed-layer composition plays an important role in determining device performance and correlate device efficiency to the morphological and spectroscopic properties of the organic layers. A maximum power conversion efficiency of η p = 1.17% is achieved for devices containing a mixed layer of ratio 75:25 CuPc:C 6 surrounded by thin continuous layers of pure organic material at the electrode interfaces. A structure containing a compositional gradient where the CuPc:C 6 composition is varied from purely D to purely A via three mixed layers of increasing A composition leads to a further improvements in efficiency (η p = 1.36%). Finally, we use thermal annealing to show how structural defects and morphological templating of organic thin films reduces the interfacial area for exciton separation and yields poor device performance
On the density scaling of pVT data and transport properties for molecular and ionic liquids.

Science.gov (United States)

López, Enriqueta R; Pensado, Alfonso S; Fernández, Josefa; Harris, Kenneth R

2012-06-07

In this work, a general equation of state (EOS) recently derived by Grzybowski et al. [Phys. Rev. E 83, 041505 (2011)] is applied to 51 molecular and ionic liquids in order to perform density scaling of pVT data employing the scaling exponent γ(EOS). It is found that the scaling is excellent in most cases examined. γ(EOS) values range from 6.1 for ammonia to 13.3 for the ionic liquid [C(4)C(1)im][BF(4)]. These γ(EOS) values are compared with results recently reported by us [E. R. López, A. S. Pensado, M. J. P. Comuñas, A. A. H. Pádua, J. Fernández, and K. R. Harris, J. Chem. Phys. 134, 144507 (2011)] for the scaling exponent γ obtained for several different transport properties, namely, the viscosity, self-diffusion coefficient, and electrical conductivity. For the majority of the compounds examined, γ(EOS) > γ, but for hexane, heptane, octane, cyclopentane, cyclohexane, CCl(4), dimethyl carbonate, m-xylene, and decalin, γ(EOS) liquids. For viscosities and the self-diffusion coefficient-temperature ratio, we have tested the relation linking EOS and dynamic scaling parameters, proposed by Paluch et al. [J. Phys. Chem. Lett. 1, 987-992 (2010)] and Grzybowski et al. [J. Chem. Phys. 133, 161101 (2010); Phys. Rev. E 82, 013501 (2010)], that is, γ = (γ(EOS)/φ) + γ(G), where φ is the stretching parameter of the modified Avramov relation for the density scaling of a transport property, and γ(G) is the Grüneisen constant. This relationship is based on data for structural relaxation times near the glass transition temperature for seven molecular liquids, including glass formers, and a single ionic liquid. For all the compounds examined in our much larger database the ratio (γ(EOS)/φ) is actually higher than γ, with the only exceptions of propylene carbonate and 1-methylnaphthalene. Therefore, it seems the relation proposed by Paluch et al. applies only in certain cases, and is really not generally applicable to liquid transport properties such as
Molecular modeling of the elastomeric properties of repeating units and building blocks of resilin, a disordered elastic protein.

Science.gov (United States)

Khandaker, Md Shahriar K; Dudek, Daniel M; Beers, Eric P; Dillard, David A; Bevan, David R

2016-08-01

The mechanisms responsible for the properties of disordered elastomeric proteins are not well known. To better understand the relationship between elastomeric behavior and amino acid sequence, we investigated resilin, a disordered rubber-like protein, found in specialized regions of the cuticle of insects. Resilin of Drosophila melanogaster contains Gly-rich repetitive motifs comprised of the amino acids, PSSSYGAPGGGNGGR, which confer elastic properties to resilin. The repetitive motifs of insect resilin can be divided into smaller partially conserved building blocks: PSS, SYGAP, GGGN and GGR. Using molecular dynamics (MD) simulations, we studied the relative roles of SYGAP, and its less common variants SYSAP and TYGAP, on the elastomeric properties of resilin. Results showed that SYGAP adopts a bent structure that is one-half to one-third the end-to-end length of the other motifs having an equal number of amino acids but containing SYSAP or TYGAP substituted for SYGAP. The bent structure of SYGAP forms due to conformational freedom of glycine, and hydrogen bonding within the motif apparently plays a role in maintaining this conformation. These structural features of SYGAP result in higher extensibility compared to other motifs, which may contribute to elastic properties at the macroscopic level. Overall, the results are consistent with a role for the SYGAP building block in the elastomeric properties of these disordered proteins. What we learned from simulating the repetitive motifs of resilin may be applicable to the biology and mechanics of other elastomeric biomaterials, and may provide us the deeper understanding of their unique properties. Copyright © 2016 Elsevier Ltd. All rights reserved.
Design of Molecular Materials: Supramolecular Engineering

Science.gov (United States)

Simon, Jacques; Bassoul, Pierre

2001-02-01

This timely and fascinating book is destined to be recognised as THE book on supramolecular engineering protocols. It covers this sometimes difficult subject in an approachable form, gathering together information from many sources. Supramolecular chemistry, which links organic chemistry to materials science, is one of the fastest growth areas of chemistry research. This book creates a correlation between the structure of single molecules and the physical and chemical properties of the resulting materials. By making systematic changes to the component molecules, the resulting solid can be engineered for optimum performance. There is a clearly written development from synthesis of designer molecules to properties of solids and further on to devices and complex materials systems, providing guidelines for mastering the organisation of these systems. Topics covered include: Systemic chemistry Molecular assemblies Notions of symmetry Supramolecular engineering Principe de Curie Organisation in molecular media Molecular semiconductors Industrial applications of molecular materials This superb book will be invaluable to researchers in the field of supramolecular materials and also to students and teachers of the subject.
Molecular studies by electron spectroscopy

International Nuclear Information System (INIS)

Hansteen, J.M.

1977-01-01

Experience gained in experimental nuclear physics has played a large role in the development of electron spectroscopy as a powerful tool for studying chemical systems. The use of ESCA (Electron Spectroscopy for Chemical Analysis) for the mapping of molecular properties connected with inner as well as outer electron shells is reviewed, mainly from a phenomological point of view. Molecular Auger electron spectroscopy is described as a means of gaining information on details in molecular structure, simultaneously being extensively applied for surface studies. Future highly promising research areas for molecular electron spectroscopy are suggested to be (e,2e) processes as well as continued exploitation of synchrotron radiation from high energy nuclear devices. (Auth.)
A Molecular Dynamics Study of the Structural and Dynamical Properties of Putative Arsenic Substituted Lipid Bilayers

Directory of Open Access Journals (Sweden)

Ratna Juwita

2013-04-01

Full Text Available Cell membranes are composed mainly of phospholipids which are in turn, composed of five major chemical elements: carbon, hydrogen, nitrogen, oxygen, and phosphorus. Recent studies have suggested the possibility of sustaining life if the phosphorus is substituted by arsenic. Although this issue is still controversial, it is of interest to investigate the properties of arsenated-lipid bilayers to evaluate this possibility. In this study, we simulated arsenated-lipid, 1-palmitoyl-2-oleoyl-sn-glycero-3-arsenocholine (POAC, lipid bilayers using all-atom molecular dynamics to understand basic structural and dynamical properties, in particular, the differences from analogous 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, (POPC lipid bilayers. Our simulations showed that POAC lipid bilayers have distinct structural and dynamical properties from those of native POPC lipid bilayers. Relative to POPC lipid bilayers, POAC lipid bilayers have a more compact structure with smaller lateral areas and greater order. The compact structure of POAC lipid bilayers is due to the fact that more inter-lipid salt bridges are formed with arsenate-choline compared to the phosphate-choline of POPC lipid bilayers. These inter-lipid salt bridges bind POAC lipids together and also slow down the head group rotation and lateral diffusion of POAC lipids. Thus, it would be anticipated that POAC and POPC lipid bilayers would have different biological implications.
Molecular electronic junction transport

DEFF Research Database (Denmark)

Solomon, Gemma C.; Herrmann, Carmen; Ratner, Mark

2012-01-01

Whenasinglemolecule,oracollectionofmolecules,isplacedbetween two electrodes and voltage is applied, one has a molecular transport junction. We discuss such junctions, their properties, their description, and some of their applications. The discussion is qualitative rather than quantitative, and f...
The effect of point mutations on structure and mechanical properties of collagen-like fibril: A molecular dynamics study

International Nuclear Information System (INIS)

Marlowe, Ashley E.; Singh, Abhishek; Yingling, Yaroslava G.

2012-01-01

Understanding sequence dependent mechanical and structural properties of collagen fibrils is important for the development of artificial biomaterials for medical and nanotechnological applications. Moreover, point mutations are behind many collagen associated diseases, including Osteogenesis Imperfecta (OI). We conducted a combination of classical and steered atomistic molecular dynamics simulations to examine the effect of point mutations on structure and mechanical properties of short collagen fibrils which include mutations of glycine to alanine, aspartic acid, cysteine, and serine or mutations of hydroxyproline to arginine, asparagine, glutamine, and lysine. We found that all mutations disrupt structure and reduce strength of the collagen fibrils, which may affect the hierarchical packing of the fibrils. The glycine mutations were more detrimental to mechanical strength of the fibrils (WT > Ala > Ser > Cys > Asp) than that of hydroxyproline (WT > Arg > Gln > Asn > Lys). The clinical outcome for glycine mutations agrees well with the trend in reduction of fibril's tensile strength predicted by our simulations. Overall, our results suggest that the reduction in mechanical properties of collagen fibrils may be used to predict the clinical outcome of mutations. Highlights: ► All mutations disrupt structure and bonding pattern and reduce strength of the collagen fibrils. ► Gly based mutations are worst to mechanical integrity of fibrils than that of Hyp. ► Lys and Arg mutations most dramatically destabilize collagen fibril properties. ► Clinical outcome of mutations may be related to the reduced mechanical properties of fibrils.
Highly efficient molecular simulation methods for evaluation of thermodynamic properties of crystalline phases

Science.gov (United States)

Moustafa, Sabry Gad Al-Hak Mohammad

Molecular simulation (MS) methods (e.g. Monte Carlo (MC) and molecular dynamics (MD)) provide a reliable tool (especially at extreme conditions) to measure solid properties. However, measuring them accurately and efficiently (smallest uncertainty for a given time) using MS can be a big challenge especially with ab initio-type models. In addition, comparing with experimental results through extrapolating properties from finite size to the thermodynamic limit can be a critical obstacle. We first estimate the free energy (FE) of crystalline system of simple discontinuous potential, hard-spheres (HS), at its melting condition. Several approaches are explored to determine the most efficient route. The comparison study shows a considerable improvement in efficiency over the standard MS methods that are known for solid phases. In addition, we were able to accurately extrapolate to the thermodynamic limit using relatively small system sizes. Although the method is applied to HS model, it is readily extended to more complex hard-body potentials, such as hard tetrahedra. The harmonic approximation of the potential energy surface is usually an accurate model (especially at low temperature and large density) to describe many realistic solid phases. In addition, since the analysis is done numerically the method is relatively cheap. Here, we apply lattice dynamics (LD) techniques to get the FE of clathrate hydrates structures. Rigid-bonds model is assumed to describe water molecules; this, however, requires additional orientation degree-of-freedom in order to specify each molecule. However, we were able to efficiently avoid using those degrees of freedom through a mathematical transformation that only uses the atomic coordinates of water molecules. In addition, the proton-disorder nature of hydrate water networks adds extra complexity to the problem, especially when extrapolating to the thermodynamic limit is needed. The finite-size effects of the proton disorder contribution is
Quantum Transport Through Tunable Molecular Diodes

KAUST Repository

Obodo, Tobechukwu Joshua

2017-07-31

Employing self-interaction corrected density functional theory combined with the non-equilibrium Green\\'s function method, we study the quantum transport through molecules with different numbers of phenyl (donor) and pyrimidinyl (acceptor) rings in order to evaluate the effects of the molecular composition on the transport properties. Excellent agreement with the results of recent experiments addressing the rectification behavior of molecular junctions is obtained, which demonstrates the potential of quantum transport simulations for designing high performance junctions by tuning the molecular specifications.
Molecular simulation of the role of interlayer water on the mechanical properties of montmorillonite

International Nuclear Information System (INIS)

Carrier, Benoit; Vandamme, Matthieu; Ebrahimi, Davoud; Whittle, Andrew J.; Pellenq, Roland J.M.; Van Damme, Henri

2012-01-01

Document available in extended abstract form only. Full text of publication follows: Montmorillonite - a swelling clay - is the main component of the clay fraction of the Callovo-Oxfordian argillite, which is considered as a possible host rock for radioactive waste disposal, and of the sealing bentonite plugs of storage tunnels. Montmorillonite layers have a great ability to adsorb water, resulting in the swelling of the clay. Montmorillonite consists of water molecules and sodium or calcium cations between negatively charged layers. Both the water content of the interlayer space and the nature of the charge-balancing cations are expected to have an effect on the mechanical properties of the clay layer. Computer simulations allow to reproduce the experimental swelling isotherms of the layers and to gain a deeper understanding of the physical mechanisms of the swelling process. They show how water is organized in discrete layers and how this process depends on the type of inter-layer cation. However, the effect of the swelling on the mechanical properties of the nano-scale have not been fully investigated. The objective of this work is to compute the elastic properties of a Na + - Montmorillonite and a Ca 2+ -Montmorillonite versus relative humidity at 300 K. The results of this work is the first step to build a macroscopic state equation of unsaturated clay-based materials. We use a simulation cell containing two Montmorillonite layers and sodium or calcium counterions. The partial charges of the atoms and the interatomic interaction parameters are given by the CLAYFF force field. Grand Canonical Monte-Carlo simulations are used to compute the adsorption/desorption isotherm. Each equilibrium configuration is then strained in all directions of space. Then, we perform Molecular Dynamics and compute the stress tensor and all the components of the elasticity tensor. We present the evolution of the elastic properties of the clay layers with the relative humidity. In

Atomic and molecular science with synchrotron radiation

International Nuclear Information System (INIS)

1989-01-01

This paper discusses the following topics: electron correlation in atoms; atomic innershell excitation and decay mechanisms; timing experiments; x-ray scattering; properties of ionized species; electronic properties of actinide atoms; total photon-interaction cross sections; and molecular physics. 66 refs
Generic Mathematical Programming Formulation and Solution for Computer-Aided Molecular Design

DEFF Research Database (Denmark)

Zhang, Lei; Cignitti, Stefano; Gani, Rafiqul

2015-01-01

This short communication presents a generic mathematical programming formulation for Computer-Aided Molecular Design (CAMD). A given CAMD problem, based on target properties, is formulated as a Mixed Integer Linear/Non-Linear Program (MILP/MINLP). The mathematical programming model presented here......, which is formulated as an MILP/MINLP problem, considers first-order and second-order molecular groups for molecular structure representation and property estimation. It is shown that various CAMD problems can be formulated and solved through this model....
Molecular clouds near supernova remnants

International Nuclear Information System (INIS)

Wootten, H.A.

1978-01-01

The physical properties of molecular clouds near supernova remnants were investigated. Various properties of the structure and kinematics of these clouds are used to establish their physical association with well-known remmnants. An infrared survey of the most massive clouds revealed embedded objects, probably stars whose formation was induced by the supernova blast wave. In order to understand the relationship between these and other molecular clouds, a control group of clouds was also observed. Excitation models for dense regions of all the clouds are constructed to evaluate molecular abundances in these regions. Those clouds that have embedded stars have lower molecular abundances than the clouds that do not. A cloud near the W28 supernova remnant also has low abundances. Molecular abundances are used to measure an important parameter, the electron density, which is not directly observable. In some clouds extensive deuterium fractionation is observed which confirms electron density measurements in those clouds. Where large deuterium fractionation is observed, the ionization rate in the cloud interior can also be measured. The electron density and ionization rate in the cloud near W28 are higher than in most clouds. The molecular abundances and electron densities are functions of the chemical and dynamical state of evolution of the cloud. Those clouds with lowest abundances are probably the youngest clouds. As low-abundance clouds, some clouds near supernova remnants may have been recently swept from the local interstellar material. Supernova remnants provide sites for star formation in ambient clouds by compressing them, and they sweep new clouds from more diffuse local matter
Modeling adsorption: Investigating adsorbate and adsorbent properties

Science.gov (United States)

Webster, Charles Edwin

1999-12-01

Surface catalyzed reactions play a major role in current chemical production technology. Currently, 90% of all chemicals are produced by heterogeneously catalyzed reactions. Most of these catalyzed reactions involve adsorption, concentrating the substrate(s) (the adsorbate) on the surface of the solid (the adsorbent). Pore volumes, accessible surface areas, and the thermodynamics of adsorption are essential in the understanding of solid surface characteristics fundamental to catalyst and adsorbent screening and selection. Molecular properties such as molecular volumes and projected molecular areas are needed in order to convert moles adsorbed to surface volumes and areas. Generally, these molecular properties have been estimated from bulk properties, but many assumptions are required. As a result, different literature values are employed for these essential molecular properties. Calculated molar volumes and excluded molecular areas are determined and tabulated for a variety of molecules. Molecular dimensions of molecules are important in the understanding of molecular exclusion as well as size and shape selectivity, diffusion, and adsorbent selection. Molecular dimensions can also be used in the determination of the effective catalytic pore size of a catalyst. Adsorption isotherms, on zeolites, (crystalline mineral oxides) and amorphous solids, can be analyzed with the Multiple Equilibrium Analysis (MEA) description of adsorption. The MEA produces equilibrium constants (Ki), capacities (ni), and thermodynamic parameters (enthalpies, ΔHi, and entropies, ΔSi) of adsorption for each process. Pore volumes and accessible surface areas are calculated from the process capacities. Adsorption isotherms can also be predicted for existing and new adsorbate-adsorbent systems with the MEA. The results show that MEA has the potential of becoming a standard characterization method for microporous solids that will lead to an increased understanding of their behavior in gas
Molecular boxes on a molecular printboard: encapsulation of anionic dyes in immobilized dendrimers

NARCIS (Netherlands)

Onclin, S.; Huskens, Jurriaan; Ravoo, B.J.; Reinhoudt, David

2005-01-01

Fifth-generation poly(propylene imine) dendrimers, modified with 64 apolar adamantyl groups, have been immobilized on cyclodextrin host monolayers (molecular printboards) on glass by supramolecular microcontact printing. The immobilized dendrimers retain their guest-binding properties and function
Pathogen Inactivating Properties and Increased Sensitivity in Molecular Diagnostics by PAXgene, a Novel Non-Crosslinking Tissue Fixative.

Directory of Open Access Journals (Sweden)

Martina Loibner

Full Text Available Requirements on tissue fixatives are getting more demanding as molecular analysis becomes increasingly relevant for routine diagnostics. Buffered formaldehyde in pathology laboratories for tissue fixation is known to cause chemical modifications of biomolecules which affect molecular testing. A novel non-crosslinking tissue preservation technology, PAXgene Tissue (PAXgene, was developed to preserve the integrity of nucleic acids in a comparable way to cryopreservation and also to preserve morphological features comparable to those of formalin fixed samples.Because of the excellent preservation of biomolecules by PAXgene we investigated its pathogen inactivation ability and biosafety in comparison to formalin by in-vitro testing of bacteria, human relevant fungi and human cytomegalovirus (CMV. Guidelines for testing disinfectants served as reference for inactivation assays. Furthermore, we tested the properties of PAXgene for detection of pathogens by PCR based assays.All microorganisms tested were similarly inactivated by PAXgene and formalin except Clostridium sporogenes, which remained viable in seven out of ten assays after PAXgene treatment and in three out of ten assays after formalin fixation. The findings suggest that similar biosafety measures can be applied for PAXgene and formalin fixed samples. Detection of pathogens in PCR-based diagnostics using two CMV assays resulted in a reduction of four to ten quantification cycles of PAXgene treated samples which is a remarkable increase of sensitivity.PAXgene fixation might be superior to formalin fixation when molecular diagnostics and highly sensitive detection of pathogens is required in parallel to morphology assessment.
Pathogen Inactivating Properties and Increased Sensitivity in Molecular Diagnostics by PAXgene, a Novel Non-Crosslinking Tissue Fixative.

Science.gov (United States)

Loibner, Martina; Buzina, Walter; Viertler, Christian; Groelz, Daniel; Hausleitner, Anja; Siaulyte, Gintare; Kufferath, Iris; Kölli, Bettina; Zatloukal, Kurt

2016-01-01

Requirements on tissue fixatives are getting more demanding as molecular analysis becomes increasingly relevant for routine diagnostics. Buffered formaldehyde in pathology laboratories for tissue fixation is known to cause chemical modifications of biomolecules which affect molecular testing. A novel non-crosslinking tissue preservation technology, PAXgene Tissue (PAXgene), was developed to preserve the integrity of nucleic acids in a comparable way to cryopreservation and also to preserve morphological features comparable to those of formalin fixed samples. Because of the excellent preservation of biomolecules by PAXgene we investigated its pathogen inactivation ability and biosafety in comparison to formalin by in-vitro testing of bacteria, human relevant fungi and human cytomegalovirus (CMV). Guidelines for testing disinfectants served as reference for inactivation assays. Furthermore, we tested the properties of PAXgene for detection of pathogens by PCR based assays. All microorganisms tested were similarly inactivated by PAXgene and formalin except Clostridium sporogenes, which remained viable in seven out of ten assays after PAXgene treatment and in three out of ten assays after formalin fixation. The findings suggest that similar biosafety measures can be applied for PAXgene and formalin fixed samples. Detection of pathogens in PCR-based diagnostics using two CMV assays resulted in a reduction of four to ten quantification cycles of PAXgene treated samples which is a remarkable increase of sensitivity. PAXgene fixation might be superior to formalin fixation when molecular diagnostics and highly sensitive detection of pathogens is required in parallel to morphology assessment.
The Influence of Irradiation and Accelerated Aging on the Mechanical and Tribological Properties of the Graphene Oxide/Ultra-High-Molecular-Weight Polyethylene Nanocomposites

Directory of Open Access Journals (Sweden)

Guodong Huang

2016-01-01

Full Text Available Graphene oxide/ultra-high-molecular-weight polyethylene (GO/UHMWPE nanocomposite is a potential and promising candidate for artificial joint applications. However, after irradiation and accelerated aging, the mechanical and tribological behaviors of the nanocomposites are still unclear and require further investigation. GO/UHMWPE nanocomposites were successfully fabricated using ultrasonication dispersion, ball-milling, and hot-pressing process. Then, the nanocomposites were irradiated by gamma ray at doses of 100 kGy. Finally, GO/UHMWPE nanocomposites underwent accelerated aging at 80°C for 21 days in air. The mechanical and tribological properties of GO/UHMWPE nanocomposites have been evaluated after irradiation and accelerated aging. The results indicated that the incorporation of GO could enhance the mechanical, wear, and antiscratch properties of UHMWPE. After irradiation, these properties could be further enhanced, compared to unirradiated ones. After accelerated aging, however, these properties have been significantly reduced when compared to unirradiated ones. Moreover, GO and irradiation can synergistically enhance these properties.
Anomalies in the equilibrium and nonequilibrium properties of correlated ions in complex molecular environments

Science.gov (United States)

Mahakrishnan, Sathiya; Chakraborty, Subrata; Vijay, Amrendra

2017-11-01

Emergent statistical attributes, and therefore the equations of state, of an assembly of interacting charge carriers embedded within a complex molecular environment frequently exhibit a variety of anomalies, particularly in the high-density (equivalently, the concentration) regime, which are not well understood, because they do not fall under the low-concentration phenomenologies of Debye-Hückel-Onsager and Poisson-Nernst-Planck, including their variants. To go beyond, we here use physical concepts and mathematical tools from quantum scattering theory, transport theory with the Stosszahlansatz of Boltzmann, and classical electrodynamics (Lorentz gauge) and obtain analytical expressions both for the average and the frequency-wave vector-dependent longitudinal and transverse current densities, diffusion coefficient, and the charge density, and therefore the analytical expressions for (a) the chemical potential, activity coefficient, and the equivalent conductivity for strong electrolytes and (b) the current-voltage characteristics for ion-transport processes in complex molecular environments. Using a method analogous to the notion of Debye length and thence the electrical double layer, we here identify a pair of characteristic length scales (longitudinal and the transverse), which, being wave vector and frequency dependent, manifestly exhibit nontrivial fluctuations in space-time. As a unifying theme, we advance a quantity (inverse length dimension), gscat(a ), which embodies all dynamical interactions, through various quantum scattering lengths, relevant to molecular species a, and the analytical behavior which helps us to rationalize the properties of strong electrolytes, including anomalies, in all concentration regimes. As an example, the behavior of gscat(a ) in the high-concentration regime explains the anomalous increase of the Debye length with concentration, as seen in a recent experiment on electrolyte solutions. We also put forth an extension of the
Luminescent properties of fluorophosphate glasses with lead chalcogenides molecular clusters

International Nuclear Information System (INIS)

Kolobkova, E.V.; Kukushkin, D.S.; Nikonorov, N.V.; Shakhverdov, T.A.; Sidorov, A.I.; Vasiliev, V.N.

2015-01-01

Fluorophosphate glasses containing lead, selenium, and sulfur exhibit an intense luminescence in the 400–620 nm spectral region when excited by the 240–420 nm radiation. This luminescence is due to the presence of (PbSe) n and/or (PbS) n molecular clusters in the glasses, which appear in the as-prepared glasses before quantum dots formation. The thermal treatment at temperatures less than the glass transition temperature results in the red-shift of the luminescence bands and in an increase in the luminescence intensity. Heating the thermally treated glass samples leads to the reversible thermal quenching of the luminescence. - Highlights: • Fluorophosphate glasses with Pb, Se, and S ions contain (PbSe) n or (PbS) n molecular clusters. • (PbSe) n and (PbS) n molecular clusters possess luminescence in the visible with UV excitation. • Heating the glass leads to the reversible thermal quenching of the luminescence
Molecular Design of Bioinspired Nanostructures for Biomedical Applications: Synthesis, Self-Assembly and Functional Properties

Science.gov (United States)

Xu, Hesheng Victor; Zheng, Xin Ting; Mok, Beverly Yin Leng; Ibrahim, Salwa Ali; Yu, Yong; Tan, Yen Nee

2016-08-01

Biomolecules are the nanoscale building blocks of cells, which play multifaceted roles in the critical biological processes such as biomineralization in a living organism. In these processes, the biological molecules such as protein and nucleic acids use their exclusive biorecognition properties enabled from their unique chemical composition, shape and function to initiate a cascade of cellular events. The exceptional features of these biomolecules, coupled with the recent advancement in nanotechnology, have led to the emergence of a new research field that focuses on the molecular design of bioinspired nanostructures that inherit the extraordinary function of natural biomaterials. These “bioinspired” nanostructures could be formulated by biomimetic approaches through either self-assembling of biomolecules or acting as a biomolecular template/precursor to direct the synthesis of nanocomposite. In either situation, the resulting nanomaterials exhibit phenomenal biocompatibility, superb aqueous solubility and excellent colloidal stability, branding them exceptionally desirable for both in vitro and in vivo biomedical applications. In this review, we will present the recent developments in the preparation of “bioinspired” nanostructures through biomimetic self-assembly and biotemplating synthesis, as well as highlight their functional properties and potential applications in biomedical diagnostics and therapeutic delivery. Lastly, we will conclude this topic with some personal perspective on the challenges and future outlooks of the “bioinspired” nanostructures for nanomedicine.
CONSTRAINING DUST AND MOLECULAR GAS PROPERTIES IN Ly{alpha} BLOBS AT z {approx} 3

Energy Technology Data Exchange (ETDEWEB)

Yang Yujin; Decarli, Roberto; Walter, Fabian; Leipski, Christian [Max-Planck-Institut fuer Astronomie, Koenigstuhl 17, Heidelberg (Germany); Dannerbauer, Helmut; Le Floc' h, Emeric [Laboratoire AIM, CEA/DSM-CNRS-Universite Paris Diderot, Irfu/Service d' Astrophysique, CEA-Saclay, Orme des Merisiers, 91191 Gif-sur-Yvette Cedex (France); Weiss, Axel; Menten, Karl M. [Max-Planck-Insitut fuer Radioastronomie, Auf dem Huegel 69, D-53121 Bonn (Germany); Dey, Arjun [National Optical Astronomy Observatory, 950 North Cherry Avenue, Tucson, AZ 85719 (United States); Chapman, Scott C. [Institute of Astronomy, University of Cambridge, Madingley Road, Cambridge CB3 0HA (United Kingdom); Prescott, Moire K. M. [Department of Physics, Broida Hall, Mail Code 9530, University of California, Santa Barbara, CA 93106 (United States); Neri, Roberto [IRAM-Institut de Radio Astronomie Millimetrique, 300 rue de la Piscine, 38406 Saint-Martin d' Heres (France); Borys, Colin [IPAC, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125 (United States); Matsuda, Yuichi [Department of Physics, Durham University, South Road, Durham DH1 3LE (United Kingdom); Yamada, Toru [Astronomical Institute, Tohoku University, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578 (Japan); Hayashino, Tomoki [Research Center for Neutrino Science, Graduate School of Science, Tohoku University, Sendai 980-8578 (Japan); Tapken, Christian [Leibnitz-Institut fuer Astrophysik Potsdam (AIP), An der Sternwarte 16, 14482 Potsdam (Germany)

2012-01-10

In order to constrain the bolometric luminosities, dust properties, and molecular gas content of giant Ly{alpha} nebulae, the so-called Ly{alpha} blobs, we have carried out a study of dust continuum and CO line emission in two well-studied representatives of this population at z {approx} 3: an Ly{alpha} blob discovered by its strong Spitzer Multiband Infrared Photometer 24 {mu}m detection (LABd05) and the Steidel blob 1 (SSA22-LAB01). We find that the spectral energy distribution of LABd05 is well described by an active-galactic-nucleus-starburst composite template with L{sub FIR} = (4.0 {+-} 0.5) Multiplication-Sign 10{sup 12} L{sub Sun }, comparable to high-z submillimeter galaxies and ultraluminous infrared galaxies. New Large APEX Bolometer Camera 870 {mu}m measurements rule out the reported Submillimeter Common-User Bolometer Array detection of the SSA22-LAB01 (S{sub 850{mu}m} = 16.8 mJy) at the >4{sigma} level. Consistent with this, ultradeep Plateau de Bure Interferometer observations with {approx}2'' spatial resolution also fail to detect any 1.2 mm continuum source down to Almost-Equal-To 0.45 mJy beam{sup -1} (3{sigma}). Combined with the existing (sub)millimeter observations in the literature, we conclude that the FIR luminosity of SSA22-LAB01 remains uncertain. No CO line is detected in either case down to integrated flux limits of S{sub {nu}}{Delta}V {approx}< 0.25-1.0 Jy km s{sup -1}, indicating a modest molecular gas reservoir, M(H{sub 2}) < (1-3) Multiplication-Sign 10{sup 10} M{sub Sun }. The non-detections exclude, with high significance (12{sigma}), the previous tentative detection of a CO J = 4-3 line in the SSA22-LAB01. The increased sensitivity afforded by the Atacama Large Millimeter/submillimeter Array will be critical in studying molecular gas and dust in these interesting systems.
Dynamics and Thermodynamics of Molecular Machines

DEFF Research Database (Denmark)

Golubeva, Natalia

2014-01-01

to their microscopic size, molecular motors are governed by principles fundamentally different from those describing the operation of man-made motors such as car engines. In this dissertation the dynamic and thermodynamic properties of molecular machines are studied using the tools of nonequilibrium statistical......Molecular machines, or molecular motors, are small biophysical devices that perform a variety of essential metabolic processes such as DNA replication, protein synthesis and intracellular transport. Typically, these machines operate by converting chemical energy into motion and mechanical work. Due...... mechanics. The first part focuses on noninteracting molecular machines described by a paradigmatic continuum model with the aim of comparing and contrasting such a description to the one offered by the widely used discrete models. Many molecular motors, for example, kinesin involved in cellular cargo...
Design strategies for organic semiconductors beyond the molecular formula.

Science.gov (United States)

Henson, Zachary B; Müllen, Klaus; Bazan, Guillermo C

2012-09-01

Organic semiconducting materials based on polymers and molecular systems containing an electronically delocalized structure are the basis of emerging optoelectronic technologies such as plastic solar cells and flexible transistors. For isolated molecules, guidelines exist that rely on the molecular formula to tailor the frontier (highest occupied or lowest unoccupied) molecular orbital energy levels and optical absorption profiles. Much less control can be achieved over relevant properties, however, as one makes the transition to the ensemble behaviour characteristic of the solid state. Polymeric materials are also challenging owing to the statistical description of the average number of repeat units. Here we draw attention to the limitations of molecular formulae as predictive tools for achieving properties relevant to device performances. Illustrative examples highlight the relevance of organization across multiple length scales, and how device performances--although relevant for practical applications--poorly reflect the success of molecular design.
Hydrogen production over Au-loaded mesoporous-assembled SrTiO3 nanocrystal photocatalyst: Effects of molecular structure and chemical properties of hole scavengers

International Nuclear Information System (INIS)

Puangpetch, Tarawipa; Chavadej, Sumaeth; Sreethawong, Thammanoon

2011-01-01

Graphical abstract: Formic acid, which is the smallest and completely-dissociated water-soluble carboxylic acid, exhibited the highest hydrogen production enhancement ability over the 1 wt.% Au-loaded mesoporous-assembled SrTiO 3 nanocrystal photocatalyst. Display Omitted Research highlights: → The 1 wt.% Au-loaded mesoporous-assembled SrTiO 3 nanocrystal photocatalyst was synthesized. → The molecular structure and chemical properties of hole scavengers affected H 2 production rate. → Formic acid exhibited the highest photocatalytic H 2 production enhancement ability. -- Abstract: The hydrogen production via the photocatalytic water splitting under UV irradiation using different compounds as hole scavengers (including methanol, formic acid, acetic acid, propanoic acid, hydrochloric acid, and sulfuric acid) under a low concentration range ( 3 nanocrystal photocatalyst. The results indicated that the hydrogen production efficiency greatly depended on the molecular structure, chemical properties, and concentration of the hole scavengers. Formic acid, which is the smallest and completely-dissociated water-soluble carboxylic acid, exhibited the highest hydrogen production enhancement ability. The 2.5 vol.% aqueous formic acid solution system provided the highest photocatalytic hydrogen production rate.
Properties of molecular clouds containing Herbig-Haro objects

International Nuclear Information System (INIS)

Loren, R.B.; Evans, N.J. II; Knapp, G.R.

1979-01-01

We have studied the physical conditions in the molecular clouds associated with a large number of Herbig-Haro and related objects. Formaldehyde emission at 2 mm was detected in the direction of approx.15 out of 30 objects observed. Using the 2 mm H 2 CO emission and observations of 2 cm H 2 CO absorption, along the the 2.6 mm CO line, we calculate core densities of these molecular clouds. Dense cores are found near but not necessarily coincident with the HH objects. Known embedded infrared sources are more likely to be at the position of greatest density than are the HH objects themselves. The densities determined for the cloud cores are intermediate between the densities of cold, dark clouds such as L134 N and the hot clouds associated with H II regions. Thus, a continuous spectrum of densities is observed in molecular clouds. The temperature and density of the clouds in this study are not well correlated. The cores associated with HH 29 IR and T Tau are very dense (6 x 10 4 and 9 x 10 4 cm -3 ), yet have temperatures typical of cold dark clouds.The strong inverse correlation between X (H 2 CO) and density found by Wootten et al. is also found in the clouds associated with HH objects. This correlation also holds within a single cloud, indicating that the correlation is not due to differences in cloud age and evolution toward gas-phase chemical equilibrium. The decrease of X (H 2 CO) with density is more rapid than predicted by steady state ion-molecule chemistry and may be the result of increased depletion of molecules onto grain surfaces at higher density
Effects of the molecular level dispersion of graphene oxide on the free volume characteristics of poly(vinyl alcohol) and its impact on the thermal and mechanical properties of their nanocomposites.

Science.gov (United States)

Sharma, S K; Prakash, J; Pujari, P K

2015-11-21

Poly(vinyl alcohol), PVA, reinforced with carbon nanofillers has shown drastic variations in thermal as well as mechanical properties. In order to establish structure-property correlations, these variations have been correlated with modifications in the hydrogen bonding structure as well as the crystallinity of the PVA matrix without paying much attention to molecular packing in the amorphous region of this semicrystalline polymer. In order to investigate the molecular packing in PVA-graphene oxide (GO) nanocomposites, free volume characterization of PVA-GO nanocomposites has been carried out using ortho-positronium (o-Ps) probe. The variations in free volume size, density and size distribution have been determined through o-Ps lifetime and the corresponding intensity as well as its lifetime distribution. The variation in hydrogen bonding and its effect on crystallinity has been determined by Fourier Transform Infra Red (FTIR) and X-ray diffraction (XRD) measurements. The variation in the thermal (glass transition temperature) and mechanical (Young's modulus, tensile strength and percentage strain at break) properties of the nanocomposites is explained in view of the free volume structure and crystallinity of the PVA matrix which are severely modified due to the molecular-level dispersion of GO sheets in the PVA matrix.
Effects of system size and cooling rate on the structure and properties of sodium borosilicate glasses from molecular dynamics simulations.

Science.gov (United States)

Deng, Lu; Du, Jincheng

2018-01-14

Borosilicate glasses form an important glass forming system in both glass science and technologies. The structure and property changes of borosilicate glasses as a function of thermal history in terms of cooling rate during glass formation and simulation system sizes used in classical molecular dynamics (MD) simulation were investigated with recently developed composition dependent partial charge potentials. Short and medium range structural features such as boron coordination, Si and B Q n distributions, and ring size distributions were analyzed to elucidate the effects of cooling rate and simulation system size on these structure features and selected glass properties such as glass transition temperature, vibration density of states, and mechanical properties. Neutron structure factors, neutron broadened pair distribution functions, and vibrational density of states were calculated and compared with results from experiments as well as ab initio calculations to validate the structure models. The results clearly indicate that both cooling rate and system size play an important role on the structures of these glasses, mainly by affecting the 3 B and 4 B distributions and consequently properties of the glasses. It was also found that different structure features and properties converge at different sizes or cooling rates; thus convergence tests are needed in simulations of the borosilicate glasses depending on the targeted properties. The results also shed light on the complex thermal history dependence on structure and properties in borosilicate glasses and the protocols in MD simulations of these and other glass materials.
Effects of system size and cooling rate on the structure and properties of sodium borosilicate glasses from molecular dynamics simulations

Science.gov (United States)

Deng, Lu; Du, Jincheng

2018-01-01

Borosilicate glasses form an important glass forming system in both glass science and technologies. The structure and property changes of borosilicate glasses as a function of thermal history in terms of cooling rate during glass formation and simulation system sizes used in classical molecular dynamics (MD) simulation were investigated with recently developed composition dependent partial charge potentials. Short and medium range structural features such as boron coordination, Si and B Qn distributions, and ring size distributions were analyzed to elucidate the effects of cooling rate and simulation system size on these structure features and selected glass properties such as glass transition temperature, vibration density of states, and mechanical properties. Neutron structure factors, neutron broadened pair distribution functions, and vibrational density of states were calculated and compared with results from experiments as well as ab initio calculations to validate the structure models. The results clearly indicate that both cooling rate and system size play an important role on the structures of these glasses, mainly by affecting the 3B and 4B distributions and consequently properties of the glasses. It was also found that different structure features and properties converge at different sizes or cooling rates; thus convergence tests are needed in simulations of the borosilicate glasses depending on the targeted properties. The results also shed light on the complex thermal history dependence on structure and properties in borosilicate glasses and the protocols in MD simulations of these and other glass materials.
Defined-size DNA triple crossover construct for molecular electronics: modification, positioning and conductance properties.

Science.gov (United States)

Linko, Veikko; Leppiniemi, Jenni; Paasonen, Seppo-Tapio; Hytönen, Vesa P; Toppari, J Jussi

2011-07-08

We present a novel, defined-size, small and rigid DNA template, a so-called B-A-B complex, based on DNA triple crossover motifs (TX tiles), which can be utilized in molecular scale patterning for nanoelectronics, plasmonics and sensing applications. The feasibility of the designed construct is demonstrated by functionalizing the TX tiles with one biotin-triethylene glycol (TEG) and efficiently decorating them with streptavidin, and furthermore by positioning and anchoring single thiol-modified B-A-B complexes to certain locations on a chip via dielectrophoretic trapping. Finally, we characterize the conductance properties of the non-functionalized construct, first by measuring DC conductivity and second by utilizing AC impedance spectroscopy in order to describe the conductivity mechanism of a single B-A-B complex using a detailed equivalent circuit model. This analysis also reveals further information about the conductivity of DNA structures in general.

Spin-Orbit Effect on the Molecular Properties of TeXn (X = F, Cl, Br, and I; n = 1, 2, and 4): A Density Functional Theory and Ab Initio Study.

Science.gov (United States)

Moon, Jiwon; Kim, Joonghan

2016-09-29

Density functional theory (DFT) and ab initio calculations, including spin-orbit coupling (SOC), were performed to investigate the spin-orbit (SO) effect on the molecular properties of tellurium halides, TeXn (X = F, Cl, Br, and I; n = 1, 2, and 4). SOC elongates the Te-X bond and slightly reduces the vibrational frequencies. Consideration of SOC leads to better agreement with experimental values. Møller-Plesset second-order perturbation theory (MP2) seriously underestimates the Te-X bond lengths. In contrast, B3LYP significantly overestimates them. SO-PBE0 and multireference configuration interactions with the Davidson correction (MRCI+Q), which include SOC via a state-interaction approach, give the Te-I bond length of TeI2 that matches the experimental value. On the basis of the calculated thermochemical energy and optimized molecular structure, TeI4 is unlikely to be stable. The use of PBE0 including SOC is strongly recommended for predicting the molecular properties of Te-containing compounds.
Polymer Molecular Weight Analysis by [Superscript 1]H NMR Spectroscopy

Science.gov (United States)

Izunobi, Josephat U.; Higginbotham, Clement L.

2011-01-01

The measurement and analysis of molecular weight and molecular weight distribution remain matters of fundamental importance for the characterization and physical properties of polymers. Gel permeation chromatography (GPC) is the most routinely used method for the molecular weight determination of polymers whereas matrix-assisted laser…
Molecular ferroelectrics: where electronics meet biology.

Science.gov (United States)

Li, Jiangyu; Liu, Yuanming; Zhang, Yanhang; Cai, Hong-Ling; Xiong, Ren-Gen

2013-12-28

In the last several years, we have witnessed significant advances in molecular ferroelectrics, with the ferroelectric properties of molecular crystals approaching those of barium titanate. In addition, ferroelectricity has been observed in biological systems, filling an important missing link in bioelectric phenomena. In this perspective, we will present short historical notes on ferroelectrics, followed by an overview of the fundamentals of ferroelectricity. The latest developments in molecular ferroelectrics and biological ferroelectricity will then be highlighted, and their implications and potential applications will be discussed. We close by noting molecular ferroelectric as an exciting frontier between electronics and biology, and a number of challenges ahead are also described.
Temperature and Pressure Dependences of the Elastic Properties of Tantalum Single Crystals Under Tensile Loading: A Molecular Dynamics Study

Science.gov (United States)

Li, Wei-bing; Li, Kang; Fan, Kan-qi; Zhang, Da-xing; Wang, Wei-dong

2018-04-01

Atomistic simulations are capable of providing insights into physical mechanisms responsible for mechanical properties of the transition metal of Tantalum (Ta). By using molecular dynamics (MD) method, temperature and pressure dependences of the elastic properties of Ta single crystals are investigated through tensile loading. First of all, a comparative study between two types of embedded-atom method (EAM) potentials is made in term of the elastic properties of Ta single crystals. The results show that Ravelo-EAM (Physical Review B, 2013, 88: 134101) potential behaves well at different hydrostatic pressures. Then, the MD simulation results based on the Ravelo-EAM potential show that Ta will experience a body-centered-cubic (BCC) to face-centered-cubic (FCC) phase transition before fracture under tensile loading at 1 K temperature, and model size and strain rate have no obvious effects on tensile behaviors of Ta. Next, from the simulation results at the system temperature from 1 to 1500 K, it can be derived that the elastic modulus of E 100 linearly decrease with the increasing temperature, while the yielding stress decrease with conforming a quadratic polynomial formula. Finally, the pressure dependence of the elastic properties is performed from 0 to 140 GPa and the observations show that the elastic modulus increases with the increasing pressure overall.
Molecular dynamics study of dynamic and structural properties of supercooled liquid and glassy iron in the rapid-cooling processes

Energy Technology Data Exchange (ETDEWEB)

Cao, Qi-Long; Huang, Duo-Hui; Yang, Jun-Sheng; Wan, Min-Jie; Wang, Fan-Hou, E-mail: eatonch@gmail.com

2014-10-01

Molecular dynamics simulations were applied to study the dynamic and structural properties of supercooled liquid and glassy iron in the rapid-cooling processes. The mean-square displacement and the non-Gaussian parameter were used to describe the dynamic properties. The evolution of structural properties was investigated using the pair distribution functions and bond-angle distribution functions. Results for dynamic and structural relaxations indicate that the dynamic features are consistently correlated with the structure evolution, and there are three temperature regions as the temperature decreases: (1) at higher temperatures (1500 K, 1300 K, and 1100 K), the system remains in the liquid characteristics during the overall relaxation process. (2) At medial temperatures (1050 K, 900 K, and 700 K), a fast β-relaxation is followed by a much slower α-relaxation. There is a little change in the structural properties in the β-relaxation region, while major configuration rearrangements occurred in the α-relaxation range and the crystallization process was completed at the end of α-relaxation region. (3) At lower temperature (500 K), the system shows glassy characteristics during the overall relaxation process. In addition, the melting temperature, glass transition temperature and diffusion coefficients of supercooled liquid iron are also computed.
Theoretical studies on molecular and explosive properties of 4,4',5,5'-Tetranitro-2,2'-bi-1H-imidazole (TNBI)

Energy Technology Data Exchange (ETDEWEB)

Cho, Soo Gyeong; Goh, Eun Mee; Cho, Jin Rai; Kim, Jeong Kook [High Explosives Team, Agency for Defense Development, P. O. Box 35-5, Yuseong, Daejeon, 305-600 (Korea)

2006-02-15

We performed theoretical studies to predict the molecular structure, molecular properties, and explosive performance of 4,4',5,5'-tetranitro-2,2'-bi-1H-imidazole (TNBI). High levels of ab initio and density functional theories were employed to predict the molecular structure of TNBI. Predicted TNBI structure was in good agreement with that observed by X-ray crystallography. Heat of formation in the solid phase at 298 K was predicted to be 270.3 kJ/mol. Density of TNBI was predicted to be 1.919-1.956 g/cm{sup 3} depending upon the parameter sets of group additivity method. By using these values as input data, we estimated detonation velocity and C-J pressure to be 8.69-8.80 km/s and 34.5-36.1 GPa, respectively. Impact sensitivity of TNBI was predicted to be 33 cm. (Abstract Copyright [2006], Wiley Periodicals, Inc.)
Molecular structure, photoluminescent and electroluminescent properties of bis(2-(4-methyl-2-hydroxyphenyl)benzothiazolate) zinc with excellent electron-transport characteristics

International Nuclear Information System (INIS)

Xu Huixia; Xu Bingshe; Fang Xiaohong; Yue Yan; Chen Liuqing; Wang Hua; Hao Yuying

2011-01-01

Highlights: → The synthesis, crystal structure and photophysical properties of Zn(4-MeBTZ) 2 were reported. → The electron-transport property was investigated by theoretical calculations and experimental. → We found that Zn(4-MeBTZ) 2 has a higher electron mobility than that of [Zn(BTZ) 2 ] 2 and the devices based on it have a lower turn-on voltage. - Abstract: In this article, the molecular structure, photoluminescent and electroluminescent properties of bis(2-(4-methyl-2-hydroxyphenyl) benzothiazolate) zinc (Zn(4-MeBTZ) 2 ) with good electron-transport characteristics were reported. This complex was identified as triclinic structure with the strong intermolecular π-π stacking interactions between the benzothiazolate/phenoxido rings and weak intramolecular hydrogen bonds by X-ray single-crystal diffraction. Quantum chemical method has been employed to investigate electron structure and charge transport property. The blue-green light emission was observed by fabricating double-layer devices using Zn(4-MeBTZ) 2 as electron-transport and NPB as hole-transport material. The performance of organic light-emitting devices based on Zn(4-MeBTZ) 2 is much better than that of the devices based on [Zn(BTZ) 2 ] 2 .
Synthesis, X-ray crystallography characterization, vibrational spectroscopic, molecular electrostatic potential maps, thermodynamic properties studies of N,N'-di(p-thiazole)formamidine.

Science.gov (United States)

Rofouei, M K; Fereyduni, E; Sohrabi, N; Shamsipur, M; Attar Gharamaleki, J; Sundaraganesan, N

2011-01-01

In this work, we will report a combined experimental and theoretical study on molecular and vibrational structure of N,N'-di(p-thiazole)formamidine (DpTF). DpTF has been synthesized and characterized by elemental analysis, FT-IR, FT-Raman, 1H NMR, 13C NMR spectroscopy and X-ray single crystal diffraction. The FT-IR and FT-Raman spectra of DpTF were recorded in the solid phase. The optimized geometry was calculated by HF and B3LYP methods using 6-31G(d) basis set. The FT-IR and FT-Raman spectra of DpTF was calculated at the HF/B3LYP/6-31G(d) level and were interpreted in terms of potential energy distribution (PED) analysis. The scaled theoretical wavenumber showed very good agreement with the experimental values. A detailed interpretation of the infrared and Raman spectra of DpTF was reported. On the basis of vibrational analyses, the thermodynamic properties of the title compound at different temperatures have been calculated, revealing the correlations between Cp,m°, Sm°, Hm° and temperatures. Furthermore, molecular electrostatic potential maps (MESP) and total dipole moment properties of the compound have been calculated. Copyright © 2010 Elsevier B.V. All rights reserved.
Statistical properties of antisymmetrized molecular dynamics for non-nucleon-emission and nucleon-emission processes

International Nuclear Information System (INIS)

Ono, A.; Horiuchi, H.

1996-01-01

Statistical properties of antisymmetrized molecular dynamics (AMD) are classical in the case of nucleon-emission processes, while they are quantum mechanical for the processes without nucleon emission. In order to understand this situation, we first clarify that there coexist mutually opposite two statistics in the AMD framework: One is the classical statistics of the motion of wave packet centroids and the other is the quantum statistics of the motion of wave packets which is described by the AMD wave function. We prove the classical statistics of wave packet centroids by using the framework of the microcanonical ensemble of the nuclear system with a realistic effective two-nucleon interaction. We show that the relation between the classical statistics of wave packet centroids and the quantum statistics of wave packets can be obtained by taking into account the effects of the wave packet spread. This relation clarifies how the quantum statistics of wave packets emerges from the classical statistics of wave packet centroids. It is emphasized that the temperature of the classical statistics of wave packet centroids is different from the temperature of the quantum statistics of wave packets. We then explain that the statistical properties of AMD for nucleon-emission processes are classical because nucleon-emission processes in AMD are described by the motion of wave packet centroids. We further show that when we improve the description of the nucleon-emission process so as to take into account the momentum fluctuation due to the wave packet spread, the AMD statistical properties for nucleon-emission processes change drastically into quantum statistics. Our study of nucleon-emission processes can be conversely regarded as giving another kind of proof of the fact that the statistics of wave packets is quantum mechanical while that of wave packet centroids is classical. copyright 1996 The American Physical Society
Hybrid nanomembrane-based capacitors for the determination of the dielectric constant of semiconducting molecular ensembles

Science.gov (United States)

Petrini, Paula A.; Silva, Ricardo M. L.; de Oliveira, Rafael F.; Merces, Leandro; Bof Bufon, Carlos C.

2018-06-01

Considerable advances in the field of molecular electronics have been achieved over the recent years. One persistent challenge, however, is the exploitation of the electronic properties of molecules fully integrated into devices. Typically, the molecular electronic properties are investigated using sophisticated techniques incompatible with a practical device technology, such as the scanning tunneling microscopy. The incorporation of molecular materials in devices is not a trivial task as the typical dimensions of electrical contacts are much larger than the molecular ones. To tackle this issue, we report on hybrid capacitors using mechanically-compliant nanomembranes to encapsulate ultrathin molecular ensembles for the investigation of molecular dielectric properties. As the prototype material, copper (II) phthalocyanine (CuPc) has been chosen as information on its dielectric constant (k CuPc) at the molecular scale is missing. Here, hybrid nanomembrane-based capacitors containing metallic nanomembranes, insulating Al2O3 layers, and the CuPc molecular ensembles have been fabricated and evaluated. The Al2O3 is used to prevent short circuits through the capacitor plates as the molecular layer is considerably thin (electrical measurements of devices with molecular layers of different thicknesses, the CuPc dielectric constant has been reliably determined (k CuPc = 4.5 ± 0.5). These values suggest a mild contribution of the molecular orientation on the CuPc dielectric properties. The reported nanomembrane-based capacitor is a viable strategy for the dielectric characterization of ultrathin molecular ensembles integrated into a practical, real device technology.
Theoretical study on mechanical and electron-transport properties of conjugated molecular junctions with carboxylic or methyl sulfide links

Energy Technology Data Exchange (ETDEWEB)

Bao, De-Liang; Liu, Ran [College of Physics and Electronics, Shandong Normal University, Jinan 250014 (China); Leng, Jian-Cai [College of Physics and Electronics, Shandong Normal University, Jinan 250014 (China); School of Science, Qilu University of Technology, Jinan 250353 (China); Zuo, Xi; Jiao, Yang [College of Physics and Electronics, Shandong Normal University, Jinan 250014 (China); Li, Zong-Liang, E-mail: lizongliang@sdnu.edu.cn [College of Physics and Electronics, Shandong Normal University, Jinan 250014 (China); Wang, Chuan-Kui [College of Physics and Electronics, Shandong Normal University, Jinan 250014 (China)

2014-03-01

The mechanical and electronic transport properties of 4-(methylthio)benzoic acid (M1), 1,4-bis(methylthio) benzene (M2) and methyl 4-(methylthio)benzoate (M3) molecular junctions are studied employing density functional theory and elastic scattering Green's function method. The numerical results show that the rupture force of M1 and M2 junctions are both about 0.6±0.1 nN as experiment probed, which is much smaller than the force to break COO{sup −}–Au bond. The COO{sup −} group strongly influenced on M1 molecular junction and further strengthened SMe–Au bond at the other end of the junction. The M3 junction is less stable because the CH{sub 3} group linked to COO group destroyed the mechanical stability of COO–Au connection. The conductance of M2 junction is about an order larger than that of M1 junction as the experiment probed. The less stable feature of M3 junction leads the absence of conductive peak.
A molecular dynamic simulation study of mechanical properties of graphene–polythiophene composite with Reax force field

International Nuclear Information System (INIS)

Nayebi, Payman; Zaminpayma, Esmaeil

2016-01-01

In this paper, we performed molecular dynamic simulations by Reax force field to study the mechanical properties of graphene–polythiophene nanocomposite. By computing elastic constant, breaking stress, breaking strain and Young's modulus from the stress–strain curve for the nanocomposites, we investigated effects of tension orientation, graphene loading to the polymer, temperature of nanocomposite and defect of graphene on these mechanical characters. It is found that mechanical characters of tension along the zigzag orientation are higher than other directions. Also, by increasing the weight concentration of graphene in composite, the Young's modulus and breaking strain increase. Our results showed that the Young's modulus decreased with increasing temperature. Finally by applying defect on graphene structure, we found that one atom missing defect has lower Young's modulus. Also, by increasing the defects concentration, elastic modulus decreases gradually. - Highlights: • We studied mechanical properties of graphene–polythiophene nanocomposite. • Mechanical characters of tension along the zigzag are higher than other directions. • By increasing the weight concentration of graphene in composite, the Young's modulus increases. • Young's modulus decreased with increasing temperature. • By increasing the defects concentration, elastic modulus decreases gradually.
The effect of point mutations on structure and mechanical properties of collagen-like fibril: A molecular dynamics study

Energy Technology Data Exchange (ETDEWEB)

Marlowe, Ashley E.; Singh, Abhishek; Yingling, Yaroslava G., E-mail: yara_yingling@ncsu.edu

2012-12-01

Understanding sequence dependent mechanical and structural properties of collagen fibrils is important for the development of artificial biomaterials for medical and nanotechnological applications. Moreover, point mutations are behind many collagen associated diseases, including Osteogenesis Imperfecta (OI). We conducted a combination of classical and steered atomistic molecular dynamics simulations to examine the effect of point mutations on structure and mechanical properties of short collagen fibrils which include mutations of glycine to alanine, aspartic acid, cysteine, and serine or mutations of hydroxyproline to arginine, asparagine, glutamine, and lysine. We found that all mutations disrupt structure and reduce strength of the collagen fibrils, which may affect the hierarchical packing of the fibrils. The glycine mutations were more detrimental to mechanical strength of the fibrils (WT > Ala > Ser > Cys > Asp) than that of hydroxyproline (WT > Arg > Gln > Asn > Lys). The clinical outcome for glycine mutations agrees well with the trend in reduction of fibril's tensile strength predicted by our simulations. Overall, our results suggest that the reduction in mechanical properties of collagen fibrils may be used to predict the clinical outcome of mutations. Highlights: Black-Right-Pointing-Pointer All mutations disrupt structure and bonding pattern and reduce strength of the collagen fibrils. Black-Right-Pointing-Pointer Gly based mutations are worst to mechanical integrity of fibrils than that of Hyp. Black-Right-Pointing-Pointer Lys and Arg mutations most dramatically destabilize collagen fibril properties. Black-Right-Pointing-Pointer Clinical outcome of mutations may be related to the reduced mechanical properties of fibrils.
Skin hydration: interplay between molecular dynamics, structure and water uptake in the stratum corneum.

Science.gov (United States)

Mojumdar, Enamul Haque; Pham, Quoc Dat; Topgaard, Daniel; Sparr, Emma

2017-11-16

Hydration is a key aspect of the skin that influences its physical and mechanical properties. Here, we investigate the interplay between molecular and macroscopic properties of the outer skin layer - the stratum corneum (SC) and how this varies with hydration. It is shown that hydration leads to changes in the molecular arrangement of the peptides in the keratin filaments as well as dynamics of C-H bond reorientation of amino acids in the protruding terminals of keratin protein within the SC. The changes in molecular structure and dynamics occur at a threshold hydration corresponding to ca. 85% relative humidity (RH). The abrupt changes in SC molecular properties coincide with changes in SC macroscopic swelling properties as well as mechanical properties in the SC. The flexible terminals at the solid keratin filaments can be compared to flexible polymer brushes in colloidal systems, creating long-range repulsion and extensive swelling in water. We further show that the addition of urea to the SC at reduced RH leads to similar molecular and macroscopic responses as the increase in RH for SC without urea. The findings provide new molecular insights to deepen the understanding of how intermediate filament organization responds to changes in the surrounding environment.
Spectroscopic (FT-IR, FT-Raman, NMR and UV-Visible) and quantum chemical studies of molecular geometry, Frontier molecular orbital, NLO, NBO and thermodynamic properties of salicylic acid.

Science.gov (United States)

Suresh, S; Gunasekaran, S; Srinivasan, S

2014-11-11

The solid phase FT-IR and FT-Raman spectra of 2-hydroxybenzoic acid (salicylic acid) have been recorded in the region 4000-400 and 4000-100 cm(-1) respectively. The optimized molecular geometry and fundamental vibrational frequencies are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) method and a comparative study between Hartree Fork (HF) method at 6-311++G(d,p) level basis set. The calculated harmonic vibrational frequencies are scaled and they are compared with experimentally obtained FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of this compound has been made on the basis of the calculated potential energy distribution (PED). The time dependent DFT method is employed to predict its absorption energy and oscillator strength. The linear polarizability (α) and the first order hyper polarizability (β) values of the investigated molecule have been computed. The electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MEP) are also performed. Stability of the molecule arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. Published by Elsevier B.V.
Effects of gamma irradiation on the molecular structure and mechanical properties of biodegradable polymer poly(hydroxybutyrate)

International Nuclear Information System (INIS)

Oliveira, Leticia M. de; Araujo, Elmo S.

2005-01-01

The effects of gamma irradiation ( 60 Co) on the properties of the Brazilian biodegradable polymer, Poly(hydroxybutyrate), PHB, i.e. chemical, mechanical and structural properties were investigated. PHB is a natural polyester biosynthesized by different bacteria as a form to store carbon and energy. This new biopolymer shows a great potential in the medical and pharmaceutical applications due to the biocompatibility and biodegradation capacity, since it is reabsorbed by organism without liberation of toxic substances. As it.s well known, gamma irradiation have been considered the more functional sterilization mechanism applied to medical devices. This way, it is necessary to know the effects caused by energy transfer to the polymer system. The viscosity-average molar mass (Mv) of the irradiated PHB, measured using an Ostwald-type capillary viscometer, significantly decreased. The irradiated samples (test specimens) showed a molecular degradation degree, G (scissions/100 eV) value, in the sterilization dose range (0-25 kGy) about 11.4, and 20.9 to doses above 35 kGy. Other results also indicate that the gamma irradiation significantly affected the mechanical properties of PHB. Tensile strength, impact strength and elongation at break decreased dramatically, indicating increasing on the brittleness, because significant chain scissions take place in the amorphous region of irradiated PHB. On the other hand, Young modulus does not significantly change on irradiated polymer. 13 C NMR spectra of irradiated PHB at dose of 200 kGy did not show arising of new structural groups. (author)
Neutron Scattering studies of magnetic molecular magnets

International Nuclear Information System (INIS)

Chaboussant, G.

2009-01-01

This work deals with inelastic neutron scattering studies of magnetic molecular magnets and focuses on their magnetic properties at low temperature and low energies. Several molecular magnets (Mn 12 , V 15 , Ni 12 , Mn 4 , etc.) are reviewed. Inelastic neutron scattering is shown to be a perfectly suited spectroscopy tool to -a) probe magnetic energy levels in such systems and -b) provide key information to understand the quantum tunnel effect of the magnetization in molecular spin clusters. (author)
Linear and Branched PEIs (Polyethylenimines and Their Property Space

Directory of Open Access Journals (Sweden)

Claudiu N. Lungu

2016-04-01

Full Text Available A chemical property space defines the adaptability of a molecule to changing conditions and its interaction with other molecular systems determining a pharmacological response. Within a congeneric molecular series (compounds with the same derivatization algorithm and thus the same brute formula the chemical properties vary in a monotonic manner, i.e., congeneric compounds share the same chemical property space. The chemical property space is a key component in molecular design, where some building blocks are functionalized, i.e., derivatized, and eventually self-assembled in more complex systems, such as enzyme-ligand systems, of which (physico-chemical properties/bioactivity may be predicted by QSPR/QSAR (quantitative structure-property/activity relationship studies. The system structure is determined by the binding type (temporal/permanent; electrostatic/covalent and is reflected in its local electronic (and/or magnetic properties. Such nano-systems play the role of molecular devices, important in nano-medicine. In the present article, the behavior of polyethylenimine (PEI macromolecules (linear LPEI and branched BPEI, respectively with respect to the glucose oxidase enzyme GOx is described in terms of their (interacting energy, geometry and topology, in an attempt to find the best shape and size of PEIs to be useful for a chosen (nanochemistry purpose.
Low Molecular Weight Norbornadiene Derivatives for Molecular Solar-Thermal Energy Storage.

Science.gov (United States)

Quant, Maria; Lennartson, Anders; Dreos, Ambra; Kuisma, Mikael; Erhart, Paul; Börjesson, Karl; Moth-Poulsen, Kasper

2016-09-05

Molecular solar-thermal energy storage systems are based on molecular switches that reversibly convert solar energy into chemical energy. Herein, we report the synthesis, characterization, and computational evaluation of a series of low molecular weight (193-260 g mol(-1) ) norbornadiene-quadricyclane systems. The molecules feature cyano acceptor and ethynyl-substituted aromatic donor groups, leading to a good match with solar irradiation, quantitative photo-thermal conversion between the norbornadiene and quadricyclane, as well as high energy storage densities (396-629 kJ kg(-1) ). The spectroscopic properties and energy storage capability have been further evaluated through density functional theory calculations, which indicate that the ethynyl moiety plays a critical role in obtaining the high oscillator strengths seen for these molecules. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.
Immunomodulatory Properties and Molecular Effects in Inflammatory Diseases of Low-Dose X-Irradiation

International Nuclear Information System (INIS)

Rödel, Franz; Frey, Benjamin; Manda, Katrin; Hildebrandt, Guido; Hehlgans, Stephanie; Keilholz, Ludwig; Seegenschmiedt, M. Heinrich; Gaipl, Udo S.; Rödel, Claus

2012-01-01

Inflammatory diseases are the result of complex and pathologically unbalanced multicellular interactions. For decades, low-dose X-irradiation therapy (LD-RT) has been clinically documented to exert an anti-inflammatory effect on benign diseases and chronic degenerative disorders. By contrast, experimental studies to confirm the effectiveness and to reveal underlying cellular and molecular mechanisms are still at their early stages. During the last decade, however, the modulation of a multitude of immunological processes by LD-RT has been explored in vitro and in vivo. These include leukocyte/endothelial cell adhesion, adhesion molecule and cytokine/chemokine expression, apoptosis induction, and mononuclear/polymorphonuclear cell metabolism and activity. Interestingly, these mechanisms display comparable dose dependences and dose-effect relationships with a maximum effect in the range between 0.3 and 0.7 Gy, already empirically identified to be most effective in the clinical routine. This review summarizes data and models exploring the mechanisms underlying the immunomodulatory properties of LD-RT that may serve as a prerequisite for further systematic analyses to optimize low-dose irradiation procedures in future clinical practice.

Immunomodulatory Properties and Molecular Effects in Inflammatory Diseases of Low-Dose X-Irradiation

Energy Technology Data Exchange (ETDEWEB)

Rödel, Franz [Department of Radiotherapy and Oncology, University Hospital of Frankfurt, Johann Wolfgang-Goethe Universität, Frankfurt am Main (Germany); Frey, Benjamin [Department of Radiation Oncology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen (Germany); Manda, Katrin; Hildebrandt, Guido [Department of Radiotherapy and Radiation Oncology, University of Rostock, Rostock (Germany); Hehlgans, Stephanie [Department of Radiotherapy and Oncology, University Hospital of Frankfurt, Johann Wolfgang-Goethe Universität, Frankfurt am Main (Germany); Keilholz, Ludwig [Department of Radiotherapy, Clinical Center Bayreuth, Bayreuth (Germany); Seegenschmiedt, M. Heinrich [Strahlenzentrum Hamburg Medizinisches Versorgungszentrum, Hamburg (Germany); Gaipl, Udo S. [Department of Radiation Oncology, University Hospital Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen (Germany); Rödel, Claus, E-mail: franz.roedel@kgu.de [Department of Radiotherapy and Oncology, University Hospital of Frankfurt, Johann Wolfgang-Goethe Universität, Frankfurt am Main (Germany)

2012-09-25

Inflammatory diseases are the result of complex and pathologically unbalanced multicellular interactions. For decades, low-dose X-irradiation therapy (LD-RT) has been clinically documented to exert an anti-inflammatory effect on benign diseases and chronic degenerative disorders. By contrast, experimental studies to confirm the effectiveness and to reveal underlying cellular and molecular mechanisms are still at their early stages. During the last decade, however, the modulation of a multitude of immunological processes by LD-RT has been explored in vitro and in vivo. These include leukocyte/endothelial cell adhesion, adhesion molecule and cytokine/chemokine expression, apoptosis induction, and mononuclear/polymorphonuclear cell metabolism and activity. Interestingly, these mechanisms display comparable dose dependences and dose-effect relationships with a maximum effect in the range between 0.3 and 0.7 Gy, already empirically identified to be most effective in the clinical routine. This review summarizes data and models exploring the mechanisms underlying the immunomodulatory properties of LD-RT that may serve as a prerequisite for further systematic analyses to optimize low-dose irradiation procedures in future clinical practice.
Analytic nuclear forces and molecular properties from full configuration interaction quantum Monte Carlo

International Nuclear Information System (INIS)

Thomas, Robert E.; Overy, Catherine; Opalka, Daniel; Alavi, Ali; Knowles, Peter J.; Booth, George H.

2015-01-01

Unbiased stochastic sampling of the one- and two-body reduced density matrices is achieved in full configuration interaction quantum Monte Carlo with the introduction of a second, “replica” ensemble of walkers, whose population evolves in imaginary time independently from the first and which entails only modest additional computational overheads. The matrices obtained from this approach are shown to be representative of full configuration-interaction quality and hence provide a realistic opportunity to achieve high-quality results for a range of properties whose operators do not necessarily commute with the Hamiltonian. A density-matrix formulated quasi-variational energy estimator having been already proposed and investigated, the present work extends the scope of the theory to take in studies of analytic nuclear forces, molecular dipole moments, and polarisabilities, with extensive comparison to exact results where possible. These new results confirm the suitability of the sampling technique and, where sufficiently large basis sets are available, achieve close agreement with experimental values, expanding the scope of the method to new areas of investigation
Scanning probe methods applied to molecular electronics

Energy Technology Data Exchange (ETDEWEB)

Pavlicek, Niko

2013-08-01

Scanning probe methods on insulating films offer a rich toolbox to study electronic, structural and spin properties of individual molecules. This work discusses three issues in the field of molecular and organic electronics. An STM head to be operated in high magnetic fields has been designed and built up. The STM head is very compact and rigid relying on a robust coarse approach mechanism. This will facilitate investigations of the spin properties of individual molecules in the future. Combined STM/AFM studies revealed a reversible molecular switch based on two stable configurations of DBTH molecules on ultrathin NaCl films. AFM experiments visualize the molecular structure in both states. Our experiments allowed to unambiguously determine the pathway of the switch. Finally, tunneling into and out of the frontier molecular orbitals of pentacene molecules has been investigated on different insulating films. These experiments show that the local symmetry of initial and final electron wave function are decisive for the ratio between elastic and vibration-assisted tunneling. The results can be generalized to electron transport in organic materials.
Molecular structure and spectroscopic properties of 4-nitrocatechol at different pH: UV-visible, Raman, DFT and TD-DFT calculations

International Nuclear Information System (INIS)

Cornard, Jean-Paul; Rasmiwetti; Merlin, Jean-Claude

2005-01-01

We investigated theoretically, by density functional theoretical calculations and by vibrational and electronic spectroscopies, the structure and the molecular spectroscopic properties of the 4-nitrocatechol molecule with varying pH. The lower energy stable structures of the neutral, monoanion and dianion forms were compared, and influence of water solvation was examined. The Raman and UV-visible spectra of 4-nitrocatechol and of its singly deprotonated form were recorded by varying the pH from 2 to 9. A calculation of the vibrational frequencies has allowed a complete assignment of the Raman spectra of the two forms of 4-nitrocatechol, and has permitted to investigate the evolution of vibrational normal modes upon deprotonation. Based on the molecular orbital analysis and the time dependent DFT (TD-DFT) calculations, we discussed the electronic structure and the assignment of the absorption bands in the electronic spectra of 4-nitrocatechol and mono-deprotonated 4-nitrocatechol
The tunneling magnetoresistance and spin-polarized optoelectronic properties of graphyne-based molecular magnetic tunnel junctions

International Nuclear Information System (INIS)

Yang, Zhi; Ouyang, Bin; Lan, Guoqing; Xu, Li-Chun; Liu, Ruiping; Liu, Xuguang

2017-01-01

Using density functional theory and the non-equilibrium Green’s function method, we investigate the spin-dependent transport and optoelectronic properties of the graphyne-based molecular magnetic tunnel junctions (MMTJs). We find that these MMTJs exhibit an outstanding tunneling magnetoresistance (TMR) effect. The TMR value is as high as 10 6 %. When the magnetization directions of two electrodes are antiparallel under positive or negative bias voltages, two kinds of pure spin currents can be obtained in the systems. Furthermore, under the irradiation of infrared, visible or ultraviolet light, spin-polarized photocurrents can be generated in the MMTJs, but the corresponding microscopic mechanisms are different. More importantly, if the magnetization directions of two electrodes are antiparallel, the photocurrents with different spins are spatially separated, appearing at different electrodes. This phenomenon provides a new way to simultaneously generate two spin currents. (paper)
Molecular characterization of γ gliadin from durum wheat ( Triticum ...

African Journals Online (AJOL)

gliadin protein associated with gluten strength and viscoelasticity of the dough, we performed an in silico molecular and structural analysis in order to define its putative functional properties. The latter could be a valuable candidate as molecular ...
Low-dimensional molecular metals

CERN Document Server

Toyota, Naoki; Muller, Jens

2007-01-01

Assimilating research in the field of low-dimensional metals, this monograph provides an overview of the status of research on quasi-one- and two-dimensional molecular metals, describing normal-state properties, magnetic field effects, superconductivity, and the phenomena of interacting p and d electrons.
Molecular Cloud Structures and Massive Star Formation in N159

Science.gov (United States)

Nayak, O.; Meixner, M.; Fukui, Y.; Tachihara, K.; Onishi, T.; Saigo, K.; Tokuda, K.; Harada, R.

2018-02-01

The N159 star-forming region is one of the most massive giant molecular clouds (GMCs) in the Large Magellanic Cloud (LMC). We show the 12CO, 13CO, CS molecular gas lines observed with ALMA in N159 west (N159W) and N159 east (N159E). We relate the structure of the gas clumps to the properties of 24 massive young stellar objects (YSOs) that include 10 newly identified YSOs based on our search. We use dendrogram analysis to identify properties of the molecular clumps, such as flux, mass, linewidth, size, and virial parameter. We relate the YSO properties to the molecular gas properties. We find that the CS gas clumps have a steeper size–linewidth relation than the 12CO or 13CO gas clumps. This larger slope could potentially occur if the CS gas is tracing shocks. The virial parameters of the 13CO gas clumps in N159W and N159E are low (<1). The threshold for massive star formation in N159W is 501 M ⊙ pc‑2, and the threshold for massive star formation in N159E is 794 M ⊙ pc‑2. We find that 13CO is more photodissociated in N159E than N159W. The most massive YSO in N159E has cleared out a molecular gas hole in its vicinity. All the massive YSO candidates in N159E have a more evolved spectral energy distribution type in comparison to the YSO candidates in N159W. These differences lead us to conclude that the giant molecular cloud complex in N159E is more evolved than the giant molecular cloud complex in N159W.
Elastic properties of amorphous boron suboxide based solids studied using ab initio molecular dynamics

International Nuclear Information System (INIS)

Music, Denis; Schneider, Jochen M

2008-01-01

We have studied the correlation between chemical composition, structure, chemical bonding and elastic properties of amorphous B 6 O based solids using ab initio molecular dynamics. These solids are of different chemical compositions, but the elasticity data appear to be a function of density. This is in agreement with previous experimental observations. As the density increases from 1.64 to 2.38 g cm -3 , the elastic modulus increases from 74 to 253 GPa. This may be understood by analyzing the cohesive energy and the chemical bonding of these compounds. The cohesive energy decreases from -7.051 to -7.584 eV/atom in the elastic modulus range studied. On the basis of the electron density distributions, Mulliken analysis and radial distribution functions, icosahedral bonding is the dominating bonding type. C and N promote cross-linking of icosahedra and thus increase the density, while H hinders the cross-linking by forming OH groups. The presence of icosahedral bonding is independent of the density
Growth, structural, and electrical properties of germanium-on-silicon heterostructure by molecular beam epitaxy

Science.gov (United States)

Ghosh, Aheli; Clavel, Michael B.; Nguyen, Peter D.; Meeker, Michael A.; Khodaparast, Giti A.; Bodnar, Robert J.; Hudait, Mantu K.

2017-09-01

The growth, morphological, and electrical properties of thin-film Ge grown by molecular beam epitaxy on Si using a two-step growth process were investigated. High-resolution x-ray diffraction analysis demonstrated ˜0.10% tensile-strained Ge epilayer, owing to the thermal expansion coefficient mismatch between Ge and Si, and negligible epilayer lattice tilt. Micro-Raman spectroscopic analysis corroborated the strain-state of the Ge thin-film. Cross-sectional transmission electron microscopy revealed the formation of 90° Lomer dislocation network at Ge/Si heterointerface, suggesting the rapid and complete relaxation of Ge epilayer during growth. Atomic force micrographs exhibited smooth surface morphology with surface roughness published Dit data for Ge MOS devices, as a function of threading dislocation density within the Ge layer. The results obtained were comparable with Ge MOS devices integrated on Si via alternative buffer schemes. This comprehensive study of directly-grown epitaxial Ge-on-Si provides a pathway for the development of Ge-based electronic devices on Si.
Thermophysical properties of energetic ionic liquids/nitric acid mixtures: insights from molecular dynamics simulations.

Science.gov (United States)

Hooper, Justin B; Smith, Grant D; Bedrov, Dmitry

2013-09-14

Molecular dynamics (MD) simulations of mixtures of the room temperature ionic liquids (ILs) 1-butyl-4-methyl imidazolium [BMIM]/dicyanoamide [DCA] and [BMIM][NO3(-)] with HNO3 have been performed utilizing the polarizable, quantum chemistry based APPLE&P(®) potential. Experimentally it has been observed that [BMIM][DCA] exhibits hypergolic behavior when mixed with HNO3 while [BMIM][NO3(-)] does not. The structural, thermodynamic, and transport properties of the IL/HNO3 mixtures have been determined from equilibrium MD simulations over the entire composition range (pure IL to pure HNO3) based on bulk simulations. Additional (non-equilibrium) simulations of the composition profile for IL/HNO3 interfaces as a function of time have been utilized to estimate the composition dependent mutual diffusion coefficients for the mixtures. The latter have been employed in continuum-level simulations in order to examine the nature (composition and width) of the IL/HNO3 interfaces on the millisecond time scale.
Intrinsic work function of molecular films

International Nuclear Information System (INIS)

Ivančo, Ján

2012-01-01

The electronic properties of molecular films are analysed with the consideration of the molecular orientation. The study demonstrates that surfaces of electroactive oligomeric molecular films can be classified—analogously to the elemental surfaces—by their intrinsic work functions. The intrinsic work function of molecular films is correlated with their ionisation energies; again, the behaviour is analogous to the correlation existing between the first ionisation energy of elements and the work function of the corresponding elemental surfaces. The proposed intrinsic work-function concept suggests that the mechanism for the energy-level alignment at the interfaces associated with molecular films is virtually controlled by work functions of materials brought into the contact. - Highlights: ► Molecular films exhibit their own (intrinsic) work function. ► Intrinsic work function is correlated with ionisation energy of molecular films. ► Intrinsic work function determines dipole at interface with a particular surface. ► Surface vacuum-level change upon film growth does not relate to interfacial dipole.
How Secondary and Tertiary Amide Moieties are Molecular Stations for Dibenzo-24-crown-8 in [2]Rotaxane Molecular Shuttles?

Science.gov (United States)

Riss-Yaw, Benjamin; Morin, Justine; Clavel, Caroline; Coutrot, Frédéric

2017-11-21

Interlocked molecular machines like [2]rotaxanes are intriguing aesthetic molecules. The control of the localization of the macrocycle, which surrounds a molecular axle, along the thread leads to translational isomers of very different properties. Although many moieties have been used as sites of interactions for crown ethers, the very straightforwardly obtained amide motif has more rarely been envisaged as molecular station. In this article, we report the use of secondary and tertiary amide moieties as efficient secondary molecular station in pH-sensitive molecular shuttles. Depending on the N -substitution of the amide station, and on deprotonation or deprotonation-carbamoylation, the actuation of the molecular machinery differs accordingly to very distinct interactions between the axle and the DB24C8.
Development of radiation-resisting high molecular-weight materials

International Nuclear Information System (INIS)

Nakagawa, Tsutomu

1976-01-01

The excellent radiation-resisting polyvinyl chloride developed at the opportunity of the research on the relationships between the protection of living body and the polymer-technological protection from radiation is reviewed. The report is divided into four main parts, namely 1) the change in the molecular arrangement of market-available, high molecular-weight materials by gamma-ray irradiation, 2) the protection of high molecular-weight materials from radiation, 3) the relationships between the biological radiation-protective substances and the change to radiation-resisting property of synthesized high molecular-weight substances, and 4) the development of the radiation-resisting high molecular-weight materials as metal-collecting agents. Attention is paid to the polyvinyl chloride having N-methyl-dithio-carbamate radical (PMD), synthesized by the author et. al., that has excellent radiation-resisting property. PMD has some possibility to form thiol- and amino-radicals necessary to protect living things from radiation. It is believed that the protection effects of N-methyl-dithio-carbamate radical are caused by the relatively stable S radical produced by the energy transfer. PMD film is suitable for the irradiation of foods, because it hardly changes the permeability of oxygen and carbon dioxide. PMD produces mercaptide or chelate. A new metal-collecting agent (PSDC) having reactivity with the metallic ions with radiation-resisting property was developed, which is derived from polyvinyl chloride and sodium N-methyl-N-carboxy-methyl-dithio-carbamate. (Iwakiri, K.)
Physical properties in the normal state of the molecular superconductor Κ-(BEDT)2Cu2(CN)3

International Nuclear Information System (INIS)

Papavassiliou, G.C.; Lagouvardos, D.J.; Terzis, A.; Amiell, J.; Garrigou-Lagrange, C.; Delhaes, P.; Hilti, B.; Pfeiffer, J.

1993-01-01

We have investigated the electrical, spectroscopic and magnetic properties of the K-phase molecular conductor K-(BEDT) 2 Cu 2 (CN) 3 between room temperature and the liquid He 4 temperature range. We have shown that an intermittent superconducting material is present around or below 4 K which presents above this temperature limited spin fluctuations. The influence of disorder inside the anionic layers is discussed with respect to the X-ray crystal structure, and also the intrinsic effects due to temperature or pressure to explain this situation. Finally, the specific behaviour of the ESR linewidth at low temperature is analysed as a magnetic precursor regime of the supposed superconducting ground state. (orig.)
Methodology for predicting oily mixture properties in the mathematical modeling of molecular distillation; Metodología para la predicción de propiedades de mezclas oleosas en el modelado matemático de la destilación molecular

Energy Technology Data Exchange (ETDEWEB)

Gayol, M.F.; Pramparo, M.C.; Miró Erdmann, S.M.

2017-07-01

A methodology for predicting the thermodynamic and transport properties of a multi-component oily mixture, in which the different mixture components are grouped into a small number of pseudo components is shown. This prediction of properties is used in the mathematical modeling of molecular distillation, which consists of a system of differential equations in partial derivatives, according to the principles of the Transport Phenomena and is solved by an implicit finite difference method using a computer code. The mathematical model was validated with experimental data, specifically the molecular distillation of a deodorizer distillate (DD) of sunflower oil. The results obtained were satisfactory, with errors less than 10% with respect to the experimental data in a temperature range in which it is possible to apply the proposed method. [Spanish] Se presenta una metodología para la predicción de las propiedades termodinámicas y de transporte de mezclas oleosas multicomponentes, en la cual se agrupan los diferentes componentes de la mezcla en un número reducido de pseudocomponentes. Esta predicción de propiedades se utiliza en el modelado matemático de la destilación molecular que consta de un sistema de ecuaciones diferenciales en derivadas parciales, según los principios de los fenómenos de transporte y se resuelve mediante un método implícito de diferencias finitas mediante un código computacional. El modelo matemático fue validado con datos experimentales, específicamente de la destilación molecular de un destilado de desodorización (DD) de aceite de girasol. Los resultados obtenidos fueron satisfactorios, con un error menor al 10% en un rango de temperaturas.
A tight-binding model of the transmission probability through a molecular junction; a single molecule vs. a molecular layer

International Nuclear Information System (INIS)

Landau, A.; Nitzan, A.

2006-01-01

Full Text: Molecular electronics, one of the major fields of the current effort in nano-science, may be de ed as the study of electronic behaviors, devices and applications that depend on the properties of matter at the molecular scale. If the miniaturization trend of microelectronic devices is to continue, elements such as transistors and contacts will soon shrink to single molecules. The promise of these new technological breakthroughs has been major driving force in this ld. Moreover, the consideration of molecular systems as electronic devices has raised new fundamental questions. In particular, while traditional quantum chemistry deals with electronically closed systems, we now face problems involving molecular systems that are open to their electronic environment, moreover, function in far from equilibrium situations. A generic molecular junction is made of two electrodes connected by a molecular spacer that takes the form of a molecular chain of varying length or a molecular layer of varying thickness. We use a simple nearest-neighbors tight-biding model with the non-equilibrium Green's function (NEGF) method to investigate and compare between a self-assembled monolayer (SAM), finite molecular layer (FML), and single molecule (SM) chemisorption to a surface of a metal substrate. In addition, we examine the difference in the transmission probability through a SAM, FML and SM sandwiched between two metallic electrodes. Dramatic differences are observed between the SM, FML and SAM density of electronic states and transmission functions. In addition, we analyze the effects of changing different physical parameters such as molecule-substrate interaction, molecule-molecule interactions, etc; interesting effects that pertain to the conduction properties of single molecules and molecular layers are observed. Intriguing results are attained when we investigate the commensurability of the SAM with the metallic surface
Structural, dynamic, electronic, and vibrational properties of flexible, intermediate, and stressed rigid As-Se glasses and liquids from first principles molecular dynamics

International Nuclear Information System (INIS)

Bauchy, M.; Kachmar, A.; Micoulaut, M.

2014-01-01

The structural, vibrational, electronic, and dynamic properties of amorphous and liquid As x Se 1-x (0.10 Molecular Dynamics. Within the above range of compositions, thresholds, and anomalies are found in the behavior of reciprocal and real space properties that can be correlated to the experimental location of the Boolchand intermediate phase in these glassy networks, observed at 0.27
Hybrid nanomembrane-based capacitors for the determination of the dielectric constant of semiconducting molecular ensembles.

Science.gov (United States)

Petrini, Paula Andreia; Lopes da Silva, Ricardo Magno; de Oliveira, Rafael Furlan; Merces, Leandro; Bufon, Carlos César Bof

2018-04-06

Considerable advances in the field of molecular electronics have been achieved over the recent years. One persistent challenge, however, is the exploitation of the electronic properties of molecules fully integrated into devices. Typically, the molecular electronic properties are investigated using sophisticated techniques incompatible with a practical device technology, such as the scanning tunneling microscope (STM). The incorporation of molecular materials in devices is not a trivial task since the typical dimensions of electrical contacts are much larger than the molecular ones. To tackle this issue, we report on hybrid capacitors using mechanically-compliant nanomembranes to encapsulate ultrathin molecular ensembles for the investigation of molecular dielectric properties. As the prototype material, copper (II) phthalocyanine (CuPc) has been chosen as information on its dielectric constant (kCuPc) at the molecular scale is missing. Here, hybrid nanomembrane-based capacitors containing metallic nanomembranes, insulating Al2O3 layers, and the CuPc molecular ensemble have been fabricated and evaluated. The Al2O3 is used to prevent short circuits through the capacitor plates as the molecular layer is considerably thin (< 30 nm). From the electrical measurements of devices with molecular layers of different thicknesses, the CuPc dielectric constant has been reliably determined (kCuPc = 4.5 ± 0.5). These values suggest a mild contribution of molecular orientation in the CuPc dielectric properties. The reported nanomembrane-based capacitor is a viable strategy for the dielectric characterization of ultrathin molecular ensembles integrated into a practical, real device technology. © 2018 IOP Publishing Ltd.
Molecular interactions with reference to manifestation of solvation ...

African Journals Online (AJOL)

The density and viscosity data were analyzed by some semi-empirical viscosity models, and the results have been discussed in terms of molecular interactions and structural effects. The excess properties were found to be either negative or positive depending on the molecular interactions and the nature of liquid mixtures.

Monolayer atomic crystal molecular superlattices

Science.gov (United States)

Wang, Chen; He, Qiyuan; Halim, Udayabagya; Liu, Yuanyue; Zhu, Enbo; Lin, Zhaoyang; Xiao, Hai; Duan, Xidong; Feng, Ziying; Cheng, Rui; Weiss, Nathan O.; Ye, Guojun; Huang, Yun-Chiao; Wu, Hao; Cheng, Hung-Chieh; Shakir, Imran; Liao, Lei; Chen, Xianhui; Goddard, William A., III; Huang, Yu; Duan, Xiangfeng

2018-03-01

Artificial superlattices, based on van der Waals heterostructures of two-dimensional atomic crystals such as graphene or molybdenum disulfide, offer technological opportunities beyond the reach of existing materials. Typical strategies for creating such artificial superlattices rely on arduous layer-by-layer exfoliation and restacking, with limited yield and reproducibility. The bottom-up approach of using chemical-vapour deposition produces high-quality heterostructures but becomes increasingly difficult for high-order superlattices. The intercalation of selected two-dimensional atomic crystals with alkali metal ions offers an alternative way to superlattice structures, but these usually have poor stability and seriously altered electronic properties. Here we report an electrochemical molecular intercalation approach to a new class of stable superlattices in which monolayer atomic crystals alternate with molecular layers. Using black phosphorus as a model system, we show that intercalation with cetyl-trimethylammonium bromide produces monolayer phosphorene molecular superlattices in which the interlayer distance is more than double that in black phosphorus, effectively isolating the phosphorene monolayers. Electrical transport studies of transistors fabricated from the monolayer phosphorene molecular superlattice show an on/off current ratio exceeding 107, along with excellent mobility and superior stability. We further show that several different two-dimensional atomic crystals, such as molybdenum disulfide and tungsten diselenide, can be intercalated with quaternary ammonium molecules of varying sizes and symmetries to produce a broad class of superlattices with tailored molecular structures, interlayer distances, phase compositions, electronic and optical properties. These studies define a versatile material platform for fundamental studies and potential technological applications.
Molecular Cloning and Pharmacological Properties of an Acidic PLA2 from Bothrops pauloensis Snake Venom

Science.gov (United States)

Ferreira, Francis Barbosa; Gomes, Mário Sérgio Rocha; Naves de Souza, Dayane Lorena; Gimenes, Sarah Natalie Cirilo; Castanheira, Letícia Eulalio; Borges, Márcia Helena; Rodrigues, Renata Santos; Yoneyama, Kelly Aparecida Geraldo; Homsi Brandeburgo, Maria Inês; Rodrigues, Veridiana M.

2013-01-01

In this work, we describe the molecular cloning and pharmacological properties of an acidic phospholipase A2 (PLA2) isolated from Bothrops pauloensis snake venom. This enzyme, denominated BpPLA2-TXI, was purified by four chromatographic steps and represents 2.4% of the total snake venom protein content. BpPLA2-TXI is a monomeric protein with a molecular mass of 13.6 kDa, as demonstrated by Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) analysis and its theoretical isoelectric point was 4.98. BpPLA2-TXI was catalytically active and showed some pharmacological effects such as inhibition of platelet aggregation induced by collagen or ADP and also induced edema and myotoxicity. BpPLA2-TXI displayed low cytotoxicity on TG-180 (CCRF S 180 II) and Ovarian Carcinoma (OVCAR-3), whereas no cytotoxicity was found in regard to MEF (Mouse Embryonic Fibroblast) and Sarcoma 180 (TIB-66). The N-terminal sequence of forty-eight amino acid residues was determined by Edman degradation. In addition, the complete primary structure of 122 amino acids was deduced by cDNA from the total RNA of the venom gland using specific primers, and it was significantly similar to other acidic D49 PLA2s. The phylogenetic analyses showed that BpPLA2-TXI forms a group with other acidic D49 PLA2s from the gender Bothrops, which are characterized by a catalytic activity associated with anti-platelet effects. PMID:24304676
Some aspects on the conditioning of the molecular sieves waste

International Nuclear Information System (INIS)

Deneanu, N.; Dulama, M.; Teoreanu, I.

2009-01-01

The paper deals with a systematic approach of some important problems, concerning the conditioning of the molecular sieves wastes resulted from Cernavoda Nuclear Power Plant using binder materials, ensuring the prerequisites for elaboration of the recipes of the waste forms. In order to justify the more or less different behavior of wide range of potential binder materials (high alumina cement, Type II Portland blast furnace cement, Type I normal Portland cement) in relation to the molecular sieves content, within the paper there were studied the leach rates of tritium and the compressive strengths. Moreover, the research work took into consideration the correlations between composition-processing-proprieties, mixing properties (workability) and hardening process (setting time). Typical properties and limits of the molecular sieves waste forms could meet the Waste Acceptance Criteria of the disposal site. The experimental results suggest that, the normal Portland cement is the best binder material for immobilizing molecular sieves wastes while addition of sand and dispersed agent into matrices would greatly enhance the properties of the waste forms. (authors)
Toward the identification of molecular cogs.

Science.gov (United States)

Dziubiński, Maciej; Lesyng, Bogdan

2016-04-05

Computer simulations of molecular systems allow determination of microscopic interactions between individual atoms or groups of atoms, as well as studies of intramolecular motions. Nevertheless, description of structural transformations at the mezoscopic level and identification of causal relations associated with these transformations is very difficult. Structural and functional properties are related to free energy changes. Therefore, to better understand structural and functional properties of molecular systems, it is required to deepen our knowledge of free energy contributions arising from molecular subsystems in the course of structural transformations. The method presented in this work quantifies the energetic contribution of each pair of atoms to the total free energy change along a given collective variable. Next, with the help of a genetic clustering algorithm, the method proposes a division of the system into two groups of atoms referred to as molecular cogs. Atoms which cooperate to push the system forward along a collective variable are referred to as forward cogs, and those which work in the opposite direction as reverse cogs. The procedure was tested on several small molecules for which the genetic clustering algorithm successfully found optimal partitionings into molecular cogs. The primary result of the method is a plot depicting the energetic contributions of the identified molecular cogs to the total Potential of Mean Force (PMF) change. Case-studies presented in this work should help better understand the implications of our approach, and were intended to pave the way to a future, publicly available implementation. © 2015 Wiley Periodicals, Inc.
Fullerenes, carbon nanotubes, and graphene for molecular electronics.

Science.gov (United States)

Pinzón, Julio R; Villalta-Cerdas, Adrián; Echegoyen, Luis

2012-01-01

With the constant growing complexity of electronic devices, the top-down approach used with silicon based technology is facing both technological and physical challenges. Carbon based nanomaterials are good candidates to be used in the construction of electronic circuitry using a bottom-up approach, because they have semiconductor properties and dimensions within the required physical limit to establish electrical connections. The unique electronic properties of fullerenes for example, have allowed the construction of molecular rectifiers and transistors that can operate with more than two logical states. Carbon nanotubes have shown their potential to be used in the construction of molecular wires and FET transistors that can operate in the THz frequency range. On the other hand, graphene is not only the most promising material for replacing ITO in the construction of transparent electrodes but it has also shown quantum Hall effect and conductance properties that depend on the edges or chemical doping. The purpose of this review is to present recent developments on the utilization carbon nanomaterials in molecular electronics.
Properties of the Excited States of Molecular Ions.

Science.gov (United States)

1981-04-13

FIg. 1). techniques have beest applied to the study of quartet states of Oi. The four potential curves most relevant Guyon et al., using a synchrotron...8217 a’ a a C ’U ~ ~ ~ ~ ~ ~ ~ 2 2,~ C a ’I C~- C ’ 𔃺 𔃺 𔃺 ’ ’ C- ~ C-E-38- ’- u A() A09a 265 SRI INTERNATIONAL 14FNLO PARK CA MOLECULAR PHYSICS LAB F
Molecular physics and chemistry applications of quantum Monte Carlo

International Nuclear Information System (INIS)

Reynolds, P.J.; Barnett, R.N.; Hammond, B.L.; Lester, W.A. Jr.

1985-09-01

We discuss recent work with the diffusion quantum Monte Carlo (QMC) method in its application to molecular systems. The formal correspondence of the imaginary time Schroedinger equation to a diffusion equation allows one to calculate quantum mechanical expectation values as Monte Carlo averages over an ensemble of random walks. We report work on atomic and molecular total energies, as well as properties including electron affinities, binding energies, reaction barriers, and moments of the electronic charge distribution. A brief discussion is given on how standard QMC must be modified for calculating properties. Calculated energies and properties are presented for a number of molecular systems, including He, F, F - , H 2 , N, and N 2 . Recent progress in extending the basic QMC approach to the calculation of ''analytic'' (as opposed to finite-difference) derivatives of the energy is presented, together with an H 2 potential-energy curve obtained using analytic derivatives. 39 refs., 1 fig., 2 tabs
Dielectric properties of binary solutions a data handbook

CERN Document Server

Akhadov, Y Y

1980-01-01

Dielectric Properties of Binary Solutions focuses on the investigation of the dielectric properties of solutions, as well as the molecular interactions and mechanisms of molecular processes that occur in liquids. The book first discusses the fundamental formulas describing the dielectric properties of liquids and dielectric data for binary systems of non-aqueous solutions. Topics include permittivity and dielectric dispersion parameters of non-aqueous solutions of organic and inorganic compounds. The text also tackles dielectric data for binary systems of aqueous solutions, including permittiv
On the structural affinity of macromolecules with different biological properties: Molecular dynamics simulations of a series of TEM-1 mutants

Energy Technology Data Exchange (ETDEWEB)

Giampaolo, Alessia Di [Dipartimento di Scienze Fisiche e Chimiche, Universita’ degli Studi di l’Aquila, Via Vetoio snc, 67100 Coppito (AQ) (Italy); Mazza, Fernando [Department of Health Sciences, Univ. of L’Aquila, 67010 L’Aquila (Italy); Daidone, Isabella [Dipartimento di Scienze Fisiche e Chimiche, Universita’ degli Studi di l’Aquila, Via Vetoio snc, 67100 Coppito (AQ) (Italy); Amicosante, Gianfranco; Perilli, Mariagrazia [Dipartimento di Scienze Cliniche Applicate e Biotecnologiche, Università degli Studi di l’Aquila, Via Vetoio snc, 67100 Coppito (AQ) (Italy); Aschi, Massimiliano, E-mail: massimiliano.aschi@univaq.it [Dipartimento di Scienze Fisiche e Chimiche, Universita’ degli Studi di l’Aquila, Via Vetoio snc, 67100 Coppito (AQ) (Italy)

2013-07-12

Highlights: •We have performed molecular dynamics simulations of TEM-1 mutants. •Mutations effects on the mechanical properties are considered. •Mutants do not significantly alter the average enzymes structure. •Mutants produce sharp alterations in enzyme conformational repertoire. •Mutants also produce changes in the active site volume. -- Abstract: Molecular Dynamics simulations have been carried out in order to provide a molecular rationalization of the biological and thermodynamic differences observed for a class of TEM β-lactamases. In particular we have considered the TEM-1(wt), the single point mutants TEM-40 and TEM-19 representative of IRT and ESBL classes respectively, and TEM-1 mutant M182T, TEM-32 and TEM-20 which differ from the first three for the additional of M182T mutation. Results indicate that most of the thermodynamic, and probably biological behaviour of these systems arise from subtle effects which, starting from the alterations of the local interactions, produce drastic modifications of the conformational space spanned by the enzymes. The present study suggests that systems showing essentially the same secondary and tertiary structure may differentiate their chemical–biological activity essentially (and probably exclusively) on the basis of the thermal fluctuations occurring in their physiological environment.
On the structural affinity of macromolecules with different biological properties: Molecular dynamics simulations of a series of TEM-1 mutants

International Nuclear Information System (INIS)

Giampaolo, Alessia Di; Mazza, Fernando; Daidone, Isabella; Amicosante, Gianfranco; Perilli, Mariagrazia; Aschi, Massimiliano

2013-01-01

Highlights: •We have performed molecular dynamics simulations of TEM-1 mutants. •Mutations effects on the mechanical properties are considered. •Mutants do not significantly alter the average enzymes structure. •Mutants produce sharp alterations in enzyme conformational repertoire. •Mutants also produce changes in the active site volume. -- Abstract: Molecular Dynamics simulations have been carried out in order to provide a molecular rationalization of the biological and thermodynamic differences observed for a class of TEM β-lactamases. In particular we have considered the TEM-1(wt), the single point mutants TEM-40 and TEM-19 representative of IRT and ESBL classes respectively, and TEM-1 mutant M182T, TEM-32 and TEM-20 which differ from the first three for the additional of M182T mutation. Results indicate that most of the thermodynamic, and probably biological behaviour of these systems arise from subtle effects which, starting from the alterations of the local interactions, produce drastic modifications of the conformational space spanned by the enzymes. The present study suggests that systems showing essentially the same secondary and tertiary structure may differentiate their chemical–biological activity essentially (and probably exclusively) on the basis of the thermal fluctuations occurring in their physiological environment
Computation of Dielectric Response in Molecular Solids for High Capacitance Organic Dielectrics.

Science.gov (United States)

Heitzer, Henry M; Marks, Tobin J; Ratner, Mark A

2016-09-20

The dielectric response of a material is central to numerous processes spanning the fields of chemistry, materials science, biology, and physics. Despite this broad importance across these disciplines, describing the dielectric environment of a molecular system at the level of first-principles theory and computation remains a great challenge and is of importance to understand the behavior of existing systems as well as to guide the design and synthetic realization of new ones. Furthermore, with recent advances in molecular electronics, nanotechnology, and molecular biology, it has become necessary to predict the dielectric properties of molecular systems that are often difficult or impossible to measure experimentally. In these scenarios, it is would be highly desirable to be able to determine dielectric response through efficient, accurate, and chemically informative calculations. A good example of where theoretical modeling of dielectric response would be valuable is in the development of high-capacitance organic gate dielectrics for unconventional electronics such as those that could be fabricated by high-throughput printing techniques. Gate dielectrics are fundamental components of all transistor-based logic circuitry, and the combination high dielectric constant and nanoscopic thickness (i.e., high capacitance) is essential to achieving high switching speeds and low power consumption. Molecule-based dielectrics offer the promise of cheap, flexible, and mass producible electronics when used in conjunction with unconventional organic or inorganic semiconducting materials to fabricate organic field effect transistors (OFETs). The molecular dielectrics developed to date typically have limited dielectric response, which results in low capacitances, translating into poor performance of the resulting OFETs. Furthermore, the development of better performing dielectric materials has been hindered by the current highly empirical and labor-intensive pace of synthetic
Investigation of Molecular Structure and Thermal Properties of Thermo-Oxidative Aged SBS in Blends and Their Relations.

Science.gov (United States)

Xu, Xiong; Yu, Jianying; Xue, Lihui; Zhang, Canlin; Zha, Yagang; Gu, Yi

2017-07-07

Tri-block copolymer styrene-butadiene (SBS) is extensively applied in bituminous highway construction due to its high elasticity and excellent weather resistance. With the extension of time, tri-block structural SBS automatically degrades into bi-block structural SB- with some terminal oxygen-containing groups under the comprehensive effects of light, heat, oxygen, etc. In this paper, the effects of aging temperature, aging time and oxygen concentration on the molecular structure of thermo-oxidative aged SBS were mainly investigated using Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS), and the correlation between oxygen-containing groups and thermal properties (TG-DTG) was further discussed. The FTIR and XPS results show that rapid decomposition of SBS will occur with increments of aging temperature, aging time and oxygen concentration, and a large number of oxygen-containing groups such as -OH, C=O, -COOH, etc. will be formed during thermo-oxidative aging. In short-term aging, changes in aging temperature and oxygen concentration have a significant impact on the structural damage of SBS. However, in long-term aging, it has no further effect on the molecular structure of SBS or on increasing oxygen concentration. The TG and DTG results indicate that the concentration of substances with low molecular weight gradually increases with the improvement of the degree of aging of the SBS, while the initial decomposition rate increases at the beginning of thermal weightlessness and the decomposition rate slows down in comparison with neat SBS. From the relation between the XPS and TG results, it can be seen that the initial thermal stability of SBS rapidly reduces as the relative concentration of the oxygen-containing groups accumulates around 3%, while the maximum decomposition temperature slowly decreases when the relative concentration of the oxygen-containing groups is more than 3%, due to the difficult damage to strong bonds
Molecular active plasmonics: controlling plasmon resonances with molecular machines

KAUST Repository

Zheng, Yue Bing

2009-08-26

The paper studies the molecular-level active control of localized surface plasmon resonances (LSPRs) of Au nanodisk arrays with molecular machines. Two types of molecular machines - azobenzene and rotaxane - have been demonstrated to enable the reversible tuning of the LSPRs via the controlled mechanical movements. Azobenzene molecules have the property of trans-cis photoisomerization and enable the photo-induced nematic (N)-isotropic (I) phase transition of the liquid crystals (LCs) that contain the molecules as dopant. The phase transition of the azobenzene-doped LCs causes the refractive-index difference of the LCs, resulting in the reversible peak shift of the LSPRs of the embedded Au nanodisks due to the sensitivity of the LSPRs to the disks\\' surroundings\\' refractive index. Au nanodisk array, coated with rotaxanes, switches its LSPRs reversibly when it is exposed to chemical oxidants and reductants alternatively. The correlation between the peak shift of the LSPRs and the chemically driven mechanical movement of rotaxanes is supported by control experiments and a time-dependent density functional theory (TDDFT)-based, microscopic model.
Molecular active plasmonics: controlling plasmon resonances with molecular machines

KAUST Repository

Zheng, Yue Bing; Yang, Ying-Wei; Jensen, Lasse; Fang, Lei; Juluri, Bala Krishna; Flood, Amar H.; Weiss, Paul S.; Stoddart, J. Fraser; Huang, Tony Jun

2009-01-01

The paper studies the molecular-level active control of localized surface plasmon resonances (LSPRs) of Au nanodisk arrays with molecular machines. Two types of molecular machines - azobenzene and rotaxane - have been demonstrated to enable the reversible tuning of the LSPRs via the controlled mechanical movements. Azobenzene molecules have the property of trans-cis photoisomerization and enable the photo-induced nematic (N)-isotropic (I) phase transition of the liquid crystals (LCs) that contain the molecules as dopant. The phase transition of the azobenzene-doped LCs causes the refractive-index difference of the LCs, resulting in the reversible peak shift of the LSPRs of the embedded Au nanodisks due to the sensitivity of the LSPRs to the disks' surroundings' refractive index. Au nanodisk array, coated with rotaxanes, switches its LSPRs reversibly when it is exposed to chemical oxidants and reductants alternatively. The correlation between the peak shift of the LSPRs and the chemically driven mechanical movement of rotaxanes is supported by control experiments and a time-dependent density functional theory (TDDFT)-based, microscopic model.
Molecular Weight and Structural Properties of Biodegradable PLA Synthesized with Different Catalysts by Direct Melt Polycondensation

Directory of Open Access Journals (Sweden)

Hyung Woo Lee

2015-09-01

Full Text Available Production of biodegradable polylactic acid (PLA from biomassbased lactic acid is widely studied for substituting petro-based plastics or polymers. This study investigated PLA production from commercial lactic acid in a batch reactor by applying a direct melt polycondensation method with two kinds of catalyst, γ-aluminium(III oxide (γ-Al2O3 or zinc oxide (ZnO, in reduced pressure. The molecular weight of the synthesized PLA was determined by capillary viscometry and its structural properties were analyzed by functional group analysis using FT-IR. The yields of polymer production with respect to the theoretical conversion were 47% for γ-Al2O3 and 35% for ZnO. However, the PLA from ZnO had a higher molecular weight (150,600 g/mol than that from γ-Al2O3 (81,400 g/mol. The IR spectra of the synthesized PLA from both catalysts using polycondensation show the same behavior of absorption peaks at wave numbers from 4,500 cm-1 to 500 cm-1, whereas the PLA produced by two other polymerization methods – polycondensation and ring opening polymerization –showed a significant difference in % transmittance intensity pattern as well as peak area absorption at a wave number of 3,500 cm-1 as –OH vibration peak and at 1,750 cm-1 as –C=O carbonyl vibrational peak.
The Weiss molecular field and the local molecular field; Le champ moleculaire de Weiss et le champ moleculaire local

Energy Technology Data Exchange (ETDEWEB)

Neel, L [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires; Faculte des Sciences de Grenoble, 38 (France)

1959-07-01

Initially, the present report outlines the work done by P. Weiss in the molecular field and spontaneous magnetization theory. It then stresses the success of the theory in the interpretation of the magnetic and energetic properties of ferro-magnetic bodies, and indicates recent progress: 'the energetic molecular field, and the corrective molecular field of the equation of state'. In the second part, the author reviews the difficulties encountered by the theory, and shows how they were overcome by the introduction of the notion of the 'local molecular field', thus supplying the key to the properties of anti-ferro and ferri-magnetic bodies. The present level of progress in the interpretation of the magnetic properties of pyrrhotite, which played a major part in the molecular field discoveries, is also discussed in paragraph 4 and appendices. (author) [French] Dans une premiere partie, l'auteur retrace l'historique des travaux de P. Weiss sur la theorie du champ moleculaire et l'aimantation spontanee; il en souligne les succes dans l'interpretation des proprietes magnetiques et energetiques des corps ferro-magnetiques et les perfectionnements ultimes: champ moleculaire energetique et champ moleculaire correctif de l'equation d'etat. Dans une deuxieme partie, apres avoir examine les difficultes auxquelles se heurtait la theorie, l'auteur montre qu'elles ont ete resolues en introduisant la notion de champ moleculaire local et en donnant ainsi la cle des proprietes des corps antiferro-et ferri-magnetiques. II etudie egalement (paragraphe 4 et Appendice) l'etat actuel de l'interpretation des proprietes magnetiques de la pyrrhotine qui a joue un grand role dans l'histoire du champ moleculaire. (auteur)
Insight into the effect of inhibitor resistant S130G mutant on physico-chemical properties of SHV type beta-lactamase: a molecular dynamics study.

Directory of Open Access Journals (Sweden)

Mohd Hassan Baig

Full Text Available Bacterial resistance is a serious threat to human health. The production of β-lactamase, which inactivates β-lactams is most common cause of resistance to the β-lactam antibiotics. The Class A enzymes are most frequently encountered among the four β-lactamases in the clinic isolates. Mutations in class A β-lactamases play a crucial role in substrate and inhibitor specificity. SHV and TEM type are known to be most common class A β-lactamases. In the present study, we have analyzed the effect of inhibitor resistant S130G point mutation of SHV type Class-A β-lactamase using molecular dynamics and other in silico approaches. Our study involved the use of different in silico methods to investigate the affect of S130G point mutation on the major physico-chemical properties of SHV type class A β-lactamase. We have used molecular dynamics approach to compare the dynamic behaviour of native and S130G mutant form of SHV β-lactamase by analyzing different properties like root mean square deviation (RMSD, H-bond, Radius of gyration (Rg and RMS fluctuation of mutation. The results clearly suggest notable loss in the stability of S130G mutant that may further lead to decrease in substrate specificity of SHV. Molecular docking further indicates that S130G mutation decreases the binding affinity of all the three inhibitors in clinical practice.
Learning surface molecular structures via machine vision

Science.gov (United States)

Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

2017-08-01

Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (`read out') all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds and thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. The method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.
Effect of annealing conditions on the molecular properties and wetting of viscoelastic bitumen substrates by liquids

Directory of Open Access Journals (Sweden)

Salomé dos Santos

2017-01-01

Full Text Available Typically, in the production of asphalt concrete, bitumen and mineral aggregates are heated and mixed at temperatures above 100 °C. After the mixing process bitumen ideally coats the mineral aggregates and remains in the form of thin films. Because bitumen is highly temperature sensitive, the study of its properties in terms of chemistry, microstructure and rheology as a function of different annealing conditions is very relevant. The resultant molecular properties have a direct correlation to bitumen macroscopic response to liquids such as water, which is of extreme relevance to the understanding of the detrimental effect of water on asphalt pavements. The wetting characteristics play a crucial role on the extension of detachment of bitumen from the mineral aggregates when asphalt is exposed to wet conditions. Therefore, in this work, the effect of the annealing temperature and cooling history on the chemistry, microstructure and wetting of bitumen films was studied. Crystalline microstructures were identified in bulk and on the surface of the bitumen films. Larger crystals presenting higher crystallinity degree were identified when the annealed bitumen films were cooled slowly. Moreover, higher annealing temperatures increased the oxidation level. The change of the rheological properties due to the alterations of the annealing conditions produced changes in the wetting characteristics. For instance, the advancing motion of a liquid drop on the viscoelastic bitumen substrate presented an intermittent behaviour due to the deformation of bitumen at the liquid-bitumen-air contact line. Consequently, changes in the contact angles were also observed. Keywords: Bitumen, Crystallization, Oxidation, Advancing contact angle, Wetting
Molecularly thin fluoro-polymeric nanolubricant films: tribology, rheology, morphology, and applications.

Science.gov (United States)

Chung, Pil Seung; Jhon, Myung S; Choi, Hyoung Jin

2016-03-21

Molecularly thin perfluoropolyether (PFPE) has been used extensively as a high-performance lubricant in various applications and, more importantly, on carbon overcoats to enhance the reliability and lubrication of micro-/nanoelectro-mechanical systems, where the tribological performance caused by its molecular architecture is a critical issue, as are its physical properties and rheological characteristics. This Highlight addresses recent trends in the development of fluoro-polymeric lubricant films with regard to their tribology, rheology, and physio-chemical properties as they relate to heat-assisted magnetic recording. Nanorheology has been employed to examine the dynamic response of nonfunctional and functional PFPEs, while the viscoelastic properties of nanoscale PFPE films and the relaxation processes as a function of molecular structure and end-group functionality were analyzed experimentally; furthermore, the characteristics of binary blends were reported.

Exploring the no-man's land between molecular nanomagnets and magnetic nanoparticles.

Science.gov (United States)

Gatteschi, Dante; Fittipaldi, Maria; Sangregorio, Claudio; Sorace, Lorenzo

2012-05-14

The comparison of the structural and magnetic properties of molecular nanomagnets (MNM) and magnetic nanoparticles (MNP) can be instructive to get a deeper understanding of the magnetic behavior on the intermediate scale between molecular and bulk objects. In this respect iron oxo based clusters are particularly interesting, since they provide an increasing number of molecular systems with sizes close to that of iron oxide MNP. In this Minireview we report a survey of literature data aimed at improving our understanding of the emergence of MNP properties from MNM ones. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Static structure, microscopic dynamics and electronic properties of the liquid Bi–Li alloy. An ab initio molecular dynamics study

International Nuclear Information System (INIS)

Souto, J; Alemany, M M G; Gallego, L J; González, L E; González, D J

2013-01-01

We report an ab initio molecular dynamics study of the static, dynamic and electronic properties of the liquid Bi x Li 1−x alloy, which is a complex binary system with a marked tendency to heterocoordination. The calculated total static structure factors are in good agreement with the available experimental data. The partial dynamic structure factors exhibit side peaks indicative of propagating density fluctuations, and for some concentrations we have found a density fluctuation mode with phase velocity greater than the hydrodynamic sound velocity. We have also evaluated other dynamical properties such as the diffusion coefficients, the shear viscosity and the adiabatic sound velocity. The electronic density of states show that the liquid Bi x Li 1−x alloy has a metallic character, although with strong deviations from the free-electron parabolic curve. The results reported improve the understanding of binary liquid alloys with both fast and slow propagating collective modes. (paper)
The third, molecular, form of carbon: fullerenes, carbon nanotubes and onions. Some physical properties of fullerites

International Nuclear Information System (INIS)

Zubov, V.I.

2004-01-01

A brief review is presented of the pre-history and discovery of fullerenes (and then carbon nanotubes) that make the third molecular form of carbon, and of various, predominantly physical, properties of fullerites, i.e. of crystals composed of fullerene molecules. Particular attention is being given to the intermolecular forces, especially at orientationally disordered phases. The Girifalco potential is presented for eight fullerenes from C 28 to C 96 and its generalization is made for the interactions between the different fullerene molecules, C m and C n . The thermodynamics properties of the high-temperature modifications of a family of the fullerites, from C 36 up to C 96 , calculated in equilibrium with their saturated vapors on the basis of the correlative method of the unsymmetrized self-consistent field that enables one to take into account the strong anharmonicity of the lattice vibrations, are discussed. The calculations were accomplished up to the temperature of loss of stability (spinodal point) T s . We compare our results with available experimental data. The behaviour of some characteristics is considered in their dependence on the number of atoms in the molecule. Using the Lindermann's melting criterion we estimate a possible melting curve for the C 60 fullerite. (orig.)
A Focus on Triazolium as a Multipurpose Molecular Station for pH-Sensitive Interlocked Crown-Ether-Based Molecular Machines.

Science.gov (United States)

Coutrot, Frédéric

2015-10-01

The control of motion of one element with respect to others in an interlocked architecture allows for different co-conformational states of a molecule. This can result in variations of physical or chemical properties. The increase of knowledge in the field of molecular interactions led to the design, the synthesis, and the study of various systems of molecular machinery in a wide range of interlocked architectures. In this field, the discovery of new molecular stations for macrocycles is an attractive way to conceive original molecular machines. In the very recent past, the triazolium moiety proved to interact with crown ethers in interlocked molecules, so that it could be used as an ideal molecular station. It also served as a molecular barrier in order to lock interlaced structures or to compartmentalize interlocked molecular machines. This review describes the recently reported examples of pH-sensitive triazolium-containing molecular machines and their peculiar features.
Large resistance change on magnetic tunnel junction based molecular spintronics devices

Science.gov (United States)

Tyagi, Pawan; Friebe, Edward

2018-05-01

Molecular bridges covalently bonded to two ferromagnetic electrodes can transform ferromagnetic materials and produce intriguing spin transport characteristics. This paper discusses the impact of molecule induced strong coupling on the spin transport. To study molecular coupling effect the octametallic molecular cluster (OMC) was bridged between two ferromagnetic electrodes of a magnetic tunnel junction (Ta/Co/NiFe/AlOx/NiFe/Ta) along the exposed side edges. OMCs induced strong inter-ferromagnetic electrode coupling to yield drastic changes in transport properties of the magnetic tunnel junction testbed at the room temperature. These OMCs also transformed the magnetic properties of magnetic tunnel junctions. SQUID and ferromagnetic resonance studies provided insightful data to explain transport studies on the magnetic tunnel junction based molecular spintronics devices.
Visualizing functional motions of membrane transporters with molecular dynamics simulations.

Science.gov (United States)

Shaikh, Saher A; Li, Jing; Enkavi, Giray; Wen, Po-Chao; Huang, Zhijian; Tajkhorshid, Emad

2013-01-29

Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins.
Clustering pesticides according to their molecular properties and their impacts by considering additional ecotoxicological parameters in the TyPol method

Science.gov (United States)

Traore, Harouna; Crouzet, Olivier; Mamy, Laure; Sireyjol, Christine; Rossard, Virginie; Servien, Remy; Latrille, Eric; Benoit, Pierre

2017-04-01

The understanding of the fate of pesticides and their environmental impacts largely relies on their molecular properties. We recently developed 'TyPol' (Typology of Pollutants), a clustering method based on statistical analyses combining several environmental endpoints (i.e. environmental parameters such as sorption coefficient, degradation half-life) and one ecotoxicological one (bioconcentration factor), and structural molecular descriptors (number of atoms in the molecule, molecular surface, dipole moment, energy of orbitals…). TyPol has been conceived on the available knowledge on QSAR of a wide diversity of organic compounds (Mamy et al., 2015). This approach also allows to focus on transformation products present in different clusters and to infer possible changes in environmental fate consecutively to different degradation processes (Servien et al., 2014; Benoit et al., 2016). The initial version of TyPol did not include any ecotoxicological parameters except the bioconcentration factor (BCF), which informs more on the transfer along the trophic chain rather than on the effects on non-target organisms. The objective was to implement the TyPol database with a data set of ecotoxicological data concerning pesticides and several aquatic and terrestrial organisms, in order to test the possibility to extend TyPol to ecotoxicological effects on various organisms. The data analysis (available literature and databases) revealed that relevant ecotoxicological endpoints for terrestrial organisms such as soil microorganisms and macroinvertebrates are lacking compared to aquatic organisms. We have added seven parameters for acute (EC50, LC50) and chronic (NOEC) toxicological effects for the following organisms: Daphnia, Algae, Lemna and Earthworm. In this new configuration, TyPol was used to classify about 45 pesticides in different behavioural and ecotoxicity clusters. The clustering results were analyzed to reveals relationships between molecular descriptors
Mechanical, Rheological, and Bioactivity Properties of Ultra High-Molecular-Weight Polyethylene Bioactive Composites Containing Polyethylene Glycol and Hydroxyapatite

Directory of Open Access Journals (Sweden)

Mazatusziha Ahmad

2012-01-01

Full Text Available Ultrahigh-molecular-weight polyethylene/high-density polyethylene (UHMWPE/HDPE blends prepared using polyethylene glycol PEG as the processing aid and hydroxyapatite (HA as the reinforcing filler were found to be highly processable using conventional melt blending technique. It was demonstrated that PEG reduced the melt viscosity of UHMWPE/HDPE blend significantly, thus improving the extrudability. The mechanical and bioactive properties were improved with incorporation of HA. Inclusion of HA from 10 to 50 phr resulted in a progressive increase in flexural strength and modulus of the composites. The strength increment is due to the improvement on surface contact between the irregular shape of HA and polymer matrix by formation of mechanical interlock. The HA particles were homogenously distributed even at higher percentage showed improvement in wetting ability between the polymer matrix and HA. The inclusion of HA enhanced the bioactivity properties of the composite by the formation of calcium phosphate (Ca-P precipitates on the composite surface as proven from SEM and XRD analysis.
Photophysical properties of novel small acceptor molecules and their application in hybrid small-molecular/polymeric organic solar cells

Energy Technology Data Exchange (ETDEWEB)

Inal, Sahika; Castellani, Mauro; Neher, Dieter [Universitaet Potsdam, Institut fuer Physik und Astronomie, Potsdam-Golm (Germany); Sellinger, Alan [Institute of Materials Research and Engineering, Singapore (Singapore)

2009-07-01

Recent experimental investigations revealed that the photovoltaic properties of our devices are related to the balance between recombination and field-induced dissociation of interfacial excited states such as exciplexes or geminate polaron pairs. This balance was shown to be affected by the nanomorphology at the heterojunction. We have analyzed the photophysical properties of a new materials couple comprising an electron-donating PPV copolymer and a vinazene-based small molecule acceptor. Steady state and time-resolved photoluminescence (PL) spectroscopy in solution and in the solid state showed the formation of excimers within the acceptor. The associated long-range diffusion promise efficient energy harvesting at the heterojunction. On the other hand, blends of the PPV-derivative and the small molecule revealed strong exciplex formation. Therefore, bilayered hybrid small-molecular/polymeric solar cells have been fabricated by consequently spin-coating the macromolecular donor and the small molecule acceptor from two different solvents. The bilayer architecture limits recombination processes enabling high FFs of around 44% and a technologically important open circuit voltage of 1Volt.
Effect of molecular interactions on retention and selectivity in reversed-phase liquid chromatography.

Science.gov (United States)

Szepesy, László

2002-06-25

The linear solvation energy relationships (LSERs) have been applied in the last years for description and prediction of retention and selectivity in reversed-phase liquid chromatography with good results. Widely different stationary phases have been compared and characterized by LSERs. In recent publications the influence of the type of the organic moderator and the composition of the mobile phase have also been described. However, the influence of the molecular properties of the solutes to be separated has never been discussed. According to the LSER model variation in retention factors (log k) with solute structure can be related to their potential for various intermolecular interactions. The retention factor is given as the sum of the terms of the LSER equation representing various types of molecular interactions. For this reason the influence of the structure and molecular properties of the solutes to be separated can also be investigated using the LSER equation. In this study we shall demonstrate how the specific molecular interactions influence chromatographic retention and selectivity. We intend to show that retention and selectivity depend on all participants of the system. In addition to the structure and properties of the stationary phase and the type and composition of the mobile phase the molecular properties of the solutes, characterized by the solvation parameters, will also influence the type and extent of the various molecular interactions governing retention and selectivity.
Structural, dynamic, electronic, and vibrational properties of flexible, intermediate, and stressed rigid As-Se glasses and liquids from first principles molecular dynamics

Energy Technology Data Exchange (ETDEWEB)

Bauchy, M. [Department of Civil and Environmental Engineering, University of California, Los Angeles, California 90095-1593 (United States); Kachmar, A. [Laboratoire de Physique Théorique de la Matière Condensée, Université Pierre et Marie Curie, 4 Place Jussieu, F-75252 Paris Cedex 05 (France); Qatar Environment and Energy Research Institute, Qatar Foundation, P.O. Box 5825, Doha (Qatar); Micoulaut, M., E-mail: mmi@lptl.jussieu.fr [Laboratoire de Physique Théorique de la Matière Condensée, Université Pierre et Marie Curie, 4 Place Jussieu, F-75252 Paris Cedex 05 (France)

2014-11-21

The structural, vibrational, electronic, and dynamic properties of amorphous and liquid As{sub x}Se{sub 1-x} (0.10 Molecular Dynamics. Within the above range of compositions, thresholds, and anomalies are found in the behavior of reciprocal and real space properties that can be correlated to the experimental location of the Boolchand intermediate phase in these glassy networks, observed at 0.27
The PdBI arcsecond whirlpool survey (PAWS): Environmental dependence of giant molecular cloud properties in M51

International Nuclear Information System (INIS)

Colombo, Dario; Hughes, Annie; Schinnerer, Eva; Meidt, Sharon E.; Leroy, Adam K.; Pety, Jérôme; Dumas, Gaëlle; Schuster, Karl F.; Dobbs, Clare L.; García-Burillo, Santiago; Thompson, Todd A.; Kramer, Carsten

2014-01-01

Using data from the PdBI Arcsecond Whirlpool Survey (PAWS), we have generated the largest extragalactic giant molecular cloud (GMC) catalog to date, containing 1507 individual objects. GMCs in the inner M51 disk account for only 54% of the total 12 CO(1-0) luminosity of the survey, but on average they exhibit physical properties similar to Galactic GMCs. We do not find a strong correlation between the GMC size and velocity dispersion, and a simple virial analysis suggests that ∼30% of GMCs in M51 are unbound. We have analyzed the GMC properties within seven dynamically motivated galactic environments, finding that GMCs in the spiral arms and in the central region are brighter and have higher velocity dispersions than inter-arm clouds. Globally, the GMC mass distribution does not follow a simple power-law shape. Instead, we find that the shape of the mass distribution varies with galactic environment: the distribution is steeper in inter-arm region than in the spiral arms, and exhibits a sharp truncation at high masses for the nuclear bar region. We propose that the observed environmental variations in the GMC properties and mass distributions are a consequence of the combined action of large-scale dynamical processes and feedback from high-mass star formation. We describe some challenges of using existing GMC identification techniques for decomposing the 12 CO(1-0) emission in molecule-rich environments, such as M51's inner disk.
Bayesian semiparametric regression models to characterize molecular evolution

Directory of Open Access Journals (Sweden)

Datta Saheli

2012-10-01

Full Text Available Abstract Background Statistical models and methods that associate changes in the physicochemical properties of amino acids with natural selection at the molecular level typically do not take into account the correlations between such properties. We propose a Bayesian hierarchical regression model with a generalization of the Dirichlet process prior on the distribution of the regression coefficients that describes the relationship between the changes in amino acid distances and natural selection in protein-coding DNA sequence alignments. Results The Bayesian semiparametric approach is illustrated with simulated data and the abalone lysin sperm data. Our method identifies groups of properties which, for this particular dataset, have a similar effect on evolution. The model also provides nonparametric site-specific estimates for the strength of conservation of these properties. Conclusions The model described here is distinguished by its ability to handle a large number of amino acid properties simultaneously, while taking into account that such data can be correlated. The multi-level clustering ability of the model allows for appealing interpretations of the results in terms of properties that are roughly equivalent from the standpoint of molecular evolution.
Wettability, optical properties and molecular structure of plasma polymerized diethylene glycol dimethyl ether

Energy Technology Data Exchange (ETDEWEB)

Azevedo, T C A M; Algatti, M A; Mota, R P; Honda, R Y; Kayama, M E; Kostov, K G; Fernandes, R S [FEG-DFQ-UNESP, Av. Ariberto Pereira da Cunha 333, 12516-410 - Guaratingueta, SP (Brazil); Cruz, N C; Rangel, E C, E-mail: algatti@feg.unesp.b [UNESP, Avenida Tres de Marco, 511, 18087-180 Sorocaba, SP (Brazil)

2009-05-01

Modern industry has frequently employed ethylene glycol ethers as monomers in plasma polymerization process to produce different types of coatings. In this work we used a stainless steel plasma reactor to grow thin polymeric films from low pressure RF excited plasma of diethylene glycol dimethyl ether. Plasmas were generated at 5W RF power in the range of 16 Pa to 60 Pa. The molecular structure of plasma polymerized films and their optical properties were analyzed by Fourier Transform Infrared Spectroscopy (FTIR) and Ultraviolet-Visible Spectroscopy, respectively. The IR spectra show C-H stretching at 3000-2900 cm{sup -1}, C=O stretching at 1730-1650 cm{sup -1}, C-H bending at 1440-1380 cm{sup -1}, C-O and C-O-C stretching at 1200-1000 cm{sup -1}. The refraction index was around 1.5 and the optical gap calculated from absorption coefficient presented value near 3.8 eV. Water contact angle of the films ranged from 40 deg. to 35 deg. with corresponding surface energy from 66 to 73x10{sup -7} J. Because of its favorable optical and hydrophilic characteristics these films can be used in ophthalmic industries as glass lenses coatings.
2012 Gordon Research Conference On Molecular And Ionic Clusters

International Nuclear Information System (INIS)

McCoy, Anne

2012-01-01

The Gordon Research Conference on 'Molecular and Ionic Clusters' focuses on clusters, which are the initial molecular species found in gases when condensation begins to occur. Condensation can take place solely from molecules interacting with each other, mostly at low temperatures, or when molecules condense around charged particles (electrons, protons, metal cations, molecular ions), producing ion molecule clusters. These clusters provide models for solvation, allow a pristine look at geometric as well as electronic structures of molecular complexes or matter in general, their interaction with radiation, their reactivity, their thermodynamic properties and, in particular, the related dynamics. This conference focuses on new ways to make clusters composed of different kinds of molecules, new experimental techniques to investigate the properties of the clusters and new theoretical methods with which to calculate the structures, dynamical motions and energetics of the clusters. Some of the main experimental methods employed include molecular beams, mass spectrometry, laser spectroscopy (from infrared to XUV; in the frequency as well as the time domain) and photoelectron spectroscopy. Techniques include laser absorption spectroscopy, laser induced fluorescence, resonance enhanced photoionization, mass-selected photodissociation, photofragment imaging, ZEKE photoelectron spectroscopy, etc. From the theoretical side, this conference highlights work on potential surfaces and measurable properties of the clusters. The close ties between experiment, theory and computation have been a hallmark of the Gordon Research Conference on Molecular and Ionic Clusters. In the 2012 meeting, we plan to have sessions that will focus on topics including: (1) The use of cluster studies to probe fundamental phenomena; (2) Finite size effects on structure and thermodynamics; (3) Intermolecular forces and cooperative effects; (4) Molecular clusters as models for solvation; and (5) Studies of
Engineering controllable bidirectional molecular motors based on myosin

Science.gov (United States)

Chen, Lu; Nakamura, Muneaki; Schindler, Tony D.; Parker, David; Bryant, Zev

2012-04-01

Cytoskeletal motors drive the transport of organelles and molecular cargoes within cells and have potential applications in molecular detection and diagnostic devices. Engineering molecular motors with controllable properties will allow selective perturbation of mechanical processes in living cells and provide optimized device components for tasks such as molecular sorting and directed assembly. Biological motors have previously been modified by introducing activation/deactivation switches that respond to metal ions and other signals. Here, we show that myosin motors can be engineered to reversibly change their direction of motion in response to a calcium signal. Building on previous protein engineering studies and guided by a structural model for the redirected power stroke of myosin VI, we have constructed bidirectional myosins through the rigid recombination of structural modules. The performance of the motors was confirmed using gliding filament assays and single fluorophore tracking. Our strategy, in which external signals trigger changes in the geometry and mechanics of myosin lever arms, should make it possible to achieve spatiotemporal control over a range of motor properties including processivity, stride size and branchpoint turning.
Photochromic molecules as building blocks for molecular electronics.

Science.gov (United States)

Peter, Belser

2010-01-01

Energy and electron transfer processes can be easily induced by a photonic excitation of a donor metal complex ([Ru(bpy)3]2), which is connected via a wire-type molecular fragment to an acceptor metal complex ([Os(bpy)3]2+). The rate constant for the transfer process can be determined by emission measurements of the two connected metal complexes. The system can be modified by incorporation of a switching unit or an interrupter into the wire, influencing the transfer process. Such a molecular device corresponds to an interrupter, mimic the same function applied in molecular electronics. We have used organic switches, which show photochromic properties. By irradiation with light of different wavelengths, the switch changes its functionality by a photochemical reaction from an OFF- to an ON-state and vice versa. The ON- respectively OFF-state is manifested by a color change but also in different conductivity properties for energy and electron transfer processes. Therefore, the mentioned molecular device can work as a simple interrupter, controlling the rate of the transfer processes.
Molecular Structure of Membrane Tethers

NARCIS (Netherlands)

Baoukina, Svetlana; Marrink, Siewert J.; Tieleman, D. Peter

2012-01-01

Membrane tethers are nanotubes formed by a lipid bilayer. They play important functional roles in cell biology and provide an experimental window on lipid properties. Tethers have been studied extensively in experiments and described by theoretical models, but their molecular structure remains
Controlling charge current through a DNA based molecular transistor

Energy Technology Data Exchange (ETDEWEB)

Behnia, S., E-mail: s.behnia@sci.uut.ac.ir; Fathizadeh, S.; Ziaei, J.

2017-01-05

Molecular electronics is complementary to silicon-based electronics and may induce electronic functions which are difficult to obtain with conventional technology. We have considered a DNA based molecular transistor and study its transport properties. The appropriate DNA sequence as a central chain in molecular transistor and the functional interval for applied voltages is obtained. I–V characteristic diagram shows the rectifier behavior as well as the negative differential resistance phenomenon of DNA transistor. We have observed the nearly periodic behavior in the current flowing through DNA. It is reported that there is a critical gate voltage for each applied bias which above it, the electrical current is always positive. - Highlights: • Modeling a DNA based molecular transistor and studying its transport properties. • Choosing the appropriate DNA sequence using the quantum chaos tools. • Choosing the functional interval for voltages via the inverse participation ratio tool. • Detecting the rectifier and negative differential resistance behavior of DNA.
Thermodynamic properties of fluids from Fluctuation Solution Theory

International Nuclear Information System (INIS)

O'Connell, J.P.

1990-01-01

Fluctuation Theory develops exact relations between integrals of molecular correlation functions and concentration derivatives of pressure and chemical potential. These quantities can be usefully correlated, particularly for mechanical and thermal properties of pure and mixed dense fluids and for activities of strongly nonideal liquid solutions. The expressions yield unique formulae for the desirable thermodynamic properties of activity and density. The molecular theory origins of the flucuation properties, their behavior for systems of technical interest and some of their successful correlations will be described. Suggestions for fruitful directions will be suggested

Molecular Cloning and Pharmacological Properties of an Acidic PLA2 from Bothrops pauloensis Snake Venom

Directory of Open Access Journals (Sweden)

Francis Barbosa Ferreira

2013-12-01

Full Text Available In this work, we describe the molecular cloning and pharmacological properties of an acidic phospholipase A2 (PLA2 isolated from Bothrops pauloensis snake venom. This enzyme, denominated BpPLA2-TXI, was purified by four chromatographic steps and represents 2.4% of the total snake venom protein content. BpPLA2-TXI is a monomeric protein with a molecular mass of 13.6 kDa, as demonstrated by Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF analysis and its theoretical isoelectric point was 4.98. BpPLA2-TXI was catalytically active and showed some pharmacological effects such as inhibition of platelet aggregation induced by collagen or ADP and also induced edema and myotoxicity. BpPLA2-TXI displayed low cytotoxicity on TG-180 (CCRF S 180 II and Ovarian Carcinoma (OVCAR-3, whereas no cytotoxicity was found in regard to MEF (Mouse Embryonic Fibroblast and Sarcoma 180 (TIB-66. The N-terminal sequence of forty-eight amino acid residues was determined by Edman degradation. In addition, the complete primary structure of 122 amino acids was deduced by cDNA from the total RNA of the venom gland using specific primers, and it was significantly similar to other acidic D49 PLA2s. The phylogenetic analyses showed that BpPLA2-TXI forms a group with other acidic D49 PLA2s from the gender Bothrops, which are characterized by a catalytic activity associated with anti-platelet effects.
Vibrational spectra (FT-IR, FT-Raman), frontier molecular orbital, first hyperpolarizability, NBO analysis and thermodynamics properties of Piroxicam by HF and DFT methods

Science.gov (United States)

Suresh, S.; Gunasekaran, S.; Srinivasan, S.

2015-03-01

The solid phase FT-IR and FT-Raman spectra of 4-Hydroxy-2-methyl-N-(2-pyridinyl)-2H-1,2-benzothiazine-3-carboxamide-1,1-dioxide (Piroxicam) have been recorded in the region 4000-400 and 4000-100 cm-1 respectively. The molecular geometry, harmonic vibrational frequencies and bonding features of piroxicam in the ground state have been calculated by Hartree-Fock (HF) and density functional theory (DFT) methods using 6-311++G(d,p) basis set. The calculated harmonic vibrational frequencies are scaled and they are compared with experimental obtained by FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of the title compound has been made on the basis of the calculated potential energy distribution (PED). The electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MESP) are also performed. The linear polarizability (α) and the first order hyper polarizability (β) values of the title compound have been computed. The molecular stability arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis.
Control of molecular rotation with an optical centrifuge

Science.gov (United States)

Korobenko, Aleksey

2017-04-01

The main purpose of this work is the experimental study of the applicability of an optical centrifuge - a novel tool, utilizing non-resonant broadband laser radiation to excite molecular rotation - to produce and control molecules in extremely high rotational states, so called molecular ``super rotors'', and to study their optical, magnetic, acoustic, hydrodynamic and quantum mechanical properties.
The molecular mechanism of gene-radiotherapy of tumor

International Nuclear Information System (INIS)

Zhu Xian

2004-01-01

Gene-radiotherapy of tumor is a new method which is induced by ionizing radiation. The molecular mechanism is to activate various molecular target by many ways and induce the apoptosis of tumor cell. It is a gene therapy based on the radiation-inducible property of the Egr-1 gene. It has good application prospect in therapy of tumor
Multimedia environmental chemical partitioning from molecular information

International Nuclear Information System (INIS)

Martinez, Izacar; Grifoll, Jordi; Giralt, Francesc; Rallo, Robert

2010-01-01

The prospect of assessing the environmental distribution of chemicals directly from their molecular information was analyzed. Multimedia chemical partitioning of 455 chemicals, expressed in dimensionless compartmental mass ratios, was predicted by SimpleBox 3, a Level III Fugacity model, together with the propagation of reported uncertainty for key physicochemical and transport properties, and degradation rates. Chemicals, some registered in priority lists, were selected according to the availability of experimental property data to minimize the influence of predicted information in model development. Chemicals were emitted in air or water in a fixed geographical scenario representing the Netherlands and characterized by five compartments (air, water, sediments, soil and vegetation). Quantitative structure-fate relationship (QSFR) models to predict mass ratios in different compartments were developed with support vector regression algorithms. A set of molecular descriptors, including the molecular weight and 38 counts of molecular constituents were adopted to characterize the chemical space. Out of the 455 chemicals, 375 were used for training and testing the QSFR models, while 80 were excluded from model development and were used as an external validation set. Training and test chemicals were selected and the domain of applicability (DOA) of the QSFRs established by means of self-organizing maps according to structural similarity. Best results were obtained with QSFR models developed for chemicals belonging to either the class [C] and [C; O], or the class with at least one heteroatom different than oxygen in the structure. These two class-specific models, with respectively 146 and 229 chemicals, showed a predictive squared coefficient of q 2 ≥ 0.90 both for air and water, which respectively dropped to q 2 ∼ 0.70 and 0.40 for outlying chemicals. Prediction errors were of the same order of magnitude as the deviations associated to the uncertainty of the
Molecular mechanics of DNA bricks: in situ structure, mechanical properties and ionic conductivity

International Nuclear Information System (INIS)

Slone, Scott Michael; Li, Chen-Yu; Aksimentiev, Aleksei; Yoo, Jejoong

2016-01-01

The DNA bricks method exploits self-assembly of short DNA fragments to produce custom three-dimensional objects with subnanometer precision. In contrast to DNA origami, the DNA brick method permits a variety of different structures to be realized using the same library of DNA strands. As a consequence of their design, however, assembled DNA brick structures have fewer interhelical connections in comparison to equivalent DNA origami structures. Although the overall shape of the DNA brick objects has been characterized and found to conform to the features of the target designs, the microscopic properties of DNA brick objects remain yet to be determined. Here, we use the all-atom molecular dynamics method to directly compare the structure, mechanical properties and ionic conductivity of DNA brick and DNA origami structures different only by internal connectivity of their consistituent DNA strands. In comparison to equivalent DNA origami structures, the DNA brick structures are found to be less rigid and less dense and have a larger cross-section area normal to the DNA helix direction. At the microscopic level, the junction in the DNA brick structures are found to be right-handed, similar to the structure of individual Holliday junctions (HJ) in solution, which contrasts with the left-handed structure of HJ in DNA origami. Subject to external electric field, a DNA brick plate is more leaky to ions than an equivalent DNA origami plate because of its lower density and larger cross-section area. Overall, our results indicate that the structures produced by the DNA brick method are fairly similar in their overall appearance to those created by the DNA origami method but are more compliant when subject to external forces, which likely is a consequence of their single crossover design. (paper)
Molecular basis of the triple negative breast cancer

Directory of Open Access Journals (Sweden)

Ayse Feyda Nursal

2015-06-01

Full Text Available Breast cancer is the most common type of cancer in women and more than 1 million breast cancer cases are diagnosed each year all over the world. Breast cancer is a complex and heterogeneous disease in terms of its molecular structure, mutation type, metastase properties, clinical course and therapeutic response. Breast cancer is divided into subtypes based on expression properties of molecular markers as estrogen receptor, progestron receptor, human epidermal growth factor receptor 2. Triple-negative breast cancer is characterized by the lack of tumors that estrogen receptor, progestron receptor, human epidermal growth factor receptor 2 gene expression. These type of tumors lead to agressive clinical course due to unresponsiveness to systemic endocrine therapy and poor prognosis. Triple negative breast cancer constitutes 10-20% of all breast cancers. It affects generally young and African-American women. Triple negative breast cancer have several subtypes based on the gene expression properties. The majority of them are basal-like breast cancers. In this review, current literature is revised and summarized with respect to the molecular basis of triple negative cancers. [Archives Medical Review Journal 2015; 24(2.000: 251-259
Physical properties of organic fullerene cocrystals

Science.gov (United States)

Macovez, Roberto

2017-12-01

The basic facts and fundamental properties of binary fullerene cocrystals are reviewed, focusing especially on solvates and salts of Buckminsterfullerene (C60), and hydrates of hydrophilic C60 derivatives. The examined properties include the lattice structure and the presence of orientational disorder and/or rotational dynamics (of both fullerenes and cocrystallizing moieties), thermodynamic properties such as decomposition enthalpies, and charge transport properties. Both thermodynamic properties and molecular orientational disorder shed light on the extent of intermolecular interactions in these binary solid-state systems. Comparison is carried out also with pristine fullerite and with the solid phases of functionalized C60. Interesting experimental findings on binary fullerene cocrystals include the simultaneous occurrence of rotations of both constituent molecular species, crystal morphologies reminiscent of quasi-crystalline behaviour, the observation of proton conduction in hydrate solids of hydrophilic fullerene derivatives, and the production of super-hard carbon materials by application of high pressures on solvated fullerene crystals.
Current's Fluctuations through Molecular Wires Composed of Thiophene Rings.

Science.gov (United States)

Ojeda Silva, Judith Helena; Cortés Peñaranda, Juan Camilo; Gómez Castaño, Jovanny A; Duque, Carlos Alberto

2018-04-11

We study theoretically the electronic transport and quantum fluctuations in single-molecule systems using thiophene rings as integrated elementary functions, as well as the dependence of these properties with the increase of the coupled rings, i.e., as a quantum wire. In order to analyze the current flow through these molecular systems, the thiophene rings are considered to be connected to metal contacts, which, in general terms, will be related to the application of voltages (bias voltages or gate voltages) to generate non-equilibrium behavior between the contacts. Due to the nonlinear behavior that is generated when said voltages are applied, it is possible to observe quantum fluctuations in the transport properties of these molecular wires. For the calculation of the transport properties, we applied a tight-binding approach using the Landauer-Büttiker formalism and the Fischer-Lee relationship, by means of a semi-analytic Green's function method within a real-space renormalization (decimation procedure). Our results showed an excellent agreement with results using a tight-binding model with a minimal number of parameters reported so far for these molecular systems.
Fulleropyrrolidine end-capped molecular wires for molecular electronics--synthesis, spectroscopic, electrochemical, and theoretical characterization

DEFF Research Database (Denmark)

Sørensen, Jakob Kryger; Fock, Jeppe; Pedersen, Anders Holmen

2011-01-01

In continuation of previous studies showing promising metal-molecule contact properties a variety of C(60) end-capped "molecular wires" for molecular electronics were prepared by variants of the Prato 1,3-dipolar cycloaddition reaction. Either benzene or fluorene was chosen as the central wire...... state. However, the fluorescence of C(60) was quenched by charge transfer from the wire to C(60). Quantum chemical calculations predict and explain the collapse of coherent electronic transmission through one of the fulleropyrrolidine-terminated molecular wires......., and synthetic protocols for derivatives terminated with one or two fullero[c]pyrrolidine "electrode anchoring" groups were developed. An aryl-substituted aziridine could in some cases be employed directly as the azomethine ylide precursor for the Prato reaction without the need of having an electron...
A Prediction of the Damping Properties of Hindered Phenol AO-60/polyacrylate Rubber (AO-60/ACM) Composites through Molecular Dynamics Simulation

Science.gov (United States)

Yang, Da-Wei; Zhao, Xiu-Ying; Zhang, Geng; Li, Qiang-Guo; Wu, Si-Zhu

2016-05-01

Molecule dynamics (MD) simulation, a molecular-level method, was applied to predict the damping properties of AO-60/polyacrylate rubber (AO-60/ACM) composites before experimental measures were performed. MD simulation results revealed that two types of hydrogen bond, namely, type A (AO-60) -OH•••O=C- (ACM), type B (AO-60) - OH•••O=C- (AO-60) were formed. Then, the AO-60/ACM composites were fabricated and tested to verify the accuracy of the MD simulation through dynamic mechanical thermal analysis (DMTA). DMTA results showed that the introduction of AO-60 could remarkably improve the damping properties of the composites, including the increase of glass transition temperature (Tg) alongside with the loss factor (tan δ), also indicating the AO-60/ACM(98/100) had the best damping performance amongst the composites which verified by the experimental.
Gas sorption and barrier properties of polymeric membranes from molecular dynamics and Monte Carlo simulations.

Science.gov (United States)

Cozmuta, Ioana; Blanco, Mario; Goddard, William A

2007-03-29

It is important for many industrial processes to design new materials with improved selective permeability properties. Besides diffusion, the molecule's solubility contributes largely to the overall permeation process. This study presents a method to calculate solubility coefficients of gases such as O2, H2O (vapor), N2, and CO2 in polymeric matrices from simulation methods (Molecular Dynamics and Monte Carlo) using first principle predictions. The generation and equilibration (annealing) of five polymer models (polypropylene, polyvinyl alcohol, polyvinyl dichloride, polyvinyl chloride-trifluoroethylene, and polyethylene terephtalate) are extensively described. For each polymer, the average density and Hansen solubilities over a set of ten samples compare well with experimental data. For polyethylene terephtalate, the average properties between a small (n = 10) and a large (n = 100) set are compared. Boltzmann averages and probability density distributions of binding and strain energies indicate that the smaller set is biased in sampling configurations with higher energies. However, the sample with the lowest cohesive energy density from the smaller set is representative of the average of the larger set. Density-wise, low molecular weight polymers tend to have on average lower densities. Infinite molecular weight samples do however provide a very good representation of the experimental density. Solubility constants calculated with two ensembles (grand canonical and Henry's constant) are equivalent within 20%. For each polymer sample, the solubility constant is then calculated using the faster (10x) Henry's constant ensemble (HCE) from 150 ps of NPT dynamics of the polymer matrix. The influence of various factors (bad contact fraction, number of iterations) on the accuracy of Henry's constant is discussed. To validate the calculations against experimental results, the solubilities of nitrogen and carbon dioxide in polypropylene are examined over a range of
Molecularly imprinted nanoparticles with recognition properties towards a laminin H-Tyr-Ile-Gly-Ser-Arg-OH sequence for tissue engineering applications

International Nuclear Information System (INIS)

Rosellini, Elisabetta; Barbani, Niccoletta; Giusti, Paolo; Ciardelli, Gianluca; Cristallini, Caterina

2010-01-01

Nanotechnology is an emerging field that promises to revolutionize medicine and is increasingly used in tissue engineering applications. Our research group proposed for the first time molecular imprinting as a new nanotechnology for the creation of advanced synthetic support structures for cell adhesion and proliferation. The aim of this work was the synthesis and characterization of molecularly imprinted polymers with recognition properties towards a laminin peptide sequence and their application as functionalization structures in the development of bioactive materials. Nanoparticles with an average diameter of 200 nm were synthesized by precipitation polymerization of methacrylic acid in the presence of the template molecule and trimethylpropane trimethacrylate as the cross-linking agent. The imprinted nanoparticles showed good performance in terms of recognition capacity and selectivity. The cytotoxicity tests showed normal vitality of C2C12 myoblasts cultured in the medium that was put in contact with the imprinted polymers. After the deposition on the polymeric film surface, the imprinted particles maintained their specific recognition and rebinding behaviour, showing an even higher quantitative binding than free nanoparticles. Preliminary in vitro cell culture tests demonstrated the ability of functionalized materials to promote cell adhesion, proliferation and differentiation, suggesting that molecular imprinting can be used as an innovative functionalization technique.
Black molecular adsorber coatings for spaceflight applications

Science.gov (United States)

Abraham, Nithin S.; Hasegawa, Mark M.; Straka, Sharon A.

2014-09-01

The molecular adsorber coating is a new technology that was developed to mitigate the risk of on-orbit molecular contamination on spaceflight missions. The application of this coating would be ideal near highly sensitive, interior surfaces and instruments that are negatively impacted by outgassed molecules from materials, such as plastics, adhesives, lubricants, epoxies, and other similar compounds. This current, sprayable paint technology is comprised of inorganic white materials made from highly porous zeolite. In addition to good adhesion performance, thermal stability, and adsorptive capability, the molecular adsorber coating offers favorable thermal control characteristics. However, low reflectivity properties, which are typically offered by black thermal control coatings, are desired for some spaceflight applications. For example, black coatings are used on interior surfaces, in particular, on instrument baffles for optical stray light control. Similarly, they are also used within light paths between optical systems, such as telescopes, to absorb light. Recent efforts have been made to transform the white molecular adsorber coating into a black coating with similar adsorptive properties. This result is achieved by optimizing the current formulation with black pigments, while still maintaining its adsorption capability for outgassing control. Different binder to pigment ratios, coating thicknesses, and spray application techniques were explored to develop a black version of the molecular adsorber coating. During the development process, coating performance and adsorption characteristics were studied. The preliminary work performed on black molecular adsorber coatings thus far is very promising. Continued development and testing is necessary for its use on future contamination sensitive spaceflight missions.
Molecular structure of hybrid imino-chalcone in the solid state: X-ray diffraction, spectroscopy study and third-order nonlinear optical properties

Science.gov (United States)

Custodio, J. M. F.; Santos, F. G.; Vaz, W. F.; Cunha, C. E. P.; Silveira, R. G.; Anjos, M. M.; Campos, C. E. M.; Oliveira, G. R.; Martins, F. T.; da Silva, C. C.; Valverde, C.; Baseia, B.; Napolitano, H. B.

2018-04-01

A comprehensive structural study of the compound (2E)-1-((E)-4-(4-methoxybenzylideneamino)phenyl)-3-(4-methoxyphenyl)prop-2-en-1-one was carried out in this work. Single crystal X-ray diffraction (SCXRD), X-ray powder diffraction (XRPD), NMR, Raman and Infrared spectroscopies, and DFT calculations were performed for characterization of this iminochalcone hybrid. Intermolecular interactions were described by Hirshfeld surface analysis derived from crystal structure. Reactivity and intramolecular charge transfer were investigated using the frontier molecular orbitals and molecular electrostatic potential. In addition, we have calculated the Nonlinear Optical Properties at the CAM-B3LYP/6-311+g(d) level of theory in the presence of different solvents (gas-phase, acetone, chloroform, dichloromethane, dimethyl sulfoxide, ethanol, methanol, and water), being found meaningful NLO parameters for our compound. At last, there is a good agreement between calculated and experimental IR spectrum, allowing the assignment of some of normal vibrational modes of the iminochalcone hybrid.
Molecular dynamics simulation of ribosome jam

KAUST Repository

Matsumoto, Shigenori; Takagi, Fumiko; Shimada, Takashi; Ito, Nobuyasu

2011-01-01

We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We
Molecular dynamics study on the structural and dynamic properties of xanthan gum in a dilute solution under the effect of temperature

Science.gov (United States)

Ong, Ernest E. S.; O'Byrne, Sean; Liow, Jong-Leng

2018-04-01

Xanthan gum (XG) is considered one of the most industrially important polysaccharides, with applications ranging from food products such as ice creams and salad dressings to pharmaceuticals and oil well drilling fluids. The wide application of XG is due to its favourable rheological properties and its capability to resist degradation under a high shear or high temperature environment. It is generally accepted that both inter- and intramolecular interactions, including hydrogen bonding (HB), are responsible for its unique properties. To date, there is still a lack of comprehensive examination on the HB mechanism in polysaccharides. Therefore, the study proposed here was conducted using molecular dynamics (MD) simulations that are able to provide insights with an unparalleled temporal and spatial resolution. Since XG is used over a broad range of temperatures, the implications of thermal effect on the structure and molecular interactions of XG in an aqueous solution are discussed in this paper. MD simulations were run at an isobaric-isothermal condition with 1 atm target pressure and five temperatures ranging between 283K and 353K. From the simulation results, an increasingly extended conformation of XG is observed as the temperature rises, and this finding matches qualitatively with the results published in the literature. The radius of gyration, radial pair distribution functions and intramolecular HB of XG were also discussed. The outcomes of the present study may serve as a stepping stone for the future studies on polysaccharides using MD simulations.
Prediction of molecular properties using graph-theoretical invariants

Energy Technology Data Exchange (ETDEWEB)

Helal, N.L.; Steinhaeusler, F.; Winkler-Heil, R. [Inst. of Physics and Biophysics, Univ. of Salzburg, Salzburg (Austria); Eckl, P.M. [Inst. of Genetics and General Biology, Univ. of Salzburg, Salzburg (Austria)

2002-03-01

this study we intend to determine the biological action of certain alkylating agents, and to relate this data to one or more molecular descriptors. The compounds are ''similar'' in the sense that they each have a recognised mutagenic potency, and the employed molecular descriptors allow one to: (a) characterize the chemical structure quantitatively, (b) correlate the molecular descriptors with the determined mutagenic endpoints and (c) rank the chemical compounds and also reliably predict the action of other chemicals belonging to the same family, provided that data on the structure of these is available. (orig.)
The molecular spin filter constructed from 1D organic chain

International Nuclear Information System (INIS)

Chen, Wei; Xu, Ning; Wang, Baolin; Bian, Baoan

2014-01-01

We proposed a molecular spin filter, which is constructed from the 1D metallic organic chain (Fe n+1 (C 6 H 4 ) n ). The spin-polarized transport properties of the molecular spin filter are explored by combining density functional theory with nonequilibrium Green's function formalism. Theoretical results reveal that Fe n+1 (C 6 H 4 ) n molecular chain exhibits robust spin filtering effect, and only the spin-down electrons can transmit through the molecular chain. At the given bias voltage window [−1 eV,1 eV], the calculated spin filter efficiency is close to 100% in the case of n≥3. We find that the effect of spin polarization origin from both Fe n+1 and (C 6 H 4 ) n . In addition, negative difference resistance behavior appears in Fe n+1 (C 6 H 4 ) n molecular chain. The results can help us understand the spin transport properties of organic molecular chain. - Highlights: • Theoretical results reveal that Fe n+1 (C 6 H 4 ) n molecular chain exhibits robust spin filtering effect. • The effect of spin polarization origin from both of Fe n+1 and (C 6 H 4 ) n . • Negative difference resistance behavior appears in Fe n+1 (C 6 H 4 ) n molecular chain
Effect of native oxide layers on copper thin-film tensile properties: A reactive molecular dynamics study

Energy Technology Data Exchange (ETDEWEB)

Skarlinski, Michael D., E-mail: michael.skarlinski@rochester.edu [Materials Science Program, University of Rochester, Rochester, New York 14627 (United States); Quesnel, David J. [Materials Science Program, University of Rochester, Rochester, New York 14627 (United States); Department of Mechanical Engineering, University of Rochester, Rochester, New York 14627 (United States)

2015-12-21

Metal-oxide layers are likely to be present on metallic nano-structures due to either environmental exposure during use, or high temperature processing techniques such as annealing. It is well known that nano-structured metals have vastly different mechanical properties from bulk metals; however, difficulties in modeling the transition between metallic and ionic bonding have prevented the computational investigation of the effects of oxide surface layers. Newly developed charge-optimized many body [Liang et al., Mater. Sci. Eng., R 74, 255 (2013)] potentials are used to perform fully reactive molecular dynamics simulations which elucidate the effects that metal-oxide layers have on the mechanical properties of a copper thin-film. Simulated tensile tests are performed on thin-films while using different strain-rates, temperatures, and oxide thicknesses to evaluate changes in yield stress, modulus, and failure mechanisms. Findings indicate that copper-thin film mechanical properties are strongly affected by native oxide layers. The formed oxide layers have an amorphous structure with lower Cu-O bond-densities than bulk CuO, and a mixture of Cu{sub 2}O and CuO charge character. It is found that oxidation will cause modifications to the strain response of the elastic modulii, producing a stiffened modulii at low temperatures (<75 K) and low strain values (<5%), and a softened modulii at higher temperatures. While under strain, structural reorganization within the oxide layers facilitates brittle yielding through nucleation of defects across the oxide/metal interface. The oxide-free copper thin-film yielding mechanism is found to be a tensile-axis reorientation and grain creation. The oxide layers change the observed yielding mechanism, allowing for the inner copper thin-film to sustain an FCC-to-BCC transition during yielding. The mechanical properties are fit to a thermodynamic model based on classical nucleation theory. The fit implies that the oxidation of the

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