Adaptive frozen orbital treatment for the fragment molecular orbital method combined with density-functional tight-binding

Science.gov (United States)

Nishimoto, Yoshio; Fedorov, Dmitri G.

2018-02-01

The exactly analytic gradient is derived and implemented for the fragment molecular orbital (FMO) method combined with density-functional tight-binding (DFTB) using adaptive frozen orbitals. The response contributions which arise from freezing detached molecular orbitals on the border between fragments are computed by solving Z-vector equations. The accuracy of the energy, its gradient, and optimized structures is verified on a set of representative inorganic materials and polypeptides. FMO-DFTB is applied to optimize the structure of a silicon nano-wire, and the results are compared to those of density functional theory and experiment. FMO accelerates the DFTB calculation of a boron nitride nano-ring with 7872 atoms by a factor of 406. Molecular dynamics simulations using FMO-DFTB applied to a 10.7 μm chain of boron nitride nano-rings, consisting of about 1.2 × 106 atoms, reveal the rippling and twisting of nano-rings at room temperature.

Layered interfaces between immiscible liquids studied by density-functional theory and molecular-dynamics simulations.

Science.gov (United States)

Geysermans, P; Elyeznasni, N; Russier, V

2005-11-22

We present a study of the structure in the interface between two immiscible liquids by density-functional theory and molecular-dynamics calculations. The liquids are modeled by Lennard-Jones potentials, which achieve immiscibility by suppressing the attractive interaction between unlike particles. The density profiles of the liquids display oscillations only in a limited part of the simple liquid-phase diagram (rho,T). When approaching the liquid-vapor coexistence, a significant depletion appears while the layering behavior of the density profile vanishes. By analogy with the liquid-vapor interface and the analysis of the adsorption this behavior is suggested to be strongly related to the drying transition.

Molecular acidity: An accurate description with information-theoretic approach in density functional reactivity theory.

Science.gov (United States)

Cao, Xiaofang; Rong, Chunying; Zhong, Aiguo; Lu, Tian; Liu, Shubin

2018-01-15

Molecular acidity is one of the important physiochemical properties of a molecular system, yet its accurate calculation and prediction are still an unresolved problem in the literature. In this work, we propose to make use of the quantities from the information-theoretic (IT) approach in density functional reactivity theory and provide an accurate description of molecular acidity from a completely new perspective. To illustrate our point, five different categories of acidic series, singly and doubly substituted benzoic acids, singly substituted benzenesulfinic acids, benzeneseleninic acids, phenols, and alkyl carboxylic acids, have been thoroughly examined. We show that using IT quantities such as Shannon entropy, Fisher information, Ghosh-Berkowitz-Parr entropy, information gain, Onicescu information energy, and relative Rényi entropy, one is able to simultaneously predict experimental pKa values of these different categories of compounds. Because of the universality of the quantities employed in this work, which are all density dependent, our approach should be general and be applicable to other systems as well. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Fluids density functional theory and initializing molecular dynamics simulations of block copolymers

Science.gov (United States)

Brown, Jonathan R.; Seo, Youngmi; Maula, Tiara Ann D.; Hall, Lisa M.

2016-03-01

Classical, fluids density functional theory (fDFT), which can predict the equilibrium density profiles of polymeric systems, and coarse-grained molecular dynamics (MD) simulations, which are often used to show both structure and dynamics of soft materials, can be implemented using very similar bead-based polymer models. We aim to use fDFT and MD in tandem to examine the same system from these two points of view and take advantage of the different features of each methodology. Additionally, the density profiles resulting from fDFT calculations can be used to initialize the MD simulations in a close to equilibrated structure, speeding up the simulations. Here, we show how this method can be applied to study microphase separated states of both typical diblock and tapered diblock copolymers in which there is a region with a gradient in composition placed between the pure blocks. Both methods, applied at constant pressure, predict a decrease in total density as segregation strength or the length of the tapered region is increased. The predictions for the density profiles from fDFT and MD are similar across materials with a wide range of interfacial widths.

Ground-state densities from the Rayleigh-Ritz variation principle and from density-functional theory.

Science.gov (United States)

Kvaal, Simen; Helgaker, Trygve

2015-11-14

The relationship between the densities of ground-state wave functions (i.e., the minimizers of the Rayleigh-Ritz variation principle) and the ground-state densities in density-functional theory (i.e., the minimizers of the Hohenberg-Kohn variation principle) is studied within the framework of convex conjugation, in a generic setting covering molecular systems, solid-state systems, and more. Having introduced admissible density functionals as functionals that produce the exact ground-state energy for a given external potential by minimizing over densities in the Hohenberg-Kohn variation principle, necessary and sufficient conditions on such functionals are established to ensure that the Rayleigh-Ritz ground-state densities and the Hohenberg-Kohn ground-state densities are identical. We apply the results to molecular systems in the Born-Oppenheimer approximation. For any given potential v ∈ L(3/2)(ℝ(3)) + L(∞)(ℝ(3)), we establish a one-to-one correspondence between the mixed ground-state densities of the Rayleigh-Ritz variation principle and the mixed ground-state densities of the Hohenberg-Kohn variation principle when the Lieb density-matrix constrained-search universal density functional is taken as the admissible functional. A similar one-to-one correspondence is established between the pure ground-state densities of the Rayleigh-Ritz variation principle and the pure ground-state densities obtained using the Hohenberg-Kohn variation principle with the Levy-Lieb pure-state constrained-search functional. In other words, all physical ground-state densities (pure or mixed) are recovered with these functionals and no false densities (i.e., minimizing densities that are not physical) exist. The importance of topology (i.e., choice of Banach space of densities and potentials) is emphasized and illustrated. The relevance of these results for current-density-functional theory is examined.

Synthesis, Crystal Structure, Density Function Theory, Molecular ...

African Journals Online (AJOL)

Tropical Journal of Pharmaceutical Research February 2016; 15 (2): 385-392 ... tested for its antimicrobial activities and computational studies including density function test (DFT) and docking ... agonists [4], selective dopamine D3 and D4 ...

Explicit polarization (X-Pol) potential using ab initio molecular orbital theory and density functional theory.

Science.gov (United States)

Song, Lingchun; Han, Jaebeom; Lin, Yen-lin; Xie, Wangshen; Gao, Jiali

2009-10-29

The explicit polarization (X-Pol) method has been examined using ab initio molecular orbital theory and density functional theory. The X-Pol potential was designed to provide a novel theoretical framework for developing next-generation force fields for biomolecular simulations. Importantly, the X-Pol potential is a general method, which can be employed with any level of electronic structure theory. The present study illustrates the implementation of the X-Pol method using ab initio Hartree-Fock theory and hybrid density functional theory. The computational results are illustrated by considering a set of bimolecular complexes of small organic molecules and ions with water. The computed interaction energies and hydrogen bond geometries are in good accord with CCSD(T) calculations and B3LYP/aug-cc-pVDZ optimizations.

Molecular Electron Density Theory: A Modern View of Reactivity in Organic Chemistry

OpenAIRE

Luis R. Domingo

2016-01-01

A new theory for the study of the reactivity in Organic Chemistry, named Molecular Electron Density Theory (MEDT), is proposed herein. MEDT is based on the idea that while the electron density distribution at the ground state is responsible for physical and chemical molecular properties, as proposed by the Density Functional Theory (DFT), the capability for changes in electron density is responsible for molecular reactivity. Within MEDT, the reactivity in Organic Chemistry is studied through ...

Chemical insight from density functional modeling of molecular adsorption: Tracking the bonding and diffusion of anthracene derivatives on Cu(111) with molecular orbitals

Science.gov (United States)

Wyrick, Jonathan; Einstein, T. L.; Bartels, Ludwig

2015-03-01

We present a method of analyzing the results of density functional modeling of molecular adsorption in terms of an analogue of molecular orbitals. This approach permits intuitive chemical insight into the adsorption process. Applied to a set of anthracene derivates (anthracene, 9,10-anthraquinone, 9,10-dithioanthracene, and 9,10-diselenonanthracene), we follow the electronic states of the molecules that are involved in the bonding process and correlate them to both the molecular adsorption geometry and the species' diffusive behavior. We additionally provide computational code to easily repeat this analysis on any system.

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.

Molecular surface mesh generation by filtering electron density map.

Science.gov (United States)

Giard, Joachim; Macq, Benoît

2010-01-01

Bioinformatics applied to macromolecules are now widely spread and in continuous expansion. In this context, representing external molecular surface such as the Van der Waals Surface or the Solvent Excluded Surface can be useful for several applications. We propose a fast and parameterizable algorithm giving good visual quality meshes representing molecular surfaces. It is obtained by isosurfacing a filtered electron density map. The density map is the result of the maximum of Gaussian functions placed around atom centers. This map is filtered by an ideal low-pass filter applied on the Fourier Transform of the density map. Applying the marching cubes algorithm on the inverse transform provides a mesh representation of the molecular surface.

Molecular Surface Mesh Generation by Filtering Electron Density Map

Directory of Open Access Journals (Sweden)

Joachim Giard

2010-01-01

Full Text Available Bioinformatics applied to macromolecules are now widely spread and in continuous expansion. In this context, representing external molecular surface such as the Van der Waals Surface or the Solvent Excluded Surface can be useful for several applications. We propose a fast and parameterizable algorithm giving good visual quality meshes representing molecular surfaces. It is obtained by isosurfacing a filtered electron density map. The density map is the result of the maximum of Gaussian functions placed around atom centers. This map is filtered by an ideal low-pass filter applied on the Fourier Transform of the density map. Applying the marching cubes algorithm on the inverse transform provides a mesh representation of the molecular surface.

Role of physisorption states in molecular scattering: a semilocal density-functional theory study on O2/Ag(111).

Science.gov (United States)

Goikoetxea, I; Meyer, J; Juaristi, J I; Alducin, M; Reuter, K

2014-04-18

We simulate the scattering of O2 from Ag(111) with classical dynamics simulations performed on a six-dimensional potential energy surface calculated within semilocal density-functional theory. The enigmatic experimental trends that originally required the conjecture of two types of repulsive walls, arising from a physisorption and chemisorption part of the interaction potential, are fully reproduced. Given the inadequate description of the physisorption properties in semilocal density-functional theory, our work casts severe doubts on the prevalent notion to use molecular scattering data as indirect evidence for the existence of such states.

Canonical-ensemble extended Lagrangian Born-Oppenheimer molecular dynamics for the linear scaling density functional theory.

Science.gov (United States)

Hirakawa, Teruo; Suzuki, Teppei; Bowler, David R; Miyazaki, Tsuyoshi

2017-10-11

We discuss the development and implementation of a constant temperature (NVT) molecular dynamics scheme that combines the Nosé-Hoover chain thermostat with the extended Lagrangian Born-Oppenheimer molecular dynamics (BOMD) scheme, using a linear scaling density functional theory (DFT) approach. An integration scheme for this canonical-ensemble extended Lagrangian BOMD is developed and discussed in the context of the Liouville operator formulation. Linear scaling DFT canonical-ensemble extended Lagrangian BOMD simulations are tested on bulk silicon and silicon carbide systems to evaluate our integration scheme. The results show that the conserved quantity remains stable with no systematic drift even in the presence of the thermostat.

Molecular docking and spectroscopic investigations aided by density functional theory of Parkinson's drug 2-(3,4-dihydroxyphenyl)ethylamine

Science.gov (United States)

Sherlin, Y. Sheeba; Vijayakumar, T.; Roy, S. D. D.; Jayakumar, V. S.

2018-05-01

Molecular geometry of Parkinson's drug 2-(3,4-Dihydroxyphenyl)ethylamine hydrochloride (Dopamine, DA) has been evaluated and compared with experimental XRD data. Molecular docking and vibrational spectral analysis of DA have been carried out using FT-Raman and FT-IR spectra aided by Density Functional Theory at B3LYP/6-311++G(d,p). The present investigation deals with the analysis of structural and spectral features responsible for drug activities, nature of hydrogen bonding interactions of the molecule and the correlation of Parkinson's nature with its molecular structural features.

Fast Computation of Solvation Free Energies with Molecular Density Functional Theory: Thermodynamic-Ensemble Partial Molar Volume Corrections.

Science.gov (United States)

Sergiievskyi, Volodymyr P; Jeanmairet, Guillaume; Levesque, Maximilien; Borgis, Daniel

2014-06-05

Molecular density functional theory (MDFT) offers an efficient implicit-solvent method to estimate molecule solvation free-energies, whereas conserving a fully molecular representation of the solvent. Even within a second-order approximation for the free-energy functional, the so-called homogeneous reference fluid approximation, we show that the hydration free-energies computed for a data set of 500 organic compounds are of similar quality as those obtained from molecular dynamics free-energy perturbation simulations, with a computer cost reduced by 2-3 orders of magnitude. This requires to introduce the proper partial volume correction to transform the results from the grand canonical to the isobaric-isotherm ensemble that is pertinent to experiments. We show that this correction can be extended to 3D-RISM calculations, giving a sound theoretical justification to empirical partial molar volume corrections that have been proposed recently.

Molecular Electron Density Theory: A Modern View of Reactivity in Organic Chemistry.

Science.gov (United States)

Domingo, Luis R

2016-09-30

A new theory for the study of the reactivity in Organic Chemistry, named Molecular Electron Density Theory (MEDT), is proposed herein. MEDT is based on the idea that while the electron density distribution at the ground state is responsible for physical and chemical molecular properties, as proposed by the Density Functional Theory (DFT), the capability for changes in electron density is responsible for molecular reactivity. Within MEDT, the reactivity in Organic Chemistry is studied through a rigorous quantum chemical analysis of the changes of the electron density as well as the energies associated with these changes along the reaction path in order to understand experimental outcomes. Studies performed using MEDT allow establishing a modern rationalisation and to gain insight into molecular mechanisms and reactivity in Organic Chemistry.

Molecular Electron Density Theory: A Modern View of Reactivity in Organic Chemistry

Directory of Open Access Journals (Sweden)

Luis R. Domingo

2016-09-01

Full Text Available A new theory for the study of the reactivity in Organic Chemistry, named Molecular Electron Density Theory (MEDT, is proposed herein. MEDT is based on the idea that while the electron density distribution at the ground state is responsible for physical and chemical molecular properties, as proposed by the Density Functional Theory (DFT, the capability for changes in electron density is responsible for molecular reactivity. Within MEDT, the reactivity in Organic Chemistry is studied through a rigorous quantum chemical analysis of the changes of the electron density as well as the energies associated with these changes along the reaction path in order to understand experimental outcomes. Studies performed using MEDT allow establishing a modern rationalisation and to gain insight into molecular mechanisms and reactivity in Organic Chemistry.

Density-Functional formalism

International Nuclear Information System (INIS)

Szasz, L.; Berrios-Pagan, I.; McGinn, G.

1975-01-01

A new Density-Functional formula is constructed for atoms. The kinetic energy of the electron is divided into two parts: the kinetic self-energy and the orthogonalization energy. Calculations were made for the total energies of neutral atoms, positive ions and for the He isoelectronic series. For neutral atoms the results match the Hartree-Fock energies within 1% for atoms with N 36 the results generally match the HF energies within 0.1%. For positive ions the results are fair; for the molecular applications a simplified model is developed in which the kinetic energy consists of the Weizsaecker term plus the Fermi energy reduced by a continuous function. (orig.) [de

Bridging scales from molecular simulations to classical thermodynamics: density functional theory of capillary condensation in nanopores

International Nuclear Information System (INIS)

Neimark, Alexander V; Ravikovitch, Peter I; Vishnyakov, Aleksey

2003-01-01

With the example of the capillary condensation of Lennard-Jones fluid in nanopores ranging from 1 to 10 nm, we show that the non-local density functional theory (NLDFT) with properly chosen parameters of intermolecular interactions bridges the scale gap from molecular simulations to macroscopic thermodynamics. On the one hand, NLDFT correctly approximates the results of Monte Carlo simulations (shift of vapour-liquid equilibrium, spinodals, density profiles, adsorption isotherms) for pores wider than about 2 nm. On the other hand, NLDFT smoothly merges (above 7-10 nm) with the Derjaguin-Broekhoff-de Boer equations which represent augmented Laplace-Kelvin equations of capillary condensation and desorption

Subsystem density functional theory with meta-generalized gradient approximation exchange-correlation functionals.

Science.gov (United States)

Śmiga, Szymon; Fabiano, Eduardo; Laricchia, Savio; Constantin, Lucian A; Della Sala, Fabio

2015-04-21

We analyze the methodology and the performance of subsystem density functional theory (DFT) with meta-generalized gradient approximation (meta-GGA) exchange-correlation functionals for non-bonded molecular systems. Meta-GGA functionals depend on the Kohn-Sham kinetic energy density (KED), which is not known as an explicit functional of the density. Therefore, they cannot be directly applied in subsystem DFT calculations. We propose a Laplacian-level approximation to the KED which overcomes this limitation and provides a simple and accurate way to apply meta-GGA exchange-correlation functionals in subsystem DFT calculations. The so obtained density and energy errors, with respect to the corresponding supermolecular calculations, are comparable with conventional approaches, depending almost exclusively on the approximations in the non-additive kinetic embedding term. An embedding energy error decomposition explains the accuracy of our method.

Threshold defect production in silicon determined by density functional theory molecular dynamics simulations

International Nuclear Information System (INIS)

Holmstroem, E.; Kuronen, A.; Nordlund, K.

2008-01-01

We studied threshold displacement energies for creating stable Frenkel pairs in silicon using density functional theory molecular dynamics simulations. The average threshold energy over all lattice directions was found to be 36±2 STAT ±2 SYST eV, and thresholds in the directions and were found to be 20±2 SYST eV and 12.5±1.5 SYST eV, respectively. Moreover, we found that in most studied lattice directions, a bond defect complex is formed with a lower threshold than a Frenkel pair. The average threshold energy for producing either a bond defect or a Frenkel pair was found to be 24±1 STAT ±2 SYST eV

Recent developments in LIBXC - A comprehensive library of functionals for density functional theory

Science.gov (United States)

Lehtola, Susi; Steigemann, Conrad; Oliveira, Micael J. T.; Marques, Miguel A. L.

2018-01-01

LIBXC is a library of exchange-correlation functionals for density-functional theory. We are concerned with semi-local functionals (or the semi-local part of hybrid functionals), namely local-density approximations, generalized-gradient approximations, and meta-generalized-gradient approximations. Currently we include around 400 functionals for the exchange, correlation, and the kinetic energy, spanning more than 50 years of research. Moreover, LIBXC is by now used by more than 20 codes, not only from the atomic, molecular, and solid-state physics, but also from the quantum chemistry communities.

The force distribution probability function for simple fluids by density functional theory.

Science.gov (United States)

Rickayzen, G; Heyes, D M

2013-02-28

Classical density functional theory (DFT) is used to derive a formula for the probability density distribution function, P(F), and probability distribution function, W(F), for simple fluids, where F is the net force on a particle. The final formula for P(F) ∝ exp(-AF(2)), where A depends on the fluid density, the temperature, and the Fourier transform of the pair potential. The form of the DFT theory used is only applicable to bounded potential fluids. When combined with the hypernetted chain closure of the Ornstein-Zernike equation, the DFT theory for W(F) agrees with molecular dynamics computer simulations for the Gaussian and bounded soft sphere at high density. The Gaussian form for P(F) is still accurate at lower densities (but not too low density) for the two potentials, but with a smaller value for the constant, A, than that predicted by the DFT theory.

Multiconfiguration Pair-Density Functional Theory Outperforms Kohn-Sham Density Functional Theory and Multireference Perturbation Theory for Ground-State and Excited-State Charge Transfer.

Science.gov (United States)

Ghosh, Soumen; Sonnenberger, Andrew L; Hoyer, Chad E; Truhlar, Donald G; Gagliardi, Laura

2015-08-11

The correct description of charge transfer in ground and excited states is very important for molecular interactions, photochemistry, electrochemistry, and charge transport, but it is very challenging for Kohn-Sham (KS) density functional theory (DFT). KS-DFT exchange-correlation functionals without nonlocal exchange fail to describe both ground- and excited-state charge transfer properly. We have recently proposed a theory called multiconfiguration pair-density functional theory (MC-PDFT), which is based on a combination of multiconfiguration wave function theory with a new type of density functional called an on-top density functional. Here we have used MC-PDFT to study challenging ground- and excited-state charge-transfer processes by using on-top density functionals obtained by translating KS exchange-correlation functionals. For ground-state charge transfer, MC-PDFT performs better than either the PBE exchange-correlation functional or CASPT2 wave function theory. For excited-state charge transfer, MC-PDFT (unlike KS-DFT) shows qualitatively correct behavior at long-range with great improvement in predicted excitation energies.

ALMA SPECTROSCOPIC SURVEY IN THE HUBBLE ULTRA DEEP FIELD: CO LUMINOSITY FUNCTIONS AND THE EVOLUTION OF THE COSMIC DENSITY OF MOLECULAR GAS

Energy Technology Data Exchange (ETDEWEB)

Decarli, Roberto; Walter, Fabian [Max-Planck Institut für Astronomie, Königstuhl 17, D-69117, Heidelberg (Germany); Aravena, Manuel; Assef, Roberto J. [Núcleo de Astronomía, Facultad de Ingeniería, Universidad Diego Portales, Av. Ejército 441, Santiago (Chile); Carilli, Chris [National Radio Astronomy Observatory, Pete V. Domenici Array Science Center, P.O. Box O, Socorro, NM 87801 (United States); Bouwens, Rychard [Leiden Observatory, Leiden University, P.O. Box 9513, NL2300 RA Leiden (Netherlands); Da Cunha, Elisabete [Centre for Astrophysics and Supercomputing, Swinburne University of Technology, Hawthorn, Victoria 3122 (Australia); Daddi, Emanuele [Laboratoire AIM, CEA/DSM-CNRS-Université Paris Diderot, Irfu/Service d’Astrophysique, CEA Saclay, Orme des Merisiers, F-91191 Gif-sur-Yvette cedex (France); Ivison, R. J.; Popping, Gergö [European Southern Observatory, Karl-Schwarzschild-Strasse 2, D-85748, Garching (Germany); Riechers, Dominik [Cornell University, 220 Space Sciences Building, Ithaca, NY 14853 (United States); Smail, Ian R. [6 Centre for Extragalactic Astronomy, Department of Physics, Durham University, South Road, Durham DH1 3LE (United Kingdom); Swinbank, Mark [Max-Planck-Institut für Radioastronomie, Auf dem Hügel 69, D-053121 Bonn (Germany); Weiss, Axel; Anguita, Timo, E-mail: decarli@mpia.de [Departamento de Ciencias Físicas, Universidad Andres Bello, Fernandez Concha 700, Las Condes, Santiago (Chile); and others

2016-12-10

In this paper we use ASPECS, the ALMA Spectroscopic Survey in the Hubble Ultra Deep Field in band 3 and band 6, to place blind constraints on the CO luminosity function and the evolution of the cosmic molecular gas density as a function of redshift up to z  ∼ 4.5. This study is based on galaxies that have been selected solely through their CO emission and not through any other property. In all of the redshift bins the ASPECS measurements reach the predicted “knee” of the CO luminosity function (around 5 × 10{sup 9} K km s{sup −1} pc{sup 2}). We find clear evidence of an evolution in the CO luminosity function with respect to z  ∼ 0, with more CO-luminous galaxies present at z  ∼ 2. The observed galaxies at z  ∼ 2 also appear more gas-rich than predicted by recent semi-analytical models. The comoving cosmic molecular gas density within galaxies as a function of redshift shows a drop by a factor of 3–10 from z  ∼ 2 to z  ∼ 0 (with significant error bars), and possibly a decline at z  > 3. This trend is similar to the observed evolution of the cosmic star formation rate density. The latter therefore appears to be at least partly driven by the increased availability of molecular gas reservoirs at the peak of cosmic star formation ( z  ∼ 2).

Studies of the energy density functional and its derivatives in atomic and molecular systems

International Nuclear Information System (INIS)

Robles, J.

1986-01-01

The first chapter is a review of formal density functional theory, (DFT). In the second chapter, approximations to exact DFT are reviewed. In chapter three, the author proposes a modified molecular Thomas-Fermi, (TF) theory. He proceeds by imposing a continuity condition on the density. This avoids the singularities at the nuclei of classical TF. The method is sanctioned by Teller and Balasz theorems. However, it is found that while the classical TF theory is improved, the present method still predicts no-binding. In chapter four, it is suggested that the correlation energy, (E/sub c/), is proportional to the exchange energy, (K), E/sub c/ = cK. This idea is tested with Hartree-Fock (HF) and DFT data. In HF, c = 1/40 for atoms and c = 1/25 for molecules. Furthermore, the method is used to estimate dissociation energies. Thereafter, the author studies the chemical potential, (μ), of atoms (chapter five) and molecules (chapter six). In chapter seven, the concept of local pressure in an inhomogeneous electronic system is studied and extended, within the local thermodynamic formulation of DFT. Finally, appendix A provides the required mathematical framework (basic functional calculus) to understand this work, while appendix B is essentially a summary of the HF method

The heat current density correlation function: sum rules and thermal conductivity

International Nuclear Information System (INIS)

Singh, Shaminder; Tankeshwar, K; Pathak, K N; Ranganathan, S

2006-01-01

Expressions for the second and fourth sum rules of the heat current density correlation function have been derived in an appropriate ensemble. The thermal conductivity of Lennard-Jones fluids has been calculated using these sum rules for the heat current density correlation function and the Gaussian form of the memory function. It is found that the results obtained for the thermal conductivity are in good agreement with the molecular dynamics simulation results over a wide range of densities and temperatures. Earlier results obtained using the energy current density correlation function are also discussed

The heat current density correlation function: sum rules and thermal conductivity

Energy Technology Data Exchange (ETDEWEB)

Singh, Shaminder [Department of Physics, Panjab University, Chandigarh-160 014 (India); Tankeshwar, K [Department of Physics, Panjab University, Chandigarh-160 014 (India); Pathak, K N [Department of Physics, Panjab University, Chandigarh-160 014 (India); Ranganathan, S [Department of Physics, Royal Military College, Kingston, ON, K7K 7B4 (Canada)

2006-02-01

Expressions for the second and fourth sum rules of the heat current density correlation function have been derived in an appropriate ensemble. The thermal conductivity of Lennard-Jones fluids has been calculated using these sum rules for the heat current density correlation function and the Gaussian form of the memory function. It is found that the results obtained for the thermal conductivity are in good agreement with the molecular dynamics simulation results over a wide range of densities and temperatures. Earlier results obtained using the energy current density correlation function are also discussed.

Linear scaling of density functional algorithms

International Nuclear Information System (INIS)

Stechel, E.B.; Feibelman, P.J.; Williams, A.R.

1993-01-01

An efficient density functional algorithm (DFA) that scales linearly with system size will revolutionize electronic structure calculations. Density functional calculations are reliable and accurate in determining many condensed matter and molecular ground-state properties. However, because current DFA's, including methods related to that of Car and Parrinello, scale with the cube of the system size, density functional studies are not routinely applied to large systems. Linear scaling is achieved by constructing functions that are both localized and fully occupied, thereby eliminating the need to calculate global eigenfunctions. It is, however, widely believed that exponential localization requires the existence of an energy gap between the occupied and unoccupied states. Despite this, the authors demonstrate that linear scaling can still be achieved for metals. Using a linear scaling algorithm, they have explicitly constructed localized, almost fully occupied orbitals for the quintessential metallic system, jellium. The algorithm is readily generalizable to any system geometry and Hamiltonian. They will discuss the conceptual issues involved, convergence properties and scaling for their new algorithm

The molecular, electronic structures and vibrational spectra of metal-free, N,N'-dideuterio and magnesium tetra-2,3-pyridino-porphyrazines: Density functional calculations.

Science.gov (United States)

Liu, Zhongqiang; Zhang, Xianxi; Zhang, Yuexing; Li, Renjie; Jiang, Jianzhuang

2006-10-01

A theoretical investigation of the fully optimized geometries and electronic structures of the metal-free (TPdPzH(2)), N,N'-dideuterio (TPdPzD(2)), and magnesium (TPdPzMg) tetra-2,3-pyridino-porphyrazine has been conducted based on density functional theory. The optimized geometries at density functional theory level for these compounds are reported here for the first time. A comparison between the different molecules for the geometry, molecular orbital, and atomic charge is made. The substituent effect of the N atoms on the molecular structures of these compounds is discussed. The IR and Raman spectra for these three compounds have also been calculated at density functional B3LYP level using the 6-31G(d) basis set. Detailed assignments of the NH, NM, and pyridine ring vibrational bands in the IR and Raman spectra have been made based on assistance of animated pictures. The simulated IR spectra of TPdPzH(2) are compared with the experimental absorption spectra, and very good consistency has been found. The isotope effect on the IR and Raman spectra is also discussed.

Fast plane wave density functional theory molecular dynamics calculations on multi-GPU machines

International Nuclear Information System (INIS)

Jia, Weile; Fu, Jiyun; Cao, Zongyan; Wang, Long; Chi, Xuebin; Gao, Weiguo; Wang, Lin-Wang

2013-01-01

Plane wave pseudopotential (PWP) density functional theory (DFT) calculation is the most widely used method for material simulations, but its absolute speed stagnated due to the inability to use large scale CPU based computers. By a drastic redesign of the algorithm, and moving all the major computation parts into GPU, we have reached a speed of 12 s per molecular dynamics (MD) step for a 512 atom system using 256 GPU cards. This is about 20 times faster than the CPU version of the code regardless of the number of CPU cores used. Our tests and analysis on different GPU platforms and configurations shed lights on the optimal GPU deployments for PWP-DFT calculations. An 1800 step MD simulation is used to study the liquid phase properties of GaInP

A third-generation density-functional-theory-based method for calculating canonical molecular orbitals of large molecules.

Science.gov (United States)

Hirano, Toshiyuki; Sato, Fumitoshi

2014-07-28

We used grid-free modified Cholesky decomposition (CD) to develop a density-functional-theory (DFT)-based method for calculating the canonical molecular orbitals (CMOs) of large molecules. Our method can be used to calculate standard CMOs, analytically compute exchange-correlation terms, and maximise the capacity of next-generation supercomputers. Cholesky vectors were first analytically downscaled using low-rank pivoted CD and CD with adaptive metric (CDAM). The obtained Cholesky vectors were distributed and stored on each computer node in a parallel computer, and the Coulomb, Fock exchange, and pure exchange-correlation terms were calculated by multiplying the Cholesky vectors without evaluating molecular integrals in self-consistent field iterations. Our method enables DFT and massively distributed memory parallel computers to be used in order to very efficiently calculate the CMOs of large molecules.

Adsorption of hairy particles with mobile ligands: Molecular dynamics and density functional study

Science.gov (United States)

Borówko, M.; Sokołowski, S.; Staszewski, T.; Pizio, O.

2018-01-01

We study models of hairy nanoparticles in contact with a hard wall. Each particle is built of a spherical core with a number of ligands attached to it and each ligand is composed of several spherical, tangentially jointed segments. The number of segments is the same for all ligands. Particular models differ by the numbers of ligands and of segments per ligand, but the total number of segments is constant. Moreover, our model assumes that the ligands are tethered to the core in such a manner that they can "slide" over the core surface. Using molecular dynamics simulations we investigate the differences in the structure of a system close to the wall. In order to characterize the distribution of the ligands around the core, we have calculated the end-to-end distances of the ligands and the lengths and orientation of the mass dipoles. Additionally, we also employed a density functional approach to obtain the density profiles. We have found that if the number of ligands is not too high, the proposed version of the theory is capable to predict the structure of the system with a reasonable accuracy.

The solid molecular hydrogens in the ordered state as function of density and ortho-para concentration: a far infrared study

International Nuclear Information System (INIS)

Jochemsen, R.

1978-01-01

In this thesis, the results of far infrared absorption experiments on solid molecular hydrogen and deuterium are presented. In Chapter I an introduction to the properties of solid molecular hydrogens in given. The experimental system used for the high pressure infrared measurements and the data handling procedures are discussed in Chapter II. The theory of infrared absorption and the averaging of the dipole moment over the motion of the molecules is contained in Chapter III. In this chapter a general sum rule for the integrated absorption is derived. The remaining chapters present the results of the measurements and the discussion. In Chapter IV the author concentrates on the phonon frequencies as a function of ortho-para concentration and density, while in Chapter V measuremtns of phonon lineshape and integrated absorption intensities are presented. Finally, in Chapter VI, a study is given of the phase transition in solid hydrogen and deuterium. This study provides accurate values for the transition temperature as a function of density (in deuterium) and as a function of ortho-para concentration (in hydrogen) as well as the dependence of the order parameter on the temperature and the ortho-para concentration. (Auth.)

Structure and Stability of Molecular Crystals with Many-Body Dispersion-Inclusive Density Functional Tight Binding.

Science.gov (United States)

Mortazavi, Majid; Brandenburg, Jan Gerit; Maurer, Reinhard J; Tkatchenko, Alexandre

2018-01-18

Accurate prediction of structure and stability of molecular crystals is crucial in materials science and requires reliable modeling of long-range dispersion interactions. Semiempirical electronic structure methods are computationally more efficient than their ab initio counterparts, allowing structure sampling with significant speedups. We combine the Tkatchenko-Scheffler van der Waals method (TS) and the many-body dispersion method (MBD) with third-order density functional tight-binding (DFTB3) via a charge population-based method. We find an overall good performance for the X23 benchmark database of molecular crystals, despite an underestimation of crystal volume that can be traced to the DFTB parametrization. We achieve accurate lattice energy predictions with DFT+MBD energetics on top of vdW-inclusive DFTB3 structures, resulting in a speedup of up to 3000 times compared with a full DFT treatment. This suggests that vdW-inclusive DFTB3 can serve as a viable structural prescreening tool in crystal structure prediction.

Density distribution function of a self-gravitating isothermal compressible turbulent fluid in the context of molecular clouds ensembles

Science.gov (United States)

Donkov, Sava; Stefanov, Ivan Z.

2018-03-01

We have set ourselves the task of obtaining the probability distribution function of the mass density of a self-gravitating isothermal compressible turbulent fluid from its physics. We have done this in the context of a new notion: the molecular clouds ensemble. We have applied a new approach that takes into account the fractal nature of the fluid. Using the medium equations, under the assumption of steady state, we show that the total energy per unit mass is an invariant with respect to the fractal scales. As a next step we obtain a non-linear integral equation for the dimensionless scale Q which is the third root of the integral of the probability distribution function. It is solved approximately up to the leading-order term in the series expansion. We obtain two solutions. They are power-law distributions with different slopes: the first one is -1.5 at low densities, corresponding to an equilibrium between all energies at a given scale, and the second one is -2 at high densities, corresponding to a free fall at small scales.

Density Functional Methods for Shock Physics and High Energy Density Science

Science.gov (United States)

Desjarlais, Michael

2017-06-01

Molecular dynamics with density functional theory has emerged over the last two decades as a powerful and accurate framework for calculating thermodynamic and transport properties with broad application to dynamic compression, high energy density science, and warm dense matter. These calculations have been extensively validated against shock and ramp wave experiments, are a principal component of high-fidelity equation of state generation, and are having wide-ranging impacts on inertial confinement fusion, planetary science, and shock physics research. In addition to thermodynamic properties, phase boundaries, and the equation of state, one also has access to electrical conductivity, thermal conductivity, and lower energy optical properties. Importantly, all these properties are obtained within the same theoretical framework and are manifestly consistent. In this talk I will give a brief history and overview of molecular dynamics with density functional theory and its use in calculating a wide variety of thermodynamic and transport properties for materials ranging from ambient to extreme conditions and with comparisons to experimental data. I will also discuss some of the limitations and difficulties, as well as active research areas. Sandia is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Kohn-Sham orbitals and potentials from quantum Monte Carlo molecular densities

International Nuclear Information System (INIS)

Varsano, Daniele; Barborini, Matteo; Guidoni, Leonardo

2014-01-01

In this work we show the possibility to extract Kohn-Sham orbitals, orbital energies, and exchange correlation potentials from accurate Quantum Monte Carlo (QMC) densities for atoms (He, Be, Ne) and molecules (H 2 , Be 2 , H 2 O, and C 2 H 4 ). The Variational Monte Carlo (VMC) densities based on accurate Jastrow Antisymmetrised Geminal Power wave functions are calculated through different estimators. Using these reference densities, we extract the Kohn-Sham quantities with the method developed by Zhao, Morrison, and Parr (ZMP) [Phys. Rev. A 50, 2138 (1994)]. We compare these extracted quantities with those obtained form CISD densities and with other data reported in the literature, finding a good agreement between VMC and other high-level quantum chemistry methods. Our results demonstrate the applicability of the ZMP procedure to QMC molecular densities, that can be used for the testing and development of improved functionals and for the implementation of embedding schemes based on QMC and Density Functional Theory

Molecular Structure And Vibrational Frequencies of Tetrafluoro isophthalonitrile By Hartree-Fock And Density Functional Theory Calculations

International Nuclear Information System (INIS)

Ayikoglu, A.

2008-01-01

The molecular structure, vibrational frequencies and corresponding vibrational assignments of tetrafluoro isophthalonitrile (TFPN) in the ground state have been calculated using the Hartree-Fock (HF) and density functional methods (B3LYP) with 6-311++G (d, p) basis set. The calculations were utilized in the CS symmetry of TFPN. The obtained vibrational frequencies and optimized geometric parameters (bond lengths and bond angles) were seen to be in good agreement with the experimental data. The comparison of the observed and calculated results showed that the B3LYP method is superior to the HF method for both the vibrational frequencies and geometric parameters

Coupling of ab initio density functional theory and molecular dynamics for the multiscale modeling of carbon nanotubes

International Nuclear Information System (INIS)

Ng, T Y; Yeak, S H; Liew, K M

2008-01-01

A multiscale technique is developed that couples empirical molecular dynamics (MD) and ab initio density functional theory (DFT). An overlap handshaking region between the empirical MD and ab initio DFT regions is formulated and the interaction forces between the carbon atoms are calculated based on the second-generation reactive empirical bond order potential, the long-range Lennard-Jones potential as well as the quantum-mechanical DFT derived forces. A density of point algorithm is also developed to track all interatomic distances in the system, and to activate and establish the DFT and handshaking regions. Through parallel computing, this multiscale method is used here to study the dynamic behavior of single-walled carbon nanotubes (SWCNTs) under asymmetrical axial compression. The detection of sideways buckling due to the asymmetrical axial compression is reported and discussed. It is noted from this study on SWCNTs that the MD results may be stiffer compared to those with electron density considerations, i.e. first-principle ab initio methods

Liquid ammonia: Molecular correlation functions from x-ray diffraction

International Nuclear Information System (INIS)

Narten, A.H.

1977-01-01

For nearly spherical molecules the x-ray scattering from liquids yields structure and correlation functions for molecular centers. The distribution of electron density in an ammonia molecular is very nearly spherical, and orientational correlation between molecules in the liquid is not ''seen'' by x rays. Structure and correlation functions for molecular centers (nitrogen atoms) are derived from x-ray data on liquid NH 3 at 4 degreeC and tabulated. They provide a sensitive test for future work on a molecular theory of liquid ammonia

Optimal control theory for quantum-classical systems: Ehrenfest molecular dynamics based on time-dependent density-functional theory

International Nuclear Information System (INIS)

Castro, A; Gross, E K U

2014-01-01

We derive the fundamental equations of an optimal control theory for systems containing both quantum electrons and classical ions. The system is modeled with Ehrenfest dynamics, a non-adiabatic variant of molecular dynamics. The general formulation, that needs the fully correlated many-electron wavefunction, can be simplified by making use of time-dependent density-functional theory. In this case, the optimal control equations require some modifications that we will provide. The abstract general formulation is complemented with the simple example of the H 2 + molecule in the presence of a laser field. (paper)

Teaching Density Functional Theory Through Experiential Learning

International Nuclear Information System (INIS)

Narasimhan, Shobhana

2015-01-01

Today, quantum mechanical density functional theory is often the method of choice for performing accurate calculations on atomic, molecular and condensed matter systems. Here, I share some of my experiences in teaching the necessary basics of solid state physics, as well as the theory and practice of density functional theory, in a number of workshops held in developing countries over the past two decades. I discuss the advantages of supplementing the usual mathematically formal teaching methods, characteristic of graduate courses, with the use of visual imagery and analogies. I also describe a successful experiment we carried out, which resulted in a joint publication co-authored by 67 lecturers and students participating in a summer school. (paper)

Density functional representation of quantum chemistry. II. Local quantum field theories of molecular matter in terms of the charge density operator do not work

International Nuclear Information System (INIS)

Primas, H.; Schleicher, M.

1975-01-01

A comprehensive review of the attempts to rephrase molecular quantum mechanics in terms of the particle density operator and the current density or phase density operator is given. All pertinent investigations which have come to attention suffer from severe mathematical inconsistencies and are not adequate to the few-body problem of quantum chemistry. The origin of the failure of these attempts is investigated, and it is shown that a realization of a local quantum field theory of molecular matter in terms of observables would presuppose the solution of many highly nontrivial mathematical problems

Spin theory of the density functional: reduced matrices and density functions

International Nuclear Information System (INIS)

Pavlov, R.; Delchev, Y.; Pavlova, K.; Maruani, J.

1993-01-01

Expressions for the reduced matrices and density functions of N-fermion systems of arbitrary order s (1<=s<=N) are derived within the frame of rigorous spin approach to the density functional theory (DFT). Using the local-scale transformation method and taking into account the particle spin it is shown that the reduced matrices and density functions are functionals of the total one-fermion density. Similar dependence is found for the distribution density of s-particle aggregates. Generalization and applicability of DFT to the case of s-particle ensembles and aggregates is discussed. 14 refs

Molecular Excitation Energies from Time-Dependent Density Functional Theory Employing Random-Phase Approximation Hessians with Exact Exchange.

Science.gov (United States)

Heßelmann, Andreas

2015-04-14

Molecular excitation energies have been calculated with time-dependent density-functional theory (TDDFT) using random-phase approximation Hessians augmented with exact exchange contributions in various orders. It has been observed that this approach yields fairly accurate local valence excitations if combined with accurate asymptotically corrected exchange-correlation potentials used in the ground-state Kohn-Sham calculations. The inclusion of long-range particle-particle with hole-hole interactions in the kernel leads to errors of 0.14 eV only for the lowest excitations of a selection of three alkene, three carbonyl, and five azabenzene molecules, thus surpassing the accuracy of a number of common TDDFT and even some wave function correlation methods. In the case of long-range charge-transfer excitations, the method typically underestimates accurate reference excitation energies by 8% on average, which is better than with standard hybrid-GGA functionals but worse compared to range-separated functional approximations.

A simple scaling law for the equation of state and the radial distribution functions calculated by density-functional theory molecular dynamics

Science.gov (United States)

Danel, J.-F.; Kazandjian, L.

2018-06-01

It is shown that the equation of state (EOS) and the radial distribution functions obtained by density-functional theory molecular dynamics (DFT-MD) obey a simple scaling law. At given temperature, the thermodynamic properties and the radial distribution functions given by a DFT-MD simulation remain unchanged if the mole fractions of nuclei of given charge and the average volume per atom remain unchanged. A practical interest of this scaling law is to obtain an EOS table for a fluid from that already obtained for another fluid if it has the right characteristics. Another practical interest of this result is that an asymmetric mixture made up of light and heavy atoms requiring very different time steps can be replaced by a mixture of atoms of equal mass, which facilitates the exploration of the configuration space in a DFT-MD simulation. The scaling law is illustrated by numerical results.

FTIR and FT-Raman spectra and density functional computations of the vibrational spectra, molecular geometry and atomic charges of the biomolecule: 5-bromouracil

Czech Academy of Sciences Publication Activity Database

Rastogi, V.K.; Palafox, M. A.; Mittal, L.; Peica, N.; Keifer, W.; Lang, Kamil; Ojha, S.P.

2007-01-01

Roč. 38, č. 10 (2007), s. 1227-1241 ISSN 0377-0486 Institutional research plan: CEZ:AV0Z40320502 Keywords : FTIR and FT-Raman spectra * density functional computations * molecular geometry Subject RIV: CA - Inorganic Chemistry Impact factor: 3.514, year: 2007

Extending density functional embedding theory for covalently bonded systems.

Science.gov (United States)

Yu, Kuang; Carter, Emily A

2017-12-19

Quantum embedding theory aims to provide an efficient solution to obtain accurate electronic energies for systems too large for full-scale, high-level quantum calculations. It adopts a hierarchical approach that divides the total system into a small embedded region and a larger environment, using different levels of theory to describe each part. Previously, we developed a density-based quantum embedding theory called density functional embedding theory (DFET), which achieved considerable success in metals and semiconductors. In this work, we extend DFET into a density-matrix-based nonlocal form, enabling DFET to study the stronger quantum couplings between covalently bonded subsystems. We name this theory density-matrix functional embedding theory (DMFET), and we demonstrate its performance in several test examples that resemble various real applications in both chemistry and biochemistry. DMFET gives excellent results in all cases tested thus far, including predicting isomerization energies, proton transfer energies, and highest occupied molecular orbital-lowest unoccupied molecular orbital gaps for local chromophores. Here, we show that DMFET systematically improves the quality of the results compared with the widely used state-of-the-art methods, such as the simple capped cluster model or the widely used ONIOM method.

Normal co-ordinate analysis, molecular structural, non-linear optical, second order perturbation studies of Tizanidine by density functional theory.

Science.gov (United States)

Sheela, N R; Muthu, S; Sampathkrishnan, S; Al-Saadi, Abdulaziz A

2015-03-15

The spectroscopic techniques and semi-empirical molecular calculations have been utilized to analyze the drug Tizanidine (5CDIBTA). The solid phase Fourier Transform Infrared (FTIR) and Fourier Transform Raman (FTR) spectral analysis of 5CDIBTA is carried out along with density functional theory (DFT) calculations (B3LYP) with the 6-311++G(d,p) basis set. Detailed interpretation of the vibrational spectra of the compound has been made on the basis of the calculated potential energy distribution (PED). The individual atomic charges by NPA using B3LYP method is studied. A study on the Mulliken atomic charges, frontier molecular orbitals (HOMO-LUMO), molecular electrostatic potential (MEP) and thermodynamic properties were performed. The electric dipole moment (μ) and the first hyperpolarizability (α) values of the investigated molecule were also computed. Copyright © 2014 Elsevier B.V. All rights reserved.

Density functional theory fragment descriptors to quantify the reactivity of a molecular family: application to amino acids.

Science.gov (United States)

Senet, P; Aparicio, F

2007-04-14

By using the exact density functional theory, one demonstrates that the value of the local electronic softness of a molecular fragment is directly related to the polarization charge (Coulomb hole) induced by a test electron removed (or added) from (at) the fragment. Our finding generalizes to a chemical group a formal relation between these molecular descriptors recently obtained for an atom in a molecule using an approximate atomistic model [P. Senet and M. Yang, J. Chem. Sci. 117, 411 (2005)]. In addition, a practical ab initio computational scheme of the Coulomb hole and related local descriptors of reactivity of a molecular family having in common a similar fragment is presented. As a blind test, the method is applied to the lateral chains of the 20 isolated amino acids. One demonstrates that the local softness of the lateral chain is a quantitative measure of the similarity of the amino acids. It predicts the separation of amino acids in different biochemical groups (aliphatic, basic, acidic, sulfur contained, and aromatic). The present approach may find applications in quantitative structure activity relationship methodology.

Accurate density functional prediction of molecular electron affinity with the scaling corrected Kohn–Sham frontier orbital energies

Science.gov (United States)

Zhang, DaDi; Yang, Xiaolong; Zheng, Xiao; Yang, Weitao

2018-04-01

Electron affinity (EA) is the energy released when an additional electron is attached to an atom or a molecule. EA is a fundamental thermochemical property, and it is closely pertinent to other important properties such as electronegativity and hardness. However, accurate prediction of EA is difficult with density functional theory methods. The somewhat large error of the calculated EAs originates mainly from the intrinsic delocalisation error associated with the approximate exchange-correlation functional. In this work, we employ a previously developed non-empirical global scaling correction approach, which explicitly imposes the Perdew-Parr-Levy-Balduz condition to the approximate functional, and achieve a substantially improved accuracy for the calculated EAs. In our approach, the EA is given by the scaling corrected Kohn-Sham lowest unoccupied molecular orbital energy of the neutral molecule, without the need to carry out the self-consistent-field calculation for the anion.

Quantum master equation method based on the broken-symmetry time-dependent density functional theory: application to dynamic polarizability of open-shell molecular systems.

Science.gov (United States)

Kishi, Ryohei; Nakano, Masayoshi

2011-04-21

A novel method for the calculation of the dynamic polarizability (α) of open-shell molecular systems is developed based on the quantum master equation combined with the broken-symmetry (BS) time-dependent density functional theory within the Tamm-Dancoff approximation, referred to as the BS-DFTQME method. We investigate the dynamic α density distribution obtained from BS-DFTQME calculations in order to analyze the spatial contributions of electrons to the field-induced polarization and clarify the contributions of the frontier orbital pair to α and its density. To demonstrate the performance of this method, we examine the real part of dynamic α of singlet 1,3-dipole systems having a variety of diradical characters (y). The frequency dispersion of α, in particular in the resonant region, is shown to strongly depend on the exchange-correlation functional as well as on the diradical character. Under sufficiently off-resonant condition, the dynamic α is found to decrease with increasing y and/or the fraction of Hartree-Fock exchange in the exchange-correlation functional, which enhances the spin polarization, due to the decrease in the delocalization effects of π-diradical electrons in the frontier orbital pair. The BS-DFTQME method with the BHandHLYP exchange-correlation functional also turns out to semiquantitatively reproduce the α spectra calculated by a strongly correlated ab initio molecular orbital method, i.e., the spin-unrestricted coupled-cluster singles and doubles.

Constructive definition of functional derivatives in density-functional theory

International Nuclear Information System (INIS)

Luo Ji

2006-01-01

It is shown that the functional derivatives in density-functional theory (DFT) can be explicitly defined within the domain of electron densities restricted by the electron number, and a constructive definition of such restricted derivatives is suggested. With this definition, Kohn-Sham (KS) equations can be established for an N-electron system without extending the functional domain and introducing a Lagrange multiplier. This may clarify some of the fundamental questions raised by Nesbet (1998 Phys. Rev. A 58 R12). The definition naturally leads to the fact that the KS effective potential is determined only to within an additive constant, thus the KS levels can shift freely and the relation between the highest occupied molecular orbital (HOMO) energy and the ionization potential of the system depends on the choice of the constant. On the other hand, if the domain of functionals is indeed extended beyond the electron number restriction, conclusions depend on whether the extended functionals have unrestricted derivatives or not. It is shown that the ensemble extension of DFT to open systems of mixed states (Perdew et al 1982 Phys. Rev. Lett. 49 1691) leads to an energy functional which has no unrestricted derivative at integer electron numbers. Hence after this extension, the relation between the HOMO energy and the ionization potential for an N-electron system is still uncertain. Besides, there are different extensions of the energy functional to a domain of densities unrestricted by the integer electron number, resulting in different unrestricted derivatives and electron systems with different chemical potentials. Even for the exact exchange-correlation potential, there is still an undetermined constant, whether it is a restricted or unrestricted derivative

Intrinsic-density functionals

International Nuclear Information System (INIS)

Engel, J.

2007-01-01

The Hohenberg-Kohn theorem and Kohn-Sham procedure are extended to functionals of the localized intrinsic density of a self-bound system such as a nucleus. After defining the intrinsic-density functional, we modify the usual Kohn-Sham procedure slightly to evaluate the mean-field approximation to the functional, and carefully describe the construction of the leading corrections for a system of fermions in one dimension with a spin-degeneracy equal to the number of particles N. Despite the fact that the corrections are complicated and nonlocal, we are able to construct a local Skyrme-like intrinsic-density functional that, while different from the exact functional, shares with it a minimum value equal to the exact ground-state energy at the exact ground-state intrinsic density, to next-to-leading order in 1/N. We briefly discuss implications for real Skyrme functionals

Performance of extended Lagrangian schemes for molecular dynamics simulations with classical polarizable force fields and density functional theory.

Science.gov (United States)

Vitale, Valerio; Dziedzic, Jacek; Albaugh, Alex; Niklasson, Anders M N; Head-Gordon, Teresa; Skylaris, Chris-Kriton

2017-03-28

Iterative energy minimization with the aim of achieving self-consistency is a common feature of Born-Oppenheimer molecular dynamics (BOMD) and classical molecular dynamics with polarizable force fields. In the former, the electronic degrees of freedom are optimized, while the latter often involves an iterative determination of induced point dipoles. The computational effort of the self-consistency procedure can be reduced by re-using converged solutions from previous time steps. However, this must be done carefully, as not to break time-reversal symmetry, which negatively impacts energy conservation. Self-consistent schemes based on the extended Lagrangian formalism, where the initial guesses for the optimized quantities are treated as auxiliary degrees of freedom, constitute one elegant solution. We report on the performance of two integration schemes with the same underlying extended Lagrangian structure, which we both employ in two radically distinct regimes-in classical molecular dynamics simulations with the AMOEBA polarizable force field and in BOMD simulations with the Onetep linear-scaling density functional theory (LS-DFT) approach. Both integration schemes are found to offer significant improvements over the standard (unpropagated) molecular dynamics formulation in both the classical and LS-DFT regimes.

Joint density-functional theory and its application to systems in solution

Science.gov (United States)

Petrosyan, Sahak A.

The physics of solvation, the interaction of water with solutes, plays a central role in chemistry and biochemistry, and it is essential for the very existence of life. Despite the central importance of water and the advent of the quantum theory early in the twentieth century, the link between the fundamental laws of physics and the observable properties of water remain poorly understood to this day. The central goal of this thesis is to develop a new formalism and framework to make the study of systems (solutes or surfaces) in contact with liquid water as practical and accurate as standard electronic structure calculations without the need for explicit averaging over large ensembles of configurations of water molecules. The thesis introduces a new form of density functional theory for the ab initio description of electronic systems in contact with a molecular liquid environment. This theory rigorously joins an electron density-functional for the electrons of a solute with a classical density-functional theory for the liquid into a single variational principle for the free energy of the combined system. Using the new form of density-functional theory for the ab initio description of electronic systems in contact with a molecular liquid environment, the thesis then presents the first detailed study of the impact of a solvent on the surface chemistry of Cr2O3, the passivating layer of stainless steel alloys. In comparison to a vacuum, we predict that the presence of water has little impact on the adsorption of chloride ions to the oxygen-terminated surface but has a dramatic effect on the binding of hydrogen to that surface. A key ingredient of a successful joint density functional theory is a good approximate functional for describing the solvent. We explore how the simplest examples of the best known class of approximate forms for the classical density functional fail when applied directly to water. The thesis then presents a computationally efficient density-functional

Isobaric-Isothermal Molecular Dynamics Utilizing Density Functional Theory: An Assessment of the Structure and Density of Water at Near-Ambient Conditions

International Nuclear Information System (INIS)

Schmidt, J.; VandeVondele, J.; Kuo, I.W.; Sebastiani, D.; Siepmann, J.I.; Hutter, J.; Mundy, C.J.

2009-01-01

We present herein a comprehensive density functional theory study toward assessing the accuracy of two popular gradient-corrected exchange correlation functionals on the structure and density of liquid water at near ambient conditions in the isobaric-isothermal ensemble. Our results indicate that both PBE and BLYP functionals under predict the density and over structure the liquid. Adding the dispersion correction due to Grimme(1, 2) improves the predicted densities for both BLYP and PBE in a significant manner. Moreover, the addition of the dispersion correction for BLYP yields an oxygen-oxygen radial distribution function in excellent agreement with experiment. Thus, we conclude that one can obtain a very satisfactory model for water using BLYP and a correction for dispersion.

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.

Development and application of a 2-electron reduced density matrix approach to electron transport via molecular junctions

Science.gov (United States)

Hoy, Erik P.; Mazziotti, David A.; Seideman, Tamar

2017-11-01

Can an electronic device be constructed using only a single molecule? Since this question was first asked by Aviram and Ratner in the 1970s [Chem. Phys. Lett. 29, 277 (1974)], the field of molecular electronics has exploded with significant experimental advancements in the understanding of the charge transport properties of single molecule devices. Efforts to explain the results of these experiments and identify promising new candidate molecules for molecular devices have led to the development of numerous new theoretical methods including the current standard theoretical approach for studying single molecule charge transport, i.e., the non-equilibrium Green's function formalism (NEGF). By pairing this formalism with density functional theory (DFT), a wide variety of transport problems in molecular junctions have been successfully treated. For some systems though, the conductance and current-voltage curves predicted by common DFT functionals can be several orders of magnitude above experimental results. In addition, since density functional theory relies on approximations to the exact exchange-correlation functional, the predicted transport properties can show significant variation depending on the functional chosen. As a first step to addressing this issue, the authors have replaced density functional theory in the NEGF formalism with a 2-electron reduced density matrix (2-RDM) method, creating a new approach known as the NEGF-RDM method. 2-RDM methods provide a more accurate description of electron correlation compared to density functional theory, and they have lower computational scaling compared to wavefunction based methods of similar accuracy. Additionally, 2-RDM methods are capable of capturing static electron correlation which is untreatable by existing NEGF-DFT methods. When studying dithiol alkane chains and dithiol benzene in model junctions, the authors found that the NEGF-RDM predicts conductances and currents that are 1-2 orders of magnitude below

Density functional theory: Foundations reviewed

Energy Technology Data Exchange (ETDEWEB)

Kryachko, Eugene S., E-mail: eugene.kryachko@ulg.ac.be [Bogolyubov Institute for Theoretical Physics, Kiev, 03680 (Ukraine); Ludeña, Eduardo V., E-mail: popluabe@yahoo.es [Centro de Química, Instituto Venezolano de Investigaciones Científicas, IVIC, Apartado 21827, Caracas 1020-A (Venezuela, Bolivarian Republic of); Prometheus Program, Senescyt (Ecuador); Grupo Ecuatoriano para el Estudio Experimental y Teórico de Nanosistemas, GETNano, USFQ, N104-E, Quito (Ecuador); Escuela Politécnica Superior del Litoral, ESPOL, Guayaquil (Ecuador)

2014-11-10

-geared functionals. These problems are discussed by making reference to ab initio DFT as well as to the local-scaling-transformation version of DFT, LS-DFT. In addition, we examine the question of the accuracy of approximate exchange–correlation functionals in the light of their non-observance of the variational principle. Why do approximate functionals yield reasonable (and accurate) descriptions of many molecular and condensed matter properties? Are the conditions imposed on exchange and correlation functionals sufficiently adequate to produce accurate semi-empirical functionals? In this respect, we consider the question of whether the results reflect a true approach to chemical accuracy or are just the outcome of a virtuoso-like performance which cannot be systematically improved. We discuss the issue of the accuracy of the contemporary DFT results by contrasting them to those obtained by the alternative RDMT and NOFT. We discuss the possibility of improving DFT functionals by applying in a systematic way the N-representability conditions on the 2-RDM. In this respect, we emphasize the possibility of constructing 2-matrices in the context of the local scaling transformation version of DFT to which the N-representability condition of RDM theory may be applied. We end up our revision of HKS-DFT by considering some of the problems related to spin symmetry and discuss some current issues dealing with a proper treatment of open-shell systems. We are particularly concerned, as in the rest of this paper, mostly with foundational issues arising in the construction of functionals. We dedicate the whole Section  4 to the local-scaling transformation version of density functional theory, LS-DFT. The reason is that in this theory some of the fundamental problems that appear in HKS-DFT, have been solved. For example, in LS-DFT the functionals are, in principle, designed to fulfill v- and N-representability conditions from the outset. This is possible because LS-DFT is based on density

Probability density function method for variable-density pressure-gradient-driven turbulence and mixing

International Nuclear Information System (INIS)

Bakosi, Jozsef; Ristorcelli, Raymond J.

2010-01-01

Probability density function (PDF) methods are extended to variable-density pressure-gradient-driven turbulence. We apply the new method to compute the joint PDF of density and velocity in a non-premixed binary mixture of different-density molecularly mixing fluids under gravity. The full time-evolution of the joint PDF is captured in the highly non-equilibrium flow: starting from a quiescent state, transitioning to fully developed turbulence and finally dissipated by molecular diffusion. High-Atwood-number effects (as distinguished from the Boussinesq case) are accounted for: both hydrodynamic turbulence and material mixing are treated at arbitrary density ratios, with the specific volume, mass flux and all their correlations in closed form. An extension of the generalized Langevin model, originally developed for the Lagrangian fluid particle velocity in constant-density shear-driven turbulence, is constructed for variable-density pressure-gradient-driven flows. The persistent small-scale anisotropy, a fundamentally 'non-Kolmogorovian' feature of flows under external acceleration forces, is captured by a tensorial diffusion term based on the external body force. The material mixing model for the fluid density, an active scalar, is developed based on the beta distribution. The beta-PDF is shown to be capable of capturing the mixing asymmetry and that it can accurately represent the density through transition, in fully developed turbulence and in the decay process. The joint model for hydrodynamics and active material mixing yields a time-accurate evolution of the turbulent kinetic energy and Reynolds stress anisotropy without resorting to gradient diffusion hypotheses, and represents the mixing state by the density PDF itself, eliminating the need for dubious mixing measures. Direct numerical simulations of the homogeneous Rayleigh-Taylor instability are used for model validation.

Hot-electron-assisted femtochemistry at surfaces: A time-dependent density functional theory approach

DEFF Research Database (Denmark)

Gavnholt, Jeppe; Rubio, Angel; Olsen, Thomas

2009-01-01

Using time-evolution time-dependent density functional theory (TDDFT) within the adiabatic local-density approximation, we study the interactions between single electrons and molecular resonances at surfaces. Our system is a nitrogen molecule adsorbed on a ruthenium surface. The surface is modele...... resonance and the lowering of the resonance energy due to an image charge effect. Finally we apply the TDDFT procedure to only consider the decay of molecular excitations and find that it agrees quite well with the width of the projected density of Kohn-Sham states....

Semi-local machine-learned kinetic energy density functional with third-order gradients of electron density

Science.gov (United States)

Seino, Junji; Kageyama, Ryo; Fujinami, Mikito; Ikabata, Yasuhiro; Nakai, Hiromi

2018-06-01

A semi-local kinetic energy density functional (KEDF) was constructed based on machine learning (ML). The present scheme adopts electron densities and their gradients up to third-order as the explanatory variables for ML and the Kohn-Sham (KS) kinetic energy density as the response variable in atoms and molecules. Numerical assessments of the present scheme were performed in atomic and molecular systems, including first- and second-period elements. The results of 37 conventional KEDFs with explicit formulae were also compared with those of the ML KEDF with an implicit formula. The inclusion of the higher order gradients reduces the deviation of the total kinetic energies from the KS calculations in a stepwise manner. Furthermore, our scheme with the third-order gradient resulted in the closest kinetic energies to the KS calculations out of the presented functionals.

Semiclassical neutral atom as a reference system in density functional theory.

Science.gov (United States)

Constantin, Lucian A; Fabiano, E; Laricchia, S; Della Sala, F

2011-05-06

We use the asymptotic expansions of the semiclassical neutral atom as a reference system in density functional theory to construct accurate generalized gradient approximations (GGAs) for the exchange-correlation and kinetic energies without any empiricism. These asymptotic functionals are among the most accurate GGAs for molecular systems, perform well for solid state, and overcome current GGA state of the art in frozen density embedding calculations. Our results also provide evidence for the conjointness conjecture between exchange and kinetic energies of atomic systems.

The calculations of small molecular conformation energy differences by density functional method

Science.gov (United States)

Topol, I. A.; Burt, S. K.

1993-03-01

The differences in the conformational energies for the gauche (G) and trans(T) conformers of 1,2-difluoroethane and for myo-and scyllo-conformer of inositol have been calculated by local density functional method (LDF approximation) with geometry optimization using different sets of calculation parameters. It is shown that in the contrast to Hartree—Fock methods, density functional calculations reproduce the correct sign and value of the gauche effect for 1,2-difluoroethane and energy difference for both conformers of inositol. The results of normal vibrational analysis for1,2-difluoroethane showed that harmonic frequencies calculated in LDF approximation agree with experimental data with the accuracy typical for scaled large basis set Hartree—Fock calculations.

Density Functional Theory and Materials Modeling at Atomistic Length Scales

Directory of Open Access Journals (Sweden)

Swapan K. Ghosh

2002-04-01

Full Text Available Abstract: We discuss the basic concepts of density functional theory (DFT as applied to materials modeling in the microscopic, mesoscopic and macroscopic length scales. The picture that emerges is that of a single unified framework for the study of both quantum and classical systems. While for quantum DFT, the central equation is a one-particle Schrodinger-like Kohn-Sham equation, the classical DFT consists of Boltzmann type distributions, both corresponding to a system of noninteracting particles in the field of a density-dependent effective potential, the exact functional form of which is unknown. One therefore approximates the exchange-correlation potential for quantum systems and the excess free energy density functional or the direct correlation functions for classical systems. Illustrative applications of quantum DFT to microscopic modeling of molecular interaction and that of classical DFT to a mesoscopic modeling of soft condensed matter systems are highlighted.

The problem of the universal density functional and the density matrix functional theory

International Nuclear Information System (INIS)

Bobrov, V. B.; Trigger, S. A.

2013-01-01

The analysis in this paper shows that the Hohenberg-Kohn theorem is the constellation of two statements: (i) the mathematically rigorous Hohenberg-Kohn lemma, which demonstrates that the same ground-state density cannot correspond to two different potentials of an external field, and (ii) the hypothesis of the existence of the universal density functional. Based on the obtained explicit expression for the nonrel-ativistic particle energy in a local external field, we prove that the energy of the system of more than two non-interacting electrons cannot be a functional of the inhomogeneous density. This result is generalized to the system of interacting electrons. It means that the Hohenberg-Kohn lemma cannot provide justification of the universal density functional for fermions. At the same time, statements of the density functional theory remain valid when considering any number of noninteracting ground-state bosons due to the Bose condensation effect. In the framework of the density matrix functional theory, the hypothesis of the existence of the universal density matrix functional corresponds to the cases of noninteracting particles and to interaction in the Hartree-Fock approximation.

Density-functional errors in ionization potential with increasing system size

Energy Technology Data Exchange (ETDEWEB)

Whittleton, Sarah R.; Sosa Vazquez, Xochitl A.; Isborn, Christine M., E-mail: cisborn@ucmerced.edu [Chemistry and Chemical Biology, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, California 95343 (United States); Johnson, Erin R., E-mail: erin.johnson@dal.ca [Chemistry and Chemical Biology, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, California 95343 (United States); Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2 (Canada)

2015-05-14

This work investigates the effects of molecular size on the accuracy of density-functional ionization potentials for a set of 28 hydrocarbons, including series of alkanes, alkenes, and oligoacenes. As the system size increases, delocalization error introduces a systematic underestimation of the ionization potential, which is rationalized by considering the fractional-charge behavior of the electronic energies. The computation of the ionization potential with many density-functional approximations is not size-extensive due to excessive delocalization of the incipient positive charge. While inclusion of exact exchange reduces the observed errors, system-specific tuning of long-range corrected functionals does not generally improve accuracy. These results emphasize that good performance of a functional for small molecules is not necessarily transferable to larger systems.

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.

A density functional theory study on the molecular mechanism of the cycloaddition between (E)-methyl cinnamate and cyclopentadiene

International Nuclear Information System (INIS)

Alves, C.N.; Camilo, F.F.; Gruber, J.; Silva, A.B.F. da

2004-01-01

The molecular mechanism of the Diels-Alder reaction between (E)-methyl cinnamate and cyclopentadiene has been characterized by means of density functional theory method at the B3LYP/6-31G* theory level. Stationary points for two reactive channels, endo-cis and exo-cis, on potential energy surfaces, have been characterized. Three Lewis acids, boron trifluoride (BF 3 ), aluminum trichloride (AlCl 3 ) and catechol boron bromide (CBB), have been used as catalysts taking into account the formation of a complex between the boron or aluminum atom and the carbonyl oxygen of (E)-methyl cinnamate. The molecular mechanism of the uncatalyzed reaction corresponds to a concerted process. In the presence of BF 3 and AlCl 3 , enhancement of both the asynchronicity and charge transfer between diene and the dienophile, with small decreased energy barriers, were obtained. With CBB, the molecular mechanism changes and the reaction takes place along a stepwise mechanism. The inclusion of the CBB catalyst drastically decreases the energy barrier associated with the carbon-carbon bond formation of the first step relative to the concerted process. The results obtained in this work are compared with experimental data and AM1 semiempirical calculation

Molecular designing of nanoparticles and functional materials

Directory of Open Access Journals (Sweden)

Ignjatović Nenad L.

2017-01-01

Full Text Available The interdisciplinary research team implemented the program titled “Molecular designing of nanoparticles with controlled morphological and physicochemical characteristics and functional materials based on them” (MODENAFUNA, between 2011 and 2016, gaining new knowledge significant to the further improvement of nanomaterials and nanotechnologies. It gathered under its umbrella six main interrelated topics pertaining to the design and control of morphological and physicochemical properties of nanoparticles and functional material based on them using new methods of synthesis and processing: 1 inorganic nanoparticles, 2 cathode materials for lithium-ion batteries, 3 functional ceramics with improved electrical and optical properties, 4 full density nanostructured calcium phosphate and functionally-graded materials, 5 nano-calcium phosphate in bone tissue engineering and 6 biodegradable micro- and nano-particles for the controlled delivery of medicaments. [Project of the Serbian Ministry of Education, Science and Technological Development, Grant no. III45004: Molecular designing of nanoparticles with controlled morphological and physicochemical characteristics and functional materials based on them

Spin-Density Functionals from Current-Density Functional Theory and Vice Versa: A Road towards New Approximations

International Nuclear Information System (INIS)

Capelle, K.; Gross, E.

1997-01-01

It is shown that the exchange-correlation functional of spin-density functional theory is identical, on a certain set of densities, with the exchange-correlation functional of current-density functional theory. This rigorous connection is used to construct new approximations of the exchange-correlation functionals. These include a conceptually new generalized-gradient spin-density functional and a nonlocal current-density functional. copyright 1997 The American Physical Society

Interpretation of the U L3-edge EXAFS in uranium dioxide using molecular dynamics and density functional theory simulations

International Nuclear Information System (INIS)

Bocharov, Dmitry; Chollet, Melanie; Krack, Matthias; Bertsch, Johannes; Grolimund, Daniel; Martin, Matthias; Kuzmin, Alexei; Purans, Juris; Kotomin, Eugene

2016-01-01

X-ray absorption spectroscopy is employed to study the local structure of pure and Cr-doped UO 2 at 300 K. The U L 3 -edge EXAFS spectrum is interpreted within the multiplescattering (MS) theory using the results of the classical and ab initio molecular dynamics simulations, allowing us to validate the accuracy of theoretical models. The Cr K-edge XANES is simulated within the full-multiple-scattering formalism considering a substitutional model (Cr at U site). It is shown that both unrelaxed and relaxed structures, produced by ab initio density functional theory (DFT) calculations, fail to describe the experiment. (paper)

Local density inhomogeneities and dynamics in supercritical water: A molecular dynamics simulation approach.

Science.gov (United States)

Skarmoutsos, Ioannis; Samios, Jannis

2006-11-02

Molecular dynamics atomistic simulations in the canonical ensemble (NVT-MD) have been used to investigate the "Local Density Inhomogeneities and their Dynamics" in pure supercritical water. The simulations were carried out along a near-critical isotherm (Tr = T/Tc = 1.03) and for a wide range of densities below and above the critical one (0.2 rho(c) - 2.0 rho(c)). The results obtained reveal the existence of significant local density augmentation effects, which are found to be sufficiently larger in comparison to those reported for nonassociated fluids. The time evolution of the local density distribution around each molecule was studied in terms of the appropriate time correlation functions C(Delta)rhol(t). It is found that the shape of these functions changes significantly by increasing the density of the fluid. Finally, the local density reorganization times for the first and second coordination shell derived from these correlations exhibit a decreasing behavior by increasing the density of the system, signifying the density effect upon the dynamics of the local environment around each molecule.

Laboratory Density Functionals

OpenAIRE

Giraud, B. G.

2007-01-01

We compare several definitions of the density of a self-bound system, such as a nucleus, in relation with its center-of-mass zero-point motion. A trivial deconvolution relates the internal density to the density defined in the laboratory frame. This result is useful for the practical definition of density functionals.

Solvation and Aggregation of Meta-Aminobenzoic Acid in Water: Density Functional Theory and Molecular Dynamics Study

Directory of Open Access Journals (Sweden)

Etienne Gaines

2018-01-01

Full Text Available Meta-aminobenzoic acid, an important model system in the study of polymorphism and crystallization of active pharmaceutical ingredients, exist in water in both the nonionic (mABA and zwitterionic (mABA± forms. However, the constituent molecules of the polymorph that crystallizes from aqueous solutions are zwitterionic. This study reports atomistic simulations of the events surrounding the early stage of crystal nucleation of meta-aminobenzoic acid from aqueous solutions. Ab initio molecular dynamics was used to simulate the hydration of mABA± and mABA and to quantify the interaction of these molecules with the surrounding water molecules. Density functional theory calculations were conducted to determine the low-lying energy conformers of meta-aminobenzoic acid dimers and to compute the Gibbs free energies in water of nonionic, (mABA2, zwitterionic, (mABA±2, and nonionic-zwitterionic, (mABA(mABA±, species. Classical molecular dynamics simulations of mixed mABA–mABA± aqueous solutions were carried out to examine the aggregation of meta-aminobenzoic acid. According to these simulations, the selective crystallization of the polymorphs whose constituent molecules are zwitterionic is driven by the formation of zwitterionic dimers in solution, which are thermodynamically more stable than (mABA2 and (mABA(mABA± pairs. This work represents a paradigm of the role of molecular processes during the early stages of crystal nucleation in affecting polymorph selection during crystallization from solution.

A Comparative Density Functional Theory and Density Functional Tight Binding Study of Phases of Nitrogen Including a High Energy Density Material N8

Directory of Open Access Journals (Sweden)

Nicholas Capel

2015-11-01

Full Text Available We present a comparative dispersion-corrected Density Functional Theory (DFT and Density Functional Tight Binding (DFTB-D study of several phases of nitrogen, including the well-known alpha, beta, and gamma phases as well as recently discovered highly energetic phases: covalently bound cubic gauche (cg nitrogen and molecular (vdW-bound N8 crystals. Among several tested parametrizations of N–N interactions for DFTB, we identify only one that is suitable for modeling of all these phases. This work therefore establishes the applicability of DFTB-D to studies of phases, including highly metastable phases, of nitrogen, which will be of great use for modelling of dynamics of reactions involving these phases, which may not be practical with DFT due to large required space and time scales. We also derive a dispersion-corrected DFT (DFT-D setup (atom-centered basis parameters and Grimme dispersion parameters tuned for accurate description simultaneously of several nitrogen allotropes including covalently and vdW-bound crystals and including high-energy phases.

Density functional theory for prediction of far-infrared vibrational frequencies: molecular crystals of astrophysical interest

Science.gov (United States)

Ennis, C.; Auchettl, R.; Appadoo, D. R. T.; Robertson, E. G.

2017-11-01

Solid-state density functional theory code has been implemented for the structure optimization of crystalline methanol, acetaldehyde and acetic acid and for the calculation of infrared frequencies. The results are compared to thin film spectra obtained from low-temperature experiments performed at the Australian Synchrotron. Harmonic frequency calculations of the internal modes calculated at the B3LYP-D3/m-6-311G(d) level shows higher deviation from infrared experiment than more advanced theory applied to the gas phase. Importantly for the solid-state, the simulation of low-frequency molecular lattice modes closely resembles the observed far-infrared features after application of a 0.92 scaling factor. This allowed experimental peaks to be assigned to specific translation and libration modes, including acetaldehyde and acetic acid lattice features for the first time. These frequency calculations have been performed without the need for supercomputing resources that are required for large molecular clusters using comparable levels of theory. This new theoretical approach will find use for the rapid characterization of intermolecular interactions and bonding in crystals, and the assignment of far-infrared spectra for crystalline samples such as pharmaceuticals and molecular ices. One interesting application may be for the detection of species of prebiotic interest on the surfaces of Kuiper-Belt and Trans-Neptunian Objects. At such locations, the three small organic molecules studied here could reside in their crystalline phase. The far-infrared spectra for their low-temperature solid phases are collected under planetary conditions, allowing us to compile and assign their most intense spectral features to assist future far-infrared surveys of icy Solar system surfaces.

Solvation Mechanism of Task-Specific Ionic Liquids in Water: A Combined Investigation Using Classical Molecular Dynamics and Density Functional Theory.

Science.gov (United States)

Yuvaraj, Surya V J; Zhdanov, Ravil K; Belosludov, Rodion V; Belosludov, Vladimir R; Subbotin, Oleg S; Kanie, Kiyoshi; Funaki, Kenji; Muramatsu, Atsushi; Nakamura, Takashi; Kawazoe, Yoshiyuki

2015-10-08

The solvation behavior of task-specific ionic liquids (TSILs) containing a common, L-histidine derived imidazolium cation [C20H28N3O3](+) and different anions, bromide-[Br](-) and bis(trifluoromethylsulfonyl)amide-[NTF2](-), in water is examined, computationally. These amino acid functionalized ionic liquids (ILs) are taken into account because of their ability to react with rare earth metal salts. It has been noted that the TSIL with [Br](-) is more soluble than its counterpart TSIL with [NTF2](-), experimentally. In this theoretical work, the combined classical molecular dynamics (CMD) and density functional theory (DFT) calculations are performed to study the behavior of the bulk phase of these two TSILs in the vicinity of water (H2O) molecules with different concentrations. Initially, all the constructed systems are equilibrated using the CMD method. The final structures of the equilibrated systems are extracted for DFT calculations. Under CMD operation, the radial distribution function (RDF) plots and viscosity of TSILs are analyzed to understand the effect of water on TSILs. In the DFT regime, binding energy per H2O, charge transfer, charge density mapping, and electronic density of states (EDOS) analyses are done. The CMD results along with the DFT results are consolidated to support the hydrophilic and hydrophobic nature of the TSILs. Interestingly, we have found a strong correlation between the viscosity and the EDOS results that leads to an understanding of the hydration properties of the TSILs.

A measurement of the turbulence-driven density distribution in a non-star-forming molecular cloud

Energy Technology Data Exchange (ETDEWEB)

Ginsburg, Adam; Darling, Jeremy [CASA, University of Colorado, 389-UCB, Boulder, CO 80309 (United States); Federrath, Christoph, E-mail: Adam.G.Ginsburg@gmail.com [Monash Centre for Astrophysics, School of Mathematical Sciences, Monash University, Vic 3800 (Australia)

2013-12-10

Molecular clouds are supersonically turbulent. This turbulence governs the initial mass function and the star formation rate. In order to understand the details of star formation, it is therefore essential to understand the properties of turbulence, in particular the probability distribution of density in turbulent clouds. We present H{sub 2}CO volume density measurements of a non-star-forming cloud along the line of sight toward W49A. We use these measurements in conjunction with total mass estimates from {sup 13}CO to infer the shape of the density probability distribution function. This method is complementary to measurements of turbulence via the column density distribution and should be applicable to any molecular cloud with detected CO. We show that turbulence in this cloud is probably compressively driven, with a compressive-to-total Mach number ratio b=M{sub C}/M>0.4. We measure the standard deviation of the density distribution, constraining it to the range 1.5 < σ {sub s} < 1.9, assuming that the density is lognormally distributed. This measurement represents an essential input into star formation laws. The method of averaging over different excitation conditions to produce a model of emission from a turbulent cloud is generally applicable to optically thin line observations.

External field as the functional of inhomogeneous density and the density matrix functional approach

NARCIS (Netherlands)

Bobrov, V.B.; Trigger, S.A.; Vlasov, Y.P.

2012-01-01

Based on the Hohenberg-Kohn lemma and the hypotheses of the density functional existence for the external-field potential, it is shown that the strict result of the density functional theory is the equation of the external-field potential as the density functional. This result leads to the

Orbital functionals in density-matrix- and current-density-functional theory

Energy Technology Data Exchange (ETDEWEB)

Helbig, N

2006-05-15

Density-Functional Theory (DFT), although widely used and very successful in the calculation of several observables, fails to correctly describe strongly correlated materials. In the first part of this work we, therefore, introduce reduced-densitymatrix- functional theory (RDMFT) which is one possible way to treat electron correlation beyond DFT. Within this theory the one-body reduced density matrix (1- RDM) is used as the basic variable. Our main interest is the calculation of the fundamental gap which proves very problematic within DFT. In order to calculate the fundamental gap we generalize RDMFT to fractional particle numbers M by describing the system as an ensemble of an N and an N+1 particle system (with N{<=}M{<=}N+1). For each fixed particle number, M, the total energy is minimized with respect to the natural orbitals and their occupation numbers. This leads to the total energy as a function of M. The derivative of this function with respect to the particle number has a discontinuity at integer particle number which is identical to the gap. In addition, we investigate the necessary and sufficient conditions for the 1- RDM of a system with fractional particle number to be N-representable. Numerical results are presented for alkali atoms, small molecules, and periodic systems. Another problem within DFT is the description of non-relativistic many-electron systems in the presence of magnetic fields. It requires the paramagnetic current density and the spin magnetization to be used as basic variables besides the electron density. However, electron-gas-based functionals of current-spin-density-functional Theory (CSDFT) exhibit derivative discontinuities as a function of the magnetic field whenever a new Landau level is occupied, which makes them difficult to use in practice. Since the appearance of Landau levels is, intrinsically, an orbital effect it is appealing to use orbital-dependent functionals. We have developed a CSDFT version of the optimized

Molecular Structure And Vibrational Frequencies of 2,3,4 Nitro anilines By Hartree-Fock And Density Functional Theory Calculations

International Nuclear Information System (INIS)

Sert, Y.

2008-01-01

The optimised molecular structure, vibrational frequencies and corresponding vibrational assignments of 2-, 3- and 4- nitro anilines have been calculated using the Hartree-Fock (HF) and density functional methods (B3LYP) with 6-311++G (d, p) basis set. The calculations were adapted to the C S symmetries of all the molecules. The calculated vibrational frequencies and geometric parameters (bond lengths and bond angles) were seen to be in good agreement with the experimental data. The comparison of the experimental and theoretical results showed that the HF method is superior to the B3LYP method for both the vibrational frequencies and geometric parameters

Local-scaling density-functional method: Intraorbit and interorbit density optimizations

International Nuclear Information System (INIS)

Koga, T.; Yamamoto, Y.; Ludena, E.V.

1991-01-01

The recently proposed local-scaling density-functional theory provides us with a practical method for the direct variational determination of the electron density function ρ(r). The structure of ''orbits,'' which ensures the one-to-one correspondence between the electron density ρ(r) and the N-electron wave function Ψ({r k }), is studied in detail. For the realization of the local-scaling density-functional calculations, procedures for intraorbit and interorbit optimizations of the electron density function are proposed. These procedures are numerically illustrated for the helium atom in its ground state at the beyond-Hartree-Fock level

Electrostatic solvation free energies of charged hard spheres using molecular dynamics with density functional theory interactions

Science.gov (United States)

Duignan, Timothy T.; Baer, Marcel D.; Schenter, Gregory K.; Mundy, Chistopher J.

2017-10-01

Determining the solvation free energies of single ions in water is one of the most fundamental problems in physical chemistry and yet many unresolved questions remain. In particular, the ability to decompose the solvation free energy into simple and intuitive contributions will have important implications for models of electrolyte solution. Here, we provide definitions of the various types of single ion solvation free energies based on different simulation protocols. We calculate solvation free energies of charged hard spheres using density functional theory interaction potentials with molecular dynamics simulation and isolate the effects of charge and cavitation, comparing to the Born (linear response) model. We show that using uncorrected Ewald summation leads to unphysical values for the single ion solvation free energy and that charging free energies for cations are approximately linear as a function of charge but that there is a small non-linearity for small anions. The charge hydration asymmetry for hard spheres, determined with quantum mechanics, is much larger than for the analogous real ions. This suggests that real ions, particularly anions, are significantly more complex than simple charged hard spheres, a commonly employed representation.

Cranked cluster wave function for molecular states

International Nuclear Information System (INIS)

Horiuchi, Hisashi; Yabana, Kazuhiro; Wada, Takahiro.

1986-01-01

Construction of the cranked cluster wave function is discussed by focussing on three problems; the self-consistency between the potential and the density distribution, the properties of the rotational angular frequency which is strongly influenced by the inter-cluster Pauli principle and by the parity projection, and the spin alignment along the rotation axis with the resulting structure-change of the molecular state. (author)

Density functional calculations for atoms, molecules and clusters

International Nuclear Information System (INIS)

Gunnarsson, O.; Jones, R.O.

1980-01-01

The density functional formalism provides a framework for including exchange and correlation effects in the calculation of ground state properties of many-electron systems. The reduction of the problem to the solution of single-particle equations leads to important numerical advantages over other ab initio methods of incorporating correlation effects. The essential features of the scheme are outlined and results obtained for atomic and molecular systems are surveyed. The local spin density (LSD) approximation gives generally good results for systems where the bonding involves s and p electrons, but results are less satisfactory for d-bonded systems. Non-local modifications to the LSD approximation have been tested on atomic systems yielding much improved total energies. (Auth.)

Multicomponent Time-Dependent Density Functional Theory: Proton and Electron Excitation Energies.

Science.gov (United States)

Yang, Yang; Culpitt, Tanner; Hammes-Schiffer, Sharon

2018-04-05

The quantum mechanical treatment of both electrons and protons in the calculation of excited state properties is critical for describing nonadiabatic processes such as photoinduced proton-coupled electron transfer. Multicomponent density functional theory enables the consistent quantum mechanical treatment of more than one type of particle and has been implemented previously for studying ground state molecular properties within the nuclear-electronic orbital (NEO) framework, where all electrons and specified protons are treated quantum mechanically. To enable the study of excited state molecular properties, herein the linear response multicomponent time-dependent density functional theory (TDDFT) is derived and implemented within the NEO framework. Initial applications to FHF - and HCN illustrate that NEO-TDDFT provides accurate proton and electron excitation energies within a single calculation. As its computational cost is similar to that of conventional electronic TDDFT, the NEO-TDDFT approach is promising for diverse applications, particularly nonadiabatic proton transfer reactions, which may exhibit mixed electron-proton vibronic excitations.

Mean-field density functional theory of a nanoconfined classical, three-dimensional Heisenberg fluid. I. The role of molecular anchoring

Science.gov (United States)

Cattes, Stefanie M.; Gubbins, Keith E.; Schoen, Martin

2016-05-01

In this work, we employ classical density functional theory (DFT) to investigate for the first time equilibrium properties of a Heisenberg fluid confined to nanoscopic slit pores of variable width. Within DFT pair correlations are treated at modified mean-field level. We consider three types of walls: hard ones, where the fluid-wall potential becomes infinite upon molecular contact but vanishes otherwise, and hard walls with superimposed short-range attraction with and without explicit orientation dependence. To model the distance dependence of the attractions, we employ a Yukawa potential. The orientation dependence is realized through anchoring of molecules at the substrates, i.e., an energetic discrimination of specific molecular orientations. If the walls are hard or attractive without specific anchoring, the results are "quasi-bulk"-like in that they can be linked to a confinement-induced reduction of the bulk mean field. In these cases, the precise nature of the walls is completely irrelevant at coexistence. Only for specific anchoring nontrivial features arise, because then the fluid-wall interaction potential affects the orientation distribution function in a nontrivial way and thus appears explicitly in the Euler-Lagrange equations to be solved for minima of the grand potential of coexisting phases.

Evaluation of hydrogen bond networks in cellulose Iβ and II crystals using density functional theory and Car-Parrinello molecular dynamics.

Science.gov (United States)

Hayakawa, Daichi; Nishiyama, Yoshiharu; Mazeau, Karim; Ueda, Kazuyoshi

2017-09-08

Crystal models of cellulose Iβ and II, which contain various hydrogen bonding (HB) networks, were analyzed using density functional theory and Car-Parrinello molecular dynamics (CPMD) simulations. From the CPMD trajectories, the power spectra of the velocity correlation functions of hydroxyl groups involved in hydrogen bonds were calculated. For the Iβ allomorph, HB network A, which is dominant according to the neutron diffraction data, was stable, and the power spectrum represented the essential features of the experimental IR spectra. In contrast, network B, which is a minor structure, was unstable because its hydroxymethyl groups reoriented during the CPMD simulation, yielding a different crystal structure to that determined by experiments. For the II allomorph, a HB network A is proposed based on diffraction data, whereas molecular modeling identifies an alternative network B. Our simulations showed that the interaction energies of the cellulose II (B) model are slightly more favorable than model II(A). However, the evaluation of the free energy should be waited for the accurate determination from the energy point of view. For the IR calculation, cellulose II (B) model reproduces the spectra better than model II (A). Copyright © 2017 Elsevier Ltd. All rights reserved.

Three pillars for achieving quantum mechanical molecular dynamics simulations of huge systems: Divide-and-conquer, density-functional tight-binding, and massively parallel computation.

Science.gov (United States)

Nishizawa, Hiroaki; Nishimura, Yoshifumi; Kobayashi, Masato; Irle, Stephan; Nakai, Hiromi

2016-08-05

The linear-scaling divide-and-conquer (DC) quantum chemical methodology is applied to the density-functional tight-binding (DFTB) theory to develop a massively parallel program that achieves on-the-fly molecular reaction dynamics simulations of huge systems from scratch. The functions to perform large scale geometry optimization and molecular dynamics with DC-DFTB potential energy surface are implemented to the program called DC-DFTB-K. A novel interpolation-based algorithm is developed for parallelizing the determination of the Fermi level in the DC method. The performance of the DC-DFTB-K program is assessed using a laboratory computer and the K computer. Numerical tests show the high efficiency of the DC-DFTB-K program, a single-point energy gradient calculation of a one-million-atom system is completed within 60 s using 7290 nodes of the K computer. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Wave-function functionals for the density

International Nuclear Information System (INIS)

Slamet, Marlina; Pan Xiaoyin; Sahni, Viraht

2011-01-01

We extend the idea of the constrained-search variational method for the construction of wave-function functionals ψ[χ] of functions χ. The search is constrained to those functions χ such that ψ[χ] reproduces the density ρ(r) while simultaneously leading to an upper bound to the energy. The functionals are thereby normalized and automatically satisfy the electron-nucleus coalescence condition. The functionals ψ[χ] are also constructed to satisfy the electron-electron coalescence condition. The method is applied to the ground state of the helium atom to construct functionals ψ[χ] that reproduce the density as given by the Kinoshita correlated wave function. The expectation of single-particle operators W=Σ i r i n , n=-2,-1,1,2, W=Σ i δ(r i ) are exact, as must be the case. The expectations of the kinetic energy operator W=-(1/2)Σ i ∇ i 2 , the two-particle operators W=Σ n u n , n=-2,-1,1,2, where u=|r i -r j |, and the energy are accurate. We note that the construction of such functionals ψ[χ] is an application of the Levy-Lieb constrained-search definition of density functional theory. It is thereby possible to rigorously determine which functional ψ[χ] is closer to the true wave function.

Density functional theory

International Nuclear Information System (INIS)

Das, M.P.

1984-07-01

The state of the art of the density functional formalism (DFT) is reviewed. The theory is quantum statistical in nature; its simplest version is the well-known Thomas-Fermi theory. The DFT is a powerful formalism in which one can treat the effect of interactions in inhomogeneous systems. After some introductory material, the DFT is outlined from the two basic theorems, and various generalizations of the theorems appropriate to several physical situations are pointed out. Next, various approximations to the density functionals are presented and some practical schemes, discussed; the approximations include an electron gas of almost constant density and an electron gas of slowly varying density. Then applications of DFT in various diverse areas of physics (atomic systems, plasmas, liquids, nuclear matter) are mentioned, and its strengths and weaknesses are pointed out. In conclusion, more recent developments of DFT are indicated

Local Fitting of the Kohn-Sham Density in a Gaussian and Plane Waves Scheme for Large-Scale Density Functional Theory Simulations.

Science.gov (United States)

Golze, Dorothea; Iannuzzi, Marcella; Hutter, Jürg

2017-05-09

A local resolution-of-the-identity (LRI) approach is introduced in combination with the Gaussian and plane waves (GPW) scheme to enable large-scale Kohn-Sham density functional theory calculations. In GPW, the computational bottleneck is typically the description of the total charge density on real-space grids. Introducing the LRI approximation, the linear scaling of the GPW approach with respect to system size is retained, while the prefactor for the grid operations is reduced. The density fitting is an O(N) scaling process implemented by approximating the atomic pair densities by an expansion in one-center fit functions. The computational cost for the grid-based operations becomes negligible in LRIGPW. The self-consistent field iteration is up to 30 times faster for periodic systems dependent on the symmetry of the simulation cell and on the density of grid points. However, due to the overhead introduced by the local density fitting, single point calculations and complete molecular dynamics steps, including the calculation of the forces, are effectively accelerated by up to a factor of ∼10. The accuracy of LRIGPW is assessed for different systems and properties, showing that total energies, reaction energies, intramolecular and intermolecular structure parameters are well reproduced. LRIGPW yields also high quality results for extended condensed phase systems such as liquid water, ice XV, and molecular crystals.

Molecular dynamics and density functional simulations of tungsten nanostructure formation by helium plasma irradiation

International Nuclear Information System (INIS)

Ito, A.M.; Takayama, A.; Oda, Y.

2014-10-01

For the purposes of long-term use of tungsten diverter walls, it is necessary to suppress the surface deterioration due to the helium ash which induces the formations of helium bubbles and tungsten fuzzy nanostructures. In the present paper, the formation mechanisms of helium bubbles and tungsten fuzzy nanostructures were explained by the four-step process which is composed of the penetration process, the diffusion and agglomeration process, the helium bubble growth process and the tungsten fuzzy nanostructure formation process. The first to third step processes of the four-step process were investigated by using binary collision approximation, density functional theory and molecular dynamics, respectively. Furthermore, newly developed molecular dynamics and Monte-Carlo hybrid simulation has successfully reproduced the early formation process of tungsten fuzzy nanostructure. From these simulations, we here suggest the following key mechanisms of the formations of helium bubbles and tungsten fuzzy nanostructures: (1) By comparison between helium, neon, argon and hydrogen, the noble gas atoms can agglomerate limitlessly not only at a vacancy but also at an interstitial site. In particular, at the low incident energy, only helium atoms bring about the nucleation for helium bubble. (2) In the helium bubble growth process, the strain of the tungsten material around a helium atom is released as a dislocation loop, which is regarded as the loop punching phenomenon. (3) In the tungsten nanostructure formation process, the bursting of a helium bubble forms cavity and convexity in the surface. The helium bubbles tend to be grown and to burst at the cavity region, and then the difference of height between the cavity and convexity on the surface are enhanced. Consequently, the tungsten fuzzy nanostructure is formed. (author)

Open-system Kohn-Sham density functional theory.

Science.gov (United States)

Zhou, Yongxi; Ernzerhof, Matthias

2012-03-07

A simple model for electron transport through molecules is provided by the source-sink potential (SSP) method [F. Goyer, M. Ernzerhof, and M. Zhuang, J. Chem. Phys. 126, 144104 (2007)]. In SSP, the boundary conditions of having an incoming and outgoing electron current are enforced through complex potentials that are added to the Hamiltonian. Depending on the sign of the imaginary part of the potentials, current density is generated or absorbed. In this way, a finite system can be used to model infinite molecular electronic devices. The SSP has originally been developed for the Hückel method and subsequently it has been extended [F. Goyer and M. Ernzerhof, J. Chem. Phys. 134, 174101 (2011)] to the Hubbard model. Here we present a step towards its generalization for first-principles electronic structure theory methods. In particular, drawing on our earlier work, we discuss a new generalized density functional theory for complex non-Hermitian Hamiltonians. This theory enables us to combine SSP and Kohn-Sham theory to obtain a method for the description of open systems that exchange current density with their environment. Similarly, the Hartree-Fock method is extended to the realm of non-Hermitian, SSP containing Hamiltonians. As a proof of principle, we present the first applications of complex-density functional theory (CODFT) as well as non-Hermitian Hartree-Fock theory to electron transport through molecules. © 2012 American Institute of Physics

Low density molecular cloud in the vicinity of the Pleiades

International Nuclear Information System (INIS)

Federman, S.R.; Wilson, R.F.

1984-01-01

The central region of a small, low density molecular cloud, which lies to the south of the Pleiades cluster, has been studied through the use of molecular line observations. Column densities for CH, OH, 12 CO, and 13 CO are derived from the radio data. The CH and OH data yield a visual extinction through the center of the cloud of about 3 mag. The ratio of the antenna temperatures for the OH main lines is consistent with optically thin emission; therefore, the OH results are a good indication of the total extinction through the optically thin emission; therefore, the OH results are a good indication of the total extinction through the cloud. The analysis of the carbon monoxide data produces a relatively high kinetic temperature of at least 20 K, a low total gas density of approx.300-500 cm -3 , and a column density of approx.4 x 10 17 cm -2 for 12 CO. Thus this small molecular cloud is not typical of the molecular material generally studied in Taurus

Density Functional Investigation of Graphene Doped with Amine-Based Organic Molecules

Directory of Open Access Journals (Sweden)

Yeun Hee Hwang

2015-01-01

Full Text Available To improve the electronic properties of graphene, many doping techniques have been studied. Herein, we investigate the electronic and molecular structure of doped graphene using density functional theory, and we report the effects of amine-based benzene dopants adsorbed on graphene. Density functional theory (DFT calculations were performed to determine the role of amine-based aromatic compounds in graphene doping. These organic molecules bind to graphene through long-range interactions such as π-π interactions and C-H⋯π hydrogen bonding. We compared the electronic structures of pristine graphene and doped graphene to understand the electronic structure of doped graphene at the molecular level. Also, work functions of doped graphene were obtained from electrostatic potential calculations. A decrease in the work function was observed when the amine-based organic compounds were adsorbed onto graphene. Because these systems are based on physisorption, there was no obvious band structure change at point K at the Fermi level after doping. However, the amine-based organic dopants did change the absolute Fermi energy levels. In this study, we showed that the Fermi levels of the doped graphene were affected by the HOMO energy level of the dopants and by the intermolecular charge transfer between the adsorbed molecules and graphene.

Tunable non-interacting free-energy functionals: development and applications to low-density aluminum

Science.gov (United States)

Trickey, Samuel; Karasiev, Valentin

We introduce the concept of tunable orbital-free non-interacting free-energy density functionals and present a generalized gradient approximation (GGA) with a subset of parameters defined from constraints and a few free parameters. Those free parameters are tuned to reproduce reference Kohn-Sham (KS) static-lattice pressures for Al at T=8 kK for bulk densities between 0.6 and 2 g/cm3. The tuned functional then is used in OF molecular dynamics (MD) simulations for Al with densities between 0.1 and 2 g/cm3 and T between 6 and 50 kK to calculate the equation of state and generate configurations for electrical conductivity calculations. The tunable functional produces accurate results. Computationally it is very effective especially at elevated temperature. Kohn-Shiam calculations for such low densities are affordable only up to T=10 kK, while other OF approximations, including two-point functionals, fail badly in that regime. Work supported by US DoE Grant DE-SC0002139.

Phylogenetic molecular function annotation

International Nuclear Information System (INIS)

Engelhardt, Barbara E; Jordan, Michael I; Repo, Susanna T; Brenner, Steven E

2009-01-01

It is now easier to discover thousands of protein sequences in a new microbial genome than it is to biochemically characterize the specific activity of a single protein of unknown function. The molecular functions of protein sequences have typically been predicted using homology-based computational methods, which rely on the principle that homologous proteins share a similar function. However, some protein families include groups of proteins with different molecular functions. A phylogenetic approach for predicting molecular function (sometimes called 'phylogenomics') is an effective means to predict protein molecular function. These methods incorporate functional evidence from all members of a family that have functional characterizations using the evolutionary history of the protein family to make robust predictions for the uncharacterized proteins. However, they are often difficult to apply on a genome-wide scale because of the time-consuming step of reconstructing the phylogenies of each protein to be annotated. Our automated approach for function annotation using phylogeny, the SIFTER (Statistical Inference of Function Through Evolutionary Relationships) methodology, uses a statistical graphical model to compute the probabilities of molecular functions for unannotated proteins. Our benchmark tests showed that SIFTER provides accurate functional predictions on various protein families, outperforming other available methods.

Vibrational spectra, molecular structure, natural bond orbital, first order hyperpolarizability, thermodynamic analysis and normal coordinate analysis of Salicylaldehyde p-methylphenylthiosemicarbazone by density functional method

Science.gov (United States)

Porchelvi, E. Elamurugu; Muthu, S.

2015-01-01

The thiosemicarbazone compound, Salicylaldehyde p-methylphenylthiosemicarbazone (abbreviated as SMPTSC) was synthesized and characterized by FTIR, FT-Raman and UV. Density functional (DFT) calculations have been carried out for the title compound by performing DFT level of theory using B3LYP/6-31++G(d,p) basis set. The molecular geometry and vibrational frequencies were calculated and compared with the experimental data. The detailed interpretation of the vibrational spectra has been carried out with aid of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology. The electronic dipole moment (μD) and the first hyperpolarizability (βtot) values of the investigated molecule were computed using density functional theory (DFT/B3LYP) with 6-311++G(d,p) basis set. The stability and charge delocalization of the molecule was studied by natural bond orbital (NBO) analysis. Thearomaticities of the phenyl rings were studied using the standard harmonic oscillator model of aromaticity (HOMA) index. Mulliken population analysis on atomic charges is also calculated. The molecule orbital contributions are studied by density of energy states (DOSs).

Radical scavenging activity of some natural tropolones by density functional theory

Directory of Open Access Journals (Sweden)

A. G. Al-Sehemi

2017-07-01

Full Text Available The ground state neutral geometries of some natural tropolones, i.e. stipitatonic acid (AF1, stipitalide (AF2, stipitaldehydic acid (AF3 and methyl stipitate (AF4 have been optimized by using Density Functional Theory (DFT at B3LYP/6-31G*, B3LYP/6-31G**, B3LYP/6-31+G* and B3LYP/6-31+G** levels of theory. The excited state geometries of AF1-AF4 were optimized by adopting the Time Dependent Density Functional Theory (TDDFT at the same levels of theory. The frequencies and cation species of AF1-AF4 were also computed at all the above mentioned levels of theory. We shed light on the electro-optical and molecular properties, e.g. energy gaps, highest occupied molecular orbitals, lowest unoccupied molecular orbitals, absorption wavelengths, electronegativity (χ, hardness (η, electrophilicity (ω, softness (S, electrophilicity index (ωi and the radical scavenging activity (RSA. Hydrogen atom transfer (HAT and one-electron transfer mechanisms have been discussed to shed light on the RSA. The smallest ionization potential and bond dissociation energy of AF4 are revealing that this compound would have more RSA than those of other counterparts.

Density functional/molecular dynamics simulations of nucleus-driven crystallization of amorphous Ge2Sb2Te5

Energy Technology Data Exchange (ETDEWEB)

Akola, Jaakko [Department of Physics, Tampere University of Technology (Finland); COMP Centre of Excellence, Department of Applied Physics, Aalto University (Finland); GRSS and PGI-1, Forschungszentrum Juelich (Germany); Kalikka, Janne; Larrucea, Julen [Nanoscience Center, Department of Physics, University of Jyvaeskylae (Finland); Jones, Robert O. [GRSS and PGI-1, Forschungszentrum Juelich (Germany)

2013-07-01

Early stages of nucleus-driven crystallization of the prototype phase change material Ge{sub 2}Sb{sub 2}Te{sub 5} have been studied by massively-parallel density functional/molecular dynamics simulations for amorphous samples (460 and 648 atoms) at 500, 600, and 700 K. All systems assumed a fixed cubic seed of 58 atoms and 6 vacancies in order to achieve sub-nanosecond phase transition. Crystallization occurs within 600 ps for the 460-atom system at 600 and 700 K, and signs of crystallization (nucleus growth, percolation) are present in the others. Crystallization is accompanied by an increase in the number of ABAB squares (A: Ge,Sb, B: Te), and atoms of all elements move significantly. The evolution of cavities/vacancies is closely monitored. The existence of Te-Te, Ge-Ge, Ge-Sb, and Sb-Sb (wrong) bonds is an inevitable consequence of rapid crystallization.

Application of numerical methods to the determination of molecular wave functions

International Nuclear Information System (INIS)

Douady, Jerome

1969-01-01

A simplified SCF Method is developed. The wave function of molecular systems and spin densities in the case of free radicals are computed from geometrical data. This method, including at the beginning a delocalization of electrons over all the molecular system, two methods which clear out bonding and anti-bonding interactions have been studied and programmed: a) overlap population analysis, b) localisation of molecular orbitals. These methods have been carried out in the case of organic compounds and free radicals. (author) [fr

Density functionals from deep learning

OpenAIRE

McMahon, Jeffrey M.

2016-01-01

Density-functional theory is a formally exact description of a many-body quantum system in terms of its density; in practice, however, approximations to the universal density functional are required. In this work, a model based on deep learning is developed to approximate this functional. Deep learning allows computational models that are capable of naturally discovering intricate structure in large and/or high-dimensional data sets, with multiple levels of abstraction. As no assumptions are ...

Vibrational signatures of cation-anion hydrogen bonding in ionic liquids: a periodic density functional theory and molecular dynamics study.

Science.gov (United States)

Mondal, Anirban; Balasubramanian, Sundaram

2015-02-05

Hydrogen bonding in alkylammonium based protic ionic liquids was studied using density functional theory (DFT) and ab initio molecular dynamics (AIMD) simulations. Normal-mode analysis within the harmonic approximation and power spectra of velocity autocorrelation functions were used as tools to obtain the vibrational spectra in both the gas phase and the crystalline phases of these protic ionic liquids. The hydrogen bond vibrational modes were identified in the 150-240 cm(-1) region of the far-infrared (far-IR) spectra. A blue shift in the far-IR mode was observed with an increasing number of hydrogen-bonding sites on the cation; the exact peak position is modulated by the cation-anion hydrogen bond strength. Sub-100 cm(-1) bands in the far-IR spectrum are assigned to the rattling motion of the anions. Calculated NMR chemical shifts of the acidic protons in the crystalline phase of these salts also exhibit the signature of cation-anion hydrogen bonding.

Density functional calculations of potential energy surface and charge transfer integrals in molecular triphenylene derivative HAT6

NARCIS (Netherlands)

Zbiri, M.; Johnson, M.R.; Kearley, G.J.; Mulder, F.M.

2009-01-01

We investigate the effect of structural fluctuations on charge transfer integrals, overlap integrals, and site energies in a system of two stacked molecular 2,3,6,7,10,11-hexakishexyloxytriphenylene (HAT6), which is a model system for conducting devices in organic photocell applications. A density

Multicomponent density functional theory embedding formulation

Energy Technology Data Exchange (ETDEWEB)

Culpitt, Tanner; Brorsen, Kurt R.; Pak, Michael V.; Hammes-Schiffer, Sharon, E-mail: shs3@illinois.edu [Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Ave, Urbana, Illinois 61801 (United States)

2016-07-28

Multicomponent density functional theory (DFT) methods have been developed to treat two types of particles, such as electrons and nuclei, quantum mechanically at the same level. In the nuclear-electronic orbital (NEO) approach, all electrons and select nuclei, typically key protons, are treated quantum mechanically. For multicomponent DFT methods developed within the NEO framework, electron-proton correlation functionals based on explicitly correlated wavefunctions have been designed and used in conjunction with well-established electronic exchange-correlation functionals. Herein a general theory for multicomponent embedded DFT is developed to enable the accurate treatment of larger systems. In the general theory, the total electronic density is separated into two subsystem densities, denoted as regular and special, and different electron-proton correlation functionals are used for these two electronic densities. In the specific implementation, the special electron density is defined in terms of spatially localized Kohn-Sham electronic orbitals, and electron-proton correlation is included only for the special electron density. The electron-proton correlation functional depends on only the special electron density and the proton density, whereas the electronic exchange-correlation functional depends on the total electronic density. This scheme includes the essential electron-proton correlation, which is a relatively local effect, as well as the electronic exchange-correlation for the entire system. This multicomponent DFT-in-DFT embedding theory is applied to the HCN and FHF{sup −} molecules in conjunction with two different electron-proton correlation functionals and three different electronic exchange-correlation functionals. The results illustrate that this approach provides qualitatively accurate nuclear densities in a computationally tractable manner. The general theory is also easily extended to other types of partitioning schemes for multicomponent systems.

Scattering of a proton with the Li{sub 4} cluster: Non-adiabatic molecular dynamics description based on time-dependent density-functional theory

Energy Technology Data Exchange (ETDEWEB)

Castro, A., E-mail: acastro@bifi.es [Institute for Biocomputation and Physics of Complex Systems (BIFI) and Zaragoza Scientific Center for Advanced Modelling (ZCAM), University of Zaragoza, 50018 Zaragoza (Spain); Isla, M. [Departamento de Fisica Teorica, Atomica y Optica, Universidad de Valladolid, 47005 Valladolid (Spain); Martinez, Jose I. [Departamento de Fisica Teorica de la Materia Condensada, Universidad Autonoma de Madrid, ES-28049 Madrid (Spain); Alonso, J.A. [Departamento de Fisica Teorica, Atomica y Optica, Universidad de Valladolid, 47005 Valladolid (Spain)

2012-05-03

Graphical abstract: Two trajectories for the collision of a proton with the Lithium tetramer. On the left, the proton is scattered away, and a Li{sub 2} molecule plus two isolated Lithium atoms result. On the right, the proton is captured and a LiH molecule is created. Highlights: Black-Right-Pointing-Pointer Scattering of a proton with Lithium clusters described from first principles. Black-Right-Pointing-Pointer Description based on non-adiabatic molecular dynamics. Black-Right-Pointing-Pointer The electronic structure is described with time-dependent density-functional theory. Black-Right-Pointing-Pointer The method allows to discern reaction channels depending on initial parameters. - Abstract: We have employed non-adiabatic molecular dynamics based on time-dependent density-functional theory to characterize the scattering behavior of a proton with the Li{sub 4} cluster. This technique assumes a classical approximation for the nuclei, effectively coupled to the quantum electronic system. This time-dependent theoretical framework accounts, by construction, for possible charge transfer and ionization processes, as well as electronic excitations, which may play a role in the non-adiabatic regime. We have varied the incidence angles in order to analyze the possible reaction patterns. The initial proton kinetic energy of 10 eV is sufficiently high to induce non-adiabatic effects. For all the incidence angles considered the proton is scattered away, except in one interesting case in which one of the Lithium atoms captures it, forming a LiH molecule. This theoretical formalism proves to be a powerful, effective and predictive tool for the analysis of non-adiabatic processes at the nanoscale.

Molecular excited states from the SCAN functional

Science.gov (United States)

Tozer, David J.; Peach, Michael J. G.

2018-06-01

The performance of the strongly constrained and appropriately normed (SCAN) meta-generalised gradient approximation exchange-correlation functional is investigated for the calculation of time-dependent density-functional theory molecular excitation energies of local, charge-transfer and Rydberg character, together with the excited ? potential energy curve in H2. The SCAN results frequently resemble those obtained using a global hybrid functional, with either a standard or increased fraction of exact orbital exchange. For local excitations, SCAN can exhibit significant triplet instability problems, resulting in imaginary triplet excitation energies for a number of cases. The Tamm-Dancoff approximation offers a simple approach to improve the situation, but the excitation energies are still significantly underestimated. Understanding the origin of these (near)-triplet instabilities may provide useful insight into future functional development.

Solvation in atomic liquids: connection between Gaussian field theory and density functional theory

Directory of Open Access Journals (Sweden)

V. Sergiievskyi

2017-12-01

Full Text Available For the problem of molecular solvation, formulated as a liquid submitted to the external potential field created by a molecular solute of arbitrary shape dissolved in that solvent, we draw a connection between the Gaussian field theory derived by David Chandler [Phys. Rev. E, 1993, 48, 2898] and classical density functional theory. We show that Chandler's results concerning the solvation of a hard core of arbitrary shape can be recovered by either minimising a linearised HNC functional using an auxiliary Lagrange multiplier field to impose a vanishing density inside the core, or by minimising this functional directly outside the core — indeed a simpler procedure. Those equivalent approaches are compared to two other variants of DFT, either in the HNC, or partially linearised HNC approximation, for the solvation of a Lennard-Jones solute of increasing size in a Lennard-Jones solvent. Compared to Monte-Carlo simulations, all those theories give acceptable results for the inhomogeneous solvent structure, but are completely out-of-range for the solvation free-energies. This can be fixed in DFT by adding a hard-sphere bridge correction to the HNC functional.

Exact density functional and wave function embedding schemes based on orbital localization

International Nuclear Information System (INIS)

Hégely, Bence; Nagy, Péter R.; Kállay, Mihály; Ferenczy, György G.

2016-01-01

Exact schemes for the embedding of density functional theory (DFT) and wave function theory (WFT) methods into lower-level DFT or WFT approaches are introduced utilizing orbital localization. First, a simple modification of the projector-based embedding scheme of Manby and co-workers [J. Chem. Phys. 140, 18A507 (2014)] is proposed. We also use localized orbitals to partition the system, but instead of augmenting the Fock operator with a somewhat arbitrary level-shift projector we solve the Huzinaga-equation, which strictly enforces the Pauli exclusion principle. Second, the embedding of WFT methods in local correlation approaches is studied. Since the latter methods split up the system into local domains, very simple embedding theories can be defined if the domains of the active subsystem and the environment are treated at a different level. The considered embedding schemes are benchmarked for reaction energies and compared to quantum mechanics (QM)/molecular mechanics (MM) and vacuum embedding. We conclude that for DFT-in-DFT embedding, the Huzinaga-equation-based scheme is more efficient than the other approaches, but QM/MM or even simple vacuum embedding is still competitive in particular cases. Concerning the embedding of wave function methods, the clear winner is the embedding of WFT into low-level local correlation approaches, and WFT-in-DFT embedding can only be more advantageous if a non-hybrid density functional is employed.

Exact density functional and wave function embedding schemes based on orbital localization

Science.gov (United States)

Hégely, Bence; Nagy, Péter R.; Ferenczy, György G.; Kállay, Mihály

2016-08-01

Exact schemes for the embedding of density functional theory (DFT) and wave function theory (WFT) methods into lower-level DFT or WFT approaches are introduced utilizing orbital localization. First, a simple modification of the projector-based embedding scheme of Manby and co-workers [J. Chem. Phys. 140, 18A507 (2014)] is proposed. We also use localized orbitals to partition the system, but instead of augmenting the Fock operator with a somewhat arbitrary level-shift projector we solve the Huzinaga-equation, which strictly enforces the Pauli exclusion principle. Second, the embedding of WFT methods in local correlation approaches is studied. Since the latter methods split up the system into local domains, very simple embedding theories can be defined if the domains of the active subsystem and the environment are treated at a different level. The considered embedding schemes are benchmarked for reaction energies and compared to quantum mechanics (QM)/molecular mechanics (MM) and vacuum embedding. We conclude that for DFT-in-DFT embedding, the Huzinaga-equation-based scheme is more efficient than the other approaches, but QM/MM or even simple vacuum embedding is still competitive in particular cases. Concerning the embedding of wave function methods, the clear winner is the embedding of WFT into low-level local correlation approaches, and WFT-in-DFT embedding can only be more advantageous if a non-hybrid density functional is employed.

Exact density functional and wave function embedding schemes based on orbital localization

Energy Technology Data Exchange (ETDEWEB)

Hégely, Bence; Nagy, Péter R.; Kállay, Mihály, E-mail: kallay@mail.bme.hu [MTA-BME Lendület Quantum Chemistry Research Group, Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, P.O. Box 91, H-1521 Budapest (Hungary); Ferenczy, György G. [Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest (Hungary); Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47, H-1094 Budapest (Hungary)

2016-08-14

Exact schemes for the embedding of density functional theory (DFT) and wave function theory (WFT) methods into lower-level DFT or WFT approaches are introduced utilizing orbital localization. First, a simple modification of the projector-based embedding scheme of Manby and co-workers [J. Chem. Phys. 140, 18A507 (2014)] is proposed. We also use localized orbitals to partition the system, but instead of augmenting the Fock operator with a somewhat arbitrary level-shift projector we solve the Huzinaga-equation, which strictly enforces the Pauli exclusion principle. Second, the embedding of WFT methods in local correlation approaches is studied. Since the latter methods split up the system into local domains, very simple embedding theories can be defined if the domains of the active subsystem and the environment are treated at a different level. The considered embedding schemes are benchmarked for reaction energies and compared to quantum mechanics (QM)/molecular mechanics (MM) and vacuum embedding. We conclude that for DFT-in-DFT embedding, the Huzinaga-equation-based scheme is more efficient than the other approaches, but QM/MM or even simple vacuum embedding is still competitive in particular cases. Concerning the embedding of wave function methods, the clear winner is the embedding of WFT into low-level local correlation approaches, and WFT-in-DFT embedding can only be more advantageous if a non-hybrid density functional is employed.

Finding the best density functional approximation to describe interaction energies and structures of ionic liquids in molecular dynamics studies

Science.gov (United States)

Perlt, Eva; Ray, Promit; Hansen, Andreas; Malberg, Friedrich; Grimme, Stefan; Kirchner, Barbara

2018-05-01

Ionic liquids raise interesting but complicated questions for theoretical investigations due to the fact that a number of different inter-molecular interactions, e.g., hydrogen bonding, long-range Coulomb interactions, and dispersion interactions, need to be described properly. Here, we present a detailed study on the ionic liquids ethylammonium nitrate and 1-ethyl-3-methylimidazolium acetate, in which we compare different dispersion corrected density functional approximations to accurate local coupled cluster data in static calculations on ionic liquid clusters. The efficient new composite method B97-3c is tested and has been implemented in CP2K for future studies. Furthermore, tight-binding based approaches which may be used in large scale simulations are assessed. Subsequently, ab initio as well as classical molecular dynamics simulations are conducted and structural analyses are presented in order to shed light on the different short- and long-range structural patterns depending on the method and the system size considered in the simulation. Our results indicate the presence of strong hydrogen bonds in ionic liquids as well as the aggregation of alkyl side chains due to dispersion interactions.

Temperature-dependent study of isotropic-nematic transition for a Gay-Berne fluid using density-functional theory

International Nuclear Information System (INIS)

Singh, Ram Chandra

2007-01-01

We have used the density-functional theory to study the effect of varying temperature on the isotropic-nematic transition of a fluid of molecules interacting via the Gay-Berne intermolecular potential. The nematic phase is found to be stable with respect to isotropic phase in the temperature range 0.80≤T*≤1.25. Pair correlation functions needed as input information in density-functional theory is calculated using the Percus-Yevick integral equation theory. We find that the density-functional theory is good for studying the isotropic-nematic transition in molecular fluids if the values of the pair-correlation functions in the isotropic phase are known accurately. We have also compared our results with computer simulation results wherever they are available

Magnetic fields and density functional theory

Energy Technology Data Exchange (ETDEWEB)

Salsbury Jr., Freddie [Univ. of California, Berkeley, CA (United States)

1999-02-01

A major focus of this dissertation is the development of functionals for the magnetic susceptibility and the chemical shielding within the context of magnetic field density functional theory (BDFT). These functionals depend on the electron density in the absence of the field, which is unlike any other treatment of these responses. There have been several advances made within this theory. The first of which is the development of local density functionals for chemical shieldings and magnetic susceptibilities. There are the first such functionals ever proposed. These parameters have been studied by constructing functionals for the current density and then using the Biot-Savart equations to obtain the responses. In order to examine the advantages and disadvantages of the local functionals, they were tested numerically on some small molecules.

Magnetic fields and density functional theory

International Nuclear Information System (INIS)

Salsbury, Freddie Jr.

1999-01-01

A major focus of this dissertation is the development of functionals for the magnetic susceptibility and the chemical shielding within the context of magnetic field density functional theory (BDFT). These functionals depend on the electron density in the absence of the field, which is unlike any other treatment of these responses. There have been several advances made within this theory. The first of which is the development of local density functionals for chemical shieldings and magnetic susceptibilities. There are the first such functionals ever proposed. These parameters have been studied by constructing functionals for the current density and then using the Biot-Savart equations to obtain the responses. In order to examine the advantages and disadvantages of the local functionals, they were tested numerically on some small molecules

Density dependence of the nuclear energy-density functional

Science.gov (United States)

Papakonstantinou, Panagiota; Park, Tae-Sun; Lim, Yeunhwan; Hyun, Chang Ho

2018-01-01

Background: The explicit density dependence in the coupling coefficients entering the nonrelativistic nuclear energy-density functional (EDF) is understood to encode effects of three-nucleon forces and dynamical correlations. The necessity for the density-dependent coupling coefficients to assume the form of a preferably small fractional power of the density ρ is empirical and the power is often chosen arbitrarily. Consequently, precision-oriented parametrizations risk overfitting in the regime of saturation and extrapolations in dilute or dense matter may lose predictive power. Purpose: Beginning with the observation that the Fermi momentum kF, i.e., the cubic root of the density, is a key variable in the description of Fermi systems, we first wish to examine if a power hierarchy in a kF expansion can be inferred from the properties of homogeneous matter in a domain of densities, which is relevant for nuclear structure and neutron stars. For subsequent applications we want to determine a functional that is of good quality but not overtrained. Method: For the EDF, we fit systematically polynomial and other functions of ρ1 /3 to existing microscopic, variational calculations of the energy of symmetric and pure neutron matter (pseudodata) and analyze the behavior of the fits. We select a form and a set of parameters, which we found robust, and examine the parameters' naturalness and the quality of resulting extrapolations. Results: A statistical analysis confirms that low-order terms such as ρ1 /3 and ρ2 /3 are the most relevant ones in the nuclear EDF beyond lowest order. It also hints at a different power hierarchy for symmetric vs. pure neutron matter, supporting the need for more than one density-dependent term in nonrelativistic EDFs. The functional we propose easily accommodates known or adopted properties of nuclear matter near saturation. More importantly, upon extrapolation to dilute or asymmetric matter, it reproduces a range of existing microscopic

Total-energy Assisted Tight-binding Method Based on Local Density Approximation of Density Functional Theory

Science.gov (United States)

Fujiwara, Takeo; Nishino, Shinya; Yamamoto, Susumu; Suzuki, Takashi; Ikeda, Minoru; Ohtani, Yasuaki

2018-06-01

A novel tight-binding method is developed, based on the extended Hückel approximation and charge self-consistency, with referring the band structure and the total energy of the local density approximation of the density functional theory. The parameters are so adjusted by computer that the result reproduces the band structure and the total energy, and the algorithm for determining parameters is established. The set of determined parameters is applicable to a variety of crystalline compounds and change of lattice constants, and, in other words, it is transferable. Examples are demonstrated for Si crystals of several crystalline structures varying lattice constants. Since the set of parameters is transferable, the present tight-binding method may be applicable also to molecular dynamics simulations of large-scale systems and long-time dynamical processes.

Changes in permittivity and density of molecular liquids under high pressure.

Science.gov (United States)

Kiselev, Vladimir D; Kornilov, Dmitry A; Konovalov, Alexander I

2014-04-03

We collected and analyzed the density and permittivity of 57 nonpolar and dipolar molecular liquids at different temperatures (143 sets) and pressures (555 sets). No equation was found that could accurately predict the change to polar liquid permittivity by the change of its density in the range of the pressures and temperatures tested. Consequently, the influence of high hydrostatic pressure and temperature on liquid permittivity may be a more complicated process compared to density changes. The pressure and temperature coefficients of permittivity can be drastically larger than the pressure and temperature coefficients of density, indicating that pressure and particularly temperature significantly affect the structure of molecular liquids. These changes have less influence on the density change but can strongly affect the permittivity change. The clear relationship between the tangent and secant moduli of the permittivity curvatures under pressure for various molecular liquids at different temperatures was obtained, from which one can calculate the Tait equation coefficients from the experimental values of the pressure influence on the permittivity at ambient pressure.

Estimation of Nanodiamond Surface Charge Density from Zeta Potential and Molecular Dynamics Simulations.

Science.gov (United States)

Ge, Zhenpeng; Wang, Yi

2017-04-20

Molecular dynamics simulations of nanoparticles (NPs) are increasingly used to study their interactions with various biological macromolecules. Such simulations generally require detailed knowledge of the surface composition of the NP under investigation. Even for some well-characterized nanoparticles, however, this knowledge is not always available. An example is nanodiamond, a nanoscale diamond particle with surface dominated by oxygen-containing functional groups. In this work, we explore using the harmonic restraint method developed by Venable et al., to estimate the surface charge density (σ) of nanodiamonds. Based on the Gouy-Chapman theory, we convert the experimentally determined zeta potential of a nanodiamond to an effective charge density (σ eff ), and then use the latter to estimate σ via molecular dynamics simulations. Through scanning a series of nanodiamond models, we show that the above method provides a straightforward protocol to determine the surface charge density of relatively large (> ∼100 nm) NPs. Overall, our results suggest that despite certain limitation, the above protocol can be readily employed to guide the model construction for MD simulations, which is particularly useful when only limited experimental information on the NP surface composition is available to a modeler.

Classical density functional theory & simulations on a coarse-grained model of aromatic ionic liquids.

Science.gov (United States)

Turesson, Martin; Szparaga, Ryan; Ma, Ke; Woodward, Clifford E; Forsman, Jan

2014-05-14

A new classical density functional approach is developed to accurately treat a coarse-grained model of room temperature aromatic ionic liquids. Our major innovation is the introduction of charge-charge correlations, which are treated in a simple phenomenological way. We test this theory on a generic coarse-grained model for aromatic RTILs with oligomeric forms for both cations and anions, approximating 1-alkyl-3-methyl imidazoliums and BF₄⁻, respectively. We find that predictions by the new density functional theory for fluid structures at charged surfaces are very accurate, as compared with molecular dynamics simulations, across a range of surface charge densities and lengths of the alkyl chain. Predictions of interactions between charged surfaces are also presented.

Quasi-particle energy spectra in local reduced density matrix functional theory.

Science.gov (United States)

Lathiotakis, Nektarios N; Helbig, Nicole; Rubio, Angel; Gidopoulos, Nikitas I

2014-10-28

Recently, we introduced [N. N. Lathiotakis, N. Helbig, A. Rubio, and N. I. Gidopoulos, Phys. Rev. A 90, 032511 (2014)] local reduced density matrix functional theory (local RDMFT), a theoretical scheme capable of incorporating static correlation effects in Kohn-Sham equations. Here, we apply local RDMFT to molecular systems of relatively large size, as a demonstration of its computational efficiency and its accuracy in predicting single-electron properties from the eigenvalue spectrum of the single-particle Hamiltonian with a local effective potential. We present encouraging results on the photoelectron spectrum of molecular systems and the relative stability of C20 isotopes. In addition, we propose a modelling of the fractional occupancies as functions of the orbital energies that further improves the efficiency of the method useful in applications to large systems and solids.

High-pressure and high-temperature physical properties of LiF studied by density functional theory calculations and molecular dynamics simulations

Science.gov (United States)

Sun, Xiao-Wei; Liu, Zi-Jiang; Quan, Wei-Long; Song, Ting; Khenata, Rabah; Bin-Omran, Saad

2018-05-01

Using the revised Perdew-Burke-Ernzerhof generalized gradient approximation based on first-principles plane-wave pseudopotential density functional theory, the high-pressure structural phase transition of LiF is explored. From the analysis of Gibbs free energies, we find that no phase transition occurs for LiF in the presented pressure range from 0 to 1000 GPa, and this result is consistent with the theoretical prediction obtained via ab initio calculations [N.A. Smirnov, Phys. Rev. B 83 (2011) 014109]. Using the classical molecular dynamics technique with effective pair potentials which consist of the Coulomb, dispersion, and repulsion interaction, the melting phase diagram of LiF is determined. The obtained normalized volumes under pressure are in good agreement with our density functional theory results and the available experimental data. Meanwhile, with the help of the quasi-harmonic Debye model in which the phononic effects are considered, the thermodynamic properties of interest, including the volume thermal expansion coefficient, isothermal bulk modulus and its first and second pressure derivatives, heat capacity at constant volume, entropy, Debye temperature, and Grüneisen parameter of LiF are predicted systematically. All the properties of LiF with the stable NaCl-type structure in the temperature range of 0-4900 K and the pressure up to 1000 GPa are summarized.

Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D)

International Nuclear Information System (INIS)

Streek, Jacco van de; Neumann, Marcus A.

2014-01-01

The accuracy of 215 experimental organic crystal structures from powder diffraction data is validated against a dispersion-corrected density functional theory method. In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom

Density-functional theory for internal magnetic fields

Science.gov (United States)

Tellgren, Erik I.

2018-01-01

A density-functional theory is developed based on the Maxwell-Schrödinger equation with an internal magnetic field in addition to the external electromagnetic potentials. The basic variables of this theory are the electron density and the total magnetic field, which can equivalently be represented as a physical current density. Hence, the theory can be regarded as a physical current density-functional theory and an alternative to the paramagnetic current density-functional theory due to Vignale and Rasolt. The energy functional has strong enough convexity properties to allow a formulation that generalizes Lieb's convex analysis formulation of standard density-functional theory. Several variational principles as well as a Hohenberg-Kohn-like mapping between potentials and ground-state densities follow from the underlying convex structure. Moreover, the energy functional can be regarded as the result of a standard approximation technique (Moreau-Yosida regularization) applied to the conventional Schrödinger ground-state energy, which imposes limits on the maximum curvature of the energy (with respect to the magnetic field) and enables construction of a (Fréchet) differentiable universal density functional.

Density-density functionals and effective potentials in many-body electronic structure calculations

International Nuclear Information System (INIS)

Reboredo, Fernando A.; Kent, Paul R.

2008-01-01

We demonstrate the existence of different density-density functionals designed to retain selected properties of the many-body ground state in a non-interacting solution starting from the standard density functional theory ground state. We focus on diffusion quantum Monte Carlo applications that require trial wave functions with optimal Fermion nodes. The theory is extensible and can be used to understand current practices in several electronic structure methods within a generalized density functional framework. The theory justifies and stimulates the search of optimal empirical density functionals and effective potentials for accurate calculations of the properties of real materials, but also cautions on the limits of their applicability. The concepts are tested and validated with a near-analytic model.

Density functional theory

International Nuclear Information System (INIS)

Freyss, M.

2015-01-01

This chapter gives an introduction to first-principles electronic structure calculations based on the density functional theory (DFT). Electronic structure calculations have a crucial importance in the multi-scale modelling scheme of materials: not only do they enable one to accurately determine physical and chemical properties of materials, they also provide data for the adjustment of parameters (or potentials) in higher-scale methods such as classical molecular dynamics, kinetic Monte Carlo, cluster dynamics, etc. Most of the properties of a solid depend on the behaviour of its electrons, and in order to model or predict them it is necessary to have an accurate method to compute the electronic structure. DFT is based on quantum theory and does not make use of any adjustable or empirical parameter: the only input data are the atomic number of the constituent atoms and some initial structural information. The complicated many-body problem of interacting electrons is replaced by an equivalent single electron problem, in which each electron is moving in an effective potential. DFT has been successfully applied to the determination of structural or dynamical properties (lattice structure, charge density, magnetisation, phonon spectra, etc.) of a wide variety of solids. Its efficiency was acknowledged by the attribution of the Nobel Prize in Chemistry in 1998 to one of its authors, Walter Kohn. A particular attention is given in this chapter to the ability of DFT to model the physical properties of nuclear materials such as actinide compounds. The specificities of the 5f electrons of actinides will be presented, i.e., their more or less high degree of localisation around the nuclei and correlations. The limitations of the DFT to treat the strong 5f correlations are one of the main issues for the DFT modelling of nuclear fuels. Various methods that exist to better treat strongly correlated materials will finally be presented. (author)

Excited-state density functional theory

International Nuclear Information System (INIS)

Harbola, Manoj K; Hemanadhan, M; Shamim, Md; Samal, P

2012-01-01

Starting with a brief introduction to excited-state density functional theory, we present our method of constructing modified local density approximated (MLDA) energy functionals for the excited states. We show that these functionals give accurate results for kinetic energy and exchange energy compared to the ground state LDA functionals. Further, with the inclusion of GGA correction, highly accurate total energies for excited states are obtained. We conclude with a brief discussion on the further direction of research that include the construction of correlation energy functional and exchange potential for excited states.

Spatially heterogeneous dynamics investigated via a time-dependent four-point density correlation function

DEFF Research Database (Denmark)

Lacevic, N.; Starr, F. W.; Schrøder, Thomas

2003-01-01

correlation function g4(r,t) and corresponding "structure factor" S4(q,t) which measure the spatial correlations between the local liquid density at two points in space, each at two different times, and so are sensitive to dynamical heterogeneity. We study g4(r,t) and S4(q,t) via molecular dynamics......Relaxation in supercooled liquids above their glass transition and below the onset temperature of "slow" dynamics involves the correlated motion of neighboring particles. This correlated motion results in the appearance of spatially heterogeneous dynamics or "dynamical heterogeneity." Traditional...... two-point time-dependent density correlation functions, while providing information about the transient "caging" of particles on cooling, are unable to provide sufficiently detailed information about correlated motion and dynamical heterogeneity. Here, we study a four-point, time-dependent density...

Functional Annotation of Ion Channel Structures by Molecular Simulation.

Science.gov (United States)

Trick, Jemma L; Chelvaniththilan, Sivapalan; Klesse, Gianni; Aryal, Prafulla; Wallace, E Jayne; Tucker, Stephen J; Sansom, Mark S P

2016-12-06

Ion channels play key roles in cell membranes, and recent advances are yielding an increasing number of structures. However, their functional relevance is often unclear and better tools are required for their functional annotation. In sub-nanometer pores such as ion channels, hydrophobic gating has been shown to promote dewetting to produce a functionally closed (i.e., non-conductive) state. Using the serotonin receptor (5-HT 3 R) structure as an example, we demonstrate the use of molecular dynamics to aid the functional annotation of channel structures via simulation of the behavior of water within the pore. Three increasingly complex simulation analyses are described: water equilibrium densities; single-ion free-energy profiles; and computational electrophysiology. All three approaches correctly predict the 5-HT 3 R crystal structure to represent a functionally closed (i.e., non-conductive) state. We also illustrate the application of water equilibrium density simulations to annotate different conformational states of a glycine receptor. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Spectral function from Reduced Density Matrix Functional Theory

Science.gov (United States)

Romaniello, Pina; di Sabatino, Stefano; Berger, Jan A.; Reining, Lucia

2015-03-01

In this work we focus on the calculation of the spectral function, which determines, for example, photoemission spectra, from reduced density matrix functional theory. Starting from its definition in terms of the one-body Green's function we derive an expression for the spectral function that depends on the natural occupation numbers and on an effective energy which accounts for all the charged excitations. This effective energy depends on the two-body as well as higher-order density matrices. Various approximations to this expression are explored by using the exactly solvable Hubbard chains.

A parity function for studying the molecular electronic structure

DEFF Research Database (Denmark)

Schmider, Hartmut

1996-01-01

Sections through the molecular Wigner function with zero momentum variable are shown to provide important information about the off-diagonal regions of the spinless one-particle reduced density matrix. Since these regions are characteristic for the bonding situation in molecules, the sections...... are qualitatively even more affected by the presence of chemical bonds than a complementary projection, the reciprocal form factor. In this paper we discuss, on the grounds of a variety of examples, how this rather simple function may aid the understanding of the chemical bond on a one-particle level. (C) 1996...

Accurate density-functional calculations on large systems: Fullerenes and magnetic clusters

International Nuclear Information System (INIS)

Dunlap, B.I.

1996-01-01

Efforts to accurately compute all-electron density-functional energies for large molecules and clusters using Gaussian basis sets will be reviewed. The foundation of this effort, variational fitting, will be described and followed by three applications of the method. The first application concerns fullerenes. When first discovered, C 60 is quite unstable relative to the higher fullerenes. In addition, to raising questions about the relative abundance of the various fullerenes, this work conflicted with the then state-of-the art density-funcitonal calculations on crystalline graphite. Now high accuracy molecular and band structure calculations are in fairly good agreement. Second, we have used these methods to design transition metal clusters having the highest magnetic moment by maximizing the symmetry-required degeneracy of the one-electron orbitals. Most recently, we have developed accurate, variational generalized-gradient approximation (GGA) forces for use in geometry optimization of clusters and in molecular-dynamics simulations of friction. The GGA optimized geometries of a number of large clusters will be given

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.

Validation of missed space-group symmetry in X-ray powder diffraction structures with dispersion-corrected density functional theory

DEFF Research Database (Denmark)

Hempler, Daniela; Schmidt, Martin U.; Van De Streek, Jacco

2017-01-01

More than 600 molecular crystal structures with correct, incorrect and uncertain space-group symmetry were energy-minimized with dispersion-corrected density functional theory (DFT-D, PBE-D3). For the purpose of determining the correct space-group symmetry the required tolerance on the atomic...... with missed symmetry were investigated by dispersion-corrected density functional theory. In 98.5% of the cases the correct space group is found....

Microscopic aspects of wetting using classical density functional theory

Science.gov (United States)

Yatsyshin, P.; Durán-Olivencia, M.-A.; Kalliadasis, S.

2018-07-01

Wetting is a rather efficient mechanism for nucleation of a phase (typically liquid) on the interface between two other phases (typically solid and gas). In many experimentally accessible cases of wetting, the interplay between the substrate structure, and the fluid–fluid and fluid–substrate intermolecular interactions brings about an entire ‘zoo’ of possible fluid configurations, such as liquid films with a thickness of a few nanometers, liquid nanodrops and liquid bridges. These fluid configurations are often associated with phase transitions occurring at the solid–gas interface and at lengths of just several molecular diameters away from the substrate. In this special issue article, we demonstrate how a fully microscopic classical density-functional framework can be applied to the efficient, rational and systematic exploration of the rich phase space of wetting phenomena. We consider a number of model prototype systems such as wetting on a planar wall, a chemically patterned wall and a wedge. Through density-functional computations we demonstrate that for these simply structured substrates the behaviour of the solid–gas interface is already highly complex and non-trivial.

Density-functional theory for fluid-solid and solid-solid phase transitions.

Science.gov (United States)

Bharadwaj, Atul S; Singh, Yashwant

2017-03-01

We develop a theory to describe solid-solid phase transitions. The density functional formalism of classical statistical mechanics is used to find an exact expression for the difference in the grand thermodynamic potentials of the two coexisting phases. The expression involves both the symmetry conserving and the symmetry broken parts of the direct pair correlation function. The theory is used to calculate phase diagram of systems of soft spheres interacting via inverse power potentials u(r)=ε(σ/r)^{n}, where parameter n measures softness of the potential. We find that for 1/nfcc) structure while for 1/n≥0.154 the body-centred-cubic (bcc) structure is preferred. The bcc structure transforms into the fcc structure upon increasing the density. The calculated phase diagram is in good agreement with the one found from molecular simulations.

Single-particle energies and density of states in density functional theory

Science.gov (United States)

van Aggelen, H.; Chan, G. K.-L.

2015-07-01

Time-dependent density functional theory (TD-DFT) is commonly used as the foundation to obtain neutral excited states and transition weights in DFT, but does not allow direct access to density of states and single-particle energies, i.e. ionisation energies and electron affinities. Here we show that by extending TD-DFT to a superfluid formulation, which involves operators that break particle-number symmetry, we can obtain the density of states and single-particle energies from the poles of an appropriate superfluid response function. The standard Kohn- Sham eigenvalues emerge as the adiabatic limit of the superfluid response under the assumption that the exchange- correlation functional has no dependence on the superfluid density. The Kohn- Sham eigenvalues can thus be interpreted as approximations to the ionisation energies and electron affinities. Beyond this approximation, the formalism provides an incentive for creating a new class of density functionals specifically targeted at accurate single-particle eigenvalues and bandgaps.

Exact-exchange time-dependent density-functional theory for static and dynamic polarizabilities

International Nuclear Information System (INIS)

Hirata, So; Ivanov, Stanislav; Bartlett, Rodney J.; Grabowski, Ireneusz

2005-01-01

Time-dependent density-functional theory (TDDFT) employing the exact-exchange functional has been formulated on the basis of the optimized-effective-potential (OEP) method of Talman and Shadwick for second-order molecular properties and implemented into a Gaussian-basis-set, trial-vector algorithm. The only approximation involved, apart from the lack of correlation effects and the use of Gaussian-type basis functions, was the consistent use of the adiabatic approximation in the exchange kernel and in the linear response function. The static and dynamic polarizabilities and their anisotropy predicted by the TDDFT with exact exchange (TDOEP) agree accurately with the corresponding values from time-dependent Hartree-Fock theory, the exact-exchange counterpart in the wave function theory. The TDOEP is free from the nonphysical asymptotic decay of the exchange potential of most conventional density functionals or from any other manifestations of the incomplete cancellation of the self-interaction energy. The systematic overestimation of the absolute values and dispersion of polarizabilities that plagues most conventional TDDFT cannot be seen in the TDOEP

Recent progress in orbital-free density functional theory (recent advances in computational chemistry)

CERN Document Server

Wesolowski, Tomasz A

2013-01-01

This is a comprehensive overview of state-of-the-art computational methods based on orbital-free formulation of density functional theory completed by the most recent developments concerning the exact properties, approximations, and interpretations of the relevant quantities in density functional theory. The book is a compilation of contributions stemming from a series of workshops which had been taking place since 2002. It not only chronicles many of the latest developments but also summarises some of the more significant ones. The chapters are mainly reviews of sub-domains but also include original research. Readership: Graduate students, academics and researchers in computational chemistry. Atomic & molecular physicists, theoretical physicists, theoretical chemists, physical chemists and chemical physicists.

Electronic states of aryl radical functionalized graphenes: Density functional theory study

Science.gov (United States)

Tachikawa, Hiroto; Kawabata, Hiroshi

2016-06-01

Functionalized graphenes are known as a high-performance molecular device. In the present study, the structures and electronic states of the aryl radical functionalized graphene have been investigated by the density functional theory (DFT) method to elucidate the effects of functionalization on the electronic states of graphene (GR). Also, the mechanism of aryl radical reaction with GR was investigated. The benzene, biphenyl, p-terphenyl, and p-quaterphenyl radicals [denoted by (Bz) n (n = 1-4), where n means numbers of benzene rings in aryl radical] were examined as aryl radicals. The DFT calculation of GR-(Bz) n (n = 1-4) showed that the aryl radical binds to the carbon atom of GR, and a C-C single bond was formed. The binding energies of aryl radicals to GR were calculated to be ca. 6.0 kcal mol-1 at the CAM-B3LYP/6-311G(d,p) level. It was found that the activation barrier exists in the aryl radical addition: the barrier heights were calculated to be 10.0 kcal mol-1. The electronic states of GR-(Bz) n were examined on the basis of theoretical results.

Density of states functions for photonic crystals

International Nuclear Information System (INIS)

McPhedran, R.C.; McOrist, J.; Sterke, C.M. de; Nicorovici, N.A.; Botten, L.C.; Asatryan, A.A.

2004-01-01

We discuss density of states functions for photonic crystals, in the context of the two-dimensional problem for arrays of cylinders of arbitrary cross section. We introduce the mutual density of states (MDOS), and show that this function can be used to calculate both the local density of states (LDOS), which gives position information for emission of radiation from photonic crystals, and the spectral density of states (SDOS), which gives angular information. We establish the connection between MDOS, LDOS, SDOS and the conventional density of states, which depends only on frequency. We relate all four functions to the band structure and propagating states within the crystal, and give numerical examples of the relation between band structure and density of states functions

Nonlocal kinetic-energy-density functionals

International Nuclear Information System (INIS)

Garcia-Gonzalez, P.; Alvarellos, J.E.; Chacon, E.

1996-01-01

In this paper we present nonlocal kinetic-energy functionals T[n] within the average density approximation (ADA) framework, which do not require any extra input when applied to any electron system and recover the exact kinetic energy and the linear response function of a homogeneous system. In contrast with previous ADA functionals, these present good behavior of the long-range tail of the exact weight function. The averaging procedure for the kinetic functional (averaging the Fermi momentum of the electron gas, instead of averaging the electron density) leads to a functional without numerical difficulties in the calculation of extended systems, and it gives excellent results when applied to atoms and jellium surfaces. copyright 1996 The American Physical Society

An extended hybrid density functional (X3LYP) with improved descriptions of nonbond interactions and thermodynamic properties of molecular systems

OpenAIRE

Xu, Xin; Zhang, Qingsong; Muller, Richard P.; Goddard, William A., III

2005-01-01

We derive here the form for the exact exchange energy density for a density that decays with Gaussian-type behavior at long range. This functional is intermediate between the B88 and the PW91 exchange functionals. Using this modified functional to match the form expected for Gaussian densities, we propose the X3LYP extended functional. We find that X3LYP significantly outperforms Becke three parameter Lee–Yang–Parr (B3LYP) for describing van der Waals and hydrogen bond interactions, while per...

Density Functional Theory Study of the Interaction of Hydrogen with Li6C60.

Science.gov (United States)

Wang, Qian; Jena, Puru

2012-05-03

Hydrogen storage properties of Li-coated C60 fullerene have been studied using density functional theory within the local density as well as generalized gradient approximation. Hydrogen atoms are found to bind to Li6C60 in two distinct forms, with the first set attaching to C atoms, not linked to Li, in atomic form. Once all such C atoms are saturated with hydrogen, the second set of hydrogen atoms bind quasi-molecularly to the Li atoms, five of which remain in the exohedral and the sixth in the endohedral position. The corresponding hydrogen gravimetric density in Li6C60H40 is 5 wt %. Desorption of hydrogen takes place in succession, the ones bound quasi-molecularly desorbing at a temperature lower than the ones bound atomically. The results are compared with the recent experiment on hydrogen adsorption in Li6C60.

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.

Exchange-correlation energies of atoms from efficient density functionals: influence of the electron density

Science.gov (United States)

Tao, Jianmin; Ye, Lin-Hui; Duan, Yuhua

2017-12-01

The primary goal of Kohn-Sham density functional theory is to evaluate the exchange-correlation contribution to electronic properties. However, the accuracy of a density functional can be affected by the electron density. Here we apply the nonempirical Tao-Mo (TM) semilocal functional to study the influence of the electron density on the exchange and correlation energies of atoms and ions, and compare the results with the commonly used nonempirical semilocal functionals local spin-density approximation (LSDA), Perdew-Burke-Ernzerhof (PBE), Tao-Perdew-Staroverov-Scuseria (TPSS), and hybrid functional PBE0. We find that the spin-restricted Hartree-Fock density yields the exchange and correlation energies in good agreement with the Optimized Effective Potential method, particularly for spherical atoms and ions. However, the errors of these semilocal and hybrid functionals become larger for self-consistent densities. We further find that the quality of the electron density have greater effect on the exchange-correlation energies of kinetic energy density-dependent meta-GGA functionals TPSS and TM than on those of the LSDA and GGA, and therefore, should have greater influence on the performance of meta-GGA functionals. Finally, we show that the influence of the density quality on PBE0 is slightly reduced, compared to that of PBE, due to the exact mixing.

A multiconfigurational hybrid density-functional theory

DEFF Research Database (Denmark)

Sharkas, Kamal; Savin, Andreas; Jensen, Hans Jørgen Aagaard

2012-01-01

We propose a multiconfigurational hybrid density-functional theory which rigorously combines a multiconfiguration self-consistent-field calculation with a density-functional approximation based on a linear decomposition of the electron-electron interaction. This gives a straightforward extension ...

Local density approximation for exchange in excited-state density functional theory

OpenAIRE

Harbola, Manoj K.; Samal, Prasanjit

2004-01-01

Local density approximation for the exchange energy is made for treatment of excited-states in density-functional theory. It is shown that taking care of the state-dependence of the LDA exchange energy functional leads to accurate excitation energies.

Density functional theory study of the structural and bonding mechanism of molecular oxygen (O2) with C3Si

Science.gov (United States)

Parida, Saroj K.; Behera, C.; Sahu, Sridhar

2018-07-01

The investigations of pure and heteroatom doped carbon clusters have created great interest because of their enormous prospective applications in various research zones, for example, optoelectronics, semiconductors, material science, energy storage devices, astro-science and so on. In this article, the interaction of molecular oxygen (O2) with C3Si has explored within a density functional theory (DFT). Different possible types of structure for C3SiO2 have collected. Among five different kinds of structure, the structure-1a, 1A1 is more energetically stable. The nature of the bonding of O2 and C3Si, in C3SiO2 has been studied by using Bader's topological analysis of the electron charge density distribution ρ(r) , Laplacian ∇2 ρ(r) and total energy density H(r) at the bond critical points (BCPs) of the structures within the framework of the atoms in molecules theory (AIM). The bonding mechanism of O2 and C3Si in C3SiO2 prompts to the fundamental understanding of the interaction of C3Si with oxygen molecule. It is interesting to note that, two types of bonding mechanism are established in same C3SiO2 system such as (i) shared-kind interactions (ii) closed-shell interactions. From various kinds of structure, Csbnd C bonds in all structures are shown as shared-kind interactions whereas Csbnd Si, Osbnd O bonds are classified as closed-shell type interactions with a certain degree of covalent character.

Energy vs. density on paths toward more exact density functionals.

Science.gov (United States)

Kepp, Kasper P

2018-03-14

Recently, the progression toward more exact density functional theory has been questioned, implying a need for more formal ways to systematically measure progress, i.e. a "path". Here I use the Hohenberg-Kohn theorems and the definition of normality by Burke et al. to define a path toward exactness and "straying" from the "path" by separating errors in ρ and E[ρ]. A consistent path toward exactness involves minimizing both errors. Second, a suitably diverse test set of trial densities ρ' can be used to estimate the significance of errors in ρ without knowing the exact densities which are often inaccessible. To illustrate this, the systems previously studied by Medvedev et al., the first ionization energies of atoms with Z = 1 to 10, the ionization energy of water, and the bond dissociation energies of five diatomic molecules were investigated using CCSD(T)/aug-cc-pV5Z as benchmark at chemical accuracy. Four functionals of distinct designs was used: B3LYP, PBE, M06, and S-VWN. For atomic cations regardless of charge and compactness up to Z = 10, the energy effects of the different ρ are energy-wise insignificant. An interesting oscillating behavior in the density sensitivity is observed vs. Z, explained by orbital occupation effects. Finally, it is shown that even large "normal" problems such as the Co-C bond energy of cobalamins can use simpler (e.g. PBE) trial densities to drastically speed up computation by loss of a few kJ mol -1 in accuracy. The proposed method of using a test set of trial densities to estimate the sensitivity and significance of density errors of functionals may be useful for testing and designing new balanced functionals with more systematic improvement of densities and energies.

Total Correlation Function Integrals and Isothermal Compressibilities from Molecular Simulations

DEFF Research Database (Denmark)

Wedberg, Rasmus; Peters, Günther H.j.; Abildskov, Jens

2008-01-01

Generation of thermodynamic data, here compressed liquid density and isothermal compressibility data, using molecular dynamics simulations is investigated. Five normal alkane systems are simulated at three different state points. We compare two main approaches to isothermal compressibilities: (1...... in approximately the same amount of time. This suggests that computation of total correlation function integrals is a route to isothermal compressibility, as accurate and fast as well-established benchmark techniques. A crucial step is the integration of the radial distribution function. To obtain sensible results...

Connotation and category of functional-molecular imaging

International Nuclear Information System (INIS)

Li Tianran; Tian Jiahe

2007-01-01

Function and molecular lmaging represent medical imaging' s direction. The review article introduce function and molecular's concept and category and its characteristic. Comparing with traditionary classics radiology, function and molecular imaging have many features, such as micro-mount and specificity and quantitative. There are many technology about function and molecular imaging. Function and molecular imaging is important ingredient of modern medical and play a considerable role. (authors)

Characterizing Bonding Patterns in Diradicals and Triradicals by Density-Based Wave Function Analysis: A Uniform Approach.

Science.gov (United States)

Orms, Natalie; Rehn, Dirk R; Dreuw, Andreas; Krylov, Anna I

2018-02-13

Density-based wave function analysis enables unambiguous comparisons of the electronic structure computed by different methods and removes ambiguity of orbital choices. We use this tool to investigate the performance of different spin-flip methods for several prototypical diradicals and triradicals. In contrast to previous calibration studies that focused on energy gaps between high- and low spin-states, we focus on the properties of the underlying wave functions, such as the number of effectively unpaired electrons. Comparison of different density functional and wave function theory results provides insight into the performance of the different methods when applied to strongly correlated systems such as polyradicals. We show that canonical molecular orbitals for species like large copper-containing diradicals fail to correctly represent the underlying electronic structure due to highly non-Koopmans character, while density-based analysis of the same wave function delivers a clear picture of the bonding pattern.

Self-Consistent Optimization of Excited States within Density-Functional Tight-Binding.

Science.gov (United States)

Kowalczyk, Tim; Le, Khoa; Irle, Stephan

2016-01-12

We present an implementation of energies and gradients for the ΔDFTB method, an analogue of Δ-self-consistent-field density functional theory (ΔSCF) within density-functional tight-binding, for the lowest singlet excited state of closed-shell molecules. Benchmarks of ΔDFTB excitation energies, optimized geometries, Stokes shifts, and vibrational frequencies reveal that ΔDFTB provides a qualitatively correct description of changes in molecular geometries and vibrational frequencies due to excited-state relaxation. The accuracy of ΔDFTB Stokes shifts is comparable to that of ΔSCF-DFT, and ΔDFTB performs similarly to ΔSCF with the PBE functional for vertical excitation energies of larger chromophores where the need for efficient excited-state methods is most urgent. We provide some justification for the use of an excited-state reference density in the DFTB expansion of the electronic energy and demonstrate that ΔDFTB preserves many of the properties of its parent ΔSCF approach. This implementation fills an important gap in the extended framework of DFTB, where access to excited states has been limited to the time-dependent linear-response approach, and affords access to rapid exploration of a valuable class of excited-state potential energy surfaces.

Relativistic density functional for nuclear structure

CERN Document Server

2016-01-01

This book aims to provide a detailed introduction to the state-of-the-art covariant density functional theory, which follows the Lorentz invariance from the very beginning and is able to describe nuclear many-body quantum systems microscopically and self-consistently. Covariant density functional theory was introduced in nuclear physics in the 1970s and has since been developed and used to describe the diversity of nuclear properties and phenomena with great success. In order to provide an advanced and updated textbook of covariant density functional theory for graduate students and nuclear physics researchers, this book summarizes the enormous amount of material that has accumulated in the field of covariant density functional theory over the last few decades as well as the latest developments in this area. Moreover, the book contains enough details for readers to follow the formalism and theoretical results, and provides exhaustive references to explore the research literature.

Modeling L2,3-Edge X-ray Absorption Spectroscopy with Real-Time Exact Two-Component Relativistic Time-Dependent Density Functional Theory.

Science.gov (United States)

Kasper, Joseph M; Lestrange, Patrick J; Stetina, Torin F; Li, Xiaosong

2018-04-10

X-ray absorption spectroscopy is a powerful technique to probe local electronic and nuclear structure. There has been extensive theoretical work modeling K-edge spectra from first principles. However, modeling L-edge spectra directly with density functional theory poses a unique challenge requiring further study. Spin-orbit coupling must be included in the model, and a noncollinear density functional theory is required. Using the real-time exact two-component method, we are able to variationally include one-electron spin-orbit coupling terms when calculating the absorption spectrum. The abilities of different basis sets and density functionals to model spectra for both closed- and open-shell systems are investigated using SiCl 4 and three transition metal complexes, TiCl 4 , CrO 2 Cl 2 , and [FeCl 6 ] 3- . Although we are working in the real-time framework, individual molecular orbital transitions can still be recovered by projecting the density onto the ground state molecular orbital space and separating contributions to the time evolving dipole moment.

Spectroscopic and molecular modeling studies of N-(4-(3-methyl-3-phenylcyclobutyl-3-phenylthiazole-2(3H-ylideneaniline by using experimental and density functional methods

Directory of Open Access Journals (Sweden)

Fatih Şen

2017-05-01

Full Text Available In the present study, a combined experimental and computational study on molecular structure and spectroscopic characterization on the title compound has been reported. The crystal was synthesized and its molecular structure brought to light by X-ray single crystal structure determination. The spectroscopic properties of the compound were examined by FT-IR and NMR (1H and 13C techniques. FT-IR spectra of the target compound in solid state were observed in the region 4000–400 cm−1. The 1H and 13C NMR spectra were recorded in CDCl3 solution. The molecular geometries were those obtained from the X-ray structure determination optimized using the density functional theory (DFT/B3LYP method with the 6-31G(d, p and 6-31G+(d, p basis set in ground state. From the optimized geometry of the molecule, geometric parameters (bond lengths, bond angles and torsion angles, vibrational assignments and chemical shifts of the title compound have been calculated theoretically and compared with those of experimental data. Besides, molecular electrostatic potential (MEP, frontier molecular orbitals (FMOs, Mulliken population analysis, Thermodynamic properties and non-linear optical (NLO properties of the title molecule were investigated by theoretical calculations.

Generalized nuclear Fukui functions in the framework of spin-polarized density-functional theory

International Nuclear Information System (INIS)

Chamorro, E.; Proft, F. de; Geerlings, P.

2005-01-01

An extension of Cohen's nuclear Fukui function is presented in the spin-polarized framework of density-functional theory (SP-DFT). The resulting new nuclear Fukui function indices Φ Nα and Φ Sα are intended to be the natural descriptors for the responses of the nuclei to changes involving charge transfer at constant multiplicity and also the spin polarization at constant number of electrons. These generalized quantities allow us to gain new insights within a perturbative scheme based on DFT. Calculations of the electronic and nuclear SP-DFT quantities are presented within a Kohn-Sham framework of chemical reactivity for a sample of molecules, including H 2 O, H 2 CO, and some simple nitrenes (NX) and phosphinidenes (PX), with X=H, Li, F, Cl, OH, SH, NH 2 , and PH 2 . Results have been interpreted in terms of chemical bonding in the context of Berlin's theorem, which provides a separation of the molecular space into binding and antibinding regions

THE TURBULENCE SPECTRUM OF MOLECULAR CLOUDS IN THE GALACTIC RING SURVEY: A DENSITY-DEPENDENT PRINCIPAL COMPONENT ANALYSIS CALIBRATION

International Nuclear Information System (INIS)

Roman-Duval, Julia; Jackson, James; Federrath, Christoph; Klessen, Ralf S.; Brunt, Christopher; Heyer, Mark

2011-01-01

Turbulence plays a major role in the formation and evolution of molecular clouds. Observationally, turbulent velocities are convolved with the density of an observed region. To correct for this convolution, we investigate the relation between the turbulence spectrum of model clouds, and the statistics of their synthetic observations obtained from principal component analysis (PCA). We apply PCA to spectral maps generated from simulated density and velocity fields, obtained from hydrodynamic simulations of supersonic turbulence, and from fractional Brownian motion (fBm) fields with varying velocity, density spectra, and density dispersion. We examine the dependence of the slope of the PCA pseudo-structure function, α PCA , on intermittency, on the turbulence velocity (β v ) and density (β n ) spectral indexes, and on density dispersion. We find that PCA is insensitive to β n and to the log-density dispersion σ s , provided σ s ≤ 2. For σ s > 2, α PCA increases with σ s due to the intermittent sampling of the velocity field by the density field. The PCA calibration also depends on intermittency. We derive a PCA calibration based on fBm structures with σ s ≤ 2 and apply it to 367 13 CO spectral maps of molecular clouds in the Galactic Ring Survey. The average slope of the PCA structure function, (α PCA ) = 0.62 ± 0.2, is consistent with the hydrodynamic simulations and leads to a turbulence velocity exponent of (β v ) = 2.06 ± 0.6 for a non-intermittent, low density dispersion flow. Accounting for intermittency and density dispersion, the coincidence between the PCA slope of the GRS clouds and the hydrodynamic simulations suggests β v ≅ 1.9, consistent with both Burgers and compressible intermittent turbulence.

Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations

International Nuclear Information System (INIS)

Streek, Jacco van de; Neumann, Marcus A.

2010-01-01

The accuracy of a dispersion-corrected density functional theory method is validated against 241 experimental organic crystal structures from Acta Cryst. Section E. This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095 Å (0.084 Å for the 225 ordered structures). R.m.s. Cartesian displacements above 0.25 Å either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect

Density functional theory: Its origins, rise to prominence, and future

Science.gov (United States)

Jones, R. O.

2015-07-01

In little more than 20 years, the number of applications of the density functional (DF) formalism in chemistry and materials science has grown in an astonishing fashion. The number of publications alone shows that DF calculations make up a huge success story, and many younger colleagues are surprised to learn that the widespread application of density functional methods, particularly in chemistry, began only after 1990. This is indeed unexpected, because the origins are usually traced to the papers of Hohenberg, Kohn, and Sham more than a quarter of a century earlier. The DF formalism, its applications, and prospects were reviewed for this journal in 1989. About the same time, the combination of DF calculations with molecular dynamics promised to provide an efficient way to study structures and reactions in molecules and extended systems. This paper reviews the development of density-related methods back to the early years of quantum mechanics and follows the breakthrough in their application after 1990. The two examples from biochemistry and materials science are among the many current applications that were simply far beyond expectations in 1990. The reasons why—50 years after its modern formulation and after two decades of rapid expansion—some of the most cited practitioners in the field are concerned about its future are discussed.

Systematic theoretical investigation of the zero-field splitting in Gd(III) complexes: Wave function and density functional approaches

Energy Technology Data Exchange (ETDEWEB)

Khan, Shehryar, E-mail: sherkhan@fysik.su.se; Odelius, Michael, E-mail: odelius@fysik.su.se [Department of Physics, Stockholm University, AlbaNova University Center, S-106 91 Stockholm (Sweden); Kubica-Misztal, Aleksandra [Institute of Physics, Jagiellonian University, ul. Reymonta 4, PL-30-059 Krakow (Poland); Kruk, Danuta [Faculty of Mathematics and Computer Science, University of Warmia and Mazury in Olsztyn, Sloneczna 54, Olsztyn PL-10710 (Poland); Kowalewski, Jozef [Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm (Sweden)

2015-01-21

The zero-field splitting (ZFS) of the electronic ground state in paramagnetic ions is a sensitive probe of the variations in the electronic and molecular structure with an impact on fields ranging from fundamental physical chemistry to medical applications. A detailed analysis of the ZFS in a series of symmetric Gd(III) complexes is presented in order to establish the applicability and accuracy of computational methods using multiconfigurational complete-active-space self-consistent field wave functions and of density functional theory calculations. The various computational schemes are then applied to larger complexes Gd(III)DOTA(H{sub 2}O){sup −}, Gd(III)DTPA(H{sub 2}O){sup 2−}, and Gd(III)(H{sub 2}O){sub 8}{sup 3+} in order to analyze how the theoretical results compare to experimentally derived parameters. In contrast to approximations based on density functional theory, the multiconfigurational methods produce results for the ZFS of Gd(III) complexes on the correct order of magnitude.

Comparative molecular simulation study of low and high density polymer glasses: A competition between attractive and repulsive interactions

Science.gov (United States)

Singh, Jalim; Jose, Prasanth

Results of molecular dynamics simulations of a system of Kremer and Grest linear polymer melts are presented at moderate and high number density. A detailed study of molecular pair distribution function shows that potential of mean force between the molecules has form of Gaussian with an attractive tail at number density ρ = 0.85 (in Lennard-Jones units), which is due to the dominating attractive interactions from temperature T = 0.7. This system shows gelation assisted glass transition, which is interpreted from peaks of molecular structure factor at small wave-numbers. At low temperature, this system phase separate to form dense domains whose local density is high; these domains show many dynamical features of glass transition in monomer and molecular level of relaxation indicating glass transition is assisted by gelation in this system. In the same system, at ρ = 1.0, repulsive interactions dominate, structure does not change even at low temperatures; the system exhibits dynamic heterogeneity and known to undergo glass transition. In this work, we compare and contrast the structure and dynamics of the system near its glass transition. Also, we computed correlation length of systems from the peak value of four-point structural dynamic susceptibility. HPC facility at IIT Mandi.

Locality of correlation in density functional theory

Energy Technology Data Exchange (ETDEWEB)

Burke, Kieron [Department of Chemistry, University of California, Irvine, California 92697 (United States); Cancio, Antonio [Department of Physics and Astronomy, Ball State University, Muncie, Indiana 47306 (United States); Gould, Tim [Qld Micro- and Nanotechnology Centre, Griffith University, Nathan, Qld 4111 (Australia); Pittalis, Stefano [CNR-Istituto di Nanoscienze, Via Campi 213A, I-41125 Modena (Italy)

2016-08-07

The Hohenberg-Kohn density functional was long ago shown to reduce to the Thomas-Fermi (TF) approximation in the non-relativistic semiclassical (or large-Z) limit for all matter, i.e., the kinetic energy becomes local. Exchange also becomes local in this limit. Numerical data on the correlation energy of atoms support the conjecture that this is also true for correlation, but much less relevant to atoms. We illustrate how expansions around a large particle number are equivalent to local density approximations and their strong relevance to density functional approximations. Analyzing highly accurate atomic correlation energies, we show that E{sub C} → −A{sub C} ZlnZ + B{sub C}Z as Z → ∞, where Z is the atomic number, A{sub C} is known, and we estimate B{sub C} to be about 37 mhartree. The local density approximation yields A{sub C} exactly, but a very incorrect value for B{sub C}, showing that the local approximation is less relevant for the correlation alone. This limit is a benchmark for the non-empirical construction of density functional approximations. We conjecture that, beyond atoms, the leading correction to the local density approximation in the large-Z limit generally takes this form, but with B{sub C} a functional of the TF density for the system. The implications for the construction of approximate density functionals are discussed.

Functional derivative of noninteracting kinetic energy density functional

International Nuclear Information System (INIS)

Liu Shubin; Ayers, Paul W.

2004-01-01

Proofs from different theoretical frameworks, namely, the Hohenbergh-Kohn theorems, the Kohn-Sham scheme, and the first-order density matrix representation, have been presented in this paper to show that the functional derivative of the noninteracting kinetic energy density functional can uniquely be expressed as the negative of the Kohn-Sham effective potential, arbitrary only to an additive orbital-independent constant. Key points leading to the current result as well as confusion about the quantity in the literature are briefly discussed

Metal-ligand delocalization and spin density in the CuCl2 and [CuCl4](2-) molecules: Some insights from wave function theory.

Science.gov (United States)

Giner, Emmanuel; Angeli, Celestino

2015-09-28

The aim of this paper is to unravel the physical phenomena involved in the calculation of the spin density of the CuCl2 and [CuCl4](2-) systems using wave function methods. Various types of wave functions are used here, both variational and perturbative, to analyse the effects impacting the spin density. It is found that the spin density on the chlorine ligands strongly depends on the mixing between two types of valence bond structures. It is demonstrated that the main difficulties found in most of the previous studies based on wave function methods come from the fact that each valence bond structure requires a different set of molecular orbitals and that using a unique set of molecular orbitals in a variational procedure leads to the removal of one of them from the wave function. Starting from these results, a method to compute the spin density at a reasonable computational cost is proposed.

Hydrogen bonding in malonaldehyde: a density functional and reparametrized semiempirical approach

International Nuclear Information System (INIS)

Kovacevic, Goran; Hrenar, Tomica; Doslic, Nadja

2003-01-01

Intramolecular proton transfer in malonaldehyde (MA) has been investigated by density functional theory (DFT). The DFT results were used for the construction of a high quality semiempirical potential energy surface with a reparametrized PM3 Hamiltonian. A two-step reparameterization procedure is proposed in which (i) the PM3-MAIS core-core functions for the O-H and H-H interactions were used and a new functional form for the O-O correction function was proposed and (ii) a set of specific reaction parameters (SRP) has been obtained via genetic algorithm optimization. The quality of the reparametrized semiempirical potential energy surfaces was tested by calculating the tunneling splitting of vibrational levels and the anharmonic vibrational frequencies of the system. The applicability to multi-dimensional dynamics in large molecular systems is discussed

Adaptive local basis set for Kohn–Sham density functional theory in a discontinuous Galerkin framework II: Force, vibration, and molecular dynamics calculations

Energy Technology Data Exchange (ETDEWEB)

Zhang, Gaigong [Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Lin, Lin, E-mail: linlin@math.berkeley.edu [Department of Mathematics, University of California, Berkeley, Berkeley, CA 94720 (United States); Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Hu, Wei, E-mail: whu@lbl.gov [Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Yang, Chao, E-mail: cyang@lbl.gov [Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Pask, John E., E-mail: pask1@llnl.gov [Physics Division, Lawrence Livermore National Laboratory, Livermore, CA 94550 (United States)

2017-04-15

Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn–Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann–Feynman forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracies required in practice. Since the adaptive local basis set has implicit dependence on atomic positions, Pulay forces are in general nonzero. However, we find that the Pulay force is numerically small and systematically decreasing with increasing basis completeness, so that the Hellmann–Feynman force is sufficient for basis sizes of a few tens of basis functions per atom. We verify the accuracy of the computed forces in static calculations of quasi-1D and 3D disordered Si systems, vibration calculation of a quasi-1D Si system, and molecular dynamics calculations of H{sub 2} and liquid Al–Si alloy systems, where we show systematic convergence to benchmark planewave results and results from the literature.

Density functionals in the laboratory frame

International Nuclear Information System (INIS)

Giraud, B. G.

2008-01-01

We compare several definitions of the density of a self-bound system, such as a nucleus, in relation with its center-of-mass zero-point motion. A trivial deconvolution relates the internal density to the density defined in the laboratory frame. This result is useful for the practical definition of density functionals

Study of homogeneous bubble nucleation in liquid carbon dioxide by a hybrid approach combining molecular dynamics simulation and density gradient theory

Science.gov (United States)

Langenbach, K.; Heilig, M.; Horsch, M.; Hasse, H.

2018-03-01

A new method for predicting homogeneous bubble nucleation rates of pure compounds from vapor-liquid equilibrium (VLE) data is presented. It combines molecular dynamics simulation on the one side with density gradient theory using an equation of state (EOS) on the other. The new method is applied here to predict bubble nucleation rates in metastable liquid carbon dioxide (CO2). The molecular model of CO2 is taken from previous work of our group. PC-SAFT is used as an EOS. The consistency between the molecular model and the EOS is achieved by adjusting the PC-SAFT parameters to VLE data obtained from the molecular model. The influence parameter of density gradient theory is fitted to the surface tension of the molecular model. Massively parallel molecular dynamics simulations are performed close to the spinodal to compute bubble nucleation rates. From these simulations, the kinetic prefactor of the hybrid nucleation theory is estimated, whereas the nucleation barrier is calculated from density gradient theory. This enables the extrapolation of molecular simulation data to the whole metastable range including technically relevant densities. The results are tested against available experimental data and found to be in good agreement. The new method does not suffer from typical deficiencies of classical nucleation theory concerning the thermodynamic barrier at the spinodal and the bubble size dependence of surface tension, which is typically neglected in classical nucleation theory. In addition, the density in the center of critical bubbles and their surface tension is determined as a function of their radius. The usual linear Tolman correction to the capillarity approximation is found to be invalid.

Study of homogeneous bubble nucleation in liquid carbon dioxide by a hybrid approach combining molecular dynamics simulation and density gradient theory.

Science.gov (United States)

Langenbach, K; Heilig, M; Horsch, M; Hasse, H

2018-03-28

A new method for predicting homogeneous bubble nucleation rates of pure compounds from vapor-liquid equilibrium (VLE) data is presented. It combines molecular dynamics simulation on the one side with density gradient theory using an equation of state (EOS) on the other. The new method is applied here to predict bubble nucleation rates in metastable liquid carbon dioxide (CO 2 ). The molecular model of CO 2 is taken from previous work of our group. PC-SAFT is used as an EOS. The consistency between the molecular model and the EOS is achieved by adjusting the PC-SAFT parameters to VLE data obtained from the molecular model. The influence parameter of density gradient theory is fitted to the surface tension of the molecular model. Massively parallel molecular dynamics simulations are performed close to the spinodal to compute bubble nucleation rates. From these simulations, the kinetic prefactor of the hybrid nucleation theory is estimated, whereas the nucleation barrier is calculated from density gradient theory. This enables the extrapolation of molecular simulation data to the whole metastable range including technically relevant densities. The results are tested against available experimental data and found to be in good agreement. The new method does not suffer from typical deficiencies of classical nucleation theory concerning the thermodynamic barrier at the spinodal and the bubble size dependence of surface tension, which is typically neglected in classical nucleation theory. In addition, the density in the center of critical bubbles and their surface tension is determined as a function of their radius. The usual linear Tolman correction to the capillarity approximation is found to be invalid.

An extended hybrid density functional (X3LYP) with improved descriptions of nonbond interactions and thermodynamic properties of molecular systems

Science.gov (United States)

Xu, Xin; Zhang, Qingsong; Muller, Richard P.; Goddard, William A.

2005-01-01

We derive here the form for the exact exchange energy density for a density that decays with Gaussian-type behavior at long range. This functional is intermediate between the B88 and the PW91 exchange functionals. Using this modified functional to match the form expected for Gaussian densities, we propose the X3LYP extended functional. We find that X3LYP significantly outperforms Becke three parameter Lee-Yang-Parr (B3LYP) for describing van der Waals and hydrogen bond interactions, while performing slightly better than B3LYP for predicting heats of formation, ionization potentials, electron affinities, proton affinities, and total atomic energies as validated with the extended G2 set of atoms and molecules. Thus X3LYP greatly enlarges the field of applications for density functional theory. In particular the success of X3LYP in describing the water dimer (with Re and De within the error bars of the most accurate determinations) makes it an excellent candidate for predicting accurate ligand-protein and ligand-DNA interactions.

Density-functional expansion methods: Grand challenges.

Science.gov (United States)

Giese, Timothy J; York, Darrin M

2012-03-01

We discuss the source of errors in semiempirical density functional expansion (VE) methods. In particular, we show that VE methods are capable of well-reproducing their standard Kohn-Sham density functional method counterparts, but suffer from large errors upon using one or more of these approximations: the limited size of the atomic orbital basis, the Slater monopole auxiliary basis description of the response density, and the one- and two-body treatment of the core-Hamiltonian matrix elements. In the process of discussing these approximations and highlighting their symptoms, we introduce a new model that supplements the second-order density-functional tight-binding model with a self-consistent charge-dependent chemical potential equalization correction; we review our recently reported method for generalizing the auxiliary basis description of the atomic orbital response density; and we decompose the first-order potential into a summation of additive atomic components and many-body corrections, and from this examination, we provide new insights and preliminary results that motivate and inspire new approximate treatments of the core-Hamiltonian.

Theoretical investigation of cyromazine tautomerism using density functional theory and Møller–Plesset perturbation theory methods

Science.gov (United States)

A computational chemistry analysis of six unique tautomers of cyromazine, a pesticide used for fly control, was performed with density functional theory (DFT) and canonical second order Møller–Plesset perturbation theory (MP2) methods to gain insight into the contributions of molecular structure to ...

Lattice dynamics calculations based on density-functional perturbation theory in real space

Science.gov (United States)

Shang, Honghui; Carbogno, Christian; Rinke, Patrick; Scheffler, Matthias

2017-06-01

A real-space formalism for density-functional perturbation theory (DFPT) is derived and applied for the computation of harmonic vibrational properties in molecules and solids. The practical implementation using numeric atom-centered orbitals as basis functions is demonstrated exemplarily for the all-electron Fritz Haber Institute ab initio molecular simulations (FHI-aims) package. The convergence of the calculations with respect to numerical parameters is carefully investigated and a systematic comparison with finite-difference approaches is performed both for finite (molecules) and extended (periodic) systems. Finally, the scaling tests and scalability tests on massively parallel computer systems demonstrate the computational efficiency.

Corrections to the density-functional theory electronic spectrum: Copper phthalocyanine

DEFF Research Database (Denmark)

Vazquez, Hector; Jelinek, P.; Brandbyge, Mads

2009-01-01

A method for improving the electronic spectrum of standard Density-Functional Theory (DFT) calculations (i.e., LDA or GGA approximations) is presented, and its application is discussed for the case of the copper phthalocyanine (CuPc) molecule. The method is based on a treatment of exchange...... and correlation in a many-body Hamiltonian, and it leads to easy-to-evaluate corrections to the DFT eigenvalues. Self-interaction is largely corrected, so that the modified energy levels do not suffer from spurious crossings, as often encountered for CuPc in DFT, and they remedy the standard underestimation...... or semiempirical functionals for molecular levels, it can be easily applied to any local-orbital DFT approach, improving on several important limitations of standard DFT methods....

Testing the molecular-hydrogen Kennicutt-Schmidt law in the low-density environments of extended ultraviolet disc galaxies

Science.gov (United States)

Watson, Linda C.; Martini, Paul; Lisenfeld, Ute; Böker, Torsten; Schinnerer, Eva

2016-01-01

Studying star formation beyond the optical radius of galaxies allows us to test empirical relations in extreme conditions with low average gas density and low molecular fraction. Previous studies discovered galaxies with extended ultraviolet (XUV) discs, which often contain star-forming regions with lower Hα-to-far-UV (FUV) flux ratios compared to inner disc star-forming regions. However, most previous studies lack measurements of molecular gas, which is presumably the component of the interstellar medium out of which stars form. We analysed published CO measurements and upper limits for 15 star-forming regions in the XUV or outer disc of three nearby spiral galaxies and a new CO upper limit from the IRAM (Institut de Radioastronomie Millimétrique) 30 m telescope in one star-forming region at r = 3.4r25 in the XUV disc of NGC 4625. We found that the star-forming regions are in general consistent with the same molecular-hydrogen Kennicutt-Schmidt law that applies within the optical radius, independent of whether we used Hα or FUV as the star formation rate (SFR) tracer. However, a number of the CO detections are significantly offset towards higher SFR surface density for their molecular-hydrogen surface density. Deeper CO data may enable us to use the presence or absence of molecular gas as an evolutionary probe to break the degeneracy between age and stochastic sampling of the initial mass function as the explanation for the low Hα-to-FUV flux ratios in XUV discs.

Molecular Model for HNBR with Tunable Cross-Link Density.

Science.gov (United States)

Molinari, N; Khawaja, M; Sutton, A P; Mostofi, A A

2016-12-15

We introduce a chemically inspired, all-atom model of hydrogenated nitrile butadiene rubber (HNBR) and assess its performance by computing the mass density and glass-transition temperature as a function of cross-link density in the structure. Our HNBR structures are created by a procedure that mimics the real process used to produce HNBR, that is, saturation of the carbon-carbon double bonds in NBR, either by hydrogenation or by cross-linking. The atomic interactions are described by the all-atom "Optimized Potentials for Liquid Simulations" (OPLS-AA). In this paper, first, we assess the use of OPLS-AA in our models, especially using NBR bulk properties, and second, we evaluate the validity of the proposed model for HNBR by investigating mass density and glass transition as a function of the tunable cross-link density. Experimental densities are reproduced within 3% for both elastomers, and qualitatively correct trends in the glass-transition temperature as a function of monomer composition and cross-link density are obtained.

A density functional study of nitrogen adsorption in single-wall carbon nanotubes

International Nuclear Information System (INIS)

Zhu Jie; Wang Yao; Li Wenjun; Wei Fei; Yu Yangxin

2007-01-01

An understanding of the adsorption behaviour of nitrogen in single-wall carbon nanotubes (SWCNTs) is necessary for obtaining information on its pores by nitrogen adsorption manometry. Non-local density functional theory was used to simulate nitrogen adsorption behaviour, including the adsorption isotherms, equilibrium density profiles and potential energy of the nitrogen molecules at 77 K, inside SWCNTs with diameters ranging from 0.696 to 3.001 nm. With increasing diameter, nitrogen adsorption changes from continuous filling in one dimension to a two-stage adsorption that corresponds to monolayer formation followed by multilayer condensation. The average density of the adsorbed nitrogen and the density profiles, especially in small diameter SWCNTs, were used to analyse the adsorbate phase at the saturation pressure. The results indicate that the type of pore filling depends primarily on the ratio of the SWCNT diameter to the adsorbate molecular diameter. The filling of SWCNTs is not a simple capillary condensation process, but is dominated by geometrical limitation

Azobenzene-functionalized carbon nanotubes as high-energy density solar thermal fuels.

Science.gov (United States)

Kolpak, Alexie M; Grossman, Jeffrey C

2011-08-10

Solar thermal fuels, which reversibly store solar energy in molecular bonds, are a tantalizing prospect for clean, renewable, and transportable energy conversion/storage. However, large-scale adoption requires enhanced energy storage capacity and thermal stability. Here we present a novel solar thermal fuel, composed of azobenzene-functionalized carbon nanotubes, with the volumetric energy density of Li-ion batteries. Our work also demonstrates that the inclusion of nanoscale templates is an effective strategy for design of highly cyclable, thermally stable, and energy-dense solar thermal fuels.

Quantal density functional theory

CERN Document Server

Sahni, Viraht

2016-01-01

This book deals with quantal density functional theory (QDFT) which is a time-dependent local effective potential theory of the electronic structure of matter. The treated time-independent QDFT constitutes a special case. In the 2nd edition, the theory is extended to include the presence of external magnetostatic fields. The theory is a description of matter based on the ‘quantal Newtonian’ first and second laws which is in terms of “classical” fields that pervade all space, and their quantal sources. The fields, which are explicitly defined, are separately representative of electron correlations due to the Pauli exclusion principle, Coulomb repulsion, correlation-kinetic, correlation-current-density, and correlation-magnetic effects. The book further describes Schrödinger theory from the new physical perspective of fields and quantal sources. It also describes traditional Hohenberg-Kohn-Sham DFT, and explains via QDFT the physics underlying the various energy functionals and functional derivatives o...

Dual descriptors within the framework of spin-polarized density functional theory.

Science.gov (United States)

Chamorro, E; Pérez, P; Duque, M; De Proft, F; Geerlings, P

2008-08-14

Spin-polarized density functional theory (SP-DFT) allows both the analysis of charge-transfer (e.g., electrophilic and nucleophilic reactivity) and of spin-polarization processes (e.g., photophysical changes arising from electron transitions). In analogy with the dual descriptor introduced by Morell et al. [J. Phys. Chem. A 109, 205 (2005)], we introduce new dual descriptors intended to simultaneously give information of the molecular regions where the spin-polarization process linking states of different multiplicity will drive electron density and spin density changes. The electronic charge and spin rearrangement in the spin forbidden radiative transitions S(0)-->T(n,pi(*)) and S(0)-->T(pi,pi(*)) in formaldehyde and ethylene, respectively, have been used as benchmark examples illustrating the usefulness of the new spin-polarization dual descriptors. These quantities indicate those regions where spin-orbit coupling effects are at work in such processes. Additionally, the qualitative relationship between the topology of the spin-polarization dual descriptors and the vertical singlet triplet energy gap in simple substituted carbene series has been also discussed. It is shown that the electron density and spin density rearrangements arise in agreement with spectroscopic experimental evidence and other theoretical results on the selected target systems.

Exchange-Correlation Effects for Noncovalent Interactions in Density Functional Theory.

Science.gov (United States)

Otero-de-la-Roza, A; DiLabio, Gino A; Johnson, Erin R

2016-07-12

In this article, we develop an understanding of how errors from exchange-correlation functionals affect the modeling of noncovalent interactions in dispersion-corrected density-functional theory. Computed CCSD(T) reference binding energies for a collection of small-molecule clusters are decomposed via a molecular many-body expansion and are used to benchmark density-functional approximations, including the effect of semilocal approximation, exact-exchange admixture, and range separation. Three sources of error are identified. Repulsion error arises from the choice of semilocal functional approximation. This error affects intermolecular repulsions and is present in all n-body exchange-repulsion energies with a sign that alternates with the order n of the interaction. Delocalization error is independent of the choice of semilocal functional but does depend on the exact exchange fraction. Delocalization error misrepresents the induction energies, leading to overbinding in all induction n-body terms, and underestimates the electrostatic contribution to the 2-body energies. Deformation error affects only monomer relaxation (deformation) energies and behaves similarly to bond-dissociation energy errors. Delocalization and deformation errors affect systems with significant intermolecular orbital interactions (e.g., hydrogen- and halogen-bonded systems), whereas repulsion error is ubiquitous. Many-body errors from the underlying exchange-correlation functional greatly exceed in general the magnitude of the many-body dispersion energy term. A functional built to accurately model noncovalent interactions must contain a dispersion correction, semilocal exchange, and correlation components that minimize the repulsion error independently and must also incorporate exact exchange in such a way that delocalization error is absent.

Reduced density matrix functional theory via a wave function based approach

Energy Technology Data Exchange (ETDEWEB)

Schade, Robert; Bloechl, Peter [Institute for Theoretical Physics, Clausthal University of Technology, Clausthal (Germany); Pruschke, Thomas [Institute for Theoretical Physics, University of Goettingen, Goettingen (Germany)

2016-07-01

We propose a new method for the calculation of the electronic and atomic structure of correlated electron systems based on reduced density matrix functional theory (rDMFT). The density-matrix functional is evaluated on the fly using Levy's constrained search formalism. The present implementation rests on a local approximation of the interaction reminiscent to that of dynamical mean field theory (DMFT). We focus here on additional approximations to the exact density-matrix functional in the local approximation and evaluate their performance.

A real-space stochastic density matrix approach for density functional electronic structure.

Science.gov (United States)

Beck, Thomas L

2015-12-21

The recent development of real-space grid methods has led to more efficient, accurate, and adaptable approaches for large-scale electrostatics and density functional electronic structure modeling. With the incorporation of multiscale techniques, linear-scaling real-space solvers are possible for density functional problems if localized orbitals are used to represent the Kohn-Sham energy functional. These methods still suffer from high computational and storage overheads, however, due to extensive matrix operations related to the underlying wave function grid representation. In this paper, an alternative stochastic method is outlined that aims to solve directly for the one-electron density matrix in real space. In order to illustrate aspects of the method, model calculations are performed for simple one-dimensional problems that display some features of the more general problem, such as spatial nodes in the density matrix. This orbital-free approach may prove helpful considering a future involving increasingly parallel computing architectures. Its primary advantage is the near-locality of the random walks, allowing for simultaneous updates of the density matrix in different regions of space partitioned across the processors. In addition, it allows for testing and enforcement of the particle number and idempotency constraints through stabilization of a Feynman-Kac functional integral as opposed to the extensive matrix operations in traditional approaches.

Magnetic exchange couplings from constrained density functional theory: an efficient approach utilizing analytic derivatives.

Science.gov (United States)

Phillips, Jordan J; Peralta, Juan E

2011-11-14

We introduce a method for evaluating magnetic exchange couplings based on the constrained density functional theory (C-DFT) approach of Rudra, Wu, and Van Voorhis [J. Chem. Phys. 124, 024103 (2006)]. Our method shares the same physical principles as C-DFT but makes use of the fact that the electronic energy changes quadratically and bilinearly with respect to the constraints in the range of interest. This allows us to use coupled perturbed Kohn-Sham spin density functional theory to determine approximately the corrections to the energy of the different spin configurations and construct a priori the relevant energy-landscapes obtained by constrained spin density functional theory. We assess this methodology in a set of binuclear transition-metal complexes and show that it reproduces very closely the results of C-DFT. This demonstrates a proof-of-concept for this method as a potential tool for studying a number of other molecular phenomena. Additionally, routes to improving upon the limitations of this method are discussed. © 2011 American Institute of Physics

Decay of autoionizing states in time-dependent density functional and reduced density matrix functional theory

Energy Technology Data Exchange (ETDEWEB)

Kapoor, Varun; Brics, Martins; Bauer, Dieter [Institut fuer Physik, Universitaet Rostock, 18051 Rostock (Germany)

2013-07-01

Autoionizing states are inaccessible to time-dependent density functional theory (TDDFT) using known, adiabatic Kohn-Sham (KS) potentials. We determine the exact KS potential for a numerically exactly solvable model Helium atom interacting with a laser field that is populating an autoionizing state. The exact single-particle density of the population in the autoionizing state corresponds to that of the energetically lowest quasi-stationary state in the exact KS potential. We describe how this exact potential controls the decay by a barrier whose height and width allows for the density to tunnel out and decay with the same rate as in the ab initio time-dependent Schroedinger calculation. However, devising a useful exchange-correlation potential that is capable of governing such a scenario in general and in more complex systems is hopeless. As an improvement over TDDFT, time-dependent reduced density matrix functional theory has been proposed. We are able to obtain for the above described autoionization process the exact time-dependent natural orbitals (i.e., the eigenfunctions of the exact, time-dependent one-body reduced density matrix) and study the potentials that appear in the equations of motion for the natural orbitals and the structure of the two-body density matrix expanded in them.

Molecular density modulation type ultrahigh vacuum gauge

International Nuclear Information System (INIS)

Horikoshi, Gen-ichi; Komada, Kazutaka; Mizuno, Hajime

1978-01-01

When pressure is measured in ultrahigh vacuum region, with an ionization gauge one of the causes producing the measuring limit is its dark current due to so-called soft X-ray effect and ion desorption. A kind of the modulation gauge provided with a modulation electrode is described in this paper. If a plate is vibrating perpendicularly to its surface in the sufficiently low pressure gas to satisfy molecular conditions (molecular density n), the molecular density in the space in front of the plate is expected to vary with time, affected by the vibration of the plate. When the vacuum gauge is placed in this space, the modulated current is proportional to pressure P, which is not related to the current due to soft X-ray effect and ion desorption. The other cause of determining the pressure-measuring limit is noises, among which only the noise coherent with the vibration of the plate affects the measurement. To avoid the induced current by this type of noise, it is considered to use the pulse-counting technique using an electron multiplier. It is anticipated that the induced currents generated from electrical noises and mechanical vibrations can be avoided almost completely by this method. As a result, the theoretical measuring limit may be estimated at approximately 5 x 10 -13 Torr, if the mean residence time in the collision of molecules with the plate is assumed to be 1 sec, the sensitivity of the vacuum gauge S is 20 Torr -1 , electron current Ie is 2 x 10 -3 A and modulation coefficient m is 3 x 10 -3 . (Wakatsuki, Y.)

Large thermoelectric efficiency of doped polythiophene junction: A density functional study

Science.gov (United States)

Golsanamlou, Zahra; Bagheri Tagani, Meysam; Rahimpour Soleimani, Hamid

2018-06-01

The thermoelectric properties of polythiophene (PT) coupled to the Au (111) electrodes are studied based on density functional theory with nonequilibrium Green function formalism. Specially, the effect of Li and Cl adsorbents on the thermoelectric efficiency of the PT junction is investigated in different concentrations of the dopants for two lengths of the PT. Results show that the presence of dopants can bring the structural changes in the oligomer and modify the arrangement of the molecular levels leading to the dramatic changes in the transmission spectra of the junction. Therefore, the large enhancement in thermopower and consequently figure of merit is obtained by dopants which makes the doped PT junction as a beneficial thermoelectric device.

Fragment approach to constrained density functional theory calculations using Daubechies wavelets

International Nuclear Information System (INIS)

Ratcliff, Laura E.; Genovese, Luigi; Mohr, Stephan; Deutsch, Thierry

2015-01-01

In a recent paper, we presented a linear scaling Kohn-Sham density functional theory (DFT) code based on Daubechies wavelets, where a minimal set of localized support functions are optimized in situ and therefore adapted to the chemical properties of the molecular system. Thanks to the systematically controllable accuracy of the underlying basis set, this approach is able to provide an optimal contracted basis for a given system: accuracies for ground state energies and atomic forces are of the same quality as an uncontracted, cubic scaling approach. This basis set offers, by construction, a natural subset where the density matrix of the system can be projected. In this paper, we demonstrate the flexibility of this minimal basis formalism in providing a basis set that can be reused as-is, i.e., without reoptimization, for charge-constrained DFT calculations within a fragment approach. Support functions, represented in the underlying wavelet grid, of the template fragments are roto-translated with high numerical precision to the required positions and used as projectors for the charge weight function. We demonstrate the interest of this approach to express highly precise and efficient calculations for preparing diabatic states and for the computational setup of systems in complex environments

Fragment approach to constrained density functional theory calculations using Daubechies wavelets

Energy Technology Data Exchange (ETDEWEB)

Ratcliff, Laura E., E-mail: lratcliff@anl.gov [Argonne Leadership Computing Facility, Argonne National Laboratory, Lemont, Illinois 60439 (United States); Université de Grenoble Alpes, CEA, INAC-SP2M, L-Sim, F-38000 Grenoble (France); Genovese, Luigi; Mohr, Stephan; Deutsch, Thierry [Université de Grenoble Alpes, CEA, INAC-SP2M, L-Sim, F-38000 Grenoble (France)

2015-06-21

In a recent paper, we presented a linear scaling Kohn-Sham density functional theory (DFT) code based on Daubechies wavelets, where a minimal set of localized support functions are optimized in situ and therefore adapted to the chemical properties of the molecular system. Thanks to the systematically controllable accuracy of the underlying basis set, this approach is able to provide an optimal contracted basis for a given system: accuracies for ground state energies and atomic forces are of the same quality as an uncontracted, cubic scaling approach. This basis set offers, by construction, a natural subset where the density matrix of the system can be projected. In this paper, we demonstrate the flexibility of this minimal basis formalism in providing a basis set that can be reused as-is, i.e., without reoptimization, for charge-constrained DFT calculations within a fragment approach. Support functions, represented in the underlying wavelet grid, of the template fragments are roto-translated with high numerical precision to the required positions and used as projectors for the charge weight function. We demonstrate the interest of this approach to express highly precise and efficient calculations for preparing diabatic states and for the computational setup of systems in complex environments.

Density-functional study of photoinduced water splitting

International Nuclear Information System (INIS)

Martínez Mesa, Aliezer; Rodríguez Hernández, Fermín; Seifert, Gotthard; Tranca, Diana

2015-01-01

We investigate the dynamics of water splitting on dye-sensitized metal (Ti, Cu) oxide surfaces, induced by direct sunlight excitation. In this study, we will consider the typical photoexcitation-followed-by-injection scheme, treating electron-injection and water splitting dynamics as independent events. The simultaneous modeling of the molecular motion and the quantum nonadiabatic transitions is achieved via the computation of the low-lying electronic states along several alternative reaction paths. Electronic structure calculations are based on a B3LYP-DFT Hamiltonian. The proposed approach combines an atomistic description of the reactants and of the immediate region of the surface, while the vibrational dynamics of the substrate is modeled as an effective bath leading to dissipation effects. The use of density-functional theory to solve the many- body electronic problem allows investigating the atomic motion of the water molecules and of a representative part of the substrate, thereby providing a theoretical and computational model capable to account simultaneously for the molecular character of the dye molecule and for the bulk properties of the surface. Furthermore, the insight emerging from this fundamental modeling can be used to optimize the chemical composition of the system to attain high incident-photon-flux-to-hydrogen-yield ratios. (full text)

Fundamentals of time-dependent density functional theory

International Nuclear Information System (INIS)

Marques, Miguel A.L.; Rubio, Angel

2012-01-01

There have been many significant advances in time-dependent density functional theory over recent years, both in enlightening the fundamental theoretical basis of the theory, as well as in computational algorithms and applications. This book, as successor to the highly successful volume Time-Dependent Density Functional Theory (Lect. Notes Phys. 706, 2006) brings together for the first time all recent developments in a systematic and coherent way. First, a thorough pedagogical presentation of the fundamental theory is given, clarifying aspects of the original proofs and theorems, as well as presenting fresh developments that extend the theory into new realms such as alternative proofs of the original Runge-Gross theorem, open quantum systems, and dispersion forces to name but a few. Next, all of the basic concepts are introduced sequentially and building in complexity, eventually reaching the level of open problems of interest. Contemporary applications of the theory are discussed, from real-time coupled-electron-ion dynamics, to excited-state dynamics and molecular transport. Last but not least, the authors introduce and review recent advances in computational implementation, including massively parallel architectures and graphical processing units. Special care has been taken in editing this volume as a multi-author textbook, following a coherent line of thought, and making all the relevant connections between chapters and concepts consistent throughout. As such it will prove to be the text of reference in this field, both for beginners as well as expert researchers and lecturers teaching advanced quantum mechanical methods to model complex physical systems, from molecules to nanostructures, from biocomplexes to surfaces, solids and liquids. (orig.)

Density functional theory investigation of oxygen interaction with boron-doped graphite

Energy Technology Data Exchange (ETDEWEB)

Liu, Juan; Wang, Chen [State Key Lab of New Ceramic and Fine Processing, Institute of Nuclear and New Energy Technology, Tsinghua University, Beijing 100084 (China); Liang, Tongxiang, E-mail: txliang@tsinghua.edu.cn [State Key Lab of New Ceramic and Fine Processing, Institute of Nuclear and New Energy Technology, Tsinghua University, Beijing 100084 (China); Lai, Wensheng [Advanced Material Laboratory, School of Materials Science & Engineering, Tsinghua University, Beijing, 100084 (China)

2016-12-30

Highlights: • Density-functional approach is applied to study the interaction of oxygen with boron-doped graphite. • Adsorption and diffusion of oxygen atoms on boron doped graphite surfaces are studied. • Recombination of oxygen is investigated by ER and LH mechanisms. • Low boron concentration facilitates O{sub 2} formation while high boron loading inhibits the recombination. • The presence of B−B bonds due to boron accumulation makes it impossible for oxygen recombination. - Abstract: Boron inserted as impurity by substitution of carbon atoms in graphite is known to change (improve or deteriorate) oxidation resistance of nuclear graphite, but the reason for both catalytic and inhibiting oxidation is still uncertain. As a first step, this work is more specially devoted to the adsorption and diffusion of oxygen atoms on the surface and related to the problem of oxygen retention on the pure and boron-containing graphite surfaces. Adsorption energies and energy barriers associated to the diffusion for molecular oxygen recombination are calculated in the density functional theory framework. The existence of boron modifies the electronic structure of the surface, which results in an increase of the adsorption energy for O. However, low boron loading makes it easier for the recombination into molecular oxygen. For high boron concentration, it induces a better O retention capability in graphite because the presence of B-B bonds decreases recombination of the adsorbed oxygen atoms. A possible explanation for both catalytic and inhibiting effects of boron in graphite is proposed.

Self-Interaction Error in Density Functional Theory: An Appraisal.

Science.gov (United States)

Bao, Junwei Lucas; Gagliardi, Laura; Truhlar, Donald G

2018-05-03

Self-interaction error (SIE) is considered to be one of the major sources of error in most approximate exchange-correlation functionals for Kohn-Sham density-functional theory (KS-DFT), and it is large with all local exchange-correlation functionals and with some hybrid functionals. In this work, we consider systems conventionally considered to be dominated by SIE. For these systems, we demonstrate that by using multiconfiguration pair-density functional theory (MC-PDFT), the error of a translated local density-functional approximation is significantly reduced (by a factor of 3) when using an MCSCF density and on-top density, as compared to using KS-DFT with the parent functional; the error in MC-PDFT with local on-top functionals is even lower than the error in some popular KS-DFT hybrid functionals. Density-functional theory, either in MC-PDFT form with local on-top functionals or in KS-DFT form with some functionals having 50% or more nonlocal exchange, has smaller errors for SIE-prone systems than does CASSCF, which has no SIE.

Molecular simulations and density functional theory calculations of bromine in clathrate hydrate phases

Energy Technology Data Exchange (ETDEWEB)

Dureckova, Hana, E-mail: houci059@uottawa.ca; Woo, Tom K., E-mail: tom.woo@uottawa.ca [Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 5N6 (Canada); Alavi, Saman, E-mail: saman.alavi@nrc-cnrc.gc.ca [Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 5N6 (Canada); National Research Council of Canada, 100 Sussex Dr., Ottawa, Ontario K1N 6N5 (Canada); Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3 (Canada)

2016-01-28

Bromine forms a tetragonal clathrate hydrate structure (TS-I) very rarely observed in clathrate hydrates of other guest substances. The detailed structure, energetics, and dynamics of Br{sub 2} and Cl{sub 2} in TS-I and cubic structure I (CS-I) clathrate hydrates are studied in this work using molecular dynamics and quantum chemical calculations. X-ray diffraction studies show that the halogen-water–oxygen distances in the cages of these structures are shorter than the sum of the van der Waals radii of halogen and oxygen atoms. This suggests that the stabilizing effects of halogen bonding or other non-covalent interactions (NCIs) may contribute to the formation of the unique tetragonal bromine hydrate structure. We performed molecular dynamics simulations of Br{sub 2} and Cl{sub 2} clathrate hydrates using our previously developed five-site charge models for the dihalogen molecules [Dureckova et al. Can. J. Chem. 93, 864 (2015)] which reproduce the computed electrostatic potentials of the dihalogens and account for the electropositive σ-hole of the halogen bond donor (the dihalogen). Analysis of the radial distribution functions, enthalpies of encapsulation, velocity and orientation autocorrelation functions, and polar angle distributions are carried out for Br{sub 2} and Cl{sub 2} guests in various cages to contrast the properties of these guests in the TS-I and CS-I phases. Quantum chemical partial geometry optimizations of Br{sub 2} and Cl{sub 2} guests in the hydrate cages using the M06-2X functional give short halogen-water distances compatible with values observed in X-ray diffraction experiments. NCI plots of guest-cage structures are generated to qualitatively show the relative strength of the non-bonding interactions between dihalogens and water molecules. The differences between behaviors of Br{sub 2} and Cl{sub 2} guests in the hydrate cages may explain why bromine forms the unique TS-I phase.

Density functional theory and parallel processing

International Nuclear Information System (INIS)

Ward, R.C.; Geist, G.A.; Butler, W.H.

1987-01-01

The authors demonstrate a method for obtaining the ground state energies and charge densities of a system of atoms described within density functional theory using simulated annealing on a parallel computer

Rational Density Functional Selection Using Game Theory.

Science.gov (United States)

McAnanama-Brereton, Suzanne; Waller, Mark P

2018-01-22

Theoretical chemistry has a paradox of choice due to the availability of a myriad of density functionals and basis sets. Traditionally, a particular density functional is chosen on the basis of the level of user expertise (i.e., subjective experiences). Herein we circumvent the user-centric selection procedure by describing a novel approach for objectively selecting a particular functional for a given application. We achieve this by employing game theory to identify optimal functional/basis set combinations. A three-player (accuracy, complexity, and similarity) game is devised, through which Nash equilibrium solutions can be obtained. This approach has the advantage that results can be systematically improved by enlarging the underlying knowledge base, and the deterministic selection procedure mathematically justifies the density functional and basis set selections.

Charge Transfer Enhancement in the D-π-A Type Porphyrin Dyes: A Density Functional Theory (DFT and Time-Dependent Density Functional Theory (TD-DFT Study

Directory of Open Access Journals (Sweden)

Guo-Jun Kang

2016-11-01

Full Text Available The electronic geometries and optical properties of two D-π-A type zinc porphyrin dyes (NCH3-YD2 and TPhe-YD were systematically investigated by density functional theory (DFT and time-dependent density functional theory (TD-DFT to reveal the origin of significantly altered charge transfer enhancement by changing the electron donor of the famous porphyrin-based sensitizer YD2-o-C8. The molecular geometries and photophysical properties of dyes before and after binding to the TiO2 cluster were fully investigated. From the analyses of natural bond orbital (NBO, extended charge decomposition analysis (ECDA, and electron density variations (Δρ between the excited state and ground state, it was found that the introduction of N(CH32 and 1,1,2-triphenylethene groups enhanced the intramolecular charge-transfer (ICT character compared to YD2-o-C8. The absorption wavelength and transition possess character were significantly influenced by N(CH32 and 1,1,2-triphenylethene groups. NCH3-YD2 with N(CH32 groups in the donor part is an effective way to improve the interactions between the dyes and TiO2 surface, light having efficiency (LHE, and free energy change (ΔGinject, which is expected to be an efficient dye for use in dye-sensitized solar cells (DSSCs.

Multicomponent Density Functional Theory: Impact of Nuclear Quantum Effects on Proton Affinities and Geometries.

Science.gov (United States)

Brorsen, Kurt R; Yang, Yang; Hammes-Schiffer, Sharon

2017-08-03

Nuclear quantum effects such as zero point energy play a critical role in computational chemistry and often are included as energetic corrections following geometry optimizations. The nuclear-electronic orbital (NEO) multicomponent density functional theory (DFT) method treats select nuclei, typically protons, quantum mechanically on the same level as the electrons. Electron-proton correlation is highly significant, and inadequate treatments lead to highly overlocalized nuclear densities. A recently developed electron-proton correlation functional, epc17, has been shown to provide accurate nuclear densities for molecular systems. Herein, the NEO-DFT/epc17 method is used to compute the proton affinities for a set of molecules and to examine the role of nuclear quantum effects on the equilibrium geometry of FHF - . The agreement of the computed results with experimental and benchmark values demonstrates the promise of this approach for including nuclear quantum effects in calculations of proton affinities, pK a 's, optimized geometries, and reaction paths.

Momentum density maps for molecules

International Nuclear Information System (INIS)

Cook, J.P.D.; Brion, C.E.

1982-01-01

Momentum-space and position-space molecular orbital density functions computed from LCAO-MO-SCF wavefunctions are used to rationalize the shapes of some momentum distributions measured by binary (e,2e) spectroscopy. A set of simple rules is presented which enable one to sketch the momentum density function and the momentum distribution from a knowledge of the position-space wavefunction and the properties and effects of the Fourier Transform and the spherical average. Selected molecular orbitals of H 2 , N 2 and CO 2 are used to illustrate this work

Measurement of the density profile of pure and seeded molecular beams by femtosecond ion imaging

Energy Technology Data Exchange (ETDEWEB)

Meng, Congsen [LaserLaB Amsterdam, VU University Amsterdam, de Boelelaan 1083, 1081 HV Amsterdam (Netherlands); Department of Physics, National University of Defense Technology, Changsha 410073 (China); Janssen, Maurice H. M. [LaserLaB Amsterdam, VU University Amsterdam, de Boelelaan 1083, 1081 HV Amsterdam (Netherlands)

2015-02-15

Here, we report on femtosecond ion imaging experiments to measure the density profile of a pulsed supersonic molecular beam. Ion images are measured for both a molecular beam and bulk gas under identical experimental conditions via femtosecond multiphoton ionization of Xe atoms. We report the density profile of the molecular beam, and the measured absolute density is compared with theoretical calculations of the centre line beam density. Subsequently, we discuss reasons accounting for the differences between measurements and calculations and propose that strong skimmer interference is the most probable cause for the differences. Furthermore, we report on experiments measuring the centre line density of seeded supersonic beams. The femtosecond ion images show that seeding the heavy Xe atom at low relative seed fractions (1%-10%) in a light carrier gas like Ne results in strong relative enhancements of up to two orders of magnitude.

Uniform magnetic fields in density-functional theory

Science.gov (United States)

Tellgren, Erik I.; Laestadius, Andre; Helgaker, Trygve; Kvaal, Simen; Teale, Andrew M.

2018-01-01

We construct a density-functional formalism adapted to uniform external magnetic fields that is intermediate between conventional density functional theory and Current-Density Functional Theory (CDFT). In the intermediate theory, which we term linear vector potential-DFT (LDFT), the basic variables are the density, the canonical momentum, and the paramagnetic contribution to the magnetic moment. Both a constrained-search formulation and a convex formulation in terms of Legendre-Fenchel transformations are constructed. Many theoretical issues in CDFT find simplified analogs in LDFT. We prove results concerning N-representability, Hohenberg-Kohn-like mappings, existence of minimizers in the constrained-search expression, and a restricted analog to gauge invariance. The issue of additivity of the energy over non-interacting subsystems, which is qualitatively different in LDFT and CDFT, is also discussed.

Theoretical modelling of photoactive molecular systems: insights using the Density Functional Theory

Energy Technology Data Exchange (ETDEWEB)

Ciofini, I.; Adamo, C. [Ecole Nationale Superieure de Chimie de Paris, Lab. d' Electrochimie et Chimie Analytique, CNRS UMR 7575, 75 - Paris (France); Laine, Ph.P. [Universite Rene-Descartes, Lab. de Chimie et Biochimie Pharmacologiques et Toxicologiques, CNRS UMR 8601, 75 - Paris (France); Bedioui, F. [Ecole Nationale Superieure de Chimie de Paris, Lab. de Pharmacologie Chimique et Genetique, CNRS FRE 2463 and INSERM U 640, 75 - Paris (France); Daul, C.A. [Fribourg Univ., Dept. de Chimie (Switzerland)

2006-02-15

An account of the performance of a modern and efficient approach to Density Functional Theory (DFT) for the prediction of the photophysical behavior of a series of Ru(II) and Os(II) complexes is given. The time-dependent-DFT method was used to interpret their electronic spectra. Two different types of compounds have been analyzed: (1) a complex undergoing a light induced isomerization of one of its coordination bonds; (2) an inorganic dyads expected to undergo intramolecular photoinduced electron transfer to form a charge separated (CS) sate. Besides the noticeable quantitative agreement between computed and experimental absorption spectra, our results allow to clarify, by first principles, both the nature of the excited states and the photochemical behavior of these complex systems, thus underlying the predictive character of the theoretical approach. (authors)

Covalent addition of chitosan to graphene sheets: Density functional theory explorations of quadrupole coupling constants

Science.gov (United States)

Mokhtari, Ali; Harismah, Kun; Mirzaei, Mahmoud

2015-12-01

Density functional theory (DFT) calculations have been performed to detect the stabilities and properties of chitosan-functionalized graphene and graphene-oxide structures (G-Chit and GO-Chit). The model systems with two different sizes of sheets have been optimized and the molecular and atomic properties have been evaluated for them. The results indicated that investigated G-Chit and GO-Chit structures could be considered as stable structures but with different properties. The properties for GO and GO-Chit structures are almost similar; however, they are different from the original G and G-Chit structures. The results also indicated that the properties could be also size-dependent, in which different molecular and atomic properties have been observed for the investigate G sheets.

density functional theory approach

Indian Academy of Sciences (India)

YOGESH ERANDE

2017-07-27

Jul 27, 2017 ... a key role in all optical switching devices, since their optical properties can be .... optimized in the gas phase using Density Functional Theory. (DFT).39 The ...... The Mediation of Electrostatic Effects by Sol- vents J. Am. Chem.

Strong Correlation in Kohn-Sham Density Functional Theory

NARCIS (Netherlands)

Malet, F.; Gori Giorgi, P.

2012-01-01

We use the exact strong-interaction limit of the Hohenberg-Kohn energy density functional to approximate the exchange-correlation energy of the restricted Kohn-Sham scheme. Our approximation corresponds to a highly nonlocal density functional whose functional derivative can be easily constructed,

Functional renormalization group and Kohn-Sham scheme in density functional theory

Science.gov (United States)

Liang, Haozhao; Niu, Yifei; Hatsuda, Tetsuo

2018-04-01

Deriving accurate energy density functional is one of the central problems in condensed matter physics, nuclear physics, and quantum chemistry. We propose a novel method to deduce the energy density functional by combining the idea of the functional renormalization group and the Kohn-Sham scheme in density functional theory. The key idea is to solve the renormalization group flow for the effective action decomposed into the mean-field part and the correlation part. Also, we propose a simple practical method to quantify the uncertainty associated with the truncation of the correlation part. By taking the φ4 theory in zero dimension as a benchmark, we demonstrate that our method shows extremely fast convergence to the exact result even for the highly strong coupling regime.

Density functional theory studies on the structures and electronic communication of meso-ferrocenylporphyrins: long range orbital coupling via porphyrin core.

Science.gov (United States)

Zhang, Lijuan; Qi, Dongdong; Zhang, Yuexing; Bian, Yongzhong; Jiang, Jianzhuang

2011-02-01

The molecular and electronic structures together with the electronic absorption spectra of a series of metal free meso-ferrocenylporphyrins, namely 5-ferrocenylporphyrin (1), 5,10-diferrocenylporphyrin (2), 5,15-diferrocenylporphyrin (3), 5,10,15-triferrocenylporphyrin (4), and 5,10,15,20-tetraferrocenylporphyrin (5) have been studied with the density functional theory (DFT) and time-dependent density functional theory (TD-DFT) methods. For the purpose of comparative studies, metal free porphyrin without any ferrocenyl group (0) and isolated ferrocene (6) were also calculated. The effects of the number and position of meso-attached ferrocenyl substituents on their molecular and electronic structures, atomic charges, molecular orbitals, and electronic absorption spectra of 1-5 were systematically investigated. The orbital coupling is investigated in detail, explaining well the long range coupling of ferrocenyl substituents connected via porphyrin core and the systematic change in the electronic absorption spectra of porphyrin compounds. Copyright © 2010 Elsevier Inc. All rights reserved.

Molecular calculations with B functions

International Nuclear Information System (INIS)

Steinborn, E.O.; Homeier, H.H.H.; Ema, I.; Lopez, R.; Ramirez, G.

2000-01-01

A program for molecular calculations with B functions is reported and its performance is analyzed. All the one- and two-center integrals and the three-center nuclear attraction integrals are computed by direct procedures, using previously developed algorithms. The three- and four-center electron repulsion integrals are computed by means of Gaussian expansions of the B functions. A new procedure for obtaining these expansions is also reported. Some results on full molecular calculations are included to show the capabilities of the program and the quality of the B functions to represent the electronic functions in molecules

Thomas-Fermi molecular dynamics

International Nuclear Information System (INIS)

Clerouin, J.; Pollock, E.L.; Zerah, G.

1992-01-01

A three-dimensional density-functional molecular-dynamics code is developed for the Thomas-Fermi density functional as a prototype for density functionals using only the density. Following Car and Parrinello [Phys. Rev. Lett. 55, 2471 (1985)], the electronic density is treated as a dynamical variable. The electronic densities are verified against a multi-ion Thomas-Fermi algorithm due to Parker [Phys. Rev. A 38, 2205 (1988)]. As an initial application, the effect of electronic polarization in enhancing ionic diffusion in strongly coupled plasmas is demonstrated

THE 'TRUE' COLUMN DENSITY DISTRIBUTION IN STAR-FORMING MOLECULAR CLOUDS

International Nuclear Information System (INIS)

Goodman, Alyssa A.; Pineda, Jaime E.; Schnee, Scott L.

2009-01-01

We use the COMPLETE Survey's observations of the Perseus star-forming region to assess and intercompare the three methods used for measuring column density in molecular clouds: near-infrared (NIR) extinction mapping; thermal emission mapping in the far-IR; and mapping the intensity of CO isotopologues. Overall, the structures shown by all three tracers are morphologically similar, but important differences exist among the tracers. We find that the dust-based measures (NIR extinction and thermal emission) give similar, log-normal, distributions for the full (∼20 pc scale) Perseus region, once careful calibration corrections are made. We also compare dust- and gas-based column density distributions for physically meaningful subregions of Perseus, and we find significant variations in the distributions for those (smaller, ∼few pc scale) regions. Even though we have used 12 CO data to estimate excitation temperatures, and we have corrected for opacity, the 13 CO maps seem unable to give column distributions that consistently resemble those from dust measures. We have edited out the effects of the shell around the B-star HD 278942 from the column density distribution comparisons. In that shell's interior and in the parts where it overlaps the molecular cloud, there appears to be a dearth of 13 CO, which is likely due either to 13 CO not yet having had time to form in this young structure and/or destruction of 13 CO in the molecular cloud by the HD 278942's wind and/or radiation. We conclude that the use of either dust or gas measures of column density without extreme attention to calibration (e.g., of thermal emission zero-levels) and artifacts (e.g., the shell) is more perilous than even experts might normally admit. And, the use of 13 CO data to trace total column density in detail, even after proper calibration, is unavoidably limited in utility due to threshold, depletion, and opacity effects. If one's main aim is to map column density (rather than temperature

Density-functional, density-functional tight-binding, and wave-function calculations on biomolecular systems

Czech Academy of Sciences Publication Activity Database

Kubař, Tomáš; Jurečka, Petr; Černý, Jiří; Řezáč, Jan; Otyepka, M.; Valdes, Haydee; Hobza, Pavel

2007-01-01

Roč. 111, č. 26 (2007), s. 5642-5647 ISSN 1089-5639 R&D Projects: GA MŠk LC512; GA AV ČR IAA400550510; GA ČR(CZ) GD203/05/H001; GA ČR GA203/05/0009 Institutional research plan: CEZ:AV0Z40550506 Keywords : density functional theory * empirical dispersion-energy term * non-covalent interactions Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.918, year: 2007

Investigation of the electronic structure of the BiSBr and BiSeBr clusters by density functional method

International Nuclear Information System (INIS)

Audzijonis, A.; Gaigalas, G.; Zigas, L.; Pauliukas, A.; Zaltauskas, R.; Kvedaravicius, A.; Cerskus, A.

2008-01-01

The energy levels of valence bands (VB) of the BiSBr and BiSeBr crystals have been calculated for investigation of the photoelectron emission spectra of BiSBr, BiSeBr and BiSI crystals. The molecular model of this crystal has been used for the calculation of VB by the Density Functional Theory (DFT) method. The molecular cluster, consisting of 20 molecules of BiSBr, BiSeBr, has been used for calculations of averaged total density of states, including atom vibrations. The spectra of the averaged total density of states from VB of BiSBr and BiSeBr clusters have been compared with the experimental photoelectron emission spectra from VB of BiSI crystals. The results clarify that the atomic vibrations in A 5 B 6 C 7 type crystals with chain structure create a smoother appearance of the averaged total density of state spectrum and the experimental X-ray photoemission spectra (XPS)

Improving density functional tight binding predictions of free energy surfaces for peptide condensation reactions in solution

Science.gov (United States)

Kroonblawd, Matthew; Goldman, Nir

First principles molecular dynamics using highly accurate density functional theory (DFT) is a common tool for predicting chemistry, but the accessible time and space scales are often orders of magnitude beyond the resolution of experiments. Semi-empirical methods such as density functional tight binding (DFTB) offer up to a thousand-fold reduction in required CPU hours and can approach experimental scales. However, standard DFTB parameter sets lack good transferability and calibration for a particular system is usually necessary. Force matching the pairwise repulsive energy term in DFTB to short DFT trajectories can improve the former's accuracy for chemistry that is fast relative to DFT simulation times (Contract DE-AC52-07NA27344.

Improving Density Functional Tight Binding Predictions of Free Energy Surfaces for Slow Chemical Reactions in Solution

Science.gov (United States)

Kroonblawd, Matthew; Goldman, Nir

2017-06-01

First principles molecular dynamics using highly accurate density functional theory (DFT) is a common tool for predicting chemistry, but the accessible time and space scales are often orders of magnitude beyond the resolution of experiments. Semi-empirical methods such as density functional tight binding (DFTB) offer up to a thousand-fold reduction in required CPU hours and can approach experimental scales. However, standard DFTB parameter sets lack good transferability and calibration for a particular system is usually necessary. Force matching the pairwise repulsive energy term in DFTB to short DFT trajectories can improve the former's accuracy for reactions that are fast relative to DFT simulation times (Contract DE-AC52-07NA27344.

Versatile Density Functionals for Computational Surface Science

DEFF Research Database (Denmark)

Wellendorff, Jess

Density functional theory (DFT) emerged almost 50 years ago. Since then DFT has established itself as the central electronic structure methodology for simulating atomicscale systems from a few atoms to a few hundred atoms. This success of DFT is due to a very favorable accuracy-to-computational c......Density functional theory (DFT) emerged almost 50 years ago. Since then DFT has established itself as the central electronic structure methodology for simulating atomicscale systems from a few atoms to a few hundred atoms. This success of DFT is due to a very favorable accuracy...... resampling techniques, thereby systematically avoiding problems with overfitting. The first ever density functional presenting both reliable accuracy and convincing error estimation is generated. The methodology is general enough to be applied to more complex functional forms with higher-dimensional fitting...

Local and linear chemical reactivity response functions at finite temperature in density functional theory

International Nuclear Information System (INIS)

Franco-Pérez, Marco; Ayers, Paul W.; Gázquez, José L.; Vela, Alberto

2015-01-01

We explore the local and nonlocal response functions of the grand canonical potential density functional at nonzero temperature. In analogy to the zero-temperature treatment, local (e.g., the average electron density and the local softness) and nonlocal (e.g., the softness kernel) intrinsic response functions are defined as partial derivatives of the grand canonical potential with respect to its thermodynamic variables (i.e., the chemical potential of the electron reservoir and the external potential generated by the atomic nuclei). To define the local and nonlocal response functions of the electron density (e.g., the Fukui function, the linear density response function, and the dual descriptor), we differentiate with respect to the average electron number and the external potential. The well-known mathematical relationships between the intrinsic response functions and the electron-density responses are generalized to nonzero temperature, and we prove that in the zero-temperature limit, our results recover well-known identities from the density functional theory of chemical reactivity. Specific working equations and numerical results are provided for the 3-state ensemble model

Molecular structures and vibrational frequencies of xanthine and its methyl derivatives (caffeine and theobromine) by ab initio Hartree-Fock and density functional theory calculations

Science.gov (United States)

Ucun, Fatih; Sağlam, Adnan; Güçlü, Vesile

2007-06-01

The molecular structures, vibrational frequencies and corresponding vibrational assignments of xanthine and its methyl derivatives (caffeine and theobromine) have been calculated using ab initio Hartree-Fock (HF) and density functional theory (B3LYP) methods with 6-31G(d, p) basis set level. The calculations were utilized to the CS symmetries of the molecules. The obtained vibrational frequencies and optimised geometric parameters (bond lengths and bond angles) were seen to be well agreement with the experimental data. The used scale factors which have been obtained the ratio of the frequency values of the strongest peaks in the calculated and experimental spectra seem to cause the gained vibrations well corresponding to the experimental ones. Theoretical infrared intensities and Raman activities are also reported.

Investigation of the silicon ion density during molecular beam epitaxy growth

Science.gov (United States)

Eifler, G.; Kasper, E.; Ashurov, Kh.; Morozov, S.

2002-05-01

Ions impinging on a surface during molecular beam epitaxy influence the growth and the properties of the growing layer, for example, suppression of dopant segregation and the generation of crystal defects. The silicon electron gun in the molecular beam epitaxy (MBE) equipment is used as a source for silicon ions. To use the effect of ion bombardment the mechanism of generation and distribution of ions was investigated. A monitoring system was developed and attached at the substrate position in the MBE growth chamber to measure the ion and electron densities towards the substrate. A negative voltage was applied to the substrate to modify the ion energy and density. Furthermore the current caused by charge carriers impinging on the substrate was measured and compared with the results of the monitoring system. The electron and ion densities were measured by varying the emission current of the e-gun achieving silicon growth rates between 0.07 and 0.45 nm/s and by changing the voltage applied to the substrate between 0 to -1000 V. The dependencies of ion and electron densities were shown and discussed within the framework of a simple model. The charged carrier densities measured with the monitoring system enable to separate the ion part of the substrate current and show its correlation to the generation rate. Comparing the ion density on the whole substrate and in the center gives a hint to the ion beam focusing effect. The maximum ion and electron current densities obtained were 0.40 and 0.61 μA/cm2, respectively.

Approximate spin projected spin-unrestricted density functional theory method: Application to diradical character dependences of second hyperpolarizabilities

Energy Technology Data Exchange (ETDEWEB)

Nakano, Masayoshi, E-mail: mnaka@cheng.es.osaka-u.ac.jp; Minami, Takuya, E-mail: mnaka@cheng.es.osaka-u.ac.jp; Fukui, Hitoshi, E-mail: mnaka@cheng.es.osaka-u.ac.jp; Yoneda, Kyohei, E-mail: mnaka@cheng.es.osaka-u.ac.jp; Shigeta, Yasuteru, E-mail: mnaka@cheng.es.osaka-u.ac.jp; Kishi, Ryohei, E-mail: mnaka@cheng.es.osaka-u.ac.jp [Department of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531 (Japan); Champagne, Benoît; Botek, Edith [Laboratoire de Chimie Théorique, Facultés Universitaires Notre-Dame de la Paix (FUNDP), rue de Bruxelles, 61, 5000 Namur (Belgium)

2015-01-22

We develop a novel method for the calculation and the analysis of the one-electron reduced densities in open-shell molecular systems using the natural orbitals and approximate spin projected occupation numbers obtained from broken symmetry (BS), i.e., spin-unrestricted (U), density functional theory (DFT) calculations. The performance of this approximate spin projection (ASP) scheme is examined for the diradical character dependence of the second hyperpolarizability (γ) using several exchange-correlation functionals, i.e., hybrid and long-range corrected UDFT schemes. It is found that the ASP-LC-UBLYP method with a range separating parameter μ = 0.47 reproduces semi-quantitatively the strongly-correlated [UCCSD(T)] result for p-quinodimethane, i.e., the γ variation as a function of the diradical character.

Molecular dynamics simulations of the amino acid-ZnO (10-10) interface: A comparison between density functional theory and density functional tight binding results

Energy Technology Data Exchange (ETDEWEB)

Holthaus, Svea große; Köppen, Susan, E-mail: koeppen@hmi.uni-bremen.de; Frauenheim, Thomas; Ciacchi, Lucio Colombi [Bremen Centre for Computational Materials Science, University of Bremen, 28359 Bremen (Germany)

2014-06-21

We investigate the adsorption behavior of four different amino acids (glutamine, glutamate, serine, cysteine) on the zinc oxide (101{sup ¯}0) surface, comparing the geometry and energy associated with a number of different adsorption configurations. In doing this, we highlight the benefits and limits of using density-functional tight-binding (DFTB) with respect to standard density functional theory (DFT). The DFTB method is found to reliably reproduce the DFT adsorption geometries. Analysis of the adsorption configurations emphasizes the fundamental role of the first hydration layer in mediating the interactions between the amino acids and the surface. Direct surface-molecule bonds are found to form predominantly via the carboxylate groups of the studied amino acids. No surface-mediated chemical reactions are observed, with the notable exception of a proton transfer from the thiol group of cysteine to a hydroxyl group of the surface hydration layer. The adsorption energies are found to be dominated both by the formation of direct or indirect surface-molecule hydrogen bonds, but also by the rearrangement of the hydrogen-bond network in surface proximity in a non-intuitive way. Energetic comparisons between DFTB and DFT are made difficult on one side by the long time necessary to achieve convergence of potential energy values in MD simulations and on the other side by the necessity of including higher-order corrections to DFTB to obtain a good description of the hydrogen bond energetics. Overall, our results suggest that DFTB is a good reference method to set the correct chemical states and the initial geometries of hybrid biomolecule/ZnO systems to be simulated with non-reactive force fields.

Molecular dynamics simulations of the amino acid-ZnO (10-10) interface: a comparison between density functional theory and density functional tight binding results.

Science.gov (United States)

grosse Holthaus, Svea; Köppen, Susan; Frauenheim, Thomas; Ciacchi, Lucio Colombi

2014-06-21

We investigate the adsorption behavior of four different amino acids (glutamine, glutamate, serine, cysteine) on the zinc oxide (101̄0) surface, comparing the geometry and energy associated with a number of different adsorption configurations. In doing this, we highlight the benefits and limits of using density-functional tight-binding (DFTB) with respect to standard density functional theory (DFT). The DFTB method is found to reliably reproduce the DFT adsorption geometries. Analysis of the adsorption configurations emphasizes the fundamental role of the first hydration layer in mediating the interactions between the amino acids and the surface. Direct surface-molecule bonds are found to form predominantly via the carboxylate groups of the studied amino acids. No surface-mediated chemical reactions are observed, with the notable exception of a proton transfer from the thiol group of cysteine to a hydroxyl group of the surface hydration layer. The adsorption energies are found to be dominated both by the formation of direct or indirect surface-molecule hydrogen bonds, but also by the rearrangement of the hydrogen-bond network in surface proximity in a non-intuitive way. Energetic comparisons between DFTB and DFT are made difficult on one side by the long time necessary to achieve convergence of potential energy values in MD simulations and on the other side by the necessity of including higher-order corrections to DFTB to obtain a good description of the hydrogen bond energetics. Overall, our results suggest that DFTB is a good reference method to set the correct chemical states and the initial geometries of hybrid biomolecule/ZnO systems to be simulated with non-reactive force fields.

Chemical functionalization of graphene by carbene cycloaddition: A density functional theory study

International Nuclear Information System (INIS)

Zan, Wenyan

2014-01-01

Graphical abstract: - Highlights: • The reaction process of graphene functionalization with CCl 2 group in atomic scales was studied. • The potential candidate carbenes CR 2 (R = H, F, CN, NO 2 0 , NO 2 90 , CH 3 , OCH 3 , CCH, C 6 H 5 ) were separately combined with graphene. • The functionalization of graphene nanoribbon with dichlorocarbene group was investigated. • The electronic properties of graphene functionalized by carbene groups were discussed. - Abstract: In this work, we have systematically studied the structural, energetic and electronic properties of graphene functionalized with carbene groups by using density functional theory. Introducing a low concentration of CCl 2 group in graphene was studied in detail by DFT, and closed cyclopropane-like three-membered ring structure was formed, meanwhile, the potential candidate carbene groups CR 2 (R = H, F, CH 3 , CN, NO 2 , OCH 3 , CCH, C 6 H 5 ) were added to graphene sheet, and CR 2 (R = H, NO 2 , CH 3 ) groups were expected to be good reactive species to covalently modify graphene. The graphene functionalization with carbene groups above can open graphene's band gap. More CCl 2 molecules were added to graphene, and different concentrations of CCl 2 group can tune graphene's band gap. In addition, the addition of CCl 2 group to graphene edges was investigated, and the stronger binding energy was found. Multiple CCl 2 molecules preferred to be bound with the same edge of graphene nanoribbon. This work provides an insight into the detailed molecular mechanism of graphene functionalization with carbene groups

Quantum chemical density functional theory studies on the molecular structure and vibrational spectra of Gallic acid imprinted polymers

Science.gov (United States)

Pardeshi, Sushma; Dhodapkar, Rita; Kumar, Anupama

2013-12-01

Gallic acid (GA) is known by its antioxidant, anticarcinogenic properties and scavenger activity against several types of harmful free radicals. Molecularly imprinted polymers (MIPs) are used in separation of a pure compound from complex matrices. A stable template-monomer complex generates the MIPs with the highest affinity and selectivity for the template. The quantum chemical computations based on density functional theory (DFT) was used on the template Gallic acid (GA), monomer acrylic acid (AA) and GA-AA complex to study the nature of interactions involved in the GA-AA complex. B3LYP/6-31+G(2d,2p) model chemistry was used to optimize their structures and frequency calculations. The effect of porogen acetonitrile (ACN) on complex formation was included by using polarizable continuum model (PCM). The results demonstrated the formation of a stable GA-AA complex through the intermolecular hydrogen bonding between carboxylic acid groups of GA and AA. The Mulliken atomic charge analysis and simulated vibrational spectra also supported the stable hydrogen bonding interaction between the carboxylic acid groups of GA and AA with minimal interference of porogen ACN. Further, simulations on GA-AA mole ratio revealed that 1:4 GA-AA was optimum for synthesis of MIP for GA.

On the nodal structure of atomic and molecular Wigner functions

International Nuclear Information System (INIS)

Dahl, J.P.; Schmider, H.

1996-01-01

In previous work on the phase-space representation of quantum mechanics, we have presented detailed pictures of the electronic one-particle reduced Wigner function for atoms and small molecules. In this communication, we focus upon the nodal structure of the function. On the basis of the simplest systems, we present an expression which relates the oscillatory decay of the Wigner function solely to the dot product of the position and momentum vector, if both arguments are large. We then demonstrate the regular behavior of nodal patterns for the larger systems. For the molecular systems, an argument analogous to the open-quotes bond-oscillatory principleclose quotes for momentum densities links the nuclear framework to an additional oscillatory term in momenta parallel to bonds. It is shown that these are visible in the Wigner function in terms of characteristic nodes

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.

Reaction energetics on long-range corrected density functional theory: Diels-Alder reactions.

Science.gov (United States)

Singh, Raman K; Tsuneda, Takao

2013-02-15

The possibility of quantitative reaction analysis on the orbital energies of long-range corrected density functional theory (LC-DFT) is presented. First, we calculated the Diels-Alder reaction enthalpies that have been poorly given by conventional functionals including B3LYP functional. As a result, it is found that the long-range correction drastically improves the reaction enthalpies. The barrier height energies were also computed for these reactions. Consequently, we found that dispersion correlation correction is also crucial to give accurate barrier height energies. It is, therefore, concluded that both long-range exchange interactions and dispersion correlations are essentially required in conventional functionals to investigate Diels-Alder reactions quantitatively. After confirming that LC-DFT accurately reproduces the orbital energies of the reactant and product molecules of the Diels-Alder reactions, the global hardness responses, the halves of highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) energy gaps, along the intrinsic reaction coordinates of two Diels-Alder reactions were computed. We noticed that LC-DFT results satisfy the maximum hardness rule for overall reaction paths while conventional functionals violate this rule on the reaction pathways. Furthermore, our results also show that the HOMO-LUMO gap variations are close to the reaction enthalpies for these Diels-Alder reactions. Based on these results, we foresee quantitative reaction analysis on the orbital energies. Copyright © 2012 Wiley Periodicals, Inc.

Influence of functional groups on charge transport in molecular junctions

DEFF Research Database (Denmark)

Mowbray, Duncan; Jones, Glenn; Thygesen, Kristian Sommer

2008-01-01

Using density functional theory (DFT), we analyze the influence of five classes of functional groups, as exemplified by NO2, OCH3, CH3, CCl3, and I, on the transport properties of a 1,4-benzenedithiolate (BDT) and 1,4-benzenediamine (BDA) molecular junction with gold electrodes. Our analysis...... demonstrates how ideas from functional group chemistry may be used to engineer a molecule's transport properties, as was shown experimentally and using a semiempirical model for BDA [Nano Lett. 7, 502 (2007)]. In particular, we show that the qualitative change in conductance due to a given functional group can...... be predicted from its known electronic effect (whether it is sigma/pi donating/withdrawing). However, the influence of functional groups on a molecule's conductance is very weak, as was also found in the BDA experiments. The calculated DFT conductances for the BDA species are five times larger than...

Density functional simulations of Sb-rich GeSbTe phase change alloys

OpenAIRE

Gabardi, S; Caravati, S; Bernasconi, M; Parrinello, M

2012-01-01

We generated models of the amorphous phase of Sb rich GeSbTe phase change alloys by quenching from the melt within density functional molecular dynamics. We considered the two compositions Ge 1Sb 1Te 1 and Ge 2Sb 4Te 5. Comparison with previous results on the most studied Ge 2Sb 2Te 5 allowed us to draw some conclusions on the dependence of the structural properties of the amorphous phase on the alloy composition. Vibrational and electronic properties were also scrutinized. Phonons at high fr...

A Safari Through Density Functional Theory

Science.gov (United States)

Dreizler, Reiner M.; Lüdde, Cora S.

Density functional theory is widely used to treat quantum many body problems in many areas of physics and related fields. A brief survey of this method covering foundations, functionals and applications is presented here.

Metal-ligand delocalization and spin density in the CuCl{sub 2} and [CuCl{sub 4}]{sup 2−} molecules: Some insights from wave function theory

Energy Technology Data Exchange (ETDEWEB)

Giner, Emmanuel, E-mail: gnrmnl@unife.it; Angeli, Celestino, E-mail: anc@unife.it [Dipartimento di Scienze Chimiche e Famaceutiche, Universita di Ferrara, Via Fossato di Mortara 17, I-44121 Ferrara (Italy)

2015-09-28

The aim of this paper is to unravel the physical phenomena involved in the calculation of the spin density of the CuCl{sub 2} and [CuCl{sub 4}]{sup 2−} systems using wave function methods. Various types of wave functions are used here, both variational and perturbative, to analyse the effects impacting the spin density. It is found that the spin density on the chlorine ligands strongly depends on the mixing between two types of valence bond structures. It is demonstrated that the main difficulties found in most of the previous studies based on wave function methods come from the fact that each valence bond structure requires a different set of molecular orbitals and that using a unique set of molecular orbitals in a variational procedure leads to the removal of one of them from the wave function. Starting from these results, a method to compute the spin density at a reasonable computational cost is proposed.

Comparison of exact-exchange calculations for solids in current-spin-density- and spin-density-functional theory

DEFF Research Database (Denmark)

Sharma, S.; Pittalis, S.; Kurth, S.

2007-01-01

The relative merits of current-spin-density- and spin-density-functional theory are investigated for solids treated within the exact-exchange-only approximation. Spin-orbit splittings and orbital magnetic moments are determined at zero external magnetic field. We find that for magnetic (Fe, Co......, and Ni) and nonmagnetic (Si and Ge) solids, the exact-exchange current-spin-density functional approach does not significantly improve the accuracy of the corresponding spin-density functional results....

Dynamical density functional theory for dense atomic liquids

International Nuclear Information System (INIS)

Archer, A J

2006-01-01

Starting from Newton's equations of motion, we derive a dynamical density functional theory (DDFT) applicable to atomic liquids. The theory has the feature that it requires as input the Helmholtz free energy functional from equilibrium density functional theory. This means that, given a reliable equilibrium free energy functional, the correct equilibrium fluid density profile is guaranteed. We show that when the isothermal compressibility is small, the DDFT generates the correct value for the speed of sound in a dense liquid. We also interpret the theory as a dynamical equation for a coarse grained fluid density and show that the theory can be used (making further approximations) to derive the standard mode coupling theory that is used to describe the glass transition. The present theory should provide a useful starting point for describing the dynamics of inhomogeneous atomic fluids

Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D)

DEFF Research Database (Denmark)

van de Streek, Jacco; Neumann, Marcus A

2014-01-01

In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published...

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.

Density functional theory in quantum chemistry

CERN Document Server

Tsuneda, Takao

2014-01-01

This book examines density functional theory based on the foundation of quantum chemistry. Unconventional in approach, it reviews basic concepts, then describes the physical meanings of state-of-the-art exchange-correlation functionals and their corrections.

Comment on 'Kinetic energy as a density functional'

International Nuclear Information System (INIS)

Holas, A.; March, N.H.

2002-01-01

In a recent paper, Nesbet [Phys. Rev. A 65, 010502(R) (2001)] has proposed dropping ''the widespread but unjustified assumption that the existence of a ground-state density functional for the kinetic energy, T s [ρ], of an N-electron system implies the existence of a density-functional derivative, δT s [ρ]/δρ(r), equivalent to a local potential function,'' because, according to his arguments, this derivative 'has the mathematical character of a linear operator that acts on orbital wave functions'. Our Comment demonstrates that the statement called by Nesbet an 'unjustified assumption' happens, in fact, to be a rigorously proven theorem. Therefore, his previous conclusions stemming from his different view of this derivative, which undermined the foundations of density-functional theory, can be discounted

SYNTHESIS, CHARACTERIZATION AND DENSITY FUNCTIONAL ...

African Journals Online (AJOL)

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We synthesized a number of aniline derivatives containing acyl groups to compare their barriers of rotation around ... KEY WORDS: Monoacyl aniline, Synthesis, Density functional theory, Rotation barrier. INTRODUCTION. Developments in ...

Investigation of the silicon ion density during molecular beam epitaxy growth

CERN Document Server

Eifler, G; Ashurov, K; Morozov, S

2002-01-01

Ions impinging on a surface during molecular beam epitaxy influence the growth and the properties of the growing layer, for example, suppression of dopant segregation and the generation of crystal defects. The silicon electron gun in the molecular beam epitaxy (MBE) equipment is used as a source for silicon ions. To use the effect of ion bombardment the mechanism of generation and distribution of ions was investigated. A monitoring system was developed and attached at the substrate position in the MBE growth chamber to measure the ion and electron densities towards the substrate. A negative voltage was applied to the substrate to modify the ion energy and density. Furthermore the current caused by charge carriers impinging on the substrate was measured and compared with the results of the monitoring system. The electron and ion densities were measured by varying the emission current of the e-gun achieving silicon growth rates between 0.07 and 0.45 nm/s and by changing the voltage applied to the substrate betw...

Density functional approach to the many-body problem : Key concepts and exact functionals

NARCIS (Netherlands)

van Leeuwen, Robert

2003-01-01

We give an overview of the fundamental concepts of density functional theory. We give a careful discussion of the several density functionals and their differentiability properties. We show that for nondegenerate ground states we can calculate the necessary functional derivatives by means of linear

The effect of empirical potential functions on modeling of amorphous carbon using molecular dynamics method

International Nuclear Information System (INIS)

Li, Longqiu; Xu, Ming; Song, Wenping; Ovcharenko, Andrey; Zhang, Guangyu; Jia, Ding

2013-01-01

Empirical potentials have a strong effect on the hybridization and structure of amorphous carbon and are of great importance in molecular dynamics (MD) simulations. In this work, amorphous carbon at densities ranging from 2.0 to 3.2 g/cm 3 was modeled by a liquid quenching method using Tersoff, 2nd REBO, and ReaxFF empirical potentials. The hybridization, structure and radial distribution function G(r) of carbon atoms were analyzed as a function of the three potentials mentioned above. The ReaxFF potential is capable to model the change of the structure of amorphous carbon and MD results are in a good agreement with experimental results and density function theory (DFT) at low density of 2.6 g/cm 3 and below. The 2nd REBO potential can be used when amorphous carbon has a very low density of 2.4 g/cm 3 and below. Considering the computational efficiency, the Tersoff potential is recommended to model amorphous carbon at a high density of 2.6 g/cm 3 and above. In addition, the influence of the quenching time on the hybridization content obtained with the three potentials is discussed.

Extended screened exchange functional derived from transcorrelated density functional theory.

Science.gov (United States)

Umezawa, Naoto

2017-09-14

We propose a new formulation of the correlation energy functional derived from the transcorrelated method in use in density functional theory (TC-DFT). An effective Hamiltonian, H TC , is introduced by a similarity transformation of a many-body Hamiltonian, H, with respect to a complex function F: H TC =1FHF. It is proved that an expectation value of H TC for a normalized single Slater determinant, D n , corresponds to the total energy: E[n] = ⟨Ψ n |H|Ψ n ⟩/⟨Ψ n |Ψ n ⟩ = ⟨D n |H TC |D n ⟩ under the two assumptions: (1) The electron density nr associated with a trial wave function Ψ n = D n F is v-representable and (2) Ψ n and D n give rise to the same electron density nr. This formulation, therefore, provides an alternative expression of the total energy that is useful for the development of novel correlation energy functionals. By substituting a specific function for F, we successfully derived a model correlation energy functional, which resembles the functional form of the screened exchange method. The proposed functional, named the extended screened exchange (ESX) functional, is described within two-body integrals and is parametrized for a numerically exact correlation energy of the homogeneous electron gas. The ESX functional does not contain any ingredients of (semi-)local functionals and thus is totally free from self-interactions. The computational cost for solving the self-consistent-field equation is comparable to that of the Hartree-Fock method. We apply the ESX functional to electronic structure calculations for a solid silicon, H - ion, and small atoms. The results demonstrate that the TC-DFT formulation is promising for the systematic improvement of the correlation energy functional.

X-ray absorption in insulators with non-Hermitian real-time time-dependent density functional theory.

Science.gov (United States)

Fernando, Ranelka G; Balhoff, Mary C; Lopata, Kenneth

2015-02-10

Non-Hermitian real-time time-dependent density functional theory was used to compute the Si L-edge X-ray absorption spectrum of α-quartz using an embedded finite cluster model and atom-centered basis sets. Using tuned range-separated functionals and molecular orbital-based imaginary absorbing potentials, the excited states spanning the pre-edge to ∼20 eV above the ionization edge were obtained in good agreement with experimental data. This approach is generalizable to TDDFT studies of core-level spectroscopy and dynamics in a wide range of materials.

Quantum Crystallography: Density Matrix-Density Functional Theory and the X-Ray Diffraction Experiment

Science.gov (United States)

Soirat, Arnaud J. A.

Density Matrix Theory is a Quantum Mechanical formalism in which the wavefunction is eliminated and its role taken over by reduced density matrices. The interest of this is that, it allows one, in principle, to calculate any electronic property of a physical system, without having to solve the Schrodinger equation, using only two entities much simpler than an N-body wavefunction: first and second -order reduced density matrices. In practice, though, this very promising possibility faces the tremendous theoretical problem of N-representability, which has been solved for the former, but, until now, voids any hope of theoretically determining the latter. However, it has been shown that single determinant reduced density matrices of any order may be recovered from coherent X-ray diffraction data, if one provides a proper Quantum Mechanical description of the Crystallography experiment. A deeper investigation of this method is the purpose of this work, where we, first, further study the calculation of X-ray reduced density matrices N-representable by a single Slater determinant. In this context, we independently derive necessary and sufficient conditions for the uniqueness of the method. We then show how to account for electron correlation in this model. For the first time, indeed, we derive highly accurate, yet practical, density matrices approximately N-representable by correlated-determinant wavefunctions. The interest of such a result lies in the Quantum Mechanical validity of these density matrices, their property of being entirely obtainable from X-ray coherent diffraction data, their very high accuracy conferred by this known property of the N-representing wavefunction, as well as their definition as explicit functionals of the density. All of these properties are finally used in both a theoretical and a numerical application: in the former, we show that these density matrices may be used in the context of Density Functional Theory to highly accurately determine

Density functional theory of nuclei

International Nuclear Information System (INIS)

Terasaki, Jun

2008-01-01

The density functional theory of nuclei has come to draw attention of scientists in the field of nuclear structure because the theory is expected to provide reliable numerical data in wide range on the nuclear chart. This article is organized to present an overview of the theory to the people engaged in the theory of other fields as well as those people in the nuclear physics experiments. At first, the outline of the density functional theory widely used in the electronic systems (condensed matter, atoms, and molecules) was described starting from the Kohn-Sham equation derived on the variational principle. Then the theory used in the field of nuclear physics was presented. Hartree-Fock and Hartree-Fock-Bogolyubov approximation by using Skyrme interaction was explained. Comparison of the results of calculations and experiments of binding energies and ground state mean square charge radii of some magic number nuclei were shown. The similarity and dissimilarity between the two streams were summarized. Finally the activities of the international project of Universal Nuclear Energy Density Functional (UNEDF) which was started recently lead by US scientist was reported. This project is programmed for five years. One of the applications of the project is the calculation of the neutron capture cross section of nuclei on the r-process, which is absolutely necessary for the nucleosynthesis research. (S. Funahashi)

Molecular-Scale Electronics: From Concept to Function.

Science.gov (United States)

Xiang, Dong; Wang, Xiaolong; Jia, Chuancheng; Lee, Takhee; Guo, Xuefeng

2016-04-13

Creating functional electrical circuits using individual or ensemble molecules, often termed as "molecular-scale electronics", not only meets the increasing technical demands of the miniaturization of traditional Si-based electronic devices, but also provides an ideal window of exploring the intrinsic properties of materials at the molecular level. This Review covers the major advances with the most general applicability and emphasizes new insights into the development of efficient platform methodologies for building reliable molecular electronic devices with desired functionalities through the combination of programmed bottom-up self-assembly and sophisticated top-down device fabrication. First, we summarize a number of different approaches of forming molecular-scale junctions and discuss various experimental techniques for examining these nanoscale circuits in details. We then give a full introduction of characterization techniques and theoretical simulations for molecular electronics. Third, we highlight the major contributions and new concepts of integrating molecular functionalities into electrical circuits. Finally, we provide a critical discussion of limitations and main challenges that still exist for the development of molecular electronics. These analyses should be valuable for deeply understanding charge transport through molecular junctions, the device fabrication process, and the roadmap for future practical molecular electronics.

Local electric dipole moments for periodic systems via density functional theory embedding.

Science.gov (United States)

Luber, Sandra

2014-12-21

We describe a novel approach for the calculation of local electric dipole moments for periodic systems. Since the position operator is ill-defined in periodic systems, maximally localized Wannier functions based on the Berry-phase approach are usually employed for the evaluation of local contributions to the total electric dipole moment of the system. We propose an alternative approach: within a subsystem-density functional theory based embedding scheme, subset electric dipole moments are derived without any additional localization procedure, both for hybrid and non-hybrid exchange-correlation functionals. This opens the way to a computationally efficient evaluation of local electric dipole moments in (molecular) periodic systems as well as their rigorous splitting into atomic electric dipole moments. As examples, Infrared spectra of liquid ethylene carbonate and dimethyl carbonate are presented, which are commonly employed as solvents in Lithium ion batteries.

Local electric dipole moments for periodic systems via density functional theory embedding

Energy Technology Data Exchange (ETDEWEB)

Luber, Sandra, E-mail: sandra.luber@chem.uzh.ch [Institut für Chemie, Universität Zürich, Winterthurerstrasse 190, 8057 Zürich (Switzerland)

2014-12-21

We describe a novel approach for the calculation of local electric dipole moments for periodic systems. Since the position operator is ill-defined in periodic systems, maximally localized Wannier functions based on the Berry-phase approach are usually employed for the evaluation of local contributions to the total electric dipole moment of the system. We propose an alternative approach: within a subsystem-density functional theory based embedding scheme, subset electric dipole moments are derived without any additional localization procedure, both for hybrid and non-hybrid exchange–correlation functionals. This opens the way to a computationally efficient evaluation of local electric dipole moments in (molecular) periodic systems as well as their rigorous splitting into atomic electric dipole moments. As examples, Infrared spectra of liquid ethylene carbonate and dimethyl carbonate are presented, which are commonly employed as solvents in Lithium ion batteries.

Iron(II) and Iron(III) Spin Crossover: Toward an Optimal Density Functional

DEFF Research Database (Denmark)

Siig, Oliver S; Kepp, Kasper P.

2018-01-01

Spin crossover (SCO) plays a major role in biochemistry, catalysis, materials, and emerging technologies such as molecular electronics and sensors, and thus accurate prediction and design of SCO systems is of high priority. However, the main tool for this purpose, density functional theory (DFT......), is very sensitive to applied methodology. The most abundant SCO systems are Fe(II) and Fe(III) systems. Even with average good agreement, a functional may be significantly more accurate for Fe(II) or Fe(III) systems, preventing balanced study of SCO candidates of both types. The present work investigates....../precise, inaccurate/imprecise) are observed. More generally, our work illustrates the importance not only of overall accuracy but also of balanced accuracy for systems likely to occur in context....

Optimal Bandwidth Selection for Kernel Density Functionals Estimation

Directory of Open Access Journals (Sweden)

Su Chen

2015-01-01

Full Text Available The choice of bandwidth is crucial to the kernel density estimation (KDE and kernel based regression. Various bandwidth selection methods for KDE and local least square regression have been developed in the past decade. It has been known that scale and location parameters are proportional to density functionals ∫γ(xf2(xdx with appropriate choice of γ(x and furthermore equality of scale and location tests can be transformed to comparisons of the density functionals among populations. ∫γ(xf2(xdx can be estimated nonparametrically via kernel density functionals estimation (KDFE. However, the optimal bandwidth selection for KDFE of ∫γ(xf2(xdx has not been examined. We propose a method to select the optimal bandwidth for the KDFE. The idea underlying this method is to search for the optimal bandwidth by minimizing the mean square error (MSE of the KDFE. Two main practical bandwidth selection techniques for the KDFE of ∫γ(xf2(xdx are provided: Normal scale bandwidth selection (namely, “Rule of Thumb” and direct plug-in bandwidth selection. Simulation studies display that our proposed bandwidth selection methods are superior to existing density estimation bandwidth selection methods in estimating density functionals.

A Sparse Self-Consistent Field Algorithm and Its Parallel Implementation: Application to Density-Functional-Based Tight Binding.

Science.gov (United States)

Scemama, Anthony; Renon, Nicolas; Rapacioli, Mathias

2014-06-10

We present an algorithm and its parallel implementation for solving a self-consistent problem as encountered in Hartree-Fock or density functional theory. The algorithm takes advantage of the sparsity of matrices through the use of local molecular orbitals. The implementation allows one to exploit efficiently modern symmetric multiprocessing (SMP) computer architectures. As a first application, the algorithm is used within the density-functional-based tight binding method, for which most of the computational time is spent in the linear algebra routines (diagonalization of the Fock/Kohn-Sham matrix). We show that with this algorithm (i) single point calculations on very large systems (millions of atoms) can be performed on large SMP machines, (ii) calculations involving intermediate size systems (1000-100 000 atoms) are also strongly accelerated and can run efficiently on standard servers, and (iii) the error on the total energy due to the use of a cutoff in the molecular orbital coefficients can be controlled such that it remains smaller than the SCF convergence criterion.

Locating the rate-limiting step for the interaction of hydrogen with Mg(0001) using density-functional theory calculations and rate theory

DEFF Research Database (Denmark)

Vegge, Tejs

2004-01-01

The dissociation of molecular hydrogen on a Mgs0001d surface and the subsequent diffusion of atomic hydrogen into the magnesium substrate is investigated using Density Functional Theory (DFT) calculations and rate theory. The minimum energy path and corresponding transition states are located usi...... to be rate-limiting for the ab- and desorption of hydrogen, respectively. Zero-point energy contributions are found to be substantial for the diffusion of atomic hydrogen, but classical rates are still found to be within an order of magnitude at room temperature.......The dissociation of molecular hydrogen on a Mgs0001d surface and the subsequent diffusion of atomic hydrogen into the magnesium substrate is investigated using Density Functional Theory (DFT) calculations and rate theory. The minimum energy path and corresponding transition states are located using...

Orientation of rod molecules in selective slits: a density functional theory

International Nuclear Information System (INIS)

Xu Xiaofei; Cao Dapeng; Wang Wenchuan

2008-01-01

A density functional theory (DFT) is used to investigate molecular orientation of rod fluids in selective slits. The DFT approach combines a modified fundamental measure theory (MFMT) for excluded-volume effect, the first-order thermodynamics perturbation theory for chain connectivity and the mean-field approximation for van der Waals (vdW) attraction. To study the molecular orientation, the intramolecular bonding orientation function is introduced into the DFT. First, we investigate the orientation of the surfactant-like rod molecule of AB 6 (i.e. ABBBBBB) in a nanoslit of H 20σ, where the walls selectively adsorb segment 'A'. It is observed that, with the increase of the surface energy of the wall to head segment (i.e. 'A' segment) of the rod molecule, the rod molecules adsorbed on the wall present the perpendicular orientation gradually, and assemble into a smectic-A-like monolayer finally. In addition, we also explore the molecular orientation of the rods with both end segments preferring to the wall, i.e. AB 8 A and AB 7 A, in a nanoslit of H = 10σ. Interestingly, the AB 8 A rod monolayer is compatible with either a smectic-A-like or a smectic-C-like organization, but AB 7 A rod molecules exhibit the smectic-A-like organization. The orientation factor of the AB 7 A rod molecule reaches 1, suggesting that AB 7 A rod molecules self-assemble into an ordered structure with perfectly perpendicular orientation to the wall.

Functional Molecular Diversity of Marine Dissolved Organic Matter Is Reduced during Degradation

Directory of Open Access Journals (Sweden)

Andrea Mentges

2017-06-01

Full Text Available Dissolved organic matter (DOM is a highly diverse mixture of compounds, accounting for one of the world's largest active carbon pools. The surprising recalcitrance of some DOM compounds to bacterial degradation has recently been associated with its diversity. However, little is known about large-scale patterns of marine DOM diversity and its change through degradation, in particular considering the functional diversity of DOM. Here, we analyze the development of marine DOM diversity during degradation in two data sets comprising DOM of very different ages: a three-year mesocosm experiment and highly-resolved field samples from the Atlantic and Southern Ocean. The DOM molecular composition was determined using ultra-high resolution mass spectrometry. We quantify DOM diversity using three conceptually different diversity measures, namely richness of molecular formulas, abundance-based diversity, and functional molecular diversity. Using these measures we find stable molecular richness of DOM with age >1 year, systematic changes in the molecules' abundance distribution with degradation state, and increasing homogeneity with respect to chemical properties for more degraded DOM. Coinciding with differences in sea water density, the spatial field data separated clearly into regions of high and low diversity. The joint application of different diversity measures yields a comprehensive overview on temporal and spatial patterns of molecular diversity, valuable for general conclusions on drivers and consequences of marine DOM diversity.

Current Density Functional Theory Using Meta-Generalized Gradient Exchange-Correlation Functionals.

Science.gov (United States)

Furness, James W; Verbeke, Joachim; Tellgren, Erik I; Stopkowicz, Stella; Ekström, Ulf; Helgaker, Trygve; Teale, Andrew M

2015-09-08

We present the self-consistent implementation of current-dependent (hybrid) meta-generalized gradient approximation (mGGA) density functionals using London atomic orbitals. A previously proposed generalized kinetic energy density is utilized to implement mGGAs in the framework of Kohn-Sham current density functional theory (KS-CDFT). A unique feature of the nonperturbative implementation of these functionals is the ability to seamlessly explore a wide range of magnetic fields up to 1 au (∼235 kT) in strength. CDFT functionals based on the TPSS and B98 forms are investigated, and their performance is assessed by comparison with accurate coupled-cluster singles, doubles, and perturbative triples (CCSD(T)) data. In the weak field regime, magnetic properties such as magnetizabilities and nuclear magnetic resonance shielding constants show modest but systematic improvements over generalized gradient approximations (GGA). However, in the strong field regime, the mGGA-based forms lead to a significantly improved description of the recently proposed perpendicular paramagnetic bonding mechanism, comparing well with CCSD(T) data. In contrast to functionals based on the vorticity, these forms are found to be numerically stable, and their accuracy at high field suggests that the extension of mGGAs to CDFT via the generalized kinetic energy density should provide a useful starting point for further development of CDFT approximations.

LUMINOSITY FUNCTIONS OF SPITZER-IDENTIFIED PROTOSTARS IN NINE NEARBY MOLECULAR CLOUDS

Energy Technology Data Exchange (ETDEWEB)

Kryukova, E.; Megeath, S. T.; Allen, T. S. [Department of Physics and Astronomy, University of Toledo, Toledo, OH (United States); Gutermuth, R. A. [Department of Astronomy, University of Massachusetts, Amherst, MA (United States); Pipher, J. [Department of Physics and Astronomy, University of Rochester, Rochester, NY (United States); Allen, L. E. [National Optical Astronomy Observatories, Tucson, AZ (United States); Myers, P. C. [Harvard-Smithsonian Center for Astrophysics, Cambridge, MA (United States); Muzerolle, J. [Space Telescope Science Institute, Baltimore, MD (United States)

2012-08-15

We identify protostars in Spitzer surveys of nine star-forming (SF) molecular clouds within 1 kpc: Serpens, Perseus, Ophiuchus, Chamaeleon, Lupus, Taurus, Orion, Cep OB3, and Mon R2, which combined host over 700 protostar candidates. These clouds encompass a variety of SF environments, including both low-mass and high-mass SF regions, as well as dense clusters and regions of sparsely distributed star formation. Our diverse cloud sample allows us to compare protostar luminosity functions in these varied environments. We combine near- and mid-infrared photometry from the Two Micron All Sky Survey and Spitzer to create 1-24 {mu}m spectral energy distributions (SEDs). Using protostars from the c2d survey with well-determined bolometric luminosities, we derive a relationship between bolometric luminosity, mid-IR luminosity (integrated from 1-24 {mu}m), and SED slope. Estimations of the bolometric luminosities for protostar candidates are combined to create luminosity functions for each cloud. Contamination due to edge-on disks, reddened Class II sources, and galaxies is estimated and removed from the luminosity functions. We find that luminosity functions for high-mass SF clouds (Orion, Mon R2, and Cep OB3) peak near 1 L{sub Sun} and show a tail extending toward luminosities above 100 L{sub Sun }. The luminosity functions of the low-mass SF clouds (Serpens, Perseus, Ophiuchus, Taurus, Lupus, and Chamaeleon) do not exhibit a common peak, however the combined luminosity function of these regions peaks below 1 L{sub Sun }. Finally, we examine the luminosity functions as a function of the local surface density of young stellar objects. In the Orion molecular clouds, we find a significant difference between the luminosity functions of protostars in regions of high and low stellar density, the former of which is biased toward more luminous sources. This may be the result of primordial mass segregation, although this interpretation is not unique. We compare our luminosity

LUMINOSITY FUNCTIONS OF SPITZER-IDENTIFIED PROTOSTARS IN NINE NEARBY MOLECULAR CLOUDS

International Nuclear Information System (INIS)

Kryukova, E.; Megeath, S. T.; Allen, T. S.; Gutermuth, R. A.; Pipher, J.; Allen, L. E.; Myers, P. C.; Muzerolle, J.

2012-01-01

We identify protostars in Spitzer surveys of nine star-forming (SF) molecular clouds within 1 kpc: Serpens, Perseus, Ophiuchus, Chamaeleon, Lupus, Taurus, Orion, Cep OB3, and Mon R2, which combined host over 700 protostar candidates. These clouds encompass a variety of SF environments, including both low-mass and high-mass SF regions, as well as dense clusters and regions of sparsely distributed star formation. Our diverse cloud sample allows us to compare protostar luminosity functions in these varied environments. We combine near- and mid-infrared photometry from the Two Micron All Sky Survey and Spitzer to create 1-24 μm spectral energy distributions (SEDs). Using protostars from the c2d survey with well-determined bolometric luminosities, we derive a relationship between bolometric luminosity, mid-IR luminosity (integrated from 1-24 μm), and SED slope. Estimations of the bolometric luminosities for protostar candidates are combined to create luminosity functions for each cloud. Contamination due to edge-on disks, reddened Class II sources, and galaxies is estimated and removed from the luminosity functions. We find that luminosity functions for high-mass SF clouds (Orion, Mon R2, and Cep OB3) peak near 1 L ☉ and show a tail extending toward luminosities above 100 L ☉ . The luminosity functions of the low-mass SF clouds (Serpens, Perseus, Ophiuchus, Taurus, Lupus, and Chamaeleon) do not exhibit a common peak, however the combined luminosity function of these regions peaks below 1 L ☉ . Finally, we examine the luminosity functions as a function of the local surface density of young stellar objects. In the Orion molecular clouds, we find a significant difference between the luminosity functions of protostars in regions of high and low stellar density, the former of which is biased toward more luminous sources. This may be the result of primordial mass segregation, although this interpretation is not unique. We compare our luminosity functions to those

Comments on the locality in density-functional theory

International Nuclear Information System (INIS)

Lindgren, Ingvar; Salomonson, Sten

2003-01-01

The 'locality hypothesis' in density-functional theory (DFT), implying that the functional derivative is equivalent to a multiplicative local function, forms the basis of models of Kohn-Sham type. This has been generally accepted by the community since the advent of the model, and has later been formally proved for a large class of functionals. The hypothesis has recently been questioned by Nesbet [Phys. Rev. A 58, R12 (1998) and Phys. Rev. A 65, 010502 (2001)], who claims that it fails for the kinetic-energy functional for a system with more than two noninteracting electrons with a nondegenerate ground state. This conclusion has been questioned by Gal [Phys. Rev. A 62, 044501 (2000)] and by Holas and March [Phys. Rev. A 64, 016501 (2001)]. We claim that the arguments of Nesbet are incorrect, since the orbital functional used for the kinetic energy is not a unique functional of the total density in the domain of unnormalized orbitals. We have demonstrated that with a proper definition of the kinetic energy, which is a unique density functional also in the unnormalized region, the derivative can be represented by a single local multiplicative function for all v-representable densities. Therefore, we consider the controversy connected with the issue raised by Nesbet as resolved. We believe that the proof of the differentiability given here can be extended to larger groups of DFT functionals, and works along these lines are in progress

Collision dynamics of H+ + N2 at low energies based on time-dependent density-functional theory

Science.gov (United States)

Yu, W.; Zhang, Y.; Zhang, F. S.; Hutton, R.; Zou, Y.; Gao, C.-Z.; Wei, B.

2018-02-01

Using time-dependent density-functional theory at the level of local density approximation augmented by a self-interaction correction and coupled non-adiabatically to molecular dynamics, we study, from a theoretical perspective, scattering dynamics of the proton in collisions with the N2 molecule at 30 eV. Nine different collision configurations are employed to analyze the proton energy loss spectra, electron depletion, scattering angles and self-interaction effects. Our results agree qualitatively with the experimental data and previous theoretical calculations. The discrepancies are ascribed to the limitation of the theoretical models in use. We find that self-interaction effects can significantly influence the electron capture and the excited diatomic vibrational motion, which is in consistent with other calculations. In addition, it is found that the molecular structure can be readily retrieved from the proton energy loss spectra due to a significant momentum transfer in head-on collisions.

Molecular Dynamics Simulation of High Density DNA Arrays

Directory of Open Access Journals (Sweden)

Rudolf Podgornik

2018-01-01

Full Text Available Densely packed DNA arrays exhibit hexagonal and orthorhombic local packings, as well as a weakly first order transition between them. While we have some understanding of the interactions between DNA molecules in aqueous ionic solutions, the structural details of its ordered phases and the mechanism governing the respective phase transitions between them remains less well understood. Since at high DNA densities, i.e., small interaxial spacings, one can neither neglect the atomic details of the interacting macromolecular surfaces nor the atomic details of the intervening ionic solution, the atomistic resolution is a sine qua non to properly describe and analyze the interactions between DNA molecules. In fact, in order to properly understand the details of the observed osmotic equation of state, one needs to implement multiple levels of organization, spanning the range from the molecular order of DNA itself, the possible ordering of counterions, and then all the way to the induced molecular ordering of the aqueous solvent, all coupled together by electrostatic, steric, thermal and direct hydrogen-bonding interactions. Multiscale simulations therefore appear as singularly suited to connect the microscopic details of this system with its macroscopic thermodynamic behavior. We review the details of the simulation of dense atomistically resolved DNA arrays with different packing symmetries and the ensuing osmotic equation of state obtained by enclosing a DNA array in a monovalent salt and multivalent (spermidine counterions within a solvent permeable membrane, mimicking the behavior of DNA arrays subjected to external osmotic stress. By varying the DNA density, the local packing symmetry, and the counterion type, we are able to analyze the osmotic equation of state together with the full structural characterization of the DNA subphase, the counterion distribution and the solvent structural order in terms of its different order parameters and

Molecular dynamics simulation for the baryon-quark phase transition at finite baryon density

International Nuclear Information System (INIS)

Akimura, Y.; Maruyama, T.; Chiba, S.; Yoshinaga, N.

2005-01-01

We study the baryon-quark phase transition in the molecular dynamics (MD) of the quark degrees of freedom at finite baryon density. The baryon state at low baryon density, and the deconfined quark state at high baryon density are reproduced. We investigate the equations of state of matters with different u-d-s compositions. It is found that the baryon-quark transition is sensitive to the quark width. (orig.)

Architectonics: Design of Molecular Architecture for Functional Applications.

Science.gov (United States)

Avinash, M B; Govindaraju, Thimmaiah

2018-02-20

The term architectonics has its roots in the architectural and philosophical (as early as 1600s) literature that refers to "the theory of structure" and "the structure of theory", respectively. The concept of architectonics has been adapted to advance the field of molecular self-assembly and termed as molecular architectonics. In essence, the methodology of organizing molecular units in the required and controlled configurations to develop advanced functional systems for materials and biological applications comprises the field of molecular architectonics. This concept of designing noncovalent systems enables to focus on different functional aspects of designer molecules for biological and nonbiological applications and also strengthens our efforts toward the mastery over the art of controlled molecular self-assemblies. Programming complex molecular interactions and assemblies for specific functions has been one of the most challenging tasks in the modern era. Meticulously ordered molecular assemblies can impart remarkable developments in several areas spanning energy, health, and environment. For example, the well-defined nano-, micro-, and macroarchitectures of functional molecules with specific molecular ordering possess potential applications in flexible electronics, photovoltaics, photonic crystals, microreactors, sensors, drug delivery, biomedicine, and superhydrophobic coatings, among others. The functional molecular architectures having unparalleled properties are widely evident in various designs of Nature. By drawing inspirations from Nature, intended molecular architectures can be designed and developed to harvest various functions, as there is an inexhaustible resource and scope. In this Account, we present exquisite designer molecules developed by our group and others with an objective to master the art of molecular recognition and self-assembly for functional applications. We demonstrate the tailor-ability of molecular self-assemblies by employing

The relation between the column density structures and the magnetic field orientation in the Vela C molecular complex

Science.gov (United States)

Soler, J. D.; Ade, P. A. R.; Angilè, F. E.; Ashton, P.; Benton, S. J.; Devlin, M. J.; Dober, B.; Fissel, L. M.; Fukui, Y.; Galitzki, N.; Gandilo, N. N.; Hennebelle, P.; Klein, J.; Li, Z.-Y.; Korotkov, A. L.; Martin, P. G.; Matthews, T. G.; Moncelsi, L.; Netterfield, C. B.; Novak, G.; Pascale, E.; Poidevin, F.; Santos, F. P.; Savini, G.; Scott, D.; Shariff, J. A.; Thomas, N. E.; Tucker, C. E.; Tucker, G. S.; Ward-Thompson, D.

2017-07-01

We statistically evaluated the relative orientation between gas column density structures, inferred from Herschel submillimetre observations, and the magnetic field projected on the plane of sky, inferred from polarized thermal emission of Galactic dust observed by the Balloon-borne Large-Aperture Submillimetre Telescope for Polarimetry (BLASTPol) at 250, 350, and 500 μm, towards the Vela C molecular complex. First, we find very good agreement between the polarization orientations in the three wavelength-bands, suggesting that, at the considered common angular resolution of 3.´0 that corresponds to a physical scale of approximately 0.61 pc, the inferred magnetic field orientation is not significantly affected by temperature or dust grain alignment effects. Second, we find that the relative orientation between gas column density structures and the magnetic field changes progressively with increasing gas column density, from mostly parallel or having no preferred orientation at low column densities to mostly perpendicular at the highest column densities. This observation is in agreement with previous studies by the Planck collaboration towards more nearby molecular clouds. Finally, we find a correspondencebetween (a) the trends in relative orientation between the column density structures and the projected magnetic field; and (b) the shape of the column density probability distribution functions (PDFs). In the sub-regions of Vela C dominated by one clear filamentary structure, or "ridges", where the high-column density tails of the PDFs are flatter, we find a sharp transition from preferentially parallel or having no preferred relative orientation at low column densities to preferentially perpendicular at highest column densities. In the sub-regions of Vela C dominated by several filamentary structures with multiple orientations, or "nests", where the maximum values of the column density are smaller than in the ridge-like sub-regions and the high-column density

Trivial constraints on orbital-free kinetic energy density functionals

Science.gov (United States)

Luo, Kai; Trickey, S. B.

2018-03-01

Approximate kinetic energy density functionals (KEDFs) are central to orbital-free density functional theory. Limitations on the spatial derivative dependencies of KEDFs have been claimed from differential virial theorems. We identify a central defect in the argument: the relationships are not true for an arbitrary density but hold only for the minimizing density and corresponding chemical potential. Contrary to the claims therefore, the relationships are not constraints and provide no independent information about the spatial derivative dependencies of approximate KEDFs. A simple argument also shows that validity for arbitrary v-representable densities is not restored by appeal to the density-potential bijection.

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.

Combining Kohn-Sham and orbital-free density-functional theory for Hugoniot calculations to extreme pressures.

Science.gov (United States)

Sheppard, Daniel; Kress, Joel D; Crockett, Scott; Collins, Lee A; Desjarlais, Michael P

2014-12-01

The shock Hugoniot for lithium 6 deuteride ((6)LiD) was calculated via first principles using Kohn-Sham density-functional theory molecular dynamics (KSMD) for temperatures of 0.5-25 eV. The upper limit of 25 eV represents a practical limit where KSMD is no longer computationally feasible due to the number of electronic bands which are required to be populated. To push the Hugoniot calculations to higher temperatures we make use of orbital-free density-functional theory molecular dynamics (OFMD). Thomas-Fermi-Dirac-based OFMD gives a poor description of the electronic structure at low temperatures so the initial state is not well defined. We propose a method of bootstrapping the Hugoniot from OFMD to the Hugoniot from KSMD between 10 and 20 eV, where the two methods are in agreement. The combination of KSMD and OFMD allows construction of a first-principles Hugoniot from the initial state to 1000 eV. Theoretical shock-compression results are in good agreement with available experimental data and exhibit the appropriate high-temperature limits. We show that a unified KSMD-OFMD Hugoniot can be used to assess the quality of the existing equation-of-state (EOS) models and inform better EOS models based on justifiable physics.

Self-interaction error in density functional theory: a mean-field correction for molecules and large systems

International Nuclear Information System (INIS)

Ciofini, Ilaria; Adamo, Carlo; Chermette, Henry

2005-01-01

Corrections to the self-interaction error which is rooted in all standard exchange-correlation functionals in the density functional theory (DFT) have become the object of an increasing interest. After an introduction reminding the origin of the self-interaction error in the DFT formalism, and a brief review of the self-interaction free approximations, we present a simple, yet effective, self-consistent method to correct this error. The model is based on an average density self-interaction correction (ADSIC), where both exchange and Coulomb contributions are screened by a fraction of the electron density. The ansatz on which the method is built makes it particularly appealing, due to its simplicity and its favorable scaling with the size of the system. We have tested the ADSIC approach on one of the classical pathological problem for density functional theory: the direct estimation of the ionization potential from orbital eigenvalues. A large set of different chemical systems, ranging from simple atoms to large fullerenes, has been considered as test cases. Our results show that the ADSIC approach provides good numerical values for all the molecular systems, the agreement with the experimental values increasing, due to its average ansatz, with the size (conjugation) of the systems

Self-consistent embedding of density-matrix renormalization group wavefunctions in a density functional environment.

Science.gov (United States)

Dresselhaus, Thomas; Neugebauer, Johannes; Knecht, Stefan; Keller, Sebastian; Ma, Yingjin; Reiher, Markus

2015-01-28

We present the first implementation of a density matrix renormalization group algorithm embedded in an environment described by density functional theory. The frozen density embedding scheme is used with a freeze-and-thaw strategy for a self-consistent polarization of the orbital-optimized wavefunction and the environmental densities with respect to each other.

Molecular and vibrational structure of diphenylether and its 4,4' -dibromo derivative. Infrared linear dichroism spectroscopy and density functional theory calculations

DEFF Research Database (Denmark)

Eriksen, Troels K; Karlsen, Eva; Spanget-Larsen, Jens

2015-01-01

The title compounds were investigated by means of Linear Dichroism (LD) IR spectroscopy on samples partially aligned in uniaxially stretched low-density polyethylene and by density functional theory calculations. Satisfactory overall agreement between observed and calculated vibrational wavenumbers...

Rydberg energies using excited state density functional theory

International Nuclear Information System (INIS)

Cheng, C.-L.; Wu Qin; Van Voorhis, Troy

2008-01-01

We utilize excited state density functional theory (eDFT) to study Rydberg states in atoms. We show both analytically and numerically that semilocal functionals can give quite reasonable Rydberg energies from eDFT, even in cases where time dependent density functional theory (TDDFT) fails catastrophically. We trace these findings to the fact that in eDFT the Kohn-Sham potential for each state is computed using the appropriate excited state density. Unlike the ground state potential, which typically falls off exponentially, the sequence of excited state potentials has a component that falls off polynomially with distance, leading to a Rydberg-type series. We also address the rigorous basis of eDFT for these systems. Perdew and Levy have shown using the constrained search formalism that every stationary density corresponds, in principle, to an exact stationary state of the full many-body Hamiltonian. In the present context, this means that the excited state DFT solutions are rigorous as long as they deliver the minimum noninteracting kinetic energy for the given density. We use optimized effective potential techniques to show that, in some cases, the eDFT Rydberg solutions appear to deliver the minimum kinetic energy because the associated density is not pure state v-representable. We thus find that eDFT plays a complementary role to constrained DFT: The former works only if the excited state density is not the ground state of some potential while the latter applies only when the density is a ground state density.

Estimation of adsorption-induced pore pressure and confinement in a nanoscopic slit pore by a density functional theory

Science.gov (United States)

Grégoire, David; Malheiro, Carine; Miqueu, Christelle

2018-03-01

This study aims at characterising the adsorption-induced pore pressure and confinement in nanoscopic pores by molecular non-local density functional theory (DFT). Considering its important potential industrial applications, the adsorption of methane in graphitic slit pores has been selected as the test case. While retaining the accuracy of molecular simulations at pore scale, DFT has a very low computational cost that allows obtaining highly resolved pore pressure maps as a function of both pore width and thermodynamic conditions. The dependency of pore pressure on these parameters (pore width, pressure and temperature) is carefully analysed in order to highlight the effect of each parameter on the confined fluid properties that impact the solid matrix.

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).

Covariant Density Functionals: time-odd channel investigated

International Nuclear Information System (INIS)

Afanasjev, A. V.; Abusara, H.

2009-01-01

The description of exotic nuclear systems and phenomena requires a detailed understanding of all channels of density functional theories. The role of time-odd mean fields, their evidence in experiment, and an accurate description of these fields are subject of current interest. Recent studies advanced the understanding of these fields in energy density functional theories based on the Skyrme force [1,2]. Time-odd mean fields are related to nuclear magnetism in covariant density functional (CDF) theories [3]. They arise from space-like components of vector mesons and Lorentz invariance requires that their coupling strengths are identical to that of time-like components. There were only few limited efforts to understand the role of time-odd mean fields in covariant density functional theory [4,5]. For example, the microscopic role of nuclear magnetism and its impact on rotational properties of nuclei has been studied in Ref. [5]. It is known that time-odd mean fields modify the angular momentum content of the single-particle orbitals and thus the moments of inertia, effective alignments, alignment gains at the band crossings and other physical observables. We aim on more detailed and systematic understanding of the role of time-odd mean fields in covariant density functional theory. This investigation covers both rotating and non-rotating systems. It is shown that contrary to the Skyrme energy density functionals time-odd mean fields of CDF theory always provide additional binding in the systems with broken time-reversal symmetry (rotating nuclei, odd mass nuclei). This additional binding increases with spin and has its maximum exactly at the terminating state [6], where it can reach several MeV. The impact of time-odd mean fields on the properties of rotating systems has been studied in a systematic way (as a function of particle number and deformation) across the nuclear chart [7]. In addition, this contribution extends these studies to non-rotating systems such as

Density functional theory of the electrical double layer: the RFD functional

International Nuclear Information System (INIS)

Gillespie, Dirk; Valisko, Monika; Boda, Dezso

2005-01-01

Density functional theory (DFT) of electrolytes is applied to the electrical double layer under a wide range of conditions. The ions are charged, hard spheres of different size and valence, and the wall creating the double layer is uncharged, weakly charged, and strongly charged. Under all conditions, the density and electrostatic potential profiles calculated using the recently proposed RFD electrostatic functional (Gillespie et al 2002 J. Phys.: Condens. Matter 14 12129; 2003 Phys. Rev. E 68 031503) compare well to Monte Carlo simulations. When the wall is strongly charged, the RFD functional results agree with the results of a simpler perturbative electrostatic DFT, but the two functionals' results qualitatively disagree when the wall is uncharged or weakly charged. The RFD functional reproduces these phenomena of weakly charged double layers. It also reproduces bulk thermodynamic quantities calculated from pair correlation functions

Orthogonal bases of radial functions for charge density refinements

International Nuclear Information System (INIS)

Restori, R.

1990-01-01

Charge density determination from X-ray measurements necessitates the evaluation of the Fourier-Bessel transforms of the radial functions used to expand the charge density. Analytical expressions are given here for four sets of orthogonal functions which can substitute for the 'traditional exponential functions' set in least-squares refinements. (orig.)

Analytic derivatives for perturbatively corrected ''double hybrid'' density functionals: Theory, implementation, and applications

International Nuclear Information System (INIS)

Neese, Frank; Schwabe, Tobias; Grimme, Stefan

2007-01-01

A recently proposed new family of density functionals [S. Grimme, J. Chem. Phys. 124, 34108 (2006)] adds a fraction of nonlocal correlation as a new ingredient to density functional theory (DFT). This fractional correlation energy is calculated at the level of second-order many-body perturbation theory (PT2) and replaces some of the semilocal DFT correlation of standard hybrid DFT methods. The new ''double hybrid'' functionals (termed, e.g., B2-PLYP) contain only two empirical parameters that have been adjusted in thermochemical calculations on parts of the G2/3 benchmark set. The methods have provided the lowest errors ever obtained by any DFT method for the full G3 set of molecules. In this work, the applicability of the new functionals is extended to the exploration of potential energy surfaces with analytic gradients. The theory of the analytic gradient largely follows the standard theory of PT2 gradients with some additional subtleties due to the presence of the exchange-correlation terms in the self-consistent field operator. An implementation is reported for closed-shell as well as spin-unrestricted reference determinants. Furthermore, the implementation includes external point charge fields and also accommodates continuum solvation models at the level of the conductor like screening model. The density fitting resolution of the identity (RI) approximation can be applied to the evaluation of the PT2 part with large gains in computational efficiency. For systems with ∼500-600 basis functions the evaluation of the double hybrid gradient is approximately four times more expensive than the calculation of the standard hybrid DFT gradient. Extensive test calculations are provided for main group elements and transition metal containing species. The results reveal that the B2-PLYP functional provides excellent molecular geometries that are superior compared to those from standard DFT and MP2

Long-range corrected density functional theory with accelerated Hartree-Fock exchange integration using a two-Gaussian operator [LC-ωPBE(2Gau)].

Science.gov (United States)

Song, Jong-Won; Hirao, Kimihiko

2015-10-14

Since the advent of hybrid functional in 1993, it has become a main quantum chemical tool for the calculation of energies and properties of molecular systems. Following the introduction of long-range corrected hybrid scheme for density functional theory a decade later, the applicability of the hybrid functional has been further amplified due to the resulting increased performance on orbital energy, excitation energy, non-linear optical property, barrier height, and so on. Nevertheless, the high cost associated with the evaluation of Hartree-Fock (HF) exchange integrals remains a bottleneck for the broader and more active applications of hybrid functionals to large molecular and periodic systems. Here, we propose a very simple yet efficient method for the computation of long-range corrected hybrid scheme. It uses a modified two-Gaussian attenuating operator instead of the error function for the long-range HF exchange integral. As a result, the two-Gaussian HF operator, which mimics the shape of the error function operator, reduces computational time dramatically (e.g., about 14 times acceleration in C diamond calculation using periodic boundary condition) and enables lower scaling with system size, while maintaining the improved features of the long-range corrected density functional theory.

Time-dependent density-functional tight-binding method with the third-order expansion of electron density.

Science.gov (United States)

Nishimoto, Yoshio

2015-09-07

We develop a formalism for the calculation of excitation energies and excited state gradients for the self-consistent-charge density-functional tight-binding method with the third-order contributions of a Taylor series of the density functional theory energy with respect to the fluctuation of electron density (time-dependent density-functional tight-binding (TD-DFTB3)). The formulation of the excitation energy is based on the existing time-dependent density functional theory and the older TD-DFTB2 formulae. The analytical gradient is computed by solving Z-vector equations, and it requires one to calculate the third-order derivative of the total energy with respect to density matrix elements due to the inclusion of the third-order contributions. The comparison of adiabatic excitation energies for selected small and medium-size molecules using the TD-DFTB2 and TD-DFTB3 methods shows that the inclusion of the third-order contributions does not affect excitation energies significantly. A different set of parameters, which are optimized for DFTB3, slightly improves the prediction of adiabatic excitation energies statistically. The application of TD-DFTB for the prediction of absorption and fluorescence energies of cresyl violet demonstrates that TD-DFTB3 reproduced the experimental fluorescence energy quite well.

Measuring the Density of a Molecular Cluster Injector via Visible Emission from an Electron Beam

Energy Technology Data Exchange (ETDEWEB)

Lundberg, D. P.; Kaita, R.; Majeski, R. M.; Stotler, D. P.

2010-06-28

A method to measure the density distribution of a dense hydrogen gas jet is pre- sented. A Mach 5.5 nozzle is cooled to 80K to form a flow capable of molecular cluster formation. A 250V, 10mA electron beam collides with the jet and produces Hα emission that is viewed by a fast camera. The high density of the jet, several 10¹⁶cm^-3, results in substantial electron depletion, which attenuates the H_α emission. The attenuated emission measurement, combined with a simplified electron-molecule collision model, allows us to determine the molecular density profile via a simple iterative calculation.

Shape-Selective Syntheses of Gold and Copper Nanostructures: Insights From Density-Functional Theory and Molecular Dynamics

Science.gov (United States)

Liu, Shih-Hsien

Density-functional theory (DFT) and molecular dynamics (MD) were used to resolve the origins of shape-selective syntheses of {111}-faceted Au nanostructures mediated by polyvinylpyrrolidone (PVP) as well as {100}-faceted Cu nanostructures mediated by hex- adecylamine(HDA) seen in experiment. For the work in PVP on Au surfaces, the hexagonal reconstruction of Au(100) was considered. DFT results indicate that the Au(111) surface covered by the PVP segment, 2-pyrrolidone (2P), has a lower surface energy than the 2P- covered (5 x 1) Au(100)-hex surface, and that PVP may exhibit a binding affinity for Au(111) comparable to or greater than (5 x 1) Au(100)-hex. With MD, it is shown that the PVP-covered Au(111) surface has a lower surface energy than the PVP-covered (5 x 1) Au(100)-hex surface, and that the atactic PVP isosamer chains have a binding affinity for Au(111) comparable to (5 x 1) Au(100)-hex. Also, the (5 x 1) Au(100)-hex surface may have a higher flux of Au atoms than the Au(111) surface. Therefore, the Au(111) surface would be thermodynamically and kinetically favored in PVP-mediated syntheses, leading to {111}-faceted Au nanostructures. For the work in HDA on Cu surfaces, DFT results show that the HDA-covered Cu(100) surface has a slightly higher surface energy than the HDA- covered Cu(111) surface. However, HDA has a significant binding preference on Cu(100) over Cu(111). Therefore, the Cu(100) surface would be kinetically favored in HDA-mediated syn- theses, leading to {100}-faceted Cu nanostructures. Further, a metal-organic many-body (MOMB) force field for HDA-Cu interactions was developed based on the DFT work, and the force field was used to resolve the HDA binding patterns on Cu(100) at molecular level. With MD, it is found that decylamine (DA) may be used as an effective capping agent in the synthesis of {100}-faceted Cu nanostructures since DA as well as HDA are organized on Cu surfaces and have the same binding preference on Cu(100) over Cu(111

Dynamic analysis of electron density in the course of the internal motion of molecular system

International Nuclear Information System (INIS)

Tachibana, A.; Hori, K.; Asai, Y.; Yamabe, T.

1984-01-01

The general dynamic aspect of electron density of a molecular system is studied on the basis of the general equation of the electron orbital which is formulated for the dynamic study of electronic motion. The newly defined electron orbital incorporates the dynamics of molecular vibration into the electronic structures. In this scheme, the change of electron distribution caused by excitation of vibrational state is defined as the ''dynamic electron transfer.'' The dynamic electron density is found to have the remarkable ''additive'' property. The time-dependent aspect of the dynamic electron redistribution is also analyzed on the basis of the ''coherent state.'' The new method relates the classical vibrational amplitude to the quantum number of the vibrational state. As a preliminary application of the present treatment, the dynamic electron densities of H 2 , HD, HT, HF, and HCl molecules are calculated by use of ab initio molecular orbital method

Energy vs. density on paths toward exact density functionals

DEFF Research Database (Denmark)

Kepp, Kasper Planeta

2018-01-01

Recently, the progression toward more exact density functional theory has been questioned, implying a need for more formal ways to systematically measure progress, i.e. a “path”. Here I use the Hohenberg-Kohn theorems and the definition of normality by Burke et al. to define a path toward exactness...

Density functional theory and quantum mechanics/molecular mechanics study of cysteine protease inhibition by nitrile-based inhibitors.

Directory of Open Access Journals (Sweden)

Sam P De Visser

2013-12-01

Full Text Available Cysteine protease enzymes are important for human physiology and catalyze key protein degradation pathways. These enzymes react via a nucleophilic reaction mechanism that involves a cysteine residue and the proton of a proximal histidine. Particularly efficient inhibitors of these enzymes are nitrile-based, however, the details of the catalytic reaction mechanism currently are poorly understood. To gain further insight into the inhibition of these molecules, we have performed a combined density functional theory and quantum mechanics/molecular mechanics study on the reaction of a nitrile-based inhibitor with the enzyme active site amino acids. We show here that small perturbations to the inhibitor structure can have dramatic effects on the catalysis and inhibition processes. Thus, we investigated a range of inhibitor templates and show that specific structural changes reduce the inhibitory efficiency by several orders of magnitude. Moreover, as the reaction takes place on a polar surface, we find strong differences between the DFT and QM/MM calculated energetics. In particular, the DFT model led to dramatic distortions from the starting structure and the convergence to a structure that would not fit the enzyme active site. In the subsequent QM/MM study we investigated the use of mechanical versus electronic embedding on the kinetics, thermodynamics and geometries along the reaction mechanism. We find minor effects on the kinetics of the reaction but large geometric and thermodynamics differences as a result of inclusion of electronic embedding corrections. The work here highlights the importance of model choice in the investigation of this biochemical reaction mechanism.

Multicomponent density-functional theory for time-dependent systems

NARCIS (Netherlands)

Butriy, O.; Ebadi, H.; de Boeij, P. L.; van Leeuwen, R.; Gross, E. K. U.

2007-01-01

We derive the basic formalism of density functional theory for time-dependent electron-nuclear systems. The basic variables of this theory are the electron density in body-fixed frame coordinates and the diagonal of the nuclear N-body density matrix. The body-fixed frame transformation is carried

Improved Density Functional Tight Binding Potentials for Metalloid Aluminum Clusters

Science.gov (United States)

2016-06-01

unlimited IMPROVED DENSITY-FUNCTIONAL TIGHT BINDING POTENTIALS FOR METALLOID ALUMINUM CLUSTERS by Joon H. Kim June 2016 Thesis Advisor...DATES COVERED Master’s thesis 4. TITLE AND SUBTITLE IMPROVED DENSITY-FUNCTIONAL TIGHT BINDING POTENTIALS FOR METALLOID ALUMINUM CLUSTERS 5. FUNDING...repulsive potentials for use in density-functional tight binding (DFTB) simulations of low-valence aluminum metalloid clusters . These systems are under

Recent development of momentum density measurement of polyatomics by molecular (e,2e) spectroscopy

International Nuclear Information System (INIS)

Leung, K.T.

1996-01-01

The use of coincidence techniques to study molecular electron collisions has enabled detailed investigation of collision dynamics and development of electron scattering theories. This has in turn facilitated powerful applications in studying electron-impact ionization phenomena using the so-called (e,2e) technique. Of particular interest is the use of the triple differential cross section for modelling ionic-state-specific electronic wavefunction density in momentum space. To date, detailed electronic structural information of well over sixty atomic and molecular systems have been obtained by this method. In the past five years, there has also been intense development in the application of (e,2e) spectroscopy to study larger molecular systems and condensed matter. This paper will review the recent progress made in this field, with a special focus on the development of momentum density measurement of open-quotes largeclose quotes molecular aggregates, oligomers and bio-molecules examined in this laboratory and elsewhere

A density functional approach to ferrogels

Science.gov (United States)

Cremer, P.; Heinen, M.; Menzel, A. M.; Löwen, H.

2017-07-01

Ferrogels consist of magnetic colloidal particles embedded in an elastic polymer matrix. As a consequence, their structural and rheological properties are governed by a competition between magnetic particle-particle interactions and mechanical matrix elasticity. Typically, the particles are permanently fixed within the matrix, which makes them distinguishable by their positions. Over time, particle neighbors do not change due to the fixation by the matrix. Here we present a classical density functional approach for such ferrogels. We map the elastic matrix-induced interactions between neighboring colloidal particles distinguishable by their positions onto effective pairwise interactions between indistinguishable particles similar to a ‘pairwise pseudopotential’. Using Monte-Carlo computer simulations, we demonstrate for one-dimensional dipole-spring models of ferrogels that this mapping is justified. We then use the pseudopotential as an input into classical density functional theory of inhomogeneous fluids and predict the bulk elastic modulus of the ferrogel under various conditions. In addition, we propose the use of an ‘external pseudopotential’ when one switches from the viewpoint of a one-dimensional dipole-spring object to a one-dimensional chain embedded in an infinitely extended bulk matrix. Our mapping approach paves the way to describe various inhomogeneous situations of ferrogels using classical density functional concepts of inhomogeneous fluids.

Time-Dependent Density Functional Theory for Open Systems and Its Applications.

Science.gov (United States)

Chen, Shuguang; Kwok, YanHo; Chen, GuanHua

2018-02-20

Photovoltaic devices, electrochemical cells, catalysis processes, light emitting diodes, scanning tunneling microscopes, molecular electronics, and related devices have one thing in common: open quantum systems where energy and matter are not conserved. Traditionally quantum chemistry is confined to isolated and closed systems, while quantum dissipation theory studies open quantum systems. The key quantity in quantum dissipation theory is the reduced system density matrix. As the reduced system density matrix is an O(M! × M!) matrix, where M is the number of the particles of the system of interest, quantum dissipation theory can only be employed to simulate systems of a few particles or degrees of freedom. It is thus important to combine quantum chemistry and quantum dissipation theory so that realistic open quantum systems can be simulated from first-principles. We have developed a first-principles method to simulate the dynamics of open electronic systems, the time-dependent density functional theory for open systems (TDDFT-OS). Instead of the reduced system density matrix, the key quantity is the reduced single-electron density matrix, which is an N × N matrix where N is the number of the atomic bases of the system of interest. As the dimension of the key quantity is drastically reduced, the TDDFT-OS can thus be used to simulate the dynamics of realistic open electronic systems and efficient numerical algorithms have been developed. As an application, we apply the method to study how quantum interference develops in a molecular transistor in time domain. We include electron-phonon interaction in our simulation and show that quantum interference in the given system is robust against nuclear vibration not only in the steady state but also in the transient dynamics. As another application, by combining TDDFT-OS with Ehrenfest dynamics, we study current-induced dissociation of water molecules under scanning tunneling microscopy and follow its time dependent

On the evolution of the density probability density function in strongly self-gravitating systems

International Nuclear Information System (INIS)

Girichidis, Philipp; Konstandin, Lukas; Klessen, Ralf S.; Whitworth, Anthony P.

2014-01-01

The time evolution of the probability density function (PDF) of the mass density is formulated and solved for systems in free-fall using a simple approximate function for the collapse of a sphere. We demonstrate that a pressure-free collapse results in a power-law tail on the high-density side of the PDF. The slope quickly asymptotes to the functional form P V (ρ)∝ρ –1.54 for the (volume-weighted) PDF and P M (ρ)∝ρ –0.54 for the corresponding mass-weighted distribution. From the simple approximation of the PDF we derive analytic descriptions for mass accretion, finding that dynamically quiet systems with narrow density PDFs lead to retarded star formation and low star formation rates (SFRs). Conversely, strong turbulent motions that broaden the PDF accelerate the collapse causing a bursting mode of star formation. Finally, we compare our theoretical work with observations. The measured SFRs are consistent with our model during the early phases of the collapse. Comparison of observed column density PDFs with those derived from our model suggests that observed star-forming cores are roughly in free-fall.

Non-Born-Oppenheimer electronic and nuclear densities for a Hooke-Calogero three-particle model: non-uniqueness of density-derived molecular structure.

Science.gov (United States)

Ludeña, E V; Echevarría, L; Lopez, X; Ugalde, J M

2012-02-28

We consider the calculation of non-Born-Oppenheimer, nBO, one-particle densities for both electrons and nuclei. We show that the nBO one-particle densities evaluated in terms of translationally invariant coordinates are independent of the wavefunction describing the motion of center of mass of the whole system. We show that they depend, however, on an arbitrary reference point from which the positions of the vectors labeling the particles are determined. We examine the effect that this arbitrary choice has on the topology of the one-particle density by selecting the Hooke-Calogero model of a three-body system for which expressions for the one-particle densities can be readily obtained in analytic form. We extend this analysis to the one-particle densities obtained from full Coulomb interaction wavefunctions for three-body systems. We conclude, in view of the fact that there is a close link between the choice of the reference point and the topology of one-particle densities that the molecular structure inferred from the topology of these densities is not unique. We analyze the behavior of one-particle densities for the Hooke-Calogero Born-Oppenheimer, BO, wavefunction and show that topological transitions are also present in this case for a particular mass value of the light particles even though in the BO regime the nuclear masses are infinite. In this vein, we argue that the change in topology caused by variation of the mass ratio between light and heavy particles does not constitute a true indication in the nBO regime of the emergence of molecular structure.

Density functional study of uranyl (VI) amidoxime complexes

International Nuclear Information System (INIS)

Chi Fang-Ting; Xiong Jie; Hu Sheng; Xia Xiu-Long; Wang Xiao-Lin; Li Peng; Gao Tao

2012-01-01

Uranyl (VI) amidoxime complexes are investigated using relativistic density functional theory. The equilibrium structures, bond orders, and Mulliken populations of the complexes have been systematically investigated under a generalized gradient approximation (GGA). Comparison of (acet) uranyl amidoxime complexes ([UO 2 (AO) n ] 2−n , 1 ≤ n ≤ 4) with available experimental data shows an excellent agreement. In addition, the U−O(1), U−O(3), C(1)−N(2), and C(3)−N(4) bond lengths of [UO 2 (CH 3 AO) 4 ] 2− are longer than experimental data by about 0.088, 0.05, 0.1, and 0.056 Å. The angles of N(3)−O(3)−U, O(2)−N(1)−C(1), N(3)−C(3)−N(4), N(4)−C(3)−C(4), and C(4)−C(3)−N(3) are different from each other, which is due to existing interaction between oxygen in uranyl and hydrogen in amino group. This interaction is found to be intra-molecular hydrogen bond. Studies on the bond orders, Mulliken charges, and Mulliken populations demonstrate that uranyl oxo group functions as hydrogen-bond acceptors and H atoms in ligands act as hydrogen-bond donors forming hydrogen bonds within the complex

Functional development in density functional theory for superconductors

Energy Technology Data Exchange (ETDEWEB)

Sanna, Antonio; Gross, E.K.U.; Essenberger, Frank [Max Planck Institute of Microstructure Physics, Halle (Saale) (Germany)

2015-07-01

Density functional theory for superconductors (SCDFT) is a fully parameter-free approach to superconductivity that allows for accurate predictions of critical temperature and properties of superconductors. We report on the most recent extensions of the method, in particular the development of new functionals to: (1) incorporate in a correct fashion Migdal's theorem; (2) compute the excitation spectrum; (3) include spin-fluctuation mediated pairing Applications and predictions are shown for a set of materials, including conventional and unconventional superconductors.

Equation satisfied by electron-electron mutual Coulomb repulsion energy density functional

OpenAIRE

Joubert, Daniel P.

2011-01-01

The electron-electron mutual Coulomb repulsion energy density functional satisfies an equation that links functionals and functional derivatives at N-electron and (N-1)-electron densities for densities determined from the same adiabatic scaled external potential for the N-electron system.

Density-functional theory in one dimension for contact-interacting fermions

International Nuclear Information System (INIS)

Magyar, R.J.; Burke, K.

2004-01-01

A density-functional theory is developed for fermions in one dimension, interacting via a δ function. Such systems provide a natural testing ground for questions of principle, as the local-density approximation should be highly accurate since for this interaction type the exchange contribution to the local-density approximation is intrinsically self-interaction-free. The exact-exchange contribution to the total energy is a local functional of the density. A local-density approximation for correlation is obtained using perturbation theory and Bethe ansatz results for the one-dimensional contact-interacting uniform Fermi gas. The ground-state energies are calculated for two finite systems, the analogs of helium and of Hooke's atom. The local-density approximation is shown to be excellent as expected

Assessment of Real-Time Time-Dependent Density Functional Theory (RT-TDDFT) in Radiation Chemistry: Ionized Water Dimer.

Science.gov (United States)

Chalabala, Jan; Uhlig, Frank; Slavíček, Petr

2018-03-29

Ionization in the condensed phase and molecular clusters leads to a complicated chain of processes with coupled electron-nuclear dynamics. It is difficult to describe such dynamics with conventional nonadiabatic molecular dynamics schemes since the number of states swiftly increases as the molecular system grows. It is therefore attractive to use a direct electron and nuclear propagation such as the real-time time-dependent density functional theory (RT-TDDFT). Here we report a RT-TDDFT benchmark study on simulations of singly and doubly ionized states of a water monomer and dimer as a prototype for more complex processes in a condensed phase. We employed the RT-TDDFT based Ehrenfest molecular dynamics with a generalized gradient approximate (GGA) functional and compared it with wave-function-based surface hopping (SH) simulations. We found that the initial dynamics of a singly HOMO ionized water dimer is similar for both the RT-TDDFT/GGA and the SH simulations but leads to completely different reaction channels on a longer time scale. This failure is attributed to the self-interaction error in the GGA functionals and it can be avoided by using hybrid functionals with large fraction of exact exchange (represented here by the BHandHLYP functional). The simulations of doubly ionized states are reasonably described already at the GGA level. This suggests that the RT-TDDFT/GGA method could describe processes following the autoionization processes such as Auger emission, while its applicability to more complex processes such as intermolecular Coulombic decay remains limited.

Self-contained filtered density function

Science.gov (United States)

Nouri, A. G.; Nik, M. B.; Givi, P.; Livescu, D.; Pope, S. B.

2017-09-01

The filtered density function (FDF) closure is extended to a "self-contained" format to include the subgrid-scale (SGS) statistics of all of the hydro-thermo-chemical variables in turbulent flows. These are the thermodynamic pressure, the specific internal energy, the velocity vector, and the composition field. In this format, the model is comprehensive and facilitates large-eddy simulation (LES) of flows at both low and high compressibility levels. A transport equation is developed for the joint pressure-energy-velocity-composition filtered mass density function (PEVC-FMDF). In this equation, the effect of convection appears in closed form. The coupling of the hydrodynamics and thermochemistry is modeled via a set of stochastic differential equation for each of the transport variables. This yields a self-contained SGS closure. For demonstration, LES is conducted of a turbulent shear flow with transport of a passive scalar. The consistency of the PEVC-FMDF formulation is established, and its overall predictive capability is appraised via comparison with direct numerical simulation (DNS) data.

Density-functional molecular-dynamics study of the redox reactions of two anionic, aqueous transition-metal complexes

International Nuclear Information System (INIS)

Tateyama, Yoshitaka; Blumberger, Jochen; Sprik, Michiel; Tavernelli, Ivano

2005-01-01

The thermochemistry of the RuO 4 2- +MnO 4 - →RuO 4 - +MnO 4 2- redox reaction in aqueous solution is studied by separate density-functional-based ab initio molecular-dynamics simulations of the component half reactions RuO 4 2- →RuO 4 - +e - and MnO 4 2- →MnO 4 - +e - . We compare the results of a recently developed grand-canonical method for the computation of oxidation free energies to the predictions by the energy-gap relations of the Marcus theory that can be assumed to apply to these reactions. The calculated redox potentials are in good agreement. The subtraction of the half-reaction free energies gives an estimate of the free energy of the full reaction. The result obtained from the grand-canonical method is -0.4 eV, while the application of the Marcus theory gives -0.3 eV. These should be compared to the experimental value of 0.0 eV. Size effects, in response to increasing the number of water molecules in the periodic model system from 30 to 48, are found to be small (≅0.1 eV). The link to the Marcus theory also has enabled us to compute reorganization free energies for oxidation. For both the MnO 4 2- and RuO 4 2- redox reactions we find the same reorganization free energy of 0.8 eV (1.0 eV in the larger system). The results for the free energies and further analysis of solvation and electronic structure confirm that these two tetrahedral oxoanions show very similar behavior in solution in spite of the central transition-metal atoms occupying a different row and column in the periodic table

Microscopically based energy density functionals for nuclei using the density matrix expansion. II. Full optimization and validation

Science.gov (United States)

Navarro Pérez, R.; Schunck, N.; Dyhdalo, A.; Furnstahl, R. J.; Bogner, S. K.

2018-05-01

Background: Energy density functional methods provide a generic framework to compute properties of atomic nuclei starting from models of nuclear potentials and the rules of quantum mechanics. Until now, the overwhelming majority of functionals have been constructed either from empirical nuclear potentials such as the Skyrme or Gogny forces, or from systematic gradient-like expansions in the spirit of the density functional theory for atoms. Purpose: We seek to obtain a usable form of the nuclear energy density functional that is rooted in the modern theory of nuclear forces. We thus consider a functional obtained from the density matrix expansion of local nuclear potentials from chiral effective field theory. We propose a parametrization of this functional carefully calibrated and validated on selected ground-state properties that is suitable for large-scale calculations of nuclear properties. Methods: Our energy functional comprises two main components. The first component is a non-local functional of the density and corresponds to the direct part (Hartree term) of the expectation value of local chiral potentials on a Slater determinant. Contributions to the mean field and the energy of this term are computed by expanding the spatial, finite-range components of the chiral potential onto Gaussian functions. The second component is a local functional of the density and is obtained by applying the density matrix expansion to the exchange part (Fock term) of the expectation value of the local chiral potential. We apply the UNEDF2 optimization protocol to determine the coupling constants of this energy functional. Results: We obtain a set of microscopically constrained functionals for local chiral potentials from leading order up to next-to-next-to-leading order with and without three-body forces and contributions from Δ excitations. These functionals are validated on the calculation of nuclear and neutron matter, nuclear mass tables, single-particle shell structure

MN15-L: A New Local Exchange-Correlation Functional for Kohn-Sham Density Functional Theory with Broad Accuracy for Atoms, Molecules, and Solids.

Science.gov (United States)

Yu, Haoyu S; He, Xiao; Truhlar, Donald G

2016-03-08

Kohn-Sham density functional theory is widely used for applications of electronic structure theory in chemistry, materials science, and condensed-matter physics, but the accuracy depends on the quality of the exchange-correlation functional. Here, we present a new local exchange-correlation functional called MN15-L that predicts accurate results for a broad range of molecular and solid-state properties including main-group bond energies, transition metal bond energies, reaction barrier heights, noncovalent interactions, atomic excitation energies, ionization potentials, electron affinities, total atomic energies, hydrocarbon thermochemistry, and lattice constants of solids. The MN15-L functional has the same mathematical form as a previous meta-nonseparable gradient approximation exchange-correlation functional, MN12-L, but it is improved because we optimized it against a larger database, designated 2015A, and included smoothness restraints; the optimization has a much better representation of transition metals. The mean unsigned error on 422 chemical energies is 2.32 kcal/mol, which is the best among all tested functionals, with or without nonlocal exchange. The MN15-L functional also provides good results for test sets that are outside the training set. A key issue is that the functional is local (no nonlocal exchange or nonlocal correlation), which makes it relatively economical for treating large and complex systems and solids. Another key advantage is that medium-range correlation energy is built in so that one does not need to add damped dispersion by molecular mechanics in order to predict accurate noncovalent binding energies. We believe that the MN15-L functional should be useful for a wide variety of applications in chemistry, physics, materials science, and molecular biology.

Recent progress in predicting structural and electronic properties of organic solids with the van der Waals density functional

Energy Technology Data Exchange (ETDEWEB)

Yanagisawa, Susumu, E-mail: shou@sci.u-ryukyu.ac.jp [Department of Physics and Earth Sciences, Faculty of Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213 (Japan); Okuma, Koji; Inaoka, Takeshi [Department of Physics and Earth Sciences, Faculty of Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa 903-0213 (Japan); Hamada, Ikutaro, E-mail: Hamada.Ikutaro@nims.go.jp [International Center for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), Tsukuba 305-0044 (Japan)

2015-10-01

Highlights: • Review of theoretical studies on organic solids with the density-functional methods. • van der Waals (vdW)-inclusive methods to predict cohesive properties of oligoacenes. • A variant of the vdW density functional describes the structures accurately. • The molecular configuration and conformation crucially affects the band dispersion. - Abstract: We review recent studies on electronic properties of the organic solids with the first-principles electronic structure methods, with the emphasis on the roles of the intermolecular van der Waals (vdW) interaction in electronic properties of the organic semiconductors. After a brief summary of the recent vdW inclusive first-principle theoretical methods, we discuss their performance in predicting cohesive properties of oligoacene crystals as examples of organic crystals. We show that a variant of the van der Waals density functional describes structure and energetics of organic crystals accurately. In addition, we review our recent study on the zinc phthalocyanine crystal and discuss the importance of the intermolecular distance and orientational angle in the band dispersion. Finally, we draw some general conclusions and the future perspectives.

Recent progress in predicting structural and electronic properties of organic solids with the van der Waals density functional

International Nuclear Information System (INIS)

Yanagisawa, Susumu; Okuma, Koji; Inaoka, Takeshi; Hamada, Ikutaro

2015-01-01

Highlights: • Review of theoretical studies on organic solids with the density-functional methods. • van der Waals (vdW)-inclusive methods to predict cohesive properties of oligoacenes. • A variant of the vdW density functional describes the structures accurately. • The molecular configuration and conformation crucially affects the band dispersion. - Abstract: We review recent studies on electronic properties of the organic solids with the first-principles electronic structure methods, with the emphasis on the roles of the intermolecular van der Waals (vdW) interaction in electronic properties of the organic semiconductors. After a brief summary of the recent vdW inclusive first-principle theoretical methods, we discuss their performance in predicting cohesive properties of oligoacene crystals as examples of organic crystals. We show that a variant of the van der Waals density functional describes structure and energetics of organic crystals accurately. In addition, we review our recent study on the zinc phthalocyanine crystal and discuss the importance of the intermolecular distance and orientational angle in the band dispersion. Finally, we draw some general conclusions and the future perspectives.

Graphene on metals: A van der Waals density functional study

DEFF Research Database (Denmark)

Vanin, Marco; Mortensen, Jens Jørgen; Kelkkanen, Kari André

2010-01-01

We use density functional theory (DFT) with a recently developed van der Waals density functional (vdW-DF) to study the adsorption of graphene on Co, Ni, Pd, Ag, Au, Cu, Pt, and Al(111) surfaces. In contrast to the local-density approximation (LDA) which predicts relatively strong binding for Ni...

Bayesian error estimation in density-functional theory

DEFF Research Database (Denmark)

Mortensen, Jens Jørgen; Kaasbjerg, Kristen; Frederiksen, Søren Lund

2005-01-01

We present a practical scheme for performing error estimates for density-functional theory calculations. The approach, which is based on ideas from Bayesian statistics, involves creating an ensemble of exchange-correlation functionals by comparing with an experimental database of binding energies...

Time-dependent density functional methods for Raman spectra in open-shell systems.

Science.gov (United States)

Aquino, Fredy W; Schatz, George C

2014-01-16

We present an implementation of a time-dependent density functional theory (TD-DFT) linear response module in NWChem for unrestricted DFT calculations and apply it to the calculation of resonant Raman spectra in open-shell molecular systems using the short-time approximation. The new source code was validated and applied to simulate Raman spectra on several doublet organic radicals (e.g., benzyl, benzosemiquinone, TMPD, trans-stilbene anion and cation, and methyl viologen) and the metal complex copper phthalocyanine. We also introduce a divide-and-conquer approach for the evaluation of polarizabilities in relatively large systems (e.g., copper phthalocyanine). The implemented tool gives comparisons with experiment that are similar to what is commonly found for closed-shell systems, with good agreement for most features except for small frequency shifts, and occasionally large deviations for some modes that depend on the molecular system studied, experimental conditions not being accounted in the modeling such as solvation effects and extra solvent-based peaks, and approximations in the underlying theory. The approximations used in the quantum chemical modeling include (i) choice of exchange-correlation functional and basis set; (ii) harmonic approximation used in the frequency analysis to determine vibrational normal modes; and (iii) short-time approximation (omission of nuclear motion effects) used in calculating resonant Raman spectra.

Nuclear energy density functional from chiral pion-nucleon dynamics revisited

Science.gov (United States)

Kaiser, N.; Weise, W.

2010-05-01

We use a recently improved density-matrix expansion to calculate the nuclear energy density functional in the framework of in-medium chiral perturbation theory. Our calculation treats systematically the effects from 1 π-exchange, iterated 1 π-exchange, and irreducible 2 π-exchange with intermediate Δ-isobar excitations, including Pauli-blocking corrections up to three-loop order. We find that the effective nucleon mass M(ρ) entering the energy density functional is identical to the one of Fermi-liquid theory when employing the improved density-matrix expansion. The strength F(ρ) of the ( surface-term as provided by the pion-exchange dynamics is in good agreement with that of phenomenological Skyrme forces in the density region ρ/2short-range spin-orbit interaction. The strength function F(ρ) multiplying the square of the spin-orbit density comes out much larger than in phenomenological Skyrme forces and it has a pronounced density dependence.

Range-separated time-dependent density-functional theory with a frequency-dependent second-order Bethe-Salpeter correlation kernel

Energy Technology Data Exchange (ETDEWEB)

Rebolini, Elisa, E-mail: elisa.rebolini@kjemi.uio.no; Toulouse, Julien, E-mail: julien.toulouse@upmc.fr [Laboratoire de Chimie Théorique, Sorbonne Universités, UPMC Univ Paris 06, CNRS, 4 place Jussieu, F-75005 Paris (France)

2016-03-07

We present a range-separated linear-response time-dependent density-functional theory (TDDFT) which combines a density-functional approximation for the short-range response kernel and a frequency-dependent second-order Bethe-Salpeter approximation for the long-range response kernel. This approach goes beyond the adiabatic approximation usually used in linear-response TDDFT and aims at improving the accuracy of calculations of electronic excitation energies of molecular systems. A detailed derivation of the frequency-dependent second-order Bethe-Salpeter correlation kernel is given using many-body Green-function theory. Preliminary tests of this range-separated TDDFT method are presented for the calculation of excitation energies of the He and Be atoms and small molecules (H{sub 2}, N{sub 2}, CO{sub 2}, H{sub 2}CO, and C{sub 2}H{sub 4}). The results suggest that the addition of the long-range second-order Bethe-Salpeter correlation kernel overall slightly improves the excitation energies.

High hydrostatic pressure specifically affects molecular dynamics and shape of low-density lipoprotein particles

Science.gov (United States)

Golub, M.; Lehofer, B.; Martinez, N.; Ollivier, J.; Kohlbrecher, J.; Prassl, R.; Peters, J.

2017-04-01

Lipid composition of human low-density lipoprotein (LDL) and its physicochemical characteristics are relevant for proper functioning of lipid transport in the blood circulation. To explore dynamical and structural features of LDL particles with either a normal or a triglyceride-rich lipid composition we combined coherent and incoherent neutron scattering methods. The investigations were carried out under high hydrostatic pressure (HHP), which is a versatile tool to study the physicochemical behavior of biomolecules in solution at a molecular level. Within both neutron techniques we applied HHP to probe the shape and degree of freedom of the possible motions (within the time windows of 15 and 100 ps) and consequently the flexibility of LDL particles. We found that HHP does not change the types of motion in LDL, but influences the portion of motions participating. Contrary to our assumption that lipoprotein particles, like membranes, are highly sensitive to pressure we determined that LDL copes surprisingly well with high pressure conditions, although the lipid composition, particularly the triglyceride content of the particles, impacts the molecular dynamics and shape arrangement of LDL under pressure.

A classical density functional theory of ionic liquids.

Science.gov (United States)

Forsman, Jan; Woodward, Clifford E; Trulsson, Martin

2011-04-28

We present a simple, classical density functional approach to the study of simple models of room temperature ionic liquids. Dispersion attractions as well as ion correlation effects and excluded volume packing are taken into account. The oligomeric structure, common to many ionic liquid molecules, is handled by a polymer density functional treatment. The theory is evaluated by comparisons with simulations, with an emphasis on the differential capacitance, an experimentally measurable quantity of significant practical interest.

Measurement of the density profile of pure and seeded molecular beams by femtosecond ion imaging

NARCIS (Netherlands)

Meng, C.; Janssen, M.H.M.

2015-01-01

Here, we report on femtosecond ion imaging experiments to measure the density profile of a pulsed supersonic molecular beam. Ion images are measured for both a molecular beam and bulk gas under identical experimental conditions via femtosecond multiphoton ionization of Xe atoms. We report the

A quantum molecular similarity analysis of changes in molecular electron density caused by basis set flotation and electric field application

Science.gov (United States)

Simon, Sílvia; Duran, Miquel

1997-08-01

Quantum molecular similarity (QMS) techniques are used to assess the response of the electron density of various small molecules to application of a static, uniform electric field. Likewise, QMS is used to analyze the changes in electron density generated by the process of floating a basis set. The results obtained show an interrelation between the floating process, the optimum geometry, and the presence of an external field. Cases involving the Le Chatelier principle are discussed, and an insight on the changes of bond critical point properties, self-similarity values and density differences is performed.

Self-contained filtered density function

International Nuclear Information System (INIS)

Nouri, Arash G.; Pope, Stephen B.

2017-01-01

The filtered density function (FDF) closure is extended to a “self-contained” format to include the subgrid-scale (SGS) statistics of all of the hydro-thermo-chemical variables in turbulent flows. These are the thermodynamic pressure, the specific internal energy, the velocity vector, and the composition field. In this format, the model is comprehensive and facilitates large-eddy simulation (LES) of flows at both low and high compressibility levels. A transport equation is developed for the joint pressure-energy-velocity-composition filtered mass density function (PEVC-FMDF). In this equation, the effect of convection appears in closed form. The coupling of the hydrodynamics and thermochemistry is modeled via a set of stochastic differential equation for each of the transport variables. This yields a self-contained SGS closure. We demonstrated how LES is conducted of a turbulent shear flow with transport of a passive scalar. Finally, the consistency of the PEVC-FMDF formulation is established, and its overall predictive capability is appraised via comparison with direct numerical simulation (DNS) data.

A molecular dynamics study on the interaction between epoxy and functionalized graphene sheets

DEFF Research Database (Denmark)

Melro, Liliana Sofia S. F. P.; Pyrz, Ryszard; Jensen, Lars Rosgaard

2016-01-01

The interaction between graphene and epoxy resin was studied using molecular dynamics simulations. The interfacial shear strength and pull out force were calculated for functionalised graphene layers (carboxyl, carbonyl, and hydroxyl) and epoxy composites interfaces. The influence of functional...... groups, as well as their distribution and coverage density on the graphene sheets were also analysed through the determination of the Young's modulus. Functionalisation proved to be detrimental to the mechanical properties, nonetheless according to interfacial studies the interaction between graphene...

Multiconfiguration Pair-Density Functional Theory Is Free From Delocalization Error.

Science.gov (United States)

Bao, Junwei Lucas; Wang, Ying; He, Xiao; Gagliardi, Laura; Truhlar, Donald G

2017-11-16

Delocalization error has been singled out by Yang and co-workers as the dominant error in Kohn-Sham density functional theory (KS-DFT) with conventional approximate functionals. In this Letter, by computing the vertical first ionization energy for well separated He clusters, we show that multiconfiguration pair-density functional theory (MC-PDFT) is free from delocalization error. To put MC-PDFT in perspective, we also compare it with some Kohn-Sham density functionals, including both traditional and modern functionals. Whereas large delocalization errors are almost universal in KS-DFT (the only exception being the very recent corrected functionals of Yang and co-workers), delocalization error is removed by MC-PDFT, which bodes well for its future as a step forward from KS-DFT.

Benchmark density functional theory calculations for nanoscale conductance

DEFF Research Database (Denmark)

Strange, Mikkel; Bækgaard, Iben Sig Buur; Thygesen, Kristian Sommer

2008-01-01

We present a set of benchmark calculations for the Kohn-Sham elastic transmission function of five representative single-molecule junctions. The transmission functions are calculated using two different density functional theory methods, namely an ultrasoft pseudopotential plane-wave code...

SURFACE SYMMETRY ENERGY OF NUCLEAR ENERGY DENSITY FUNCTIONALS

Energy Technology Data Exchange (ETDEWEB)

Nikolov, N; Schunck, N; Nazarewicz, W; Bender, M; Pei, J

2010-12-20

We study the bulk deformation properties of the Skyrme nuclear energy density functionals. Following simple arguments based on the leptodermous expansion and liquid drop model, we apply the nuclear density functional theory to assess the role of the surface symmetry energy in nuclei. To this end, we validate the commonly used functional parametrizations against the data on excitation energies of superdeformed band-heads in Hg and Pb isotopes, and fission isomers in actinide nuclei. After subtracting shell effects, the results of our self-consistent calculations are consistent with macroscopic arguments and indicate that experimental data on strongly deformed configurations in neutron-rich nuclei are essential for optimizing future nuclear energy density functionals. The resulting survey provides a useful benchmark for further theoretical improvements. Unlike in nuclei close to the stability valley, whose macroscopic deformability hangs on the balance of surface and Coulomb terms, the deformability of neutron-rich nuclei strongly depends on the surface-symmetry energy; hence, its proper determination is crucial for the stability of deformed phases of the neutron-rich matter and description of fission rates for r-process nucleosynthesis.

Molecular dynamics equation designed for realizing arbitrary density: Application to sampling method utilizing the Tsallis generalized distribution

International Nuclear Information System (INIS)

Fukuda, Ikuo; Nakamura, Haruki

2010-01-01

Several molecular dynamics techniques applying the Tsallis generalized distribution are presented. We have developed a deterministic dynamics to generate an arbitrary smooth density function ρ. It creates a measure-preserving flow with respect to the measure ρdω and realizes the density ρ under the assumption of the ergodicity. It can thus be used to investigate physical systems that obey such distribution density. Using this technique, the Tsallis distribution density based on a full energy function form along with the Tsallis index q ≥ 1 can be created. From the fact that an effective support of the Tsallis distribution in the phase space is broad, compared with that of the conventional Boltzmann-Gibbs (BG) distribution, and the fact that the corresponding energy-surface deformation does not change energy minimum points, the dynamics enhances the physical state sampling, in particular for a rugged energy surface spanned by a complicated system. Other feature of the Tsallis distribution is that it provides more degree of the nonlinearity, compared with the case of the BG distribution, in the deterministic dynamics equation, which is very useful to effectively gain the ergodicity of the dynamical system constructed according to the scheme. Combining such methods with the reconstruction technique of the BG distribution, we can obtain the information consistent with the BG ensemble and create the corresponding free energy surface. We demonstrate several sampling results obtained from the systems typical for benchmark tests in MD and from biomolecular systems.

Kinetic-energy density functional: Atoms and shell structure

International Nuclear Information System (INIS)

Garcia-Gonzalez, P.; Alvarellos, J.E.; Chacon, E.

1996-01-01

We present a nonlocal kinetic-energy functional which includes an anisotropic average of the density through a symmetrization procedure. This functional allows a better description of the nonlocal effects of the electron system. The main consequence of the symmetrization is the appearance of a clear shell structure in the atomic density profiles, obtained after the minimization of the total energy. Although previous results with some of the nonlocal kinetic functionals have given incipient structures for heavy atoms, only our functional shows a clear shell structure for most of the atoms. The atomic total energies have a good agreement with the exact calculations. Discussion of the chemical potential and the first ionization potential in atoms is included. The functional is also extended to spin-polarized systems. copyright 1996 The American Physical Society

Structure and properties of simple molecular systems at very high density

International Nuclear Information System (INIS)

LeSar, R.

1989-01-01

The use of computer simulations in the study of molecular systems at very high density is reviewed. Applications to the thermodynamics of dense fluid nitrogen and phase transitions in solid oxygen are presented. The effects of changes in the atomic electronic structure on the equation of state of very dense helium are discussed. 19 refs., 2 figs

A density functional study on the adsorption of hydrogen molecule ...

Indian Academy of Sciences (India)

tive adsorption of H2 onto the minimum energy copper clusters by using the density ... theoretical study of molecular oxygen and atomic oxy- gen adsorption onto small ...... the values for all singlet spin states are zero, indicating that no ...

A classical density functional investigation of nucleation

International Nuclear Information System (INIS)

Ghosh, Satinath; Ghosh, Swapan K.

2009-01-01

Study of nucleation and growth phenomena in condensation is of prime importance in various applications such as crystal growth, nanoparticle synthesis, pattern formation etc. The knowledge of nucleation barrier in condensation is necessary to control the nucleation kinetics, size of the nanoparticles etc. Classical nucleation theory (CNT) assumes the density of the drop as bulk density irrespective of the size of the drop and overestimates the nucleation barrier. Here we are interested in solving the problem analytically using density functional theory (DFT) with square gradient approximation along the lines of Cahn and Hilliard. Nucleation barrier and density profile obtained in this work are consistent with other works based on nonclassical theory. (author)

Molecular Orbital and Density Functional Study of the Formation, Charge Transfer, Bonding and the Conformational Isomerism of the Boron Trifluoride (BF3 and Ammonia (NH3 Donor-Acceptor Complex

Directory of Open Access Journals (Sweden)

Dulal C. Ghosh

2004-09-01

Full Text Available The formation of the F3B–NH3 supermolecule by chemical interaction of its fragment parts, BF3 and NH3, and the dynamics of internal rotation about the ‘B–N’ bond have been studied in terms of parameters provided by the molecular orbital and density functional theories. It is found that the pairs of frontier orbitals of the interacting fragments have matching symmetry and are involved in the charge transfer interaction. The donation process stems from the HOMO of the donor into the LUMO of the acceptor and simultaneously, back donation stems from the HOMO of acceptor into the LUMO of the donor. The density functional computation of chemical activation in the donor and acceptor fragments, associated with the physical process of structural reorganization just prior to the event of chemical reaction, indicates that BF3 becomes more acidic and NH3 becomes more basic, compared to their separate equilibrium states. Theoretically it is observed that the chemical reaction event of the formation of the supermolecule from its fragment parts is in accordance with the chemical potential equalization principle of the density functional theory and the electronegativity equalization principle of Sanderson. The energetics of the chemical reaction, the magnitude of the net charge transfer and the energy of the newly formed bond are quite consistent, both internally and with the principle of maximum hardness, PMH. The dynamics of the internal rotation of one part with respect to the other part of the supermolecule about the ‘B–N’ bond mimics the pattern of the conformational isomerism of the isostructural ethane molecule. It is also observed that the dynamics and evolution of molecular conformations as a function of dihedral angles is also in accordance with the principle of maximum hardness, PMH. Quite consistent with spectroscopic predictions, the height of the molecule

Nonlocal exchange and kinetic-energy density functionals for electronic systems

International Nuclear Information System (INIS)

Glossman, M.D.; Rubio, A.; Balbas, L.C.; Alonso, J.A.

1992-01-01

The nonlocal weighted density approximation (WDA) to the exchange and kinetic-energy functionals of many electron systems proposed several years ago by Alonso and Girifalco is used to compute, within the framework of density functional theory, the ground-state electronic density and total energy of noble gas atoms and of neutral jellium-like sodium clusters containing up to 500 atoms. These results are compared with analogous calculations using the well known Thomas-Fermi-Weizsacker-Dirac (TFWD) approximations for the kinetic (TFW) and exchange (D) energy density functionals. An outstanding improvement of the total and exchange energies, of the density at the nucleus and of the expectation values is obtained for atoms within the WDA scheme. For sodium clusters the authors notice a sizeable contribution of the nonlocal effects to the total energy and to the density profiles. In the limit of very large clusters these effects should affect the surface energy of the bulk metal

Edge reconstruction in armchair phosphorene nanoribbons revealed by discontinuous Galerkin density functional theory.

Science.gov (United States)

Hu, Wei; Lin, Lin; Yang, Chao

2015-12-21

With the help of our recently developed massively parallel DGDFT (Discontinuous Galerkin Density Functional Theory) methodology, we perform large-scale Kohn-Sham density functional theory calculations on phosphorene nanoribbons with armchair edges (ACPNRs) containing a few thousands to ten thousand atoms. The use of DGDFT allows us to systematically achieve a conventional plane wave basis set type of accuracy, but with a much smaller number (about 15) of adaptive local basis (ALB) functions per atom for this system. The relatively small number of degrees of freedom required to represent the Kohn-Sham Hamiltonian, together with the use of the pole expansion the selected inversion (PEXSI) technique that circumvents the need to diagonalize the Hamiltonian, results in a highly efficient and scalable computational scheme for analyzing the electronic structures of ACPNRs as well as their dynamics. The total wall clock time for calculating the electronic structures of large-scale ACPNRs containing 1080-10,800 atoms is only 10-25 s per self-consistent field (SCF) iteration, with accuracy fully comparable to that obtained from conventional planewave DFT calculations. For the ACPNR system, we observe that the DGDFT methodology can scale to 5000-50,000 processors. We use DGDFT based ab initio molecular dynamics (AIMD) calculations to study the thermodynamic stability of ACPNRs. Our calculations reveal that a 2 × 1 edge reconstruction appears in ACPNRs at room temperature.

Titanium-decorated graphene for high-capacity hydrogen storage studied by density functional simulations

International Nuclear Information System (INIS)

Liu Yali; Ren Ling; He Yao; Cheng Haiping

2010-01-01

We present results of density functional theory (DFT) calculations of the adsorption of hydrogen molecules on Ti-decorated graphene. Our results indicate that the binding energies of molecular hydrogen on Ti-decorated graphene can be dramatically enhanced to 0.23-0.60 eV. The hybridization of the Ti 3d orbitals with the H 2 σ and σ* orbitals plays a central role in the enhanced binding. There is also a contribution from the attractive interaction between the surface dipole and the dipole of polarized H 2 . It can be expected that Ti-decorated graphene could be considered as a potential high-capacity hydrogen storage medium.

Constraints on parton density functions from D0

Energy Technology Data Exchange (ETDEWEB)

Hays, Jonathan M.; /Imperial Coll., London

2008-04-01

Five recent results from D0 which either impact or have the potential to impact on uncertainties in parton density functions are presented. Many analyses at D0 are sensitive to the modeling of the partonic structure of the proton. When theoretical and experimental uncertainties are well controlled there exists the possibility for additional constraints on parton density functions (PDF). Five measurements are presented which either have already been included in global parton fits or have the potential to contribute in the future.

Higher-accuracy van der Waals density functional

DEFF Research Database (Denmark)

Lee, Kyuho; Murray, Éamonn D.; Kong, Lingzhu

2010-01-01

We propose a second version of the van der Waals density functional of Dion et al. [Phys. Rev. Lett. 92, 246401 (2004)], employing a more accurate semilocal exchange functional and the use of a large-N asymptote gradient correction in determining the vdW kernel. The predicted binding energy...

A comparative study of density functional and density functional tight binding calculations of defects in graphene

Energy Technology Data Exchange (ETDEWEB)

Zobelli, Alberto [Laboratoire de Physique des Solides, Univ. Paris Sud, CNRS UMR, Orsay (France); Ivanovskaya, Viktoria; Wagner, Philipp; Yaya, Abu; Ewels, Chris P. [Institut des Materiaux Jean Rouxel (IMN), CNRS UMR, University of Nantes (France); Suarez-Martinez, Irene [Nanochemistry Research Institute, Curtin University of Technology, Perth, Western Australia (Australia)

2012-02-15

The density functional tight binding approach (DFTB) is well adapted for the study of point and line defects in graphene based systems. After briefly reviewing the use of DFTB in this area, we present a comparative study of defect structures, energies, and dynamics between DFTB results obtained using the dftb+ code, and density functional results using the localized Gaussian orbital code, AIMPRO. DFTB accurately reproduces structures and energies for a range of point defect structures such as vacancies and Stone-Wales defects in graphene, as well as various unfunctionalized and hydroxylated graphene sheet edges. Migration barriers for the vacancy and Stone-Wales defect formation barriers are accurately reproduced using a nudged elastic band approach. Finally we explore the potential for dynamic defect simulations using DFTB, taking as an example electron irradiation damage in graphene. DFTB-MD derived sputtering energy threshold map for a carbon atom in a graphene plane. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Spin Density Distribution in Open-Shell Transition Metal Systems: A Comparative Post-Hartree-Fock, Density Functional Theory, and Quantum Monte Carlo Study of the CuCl2 Molecule.

Science.gov (United States)

Caffarel, Michel; Giner, Emmanuel; Scemama, Anthony; Ramírez-Solís, Alejandro

2014-12-09

We present a comparative study of the spatial distribution of the spin density of the ground state of CuCl2 using Density Functional Theory (DFT), quantum Monte Carlo (QMC), and post-Hartree-Fock wave function theory (WFT). A number of studies have shown that an accurate description of the electronic structure of the lowest-lying states of this molecule is particularly challenging due to the interplay between the strong dynamical correlation effects in the 3d shell and the delocalization of the 3d hole over the chlorine atoms. More generally, this problem is representative of the difficulties encountered when studying open-shell metal-containing molecular systems. Here, it is shown that qualitatively different results for the spin density distribution are obtained from the various quantum-mechanical approaches. At the DFT level, the spin density distribution is found to be very dependent on the functional employed. At the QMC level, Fixed-Node Diffusion Monte Carlo (FN-DMC) results are strongly dependent on the nodal structure of the trial wave function. Regarding wave function methods, most approaches not including a very high amount of dynamic correlation effects lead to a much too high localization of the spin density on the copper atom, in sharp contrast with DFT. To shed some light on these conflicting results Full CI-type (FCI) calculations using the 6-31G basis set and based on a selection process of the most important determinants, the so-called CIPSI approach (Configuration Interaction with Perturbative Selection done Iteratively) are performed. Quite remarkably, it is found that for this 63-electron molecule and a full CI space including about 10(18) determinants, the FCI limit can almost be reached. Putting all results together, a natural and coherent picture for the spin distribution is proposed.

Existence of time-dependent density-functional theory for open electronic systems: time-dependent holographic electron density theorem.

Science.gov (United States)

Zheng, Xiao; Yam, ChiYung; Wang, Fan; Chen, GuanHua

2011-08-28

We present the time-dependent holographic electron density theorem (TD-HEDT), which lays the foundation of time-dependent density-functional theory (TDDFT) for open electronic systems. For any finite electronic system, the TD-HEDT formally establishes a one-to-one correspondence between the electron density inside any finite subsystem and the time-dependent external potential. As a result, any electronic property of an open system in principle can be determined uniquely by the electron density function inside the open region. Implications of the TD-HEDT on the practicality of TDDFT are also discussed.

Watching proteins function with picosecond X-ray crystallography and molecular dynamics simulations.

Science.gov (United States)

Anfinrud, Philip

2006-03-01

Time-resolved electron density maps of myoglobin, a ligand-binding heme protein, have been stitched together into movies that unveil with molecular dynamics (MD) calculations and picosecond time-resolved X-ray structures provides single-molecule insights into mechanisms of protein function. Ensemble-averaged MD simulations of the L29F mutant of myoglobin following ligand dissociation reproduce the direction, amplitude, and timescales of crystallographically-determined structural changes. This close agreement with experiments at comparable resolution in space and time validates the individual MD trajectories, which identify and structurally characterize a conformational switch that directs dissociated ligands to one of two nearby protein cavities. This unique combination of simulation and experiment unveils functional protein motions and illustrates at an atomic level relationships among protein structure, dynamics, and function. In collaboration with Friedrich Schotte and Gerhard Hummer, NIH.

Postfragmentation density function for bacterial aggregates in laminar flow.

Science.gov (United States)

Byrne, Erin; Dzul, Steve; Solomon, Michael; Younger, John; Bortz, David M

2011-04-01

The postfragmentation probability density of daughter flocs is one of the least well-understood aspects of modeling flocculation. We use three-dimensional positional data of Klebsiella pneumoniae bacterial flocs in suspension and the knowledge of hydrodynamic properties of a laminar flow field to construct a probability density function of floc volumes after a fragmentation event. We provide computational results which predict that the primary fragmentation mechanism for large flocs is erosion. The postfragmentation probability density function has a strong dependence on the size of the original floc and indicates that most fragmentation events result in clumps of one to three bacteria eroding from the original floc. We also provide numerical evidence that exhaustive fragmentation yields a limiting density inconsistent with the log-normal density predicted in the literature, most likely due to the heterogeneous nature of K. pneumoniae flocs. To support our conclusions, artificial flocs were generated and display similar postfragmentation density and exhaustive fragmentation. ©2011 American Physical Society

Electronic and optical properties of families of polycyclic aromatic hydrocarbons: A systematic (time-dependent) density functional theory study

International Nuclear Information System (INIS)

Malloci, G.; Cappellini, G.; Mulas, G.; Mattoni, A.

2011-01-01

Graphical abstract: Electronic absorption spectra of the neutral molecules of the four PAH classes considered, as computed using the real-time real-space TD-DFT. Highlights: →We present a systematic comparative study of families of PAHs. → We computed electronic, optical, and transport properties as a function of size. → We considered oligoacenes, phenacenes, circumacenes, and oligorylenes. → Circumacenes have the best transport properties compared to the other classes. → Oligorylenes are much more efficient in absorbing low-energy photons. - Abstract: Homologous classes of polycyclic aromatic hydrocarbons (PAHs) in their crystalline state are among the most promising materials for organic opto-electronics. Following previous works on oligoacenes we present a systematic comparative study of the electronic, optical, and transport properties of oligoacenes, phenacenes, circumacenes, and oligorylenes. Using density functional theory (DFT) and time-dependent DFT we computed: (i) electron affinities and first ionization energies; (ii) quasiparticle correction to the highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) gap; (iii) molecular reorganization energies and (iv) electronic absorption spectra of neutral and ±1 charged systems. The excitonic effects are estimated by comparing the optical gap and the quasiparticle corrected HOMO-LUMO energy gap. For each molecular property computed, general trends as a function of molecular size and charge state are discussed. Overall, we find that circumacenes have the best transport properties, displaying a steeper decrease of the molecular reorganization energy at increasing sizes, while oligorylenes are much more efficient in absorbing low-energy photons in comparison to the other classes.

Molecular solar thermal energy storage in photoswitch oligomers increases energy densities and storage times.

Science.gov (United States)

Mansø, Mads; Petersen, Anne Ugleholdt; Wang, Zhihang; Erhart, Paul; Nielsen, Mogens Brøndsted; Moth-Poulsen, Kasper

2018-05-16

Molecular photoswitches can be used for solar thermal energy storage by photoisomerization into high-energy, meta-stable isomers; we present a molecular design strategy leading to photoswitches with high energy densities and long storage times. High measured energy densities of up to 559 kJ kg -1 (155 Wh kg -1 ), long storage lifetimes up to 48.5 days, and high quantum yields of conversion of up to 94% per subunit are demonstrated in norbornadiene/quadricyclane (NBD/QC) photo-/thermoswitch couples incorporated into dimeric and trimeric structures. By changing the linker unit between the NBD units, we can at the same time fine-tune light-harvesting and energy densities of the dimers and trimers so that they exceed those of their monomeric analogs. These new oligomers thereby meet several of the criteria to be met for an optimum molecule to ultimately enter actual devices being able to undergo closed cycles of solar light-harvesting, energy storage, and heat release.

Crystal density predictions for nitramines based on quantum chemistry

International Nuclear Information System (INIS)

Qiu Ling; Xiao Heming; Gong Xuedong; Ju Xuehai; Zhu Weihua

2007-01-01

An efficient and convenient method for predicting the crystalline densities of energetic materials was established based on the quantum chemical computations. Density functional theory (DFT) with four different basis sets (6-31G**, 6-311G**, 6-31+G**, and 6-311++G**) and various semiempirical molecular orbital (MO) methods have been employed to predict the molecular volumes and densities of a series of energetic nitramines including acyclic, monocyclic, and polycyclic/cage molecules. The relationships between the calculated values and experimental data were discussed in detail, and linear correlations were suggested and compared at different levels. The calculation shows that if the selected basis set is larger, it will expend more CPU (central processing unit) time, larger molecular volume and smaller density will be obtained. And the densities predicted by the semiempirical MO methods are all systematically larger than the experimental data. In comparison with other methods, B3LYP/6-31G** is most accurate and economical to predict the solid-state densities of energetic nitramines. This may be instructive to the molecular designing and screening novel HEDMs

Linking density functional and mode coupling models for supercooled liquids.

Science.gov (United States)

Premkumar, Leishangthem; Bidhoodi, Neeta; Das, Shankar P

2016-03-28

We compare predictions from two familiar models of the metastable supercooled liquid, respectively, constructed with thermodynamic and dynamic approaches. In the so called density functional theory the free energy F[ρ] of the liquid is a functional of the inhomogeneous density ρ(r). The metastable state is identified as a local minimum of F[ρ]. The sharp density profile characterizing ρ(r) is identified as a single particle oscillator, whose frequency is obtained from the parameters of the optimum density function. On the other hand, a dynamic approach to supercooled liquids is taken in the mode coupling theory (MCT) which predict a sharp ergodicity-non-ergodicity transition at a critical density. The single particle dynamics in the non-ergodic state, treated approximately, represents a propagating mode whose characteristic frequency is computed from the corresponding memory function of the MCT. The mass localization parameters in the above two models (treated in their simplest forms) are obtained, respectively, in terms of the corresponding natural frequencies depicted and are shown to have comparable magnitudes.

Linking density functional and mode coupling models for supercooled liquids

Energy Technology Data Exchange (ETDEWEB)

Premkumar, Leishangthem; Bidhoodi, Neeta; Das, Shankar P. [School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067 (India)

2016-03-28

We compare predictions from two familiar models of the metastable supercooled liquid, respectively, constructed with thermodynamic and dynamic approaches. In the so called density functional theory the free energy F[ρ] of the liquid is a functional of the inhomogeneous density ρ(r). The metastable state is identified as a local minimum of F[ρ]. The sharp density profile characterizing ρ(r) is identified as a single particle oscillator, whose frequency is obtained from the parameters of the optimum density function. On the other hand, a dynamic approach to supercooled liquids is taken in the mode coupling theory (MCT) which predict a sharp ergodicity-non-ergodicity transition at a critical density. The single particle dynamics in the non-ergodic state, treated approximately, represents a propagating mode whose characteristic frequency is computed from the corresponding memory function of the MCT. The mass localization parameters in the above two models (treated in their simplest forms) are obtained, respectively, in terms of the corresponding natural frequencies depicted and are shown to have comparable magnitudes.

Spherical harmonics analysis of surface density fluctuations of spherical ionic SDS and nonionic C12E8 micelles: A molecular dynamics study.

Science.gov (United States)

Yoshii, Noriyuki; Nimura, Yuki; Fujimoto, Kazushi; Okazaki, Susumu

2017-07-21

The surface structure and its fluctuation of spherical micelles were investigated using a series of density correlation functions newly defined by spherical harmonics and Legendre polynomials based on the molecular dynamics calculations. To investigate the influence of head-group charges on the micelle surface structure, ionic sodium dodecyl sulfate and nonionic octaethyleneglycol monododecylether (C 12 E 8 ) micelles were investigated as model systems. Large-scale density fluctuations were observed for both micelles in the calculated surface static structure factor. The area compressibility of the micelle surface evaluated by the surface static structure factor was tens-of-times larger than a typical value of a lipid membrane surface. The structural relaxation time, which was evaluated from the surface intermediate scattering function, indicates that the relaxation mechanism of the long-range surface structure can be well described by the hydrostatic approximation. The density fluctuation on the two-dimensional micelle surface has similar characteristics to that of three-dimensional fluids near the critical point.

Primary damage in tungsten using the binary collision approximation, molecular dynamic simulations and the density functional theory

International Nuclear Information System (INIS)

De Backer, A; Sand, A; Ortiz, C J; Domain, C; Olsson, P; Berthod, E; Becquart, C S

2016-01-01

The damage produced by primary knock-on atoms (PKA) in W has been investigated from the threshold displacement energy (TDE) where it produces one self interstitial atom–vacancy pair to larger energies, up to 100 keV, where a large molten volume is formed. The TDE has been determined in different crystal directions using the Born–Oppenheimer density functional molecular dynamics (DFT-MD). A significant difference has been observed without and with the semi-core electrons. Classical MD has been used with two different empirical potentials characterized as ‘soft’ and ‘hard’ to obtain statistics on TDEs. Cascades of larger energy have been calculated, with these potentials, using a model that accounts for electronic losses (Sand et al 2013 Europhys. Lett. 103 46003). Two other sets of cascades have been produced using the binary collision approximation (BCA): a Monte Carlo BCA using SDTrimSP (Eckstein et al 2011 SDTrimSP: Version 5.00. Report IPP 12/8) (similar to SRIM www.srim.org) and MARLOWE (RSICC Home Page. (https://rsicc.ornl.gov/codes/psr/psr1/psr-137.html) (accessed May, 2014)). The comparison of these sets of cascades gave a recombination distance equal to 12 Å which is significantly larger from the one we reported in Hou et al (2010 J. Nucl. Mater. 403 89) because, here, we used bulk cascades rather than surface cascades which produce more defects (Stoller 2002 J. Nucl. Mater. 307 935, Nordlund et al 1999 Nature 398 49). Investigations on the defect clustering aspect showed that the difference between BCA and MD cascades is considerably reduced after the annealing of the cascade debris at 473 K using our Object Kinetic Monte Carlo model, LAKIMOCA (Domain et al 2004 J. Nucl. Mater. 335 121). (paper)

Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D).

Science.gov (United States)

van de Streek, Jacco; Neumann, Marcus A

2014-12-01

In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom.

Discontinuous approximate molecular electronic wave-functions

International Nuclear Information System (INIS)

Stuebing, E.W.; Weare, J.H.; Parr, R.G.

1977-01-01

Following Kohn, Schlosser and Marcus and Weare and Parr an energy functional is defined for a molecular problem which is stationary in the neighborhood of the exact solution and permits the use of trial functions that are discontinuous. The functional differs from the functional of the standard Rayleigh--Ritz method in the replacement of the usual kinetic energy operators circumflex T(μ) with operators circumflex T'(μ) = circumflex T(μ) + circumflex I(μ) generates contributions from surfaces of nonsmooth behavior. If one uses the nabla PSI . nabla PSI way of writing the usual kinetic energy contributions, one must add surface integrals of the product of the average of nabla PSI and the change of PSI across surfaces of discontinuity. Various calculations are carried out for the hydrogen molecule-ion and the hydrogen molecule. It is shown that ab initio calculations on molecules can be carried out quite generally with a basis of atomic orbitals exactly obeying the zero-differential overlap (ZDO) condition, and a firm basis is thereby provided for theories of molecular electronic structure invoking the ZDO aoproximation. It is demonstrated that a valence bond theory employing orbitals exactly obeying ZDO can provide an adequate account of chemical bonding, and several suggestions are made regarding molecular orbital methods

New Methods of Esterification of Nanodiamonds in Fighting Breast Cancer—A Density Functional Theory Approach

Directory of Open Access Journals (Sweden)

Linda-Lucila Landeros-Martinez

2017-10-01

Full Text Available The use of nanodiamonds as anticancer drug delivery vehicles has received much attention in recent years. In this theoretical paper, we propose using different esterification methods for nanodiamonds. The monomers proposed are 2-hydroxypropanal, polyethylene glycol, and polyglicolic acid. Specifically, the hydrogen bonds, infrared (IR spectra, molecular polar surface area, and reactivity parameters are analyzed. The monomers proposed for use in esterification follow Lipinski’s rule of five, meaning permeability is good, they have good permeation, and their bioactivity is high. The results show that the complex formed between tamoxifen and nanodiamond esterified with polyglicolic acid presents the greatest number of hydrogen bonds and a good amount of molecular polar surface area. Calculations concerning the esterified nanodiamond and reactivity parameters were performed using Density Functional Theory with the M06 functional and the basis set 6–31G (d; for the esterified nanodiamond–Tamoxifen complexes, the semi-empirical method PM6 was used. The solvent effect has been taken into account by using implicit modelling and the conductor-like polarizable continuum model.

Density functional theory a practical introduction

CERN Document Server

Sholl, David

2009-01-01

Demonstrates how anyone in math, science, and engineering can master DFT calculations Density functional theory (DFT) is one of the most frequently used computational tools for studying and predicting the properties of isolated molecules, bulk solids, and material interfaces, including surfaces. Although the theoretical underpinnings of DFT are quite complicated, this book demonstrates that the basic concepts underlying the calculations are simple enough to be understood by anyone with a background in chemistry, physics, engineering, or mathematics. The authors show how the widespread availability of powerful DFT codes makes it possible for students and researchers to apply this important computational technique to a broad range of fundamental and applied problems. Density Functional Theory: A Practical Introduction offers a concise, easy-to-follow introduction to the key concepts and practical applications of DFT, focusing on plane-wave DFT. The authors have many years of experience introducing DFT to studen...

Infrared spectroscopy and density functional calculations on titanium-dinitrogen complexes

Science.gov (United States)

Yoo, Hae-Wook; Choi, Changhyeok; Cho, Soo Gyeong; Jung, Yousung; Choi, Myong Yong

2018-04-01

Titanium-nitrogen complexes were generated by laser ablated titanium (Ti) atoms and N2 gas molecules in this study. These complexes were isolated on the pre-deposited solid Ar matrix on the pre-cooled KBr window (T ∼ 5.4 K), allowing infrared spectra to be measured. Laser ablation experiments with 15N2 isotope provided distinct isotopic shifts in the infrared spectra that strongly implicated the formation of titanium-nitrogen complexes, Ti(NN)x. Density functional theory (DFT) calculations were employed to investigate the molecular structures, electronic ground state, relative energies, and IR frequencies of the anticipated Ti(NN)x complexes. Based on laser ablation experiments and DFT calculations, we were able to assign multiple Ti(NN)x (x = 1-6) species. Particularly, Ti(NN)5 and Ti(NN)6, which have high nitrogen content, may serve as good precursors in preparing polynitrogens.

Theoretical Probing of Weak Anion-Cation Interactions in Certain Pyridinium-Based Ionic Liquid Ion Pairs and the Application of Molecular Electrostatic Potential in Their Ionic Crystal Density Determination: A Comparative Study Using Density Functional Approach.

Science.gov (United States)

Joseph, Aswathy; Thomas, Vibin Ipe; Żyła, Gaweł; Padmanabhan, A S; Mathew, Suresh

2018-01-11

A comprehensive study on the structure, nature of interaction, and properties of six ionic pairs of 1-butylpyridinium and 1-butyl-4-methylpyridinium cations in combination with tetrafluoroborate (BF 4 - ), chloride (Cl - ), and bromide (Br - ) anions have been carried out using density functional theory (DFT). The anion-cation interaction energy (ΔE int ), thermochemistry values, theoretical band gap, molecular orbital energy order, DFT-based chemical activity descriptors [chemical potential (μ), chemical hardness (η), and electrophilicity index (ω)], and distribution of density of states (DOS) of these ion pairs were investigated. The ascendancy of the -CH 3 substituent at the fourth position of the 1-butylpyridinium cation ring on the values of ΔE int , theoretical band gap and chemical activity descriptors was evaluated. The ΔE int values were negative for all six ion pairs and were highest for Cl - containing ion pairs. The theoretical band gap value after -CH 3 substitution increased from 3.78 to 3.96 eV (for Cl - ) and from 2.74 to 2.88 eV (for Br - ) and decreased from 4.9 to 4.89 eV (for BF 4 - ). Ion pairs of BF 4 - were more susceptible to charge transfer processes as inferred from their significantly high η values and comparatively small difference in ω value after -CH 3 substitution. The change in η and μ values due to the -CH 3 substituent is negligibly small in all cases except for the ion pairs of Cl - . Critical-point (CP) analyses were carried out to investigate the AIM topological parameters at the interionic bond critical points (BCPs). The RDG isosurface analysis indicated that the anion-cation interaction was dominated by strong H cat ···X ani and C cat ···X ani interactions in ion pairs of Cl - and Br - whereas a weak van der Waal's effect dominated in ion pairs of BF 4 - . The molecular electrostatic potential (MESP)-based parameter ΔΔV min measuring the anion-cation interaction strength showed a good linear correlation with

Relationship of Quantum Entanglement to Density Functional Theory

OpenAIRE

Rajagopal, A. K.; Rendell, R. W.

2005-01-01

The maximum von Neumann entropy principle subject to given constraints of mean values of some physical observables determines the density matrix. Similarly the stationary action principle in the case of time-dependent (dissipative) situations under similar constraints yields the density matrix. The free energy and measures of entanglement are expressed in terms of such a density matrix and thus define respective functionals of the mean values. In the light of several model calculations, it is...

Two- and three-dimensional nonlocal density functional theory for inhomogeneous fluids. 1. Algorithms and parallelization

International Nuclear Information System (INIS)

Frink, L.J.D.; Salinger, A.G.

2000-01-01

Fluids adsorbed near surfaces, near macromolecules, and in porous materials are inhomogeneous, exhibiting spatially varying density distributions. This inhomogeneity in the fluid plays an important role in controlling a wide variety of complex physical phenomena including wetting, self-assembly, corrosion, and molecular recognition. One of the key methods for studying the properties of inhomogeneous fluids in simple geometries has been density functional theory (DFT). However, there has been a conspicuous lack of calculations in complex two- and three-dimensional geometries. The computational difficulty arises from the need to perform nested integrals that are due to nonlocal terms in the free energy functional. These integral equations are expensive both in evaluation time and in memory requirements; however, the expense can be mitigated by intelligent algorithms and the use of parallel computers. This paper details the efforts to develop efficient numerical algorithms so that nonlocal DFT calculations in complex geometries that require two or three dimensions can be performed. The success of this implementation will enable the study of solvation effects at heterogeneous surfaces, in zeolites, in solvated (bio)polymers, and in colloidal suspensions

Source-Free Exchange-Correlation Magnetic Fields in Density Functional Theory.

Science.gov (United States)

Sharma, S; Gross, E K U; Sanna, A; Dewhurst, J K

2018-03-13

Spin-dependent exchange-correlation energy functionals in use today depend on the charge density and the magnetization density: E xc [ρ, m]. However, it is also correct to define the functional in terms of the curl of m for physical external fields: E xc [ρ,∇ × m]. The exchange-correlation magnetic field, B xc , then becomes source-free. We study this variation of the theory by uniquely removing the source term from local and generalized gradient approximations to the functional. By doing so, the total Kohn-Sham moments are improved for a wide range of materials for both functionals. Significantly, the moments for the pnictides are now in good agreement with experiment. This source-free method is simple to implement in all existing density functional theory codes.

Molecular sieving through a graphene nanopore: non-equilibrium molecular dynamics simulation

Institute of Scientific and Technical Information of China (English)

Chengzhen Sun; Bofeng Bai

2017-01-01

Two-dimensional graphene nanopores have shown great promise as ultra-permeable molecular sieves based on their size-sieving effects.We design a nitrogen/hydrogen modified graphene nanopore and conduct a transient non-equilibrium molecular dynamics simulation on its molecular sieving effects.The distinct time-varying molecular crossing numbers show that this special nanopore can efficiently sieve CO2 and H2S molecules from CH4 molecules with high selectivity.By analyzing the molecular structure and pore functionalization-related molecular orientation and permeable zone in the nanopore,density distribution in the molecular adsorption layer on the graphene surface,as well as other features,the molecular sieving mechanisms of graphene nanopores are revealed.Finally,several implications on the design of highly-efficient graphene nanopores,especially for determining the porosity and chemical functionalization,as gas separation membranes are summarized based on the identified phenomena and mechanisms.

Exploring the surface reactivity of 3d metal endofullerenes: a density-functional theory study.

Science.gov (United States)

Estrada-Salas, Rubén E; Valladares, Ariel A

2009-09-24

Changes in the preferential sites of electrophilic, nucleophilic, and radical attacks on the pristine C60 surface with endohedral doping using 3d transition metal atoms were studied via two useful reactivity indices, namely the Fukui functions and the molecular electrostatic potential. Both of these were calculated at the density functional BPW91 level of theory with the DNP basis set. Our results clearly show changes in the preferential reactivity sites on the fullerene surface when it is doped with Mn, Fe, Co, or Ni atoms, whereas there are no significant changes in the preferential reactivity sites on the C60 surface upon endohedral doping with Cu and Zn atoms. Electron affinities (EA), ionization potentials (IP), and HOMO-LUMO gaps (Eg) were also calculated to complete the study of the endofullerene's surface reactivity. These findings provide insight into endofullerene functionalization, an important issue in their application.

Chemical hardness and density functional theory

Indian Academy of Sciences (India)

Unknown

RALPH G PEARSON. Chemistry Department, University of California, Santa Barbara, CA 93106, USA. Abstract. The concept of chemical hardness is reviewed from a personal point of view. Keywords. Hardness; softness; hard & soft acids bases (HSAB); principle of maximum hardness. (PMH) density functional theory (DFT) ...

Density functional and neural network analysis

DEFF Research Database (Denmark)

Jalkanen, K. J.; Suhai, S.; Bohr, Henrik

1997-01-01

Density functional theory (DFT) calculations have been carried out for hydrated L-alanine, L-alanyl-L-alanine and N-acetyl L-alanine N'-methylamide and examined with respect to the effect of water on the structure, the vibrational frequencies, vibrational absorption (VA) and vibrational circular...

Nuclear energy density functional from chiral pion-nucleon dynamics revisited

OpenAIRE

Kaiser, N.; Weise, W.

2009-01-01

We use a recently improved density-matrix expansion to calculate the nuclear energy density functional in the framework of in-medium chiral perturbation theory. Our calculation treats systematically the effects from $1\\pi$-exchange, iterated $1\\pi$-exchange, and irreducible $2\\pi$-exchange with intermediate $\\Delta$-isobar excitations, including Pauli-blocking corrections up to three-loop order. We find that the effective nucleon mass $M^*(\\rho)$ entering the energy density functional is iden...

Benchmark study of ionization potentials and electron affinities of armchair single-walled carbon nanotubes using density functional theory

Science.gov (United States)

Zhou, Bin; Hu, Zhubin; Jiang, Yanrong; He, Xiao; Sun, Zhenrong; Sun, Haitao

2018-05-01

The intrinsic parameters of carbon nanotubes (CNTs) such as ionization potential (IP) and electron affinity (EA) are closely related to their unique properties and associated applications. In this work, we demonstrated the success of optimal tuning method based on range-separated (RS) density functionals for both accurate and efficient prediction of vertical IPs and electron affinities (EAs) of a series of armchair single-walled carbon nanotubes C20n H20 (n  =  2–6) compared to the high-level IP/EA equation-of-motion coupled-cluster method with single and double substitutions (IP/EA-EOM-CCSD). Notably, the resulting frontier orbital energies (–ε HOMO and –ε LUMO) from the tuning method exhibit an excellent approximation to the corresponding IPs and EAs, that significantly outperform other conventional density functionals. In addition, it is suggested that the RS density functionals that possess both a fixed amount of exact exchange in the short-range and a correct long-range asymptotic behavior are suitable for calculating electronic structures of finite-sized CNTs. Next the performance of density functionals for description of various molecular properties such as chemical potential, hardness and electrophilicity are assessed as a function of tube length. Thanks to the efficiency and accuracy of this tuning method, the related behaviors of much longer armchair single-walled CNTs until C200H20 were studied. Lastly, the present work is proved to provide an efficient theoretical tool for future materials design and reliable characterization of other interesting properties of CNT-based systems.

Combination of Wavefunction and Density Functional Approximations for Describing Electronic Correlation

Science.gov (United States)

Garza, Alejandro J.

history in quantum chemistry (practical implementations have appeared in the literature since the 1970s). However, this kind of techniques have not achieved widespread use due to problems such as double counting of correlation and the symmetry dilemma--the fact that wavefunction methods respect the symmetries of Hamiltonian, while modern functionals are designed to work with broken symmetry densities. Here, particular mathematical features of pCCD and CCD0 are exploited to avoid these problems in an efficient manner. The two resulting families of approximations, denoted as pCCD+DFT and CCD0+DFT, are shown to be able to describe static and dynamic correlation in standard benchmark calculations. Furthermore, it is also shown that CCD0+DFT lends itself to combination with correlation from the direct random phase approximation (dRPA). Inclusion of dRPA in the long-range via the technique of range-separation allows for the description of dispersion correlation, the remaining part of the correlation. Thus, when combined with the dRPA, CCD0+DFT can account for all three-types of electron correlation that are necessary to accurately describe molecular systems. Lastly, applications of CCD0+DFT to actinide chemistry are considered in this work. The accuracy of CCD0+DFT for predicting equilibrium geometries and vibrational frequencies of actinide molecules and ions is assessed and compared to that of well-established quantum chemical methods. For this purpose, the f0 actinyl series (UO2 2+, NpO 23+, PuO24+, the isoelectronic NUN, and Thorium (ThO, ThO2+) and Nobelium (NoO, NoO2) oxides are studied. It is shown that the CCD0+DFT description of these species agrees with available experimental data and is comparable with the results given by the highest-level calculations that are possible for such heavy compounds while being, at least, an order of magnitude lower in computational cost.

One Pot Selective Arylation of 2-Bromo-5-Chloro Thiophene; Molecular Structure Investigation via Density Functional Theory (DFT), X-ray Analysis, and Their Biological Activities.

Science.gov (United States)

Rasool, Nasir; Kanwal, Aqsa; Rasheed, Tehmina; Ain, Quratulain; Mahmood, Tariq; Ayub, Khurshid; Zubair, Muhammad; Khan, Khalid Mohammed; Arshad, Muhammad Nadeem; M Asiri, Abdullah; Zia-Ul-Haq, Muhammad; Jaafar, Hawa Z E

2016-06-28

Synthesis of 2,5-bisarylthiophenes was accomplished by sequential Suzuki cross coupling reaction of 2-bromo-5-chloro thiophenes. Density functional theory (DFT) studies were carried out at the B3LYP/6-31G(d, p) level of theory to compare the geometric parameters of 2,5-bisarylthiophenes with those from X-ray diffraction results. The synthesized compounds are screened for in vitro bacteria scavenging abilities. At the concentration of 50 and 100 μg/mL, compounds 2b, 2c, 2d, 3c, and 3f with IC50-values of 51.4, 52.10, 58.0, 56.2, and 56.5 μg/mL respectively, were found most potent against E. coli. Among all the synthesized compounds 2a, 2d, 3c, and 3e with the least values of IC50 77, 76.26, 79.13 μg/mL respectively showed significant antioxidant activities. Almost all of the compounds showed good antibacterial activity against Escherichia coli, whereas 2-chloro-5-(4-methoxyphenyl) thiophene (2b) was found most active among all synthesized compound with an IC50 value of 51.4 μg/mL. All of the synthesized compounds were screened for nitric oxide scavenging activity as well. Frontier molecular orbitals (FMOs) and molecular electrostatic potentials of the target compounds were also studied theoretically to account for their relative reactivity.

Reduced density matrix functional theory at finite temperature

Energy Technology Data Exchange (ETDEWEB)

Baldsiefen, Tim

2012-10-15

Density functional theory (DFT) is highly successful in many fields of research. There are, however, areas in which its performance is rather limited. An important example is the description of thermodynamical variables of a quantum system in thermodynamical equilibrium. Although the finite-temperature version of DFT (FT-DFT) rests on a firm theoretical basis and is only one year younger than its brother, groundstate DFT, it has been successfully applied to only a few problems. Because FT-DFT, like DFT, is in principle exact, these shortcomings can be attributed to the difficulties of deriving valuable functionals for FT-DFT. In this thesis, we are going to present an alternative theoretical description of quantum systems in thermal equilibrium. It is based on the 1-reduced density matrix (1RDM) of the system, rather than on its density and will rather cumbersomly be called finite-temperature reduced density matrix functional theory (FT-RDMFT). Its zero-temperature counterpart (RDMFT) proved to be successful in several fields, formerly difficult to address via DFT. These fields include, for example, the calculation of dissociation energies or the calculation of the fundamental gap, also for Mott insulators. This success is mainly due to the fact that the 1RDM carries more directly accessible ''manybody'' information than the density alone, leading for example to an exact description of the kinetic energy functional. This sparks the hope that a description of thermodynamical systems employing the 1RDM via FT-RDMFT can yield an improvement over FT-DFT. Giving a short review of RDMFT and pointing out difficulties when describing spin-polarized systems initiates our work. We then lay the theoretical framework for FT-RDMFT by proving the required Hohenberg-Kohn-like theorems, investigating and determining the domain of FT-RDMFT functionals and by deriving several properties of the exact functional. Subsequently, we present a perturbative method to

Reduced density matrix functional theory at finite temperature

International Nuclear Information System (INIS)

Baldsiefen, Tim

2012-10-01

Density functional theory (DFT) is highly successful in many fields of research. There are, however, areas in which its performance is rather limited. An important example is the description of thermodynamical variables of a quantum system in thermodynamical equilibrium. Although the finite-temperature version of DFT (FT-DFT) rests on a firm theoretical basis and is only one year younger than its brother, groundstate DFT, it has been successfully applied to only a few problems. Because FT-DFT, like DFT, is in principle exact, these shortcomings can be attributed to the difficulties of deriving valuable functionals for FT-DFT. In this thesis, we are going to present an alternative theoretical description of quantum systems in thermal equilibrium. It is based on the 1-reduced density matrix (1RDM) of the system, rather than on its density and will rather cumbersomly be called finite-temperature reduced density matrix functional theory (FT-RDMFT). Its zero-temperature counterpart (RDMFT) proved to be successful in several fields, formerly difficult to address via DFT. These fields include, for example, the calculation of dissociation energies or the calculation of the fundamental gap, also for Mott insulators. This success is mainly due to the fact that the 1RDM carries more directly accessible ''manybody'' information than the density alone, leading for example to an exact description of the kinetic energy functional. This sparks the hope that a description of thermodynamical systems employing the 1RDM via FT-RDMFT can yield an improvement over FT-DFT. Giving a short review of RDMFT and pointing out difficulties when describing spin-polarized systems initiates our work. We then lay the theoretical framework for FT-RDMFT by proving the required Hohenberg-Kohn-like theorems, investigating and determining the domain of FT-RDMFT functionals and by deriving several properties of the exact functional. Subsequently, we present a perturbative method to iteratively construct

The molecular structure and vibrational spectra of N-(2,2-diphenylacetyl)- N'-(naphthalen-1yl)-thiourea by Hartree-Fock and density functional methods

Science.gov (United States)

Arslan, Hakan; Mansuroglu, Demet Sezgin; VanDerveer, Don; Binzet, Gun

2009-04-01

N-(2,2-Diphenylacetyl)- N'-(naphthalen-1yl)-thiourea (PANT) has been synthesized and characterized by elemental analysis, IR spectroscopy and 1H NMR spectroscopy. The crystal and molecular structure of the title compound has been determined from single crystal X-ray diffraction data. It crystallizes in the triclinic space group P-1, Z = 2 with a = 10.284(2) Å, b = 10.790(2) Å, c = 11.305(2) Å, α = 64.92(3)°, β = 89.88(3)°, γ = 62.99(3)°, V = 983.7(3) Å 3 and Dcalc = 1.339 Mg/m 3. The molecular structure, vibrational frequencies and infrared intensities of PANT were calculated by the Hartree-Fock and density functional theory methods (BLYP and B3LYP) using the 6-31G* basis set. The calculated geometric parameters were compared to the corresponding X-ray structure of the title compound. We obtained 22 stable conformers for the title compound; however Conformer 1 is approximately 9.53 kcal/mol more stable than Conformer 22. The comparison of the theoretical and experimental geometry of the title compound shows that the X-ray parameters fairly well reproduce the geometry of Conformer 17. The harmonic vibrations computed for this compound by the B3LYP/6-31G* method are in good agreement with the observed IR spectral data. Theoretical vibrational spectra of the title compound were interpreted by means of PEDs using the VEDA 4 program. A general better performance of the investigated methods was calculated by PAVF 1.0 program.

Improved density functional calculations for atoms, molecules and surfaces

International Nuclear Information System (INIS)

Fricke, B.; Anton, J.; Fritzsche, S.; Sarpe-Tudoran, C.

2005-01-01

The non-collinear and collinear descriptions within relativistic density functional theory is described. We present results of both non-collinear and collinear calculations for atoms, diatomic molecules, and some surface simulations. We find that the accuracy of our density functional calculations for the smaller systems is comparable to good quantum chemical calculations, and thus this method provides a sound basis for larger systems where no such comparison is possible. (author)

Relativistic density functional theory with picture-change corrected electron density based on infinite-order Douglas-Kroll-Hess method

Science.gov (United States)

Oyama, Takuro; Ikabata, Yasuhiro; Seino, Junji; Nakai, Hiromi

2017-07-01

This Letter proposes a density functional treatment based on the two-component relativistic scheme at the infinite-order Douglas-Kroll-Hess (IODKH) level. The exchange-correlation energy and potential are calculated using the electron density based on the picture-change corrected density operator transformed by the IODKH method. Numerical assessments indicated that the picture-change uncorrected density functional terms generate significant errors, on the order of hartree for heavy atoms. The present scheme was found to reproduce the energetics in the four-component treatment with high accuracy.

Time-dependent quantum fluid density functional theory of hydrogen ...

Indian Academy of Sciences (India)

WINTEC

density functional theory; quantum fluid dynamics. 1. Introduction ... dynamics of strongly non-linear interaction of atoms with intense ... theory and quantum fluid dynamics in real space. .... clear evidence of bond softening since density in the.

The enhanced spin-polarized transport behaviors through cobalt benzene-porphyrin-benzene molecular junctions: the effect of functional groups

Science.gov (United States)

Cheng, Jue-Fei; Zhou, Liping; Wen, Zhongqian; Yan, Qiang; Han, Qin; Gao, Lei

2017-05-01

The modification effects of the groups amino (NH2) and nitro (NO2) on the spin polarized transport properties of the cobalt benzene-porphyrin-benzene (Co-BPB) molecule coupled to gold (Au) nanowire electrodes are investigated by the nonequilibrium Green’s function method combined with the density functional theory. The calculation results show that functional groups can lead to the significant spin-filter effect, enhanced low-bias negative differential resistance (NDR) behavior and novel reverse rectifying effect in Co-BPB molecular junction. The locations and types of functional groups have distinct influences on spin-polarized transport performances. The configuration with NH2 group substituting H atom in central porphyrin ring has larger spin-down current compared to that with NO2 substitution. And Co-BPB molecule junction with NH2 group substituting H atom in side benzene ring shows reverse rectifying effect. Detailed analyses confirm that NH2 and NO2 group substitution change the spin-polarized transferred charge, which makes the highest occupied molecular orbitals (HOMO) of spin-down channel of Co-BPB closer to the Fermi level. And the shift of HOMO strengthens the spin-polarized coupling between the molecular orbitals and the electrodes, leading to the enhanced spin-polarized behavior. Our findings might be useful in the design of multi-functional molecular devices in the future.

Density functional theory for polymeric systems in 2D

International Nuclear Information System (INIS)

Słyk, Edyta; Bryk, Paweł; Roth, Roland

2016-01-01

We propose density functional theory for polymeric fluids in two dimensions. The approach is based on Wertheim’s first order thermodynamic perturbation theory (TPT) and closely follows density functional theory for polymers proposed by Yu and Wu (2002 J. Chem. Phys . 117 2368). As a simple application we evaluate the density profiles of tangent hard-disk polymers at hard walls. The theoretical predictions are compared against the results of the Monte Carlo simulations. We find that for short chain lengths the theoretical density profiles are in an excellent agreement with the Monte Carlo data. The agreement is less satisfactory for longer chains. The performance of the theory can be improved by recasting the approach using the self-consistent field theory formalism. When the self-avoiding chain statistics is used, the theory yields a marked improvement in the low density limit. Further improvements for long chains could be reached by going beyond the first order of TPT. (paper)

Central depression in nucleonic densities: Trend analysis in the nuclear density functional theory approach

Science.gov (United States)

Schuetrumpf, B.; Nazarewicz, W.; Reinhard, P.-G.

2017-08-01

Background: The central depression of nucleonic density, i.e., a reduction of density in the nuclear interior, has been attributed to many factors. For instance, bubble structures in superheavy nuclei are believed to be due to the electrostatic repulsion. In light nuclei, the mechanism behind the density reduction in the interior has been discussed in terms of shell effects associated with occupations of s orbits. Purpose: The main objective of this work is to reveal mechanisms behind the formation of central depression in nucleonic densities in light and heavy nuclei. To this end, we introduce several measures of the internal nucleonic density. Through the statistical analysis, we study the information content of these measures with respect to nuclear matter properties. Method: We apply nuclear density functional theory with Skyrme functionals. Using the statistical tools of linear least square regression, we inspect correlations between various measures of central depression and model parameters, including nuclear matter properties. We study bivariate correlations with selected quantities as well as multiple correlations with groups of parameters. Detailed correlation analysis is carried out for 34Si for which a bubble structure has been reported recently, 48Ca, and N =82 , 126, and 184 isotonic chains. Results: We show that the central depression in medium-mass nuclei is very sensitive to shell effects, whereas for superheavy systems it is firmly driven by the electrostatic repulsion. An appreciable semibubble structure in proton density is predicted for 294Og, which is currently the heaviest nucleus known experimentally. Conclusion: Our correlation analysis reveals that the central density indicators in nuclei below 208Pb carry little information on parameters of nuclear matter; they are predominantly driven by shell structure. On the other hand, in the superheavy nuclei there exists a clear relationship between the central nucleonic density and symmetry energy.

The maximal-density mass function for primordial black hole dark matter

Science.gov (United States)

Lehmann, Benjamin V.; Profumo, Stefano; Yant, Jackson

2018-04-01

The advent of gravitational wave astronomy has rekindled interest in primordial black holes (PBH) as a dark matter candidate. As there are many different observational probes of the PBH density across different masses, constraints on PBH models are dependent on the functional form of the PBH mass function. This complicates general statements about the mass functions allowed by current data, and, in particular, about the maximum total density of PBH. Numerical studies suggest that some forms of extended mass functions face tighter constraints than monochromatic mass functions, but they do not preclude the existence of a functional form for which constraints are relaxed. We use analytical arguments to show that the mass function which maximizes the fraction of the matter density in PBH subject to all constraints is a finite linear combination of monochromatic mass functions. We explicitly compute the maximum fraction of dark matter in PBH for different combinations of current constraints, allowing for total freedom of the mass function. Our framework elucidates the dependence of the maximum PBH density on the form of observational constraints, and we discuss the implications of current and future constraints for the viability of the PBH dark matter paradigm.

Validation of experimental molecular crystal structures with dispersion-corrected density functional theory calculations.

Science.gov (United States)

van de Streek, Jacco; Neumann, Marcus A

2010-10-01

This paper describes the validation of a dispersion-corrected density functional theory (d-DFT) method for the purpose of assessing the correctness of experimental organic crystal structures and enhancing the information content of purely experimental data. 241 experimental organic crystal structures from the August 2008 issue of Acta Cryst. Section E were energy-minimized in full, including unit-cell parameters. The differences between the experimental and the minimized crystal structures were subjected to statistical analysis. The r.m.s. Cartesian displacement excluding H atoms upon energy minimization with flexible unit-cell parameters is selected as a pertinent indicator of the correctness of a crystal structure. All 241 experimental crystal structures are reproduced very well: the average r.m.s. Cartesian displacement for the 241 crystal structures, including 16 disordered structures, is only 0.095 Å (0.084 Å for the 225 ordered structures). R.m.s. Cartesian displacements above 0.25 A either indicate incorrect experimental crystal structures or reveal interesting structural features such as exceptionally large temperature effects, incorrectly modelled disorder or symmetry breaking H atoms. After validation, the method is applied to nine examples that are known to be ambiguous or subtly incorrect.

Calculation of the structure and IR spectrum of methyl-b-D-glucopyranoside by density functional theory

International Nuclear Information System (INIS)

Babkov, L.M.; Korolevich, M.V.; Moisejkina, E.A.

2010-01-01

Structural-dynamic models of methyl-b-D-glucopyranoside have been constructed by a density functional method using a B3LYP functional in bases 6-31G(d) and 6-31+G(d,p). Energies have been minimized. Structures, dipole moments, polarizabilities, frequencies of normal modes in the harmonic approximation, and the intensity distribution in the molecular IR spectrum have been calculated. The calculation results have been compared with both the experimental spectra of methyl-b-D-glucopyranoside in the region 400-3700 cm -1 and data obtained within the framework of an approach that uses the classical valence-force method to calculate normal mode frequencies and the quantum-chemical CNDO/2 technique to calculate the electronic structure. (authors)

Zn Coordination Chemistry:  Development of Benchmark Suites for Geometries, Dipole Moments, and Bond Dissociation Energies and Their Use To Test and Validate Density Functionals and Molecular Orbital Theory.

Science.gov (United States)

Amin, Elizabeth A; Truhlar, Donald G

2008-01-01

We present nonrelativistic and relativistic benchmark databases (obtained by coupled cluster calculations) of 10 Zn-ligand bond distances, 8 dipole moments, and 12 bond dissociation energies in Zn coordination compounds with O, S, NH3, H2O, OH, SCH3, and H ligands. These are used to test the predictions of 39 density functionals, Hartree-Fock theory, and seven more approximate molecular orbital theories. In the nonrelativisitic case, the M05-2X, B97-2, and mPW1PW functionals emerge as the most accurate ones for this test data, with unitless balanced mean unsigned errors (BMUEs) of 0.33, 0.38, and 0.43, respectively. The best local functionals (i.e., functionals with no Hartree-Fock exchange) are M06-L and τ-HCTH with BMUEs of 0.54 and 0.60, respectively. The popular B3LYP functional has a BMUE of 0.51, only slightly better than the value of 0.54 for the best local functional, which is less expensive. Hartree-Fock theory itself has a BMUE of 1.22. The M05-2X functional has a mean unsigned error of 0.008 Å for bond lengths, 0.19 D for dipole moments, and 4.30 kcal/mol for bond energies. The X3LYP functional has a smaller mean unsigned error (0.007 Å) for bond lengths but has mean unsigned errors of 0.43 D for dipole moments and 5.6 kcal/mol for bond energies. The M06-2X functional has a smaller mean unsigned error (3.3 kcal/mol) for bond energies but has mean unsigned errors of 0.017 Å for bond lengths and 0.37 D for dipole moments. The best of the semiempirical molecular orbital theories are PM3 and PM6, with BMUEs of 1.96 and 2.02, respectively. The ten most accurate functionals from the nonrelativistic benchmark analysis are then tested in relativistic calculations against new benchmarks obtained with coupled-cluster calculations and a relativistic effective core potential, resulting in M05-2X (BMUE = 0.895), PW6B95 (BMUE = 0.90), and B97-2 (BMUE = 0.93) as the top three functionals. We find significant relativistic effects (∼0.01 Å in bond lengths, ∼0

Quantum mechanical and spectroscopic (FT-IR, FT-Raman) study, NBO analysis, HOMO-LUMO, first order hyperpolarizability and molecular docking study of methyl[(3R)-3-(2-methylphenoxy)-3-phenylpropyl]amine by density functional method

Science.gov (United States)

Kuruvilla, Tintu K.; Prasana, Johanan Christian; Muthu, S.; George, Jacob; Mathew, Sheril Ann

2018-01-01

Quantum chemical techniques such as density functional theory (DFT) have become a powerful tool in the investigation of the molecular structure and vibrational spectrum and are finding increasing use in application related to biological systems. The Fourier transform infrared (FT-IR) and Fourier transform Raman (FT-Raman) techniques are employed to characterize the title compound. The vibrational frequencies were obtained by DFT/B3LYP calculations with 6-31G(d,p) and 6-311 ++G(d,p) as basis sets. The geometry of the title compound was optimized. The vibrational assignments and the calculation of Potential Energy Distribution (PED) were carried out using the Vibrational Energy Distribution Analysis (VEDA) software. Molecular electrostatic potential was calculated for the title compound to predict the reactive sites for electrophilic and nucleophilic attack. In addition, the first-order hyperpolarizability, HOMO and LUMO energies, Fukui function and NBO were computed. The thermodynamic properties of the title compound were calculated at different temperatures, revealing the correlations between heat capacity (C), entropy (S) and enthalpy changes (H) with temperatures. Molecular docking studies were also conducted as part of this study. The paper further explains the experimental results which are in line with the theoretical calculations and provide optimistic evidence through molecular docking that the title compound can act as a good antidepressant. It also provides sufficient justification for the title compound to be selected as a good candidate for further studies related to NLO properties.

Synthesis, spectroscopic and structural characterization of 5-benzoyl-4-phenyl-2-methylthio-1H-pyrimidine with theoretical calculations using density functional theory

Science.gov (United States)

İnkaya, Ersin; Dinçer, Muharrem; Şahan, Emine; Yıldırım, İsmail

2013-10-01

In this paper, we will report a combined experimental and theoretical investigation of the molecular structure and spectroscopic parameters (FT-IR, 1H NMR, 13C NMR) of 5-benzoyl-4-phenyl-2-methylthio-1H-pyrimidine. The compound crystallizes in the triclinic space group P-1 with Z = 2. The molecular geometry was also optimized using density functional theory (DFT/B3LYP) method with the 6-311G(d,p) and 6-311++G(d,p) basis sets in ground state and compared with the experimental data. All the assignments of the theoretical frequencies were performed by potential energy distributions using VEDA 4 program. Information about the size, shape, charge density distribution and site of chemical reactivity of the molecules has been obtained by mapping electron density isosurface with electrostatic potential (ESP). Also, non-linear optical properties of the title compound were performed at B3LYP/6-311++G(d,p) level. The theoretical results showed an excellent agreement with the experimental values.

Ultra-stiff metallic glasses through bond energy density design.

Science.gov (United States)

Schnabel, Volker; Köhler, Mathias; Music, Denis; Bednarcik, Jozef; Clegg, William J; Raabe, Dierk; Schneider, Jochen M

2017-07-05

The elastic properties of crystalline metals scale with their valence electron density. Similar observations have been made for metallic glasses. However, for metallic glasses where covalent bonding predominates, such as metalloid metallic glasses, this relationship appears to break down. At present, the reasons for this are not understood. Using high energy x-ray diffraction analysis of melt spun and thin film metallic glasses combined with density functional theory based molecular dynamics simulations, we show that the physical origin of the ultrahigh stiffness in both metalloid and non-metalloid metallic glasses is best understood in terms of the bond energy density. Using the bond energy density as novel materials design criterion for ultra-stiff metallic glasses, we are able to predict a Co 33.0 Ta 3.5 B 63.5 short range ordered material by density functional theory based molecular dynamics simulations with a high bond energy density of 0.94 eV Å -3 and a bulk modulus of 263 GPa, which is 17% greater than the stiffest Co-B based metallic glasses reported in literature.

Molecular and Functional Neuroscience in Immunity.

Science.gov (United States)

Pavlov, Valentin A; Chavan, Sangeeta S; Tracey, Kevin J

2018-04-26

The nervous system regulates immunity and inflammation. The molecular detection of pathogen fragments, cytokines, and other immune molecules by sensory neurons generates immunoregulatory responses through efferent autonomic neuron signaling. The functional organization of this neural control is based on principles of reflex regulation. Reflexes involving the vagus nerve and other nerves have been therapeutically explored in models of inflammatory and autoimmune conditions, and recently in clinical settings. The brain integrates neuro-immune communication, and brain function is altered in diseases characterized by peripheral immune dysregulation and inflammation. Here we review the anatomical and molecular basis of the neural interface with immunity, focusing on peripheral neural control of immune functions and the role of the brain in the model of the immunological homunculus. Clinical advances stemming from this knowledge within the framework of bioelectronic medicine are also briefly outlined.

Benchmarks for electronically excited states: Time-dependent density functional theory and density functional theory based multireference configuration interaction

DEFF Research Database (Denmark)

Silva-Junior, Mario R.; Schreiber, Marko; Sauer, Stephan P. A.

2008-01-01

Time-dependent density functional theory (TD-DFT) and DFT-based multireference configuration interaction (DFT/MRCI) calculations are reported for a recently proposed benchmark set of 28 medium-sized organic molecules. Vertical excitation energies, oscillator strengths, and excited-state dipole...

Ab initio molecular dynamics model for density, elastic properties and short range order of Co-Fe-Ta-B metallic glass thin films

International Nuclear Information System (INIS)