Ab initio molecular dynamics simulation of laser melting of silicon
Silvestrelli, P.-L.; Alavi, A.; Parrinello, M.; Frenkel, D.
1996-01-01
The method of ab initio molecular dynamics, based on finite temperature density functional theory, is used to simulate laser heating of crystal silicon. We have found that a high concentration of excited electrons dramatically weakens the covalent bond. As a result, the system undergoes a melting tr
Serine Proteases an Ab Initio Molecular Dynamics Study
De Santis, L
1999-01-01
In serine proteases (SP's), the H-bond between His-57 and Asp-102, and that between Gly-193 and the transition state intermediate play a crucial role for enzymatic function. To shed light on the nature of these interactions, we have carried out ab initio molecular dynamics simulations on complexes representing adducts between the reaction intermediate and elastase (one protein belonging to the SP family). Our calculations indicate the presence of a low--barrier H-bond between His-57 and Asp-102, in complete agreement with NMR experiments on enzyme--transition state analog complexes. Comparison with an ab initio molecular dynamics simulation on a model of the substrate--enzyme adduct indicates that the Gly-193--induced strong stabilization of the intermediate is accomplished by charge/dipole interactions and not by H-bonding as previously suggested. Inclusion of the protein electric field in the calculations does not affect significantly the charge distribution.
Ab initio molecular dynamics using hybrid density functionals
Guidon, Manuel; Schiffmann, Florian; Hutter, Jürg; Vandevondele, Joost
2008-06-01
Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.
Bicanonical ab Initio Molecular Dynamics for Open Systems.
Frenzel, Johannes; Meyer, Bernd; Marx, Dominik
2017-08-08
Performing ab initio molecular dynamics simulations of open systems, where the chemical potential rather than the number of both nuclei and electrons is fixed, still is a challenge. Here, drawing on bicanonical sampling ideas introduced two decades ago by Swope and Andersen [ J. Chem. Phys. 1995 , 102 , 2851 - 2863 ] to calculate chemical potentials of liquids and solids, an ab initio simulation technique is devised, which introduces a fictitious dynamics of two superimposed but otherwise independent periodic systems including full electronic structure, such that either the chemical potential or the average fractional particle number of a specific chemical species can be kept constant. As proof of concept, we demonstrate that solvation free energies can be computed from these bicanonical ab initio simulations upon directly superimposing pure bulk water and the respective aqueous solution being the two limiting systems. The method is useful in many circumstances, for instance for studying heterogeneous catalytic processes taking place on surfaces where the chemical potential of reactants rather than their number is controlled and opens a pathway toward ab initio simulations at constant electrochemical potential.
Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics.
Makhov, Dmitry V; Glover, William J; Martinez, Todd J; Shalashilin, Dmitrii V
2014-08-07
We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as "cloning," in analogy to the "spawning" procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, "trains," as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.
Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Makhov, Dmitry V.; Shalashilin, Dmitrii V. [Department of Chemistry, University of Leeds, Leeds LS2 9JT (United Kingdom); Glover, William J.; Martinez, Todd J. [Department of Chemistry and The PULSE Institute, Stanford University, Stanford, California 94305, USA and SLAC National Accelerator Laboratory, Menlo Park, California 94025 (United States)
2014-08-07
We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as “cloning,” in analogy to the “spawning” procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, “trains,” as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.
Arntsen, Christopher; Chen, Chen; Voth, Gregory A.
2017-09-01
We present two new multiscale molecular dynamics (MS-RMD) models for the hydrated excess proton in water developed directly from ab initio molecular dynamics (AIMD) simulation data of the same system. The potential of mean force along the proton transfer reaction coordinate and radial distribution functions for the MS-RMD models are shown to faithfully reproduce those of AIMD. The models are developed using an algorithm based on relative entropy minimization, thus demonstrating the ability of the method to rapidly generate accurate and highly efficient reactive MD force fields.
Ab initio Molecular Dynamics Study on Small Carbon Nanotubes
Institute of Scientific and Technical Information of China (English)
叶林晖; 刘邦贵; 王鼎盛
2001-01-01
Ab initio molecular dynamics simulations are performed on small single wall nanotubes. By structural relaxation,the equilibrium C-C bond lengths and bond angles are determined. Our result shows that for both zigzag and armchair nanotubes there are two nonequivalent bond lengths. One bond stretches from that of the graphene sheet, while the other shrinks. Small variations on bond angles are also shown. Energy bands are calculated for the optimized structures. It is found that the intrinsic curvature of the very small nanotube greatly modifies the energy band which can no longer be well described in the tight-binding zone-folding picture. In our calculation very small nanotubes are metallic. The energy per atom fits quite well with the relation of E(R) = E0 + f/R2 even for the extreme small radius. The implications of the results on the properties of small nanotubes are discussed.
Exploring the free energy surface using ab initio molecular dynamics
Samanta, Amit; Morales, Miguel A.; Schwegler, Eric
2016-04-01
Efficient exploration of configuration space and identification of metastable structures in condensed phase systems are challenging from both computational and algorithmic perspectives. In this regard, schemes that utilize a set of pre-defined order parameters to sample the relevant parts of the configuration space [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006); J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B 112, 15742 (2008)] have proved useful. Here, we demonstrate how these order-parameter aided temperature accelerated sampling schemes can be used within the Born-Oppenheimer and the Car-Parrinello frameworks of ab initio molecular dynamics to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways. We have used these methods to identify the metastable structures and reaction pathways in SiO2 and Ti. In addition, we have used the string method [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002); L. Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] within the density functional theory to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hexagonal closed packed to face centered cubic phase transition in Ti.
Ab initio path integral ring polymer molecular dynamics: Vibrational spectra of molecules
Shiga, Motoyuki; Nakayama, Akira
2008-01-01
The path integral ring polymer molecular dynamics method is combined with 'on-the-fly' ab initio electronic structure calculations and applied to vibrational spectra of small molecules, LiH and H 2O, at the room temperature. The results are compared with those of the numerically exact solution and ab initio path integral centroid molecular dynamics calculation. The peak positions in the calculated spectra are found to be reasonable, showing the red-shift due to potential anharmonicity. This unification enables the investigation of real-time quantum dynamics of chemically complex molecular systems on the ab initio Born-Oppenheimer potential energy surface.
Ohta, Yasuhito; Ohta, Koji; Kinugawa, Kenichi
2004-01-01
An ab initio centroid molecular dynamics (CMD) method is developed by combining the CMD method with the ab initio molecular orbital method. The ab initio CMD method is applied to vibrational dynamics of diatomic molecules, H2 and HF. For the H2 molecule, the temperature dependence of the peak frequency of the vibrational spectral density is investigated. The results are compared with those obtained by the ab initio classical molecular dynamics method and exact quantum mechanical treatment. It is shown that the vibrational frequency obtained from the ab initio CMD approaches the exact first excitation frequency as the temperature lowers. For the HF molecule, the position autocorrelation function is also analyzed in detail. The present CMD method is shown to well reproduce the exact quantum result for the information on the vibrational properties of the system.
Conformational space of clindamycin studied by ab initio and full-atom molecular dynamics.
Kulczycka-Mierzejewska, Katarzyna; Trylska, Joanna; Sadlej, Joanna
2016-01-01
Molecular dynamics (MD) simulations allow determining internal flexibility of molecules at atomic level. Using ab initio Born-Oppenheimer molecular dynamics (BOMD), one can simulate in a reasonable time frame small systems with hundreds of atoms, usually in vacuum. With quantum mechanics/molecular mechanics (QM/MM) or full-atom molecular dynamics (FAMD), the influence of the environment can also be simulated. Here, we compare three types of MD calculations: ab initio BOMD, hybrid QM/MM, and classical FAMD. As a model system, we use a small antibiotic molecule, clindamycin, which is one of the lincosamide antibiotics. Clindamycin acquires two energetically stable forms and we investigated the transition between these two experimentally known conformers. We performed 60-ps BOMD simulations in vacuum, 50-ps QM/MM, and 100-ns FAMD in explicit water. The transition between two antibiotic conformers was observed using both BOMD and FAMD methods but was not noted in the QM/MM simulations.
Ab initio molecular dynamics study of Fe-containing smectites
Liu, X.; Meijer, E.J.; Lu, X.; Wang, R.
2010-01-01
In order to identify the influences imposed by Fe substitution, density functional theory-based Car-Parrinello molecular dynamics simulations were employed to study both oxidized and reduced Fe-bearing smectites. The following basic properties were investigated: local structures in the clay layer, h
X-ray absorption Debye-Waller factors from ab initio molecular dynamics
Vila, F. D.; Lindahl, V. E.; Rehr, J. J.
2012-01-01
An ab initio equation of motion method is introduced to calculate the temperature-dependent mean-square vibrational amplitudes σ2 which appear in the Debye-Waller factors in x-ray absorption, x-ray scattering, and related spectra. The approach avoids explicit calculations of phonon modes, and is based instead on calculations of the displacement-displacement time correlation function from ab initio density functional theory molecular dynamics simulations. The method also yields the vibrational density of states and thermal quantities such as the lattice free energy. Illustrations of the method are presented for a number of systems and compared with other methods and experiment.
Ab initio molecular dynamics study of liquid methanol
Handgraaf, J W; Meijer, E J; Handgraaf, Jan-Willem; Erp, Titus S. van; Meijer, Evert Jan
2003-01-01
We present a density-functional theory based molecular-dynamics study of the structural, dynamical, and electronic properties of liquid methanol under ambient conditions. The calculated radial distribution functions involving the oxygen and hydroxyl hydrogen show a pronounced hydrogen bonding and compare well with recent neutron diffraction data, except for an underestimate of the oxygen-oxygen correlation. We observe that, in line with infrared spectroscopic data, the hydroxyl stretching mode is significantly red-shifted in the liquid. A substantial enhancement of the dipole moment is accompanied by significant fluctuations due to thermal motion. Our results provide valuable data for improvement of empirical potentials.
Liquid Be, Ca and Ba. An orbital-free ab-initio molecular dynamics study
Energy Technology Data Exchange (ETDEWEB)
Rio, B. G. del; González, L. E. [Departamento de Física Teórica, Atómica y Óptica, Universidad de Valladolid, 47011 Valladolid (Spain)
2015-08-17
Several static and dynamic properties of liquid beryllium (l-Be), liquid calcium (l-Ca) and liquid barium (l-Ba) near their triple point have been evaluated by the orbital-free ab initio molecular dynamics method (OF-AIMD), where the interaction between valence electrons and ions is described by means of local pseudopotentials. These local pseudopotentials used were constructed through a force-matching process with those obtained from a Kohn-Sham ab initio molecular dynamics study (KS-AIMD) of a reduced system with non-local pseudopotentials. The calculated static structures show good agreement with the available experimental data, including an asymmetric second peak in the structure factor which has been linked to the existence of a marked icosahedral short-range order in the liquid. As for the dynamic properties, we obtain collective density excitations whose associated dispersion relations exhibit a positive dispersion.
Li ion diffusion mechanisms in LiFePO4: an ab initio molecular dynamics study.
Yang, Jianjun; Tse, John S
2011-11-17
The mechanisms for thermal (self) diffusion of Li ions in fully lithiated LiFePO(4) have been investigated with spin polarized ab initio molecular dynamics calculations. The effect of electron correlation is taken into account with the GGA+U formalism. It was found that Li ion diffusion is not a continuous process but through a series of jumps from one site to another. A dominant process is the hopping between neighboring Li sites around the PO(4) groups, which results in a zigzag pathway along the crystallographic b-axis. This observation is in agreement with a recent neutron diffraction experiment. A second process involves the collaborative movements of the Fe ions leading to the formation of antisite defects and promotes Li diffusion across the Li ion channels. The finding of the second mechanism demonstrates the benefit of ab initio molecular dynamics simulation in sampling diffusion pathways that may not be anticipated.
Ab initio molecular dynamics simulation of hydrogen fluoride at several thermodynamic states
DEFF Research Database (Denmark)
Kreitmeir, M.; Bertagnolli, H.; Mortensen, Jens Jørgen;
2003-01-01
Liquid hydrogen fluoride is a simple but interesting system for studies of the influence of hydrogen bonds on physical properties. We have performed ab initio molecular dynamics simulations of HF at several thermodynamic states, where we examine the microscopic structure of the liquid as well...... as its static and dynamic properties. The results obtained show good agreement with well established data, and, moreover, we were able to show significant changes within the structure depending on the system's temperature and density....
Projector augmented wave method: ab initio molecular dynamics with full wave functions
Indian Academy of Sciences (India)
Peter E Blöchl; Clemens J Först; Johannes Schimpl
2003-01-01
A brief introduction to the projector augmented wave method is given and recent developments are reviewed. The projector augmented wave method is an all-electron method for efficient ab initio molecular dynamics simulations with full wave functions. It extends and combines the traditions of existing augmented wave methods and the pseudopotential approach. Without sacrificing efficiency, the PAW method avoids transferability problems of the pseudopotential approach and it has been valuable to predict properties that depend on the full wave functions.
Simulation of Ab Initio Molecular Dynamics of Shock Wave on Copper
Institute of Scientific and Technical Information of China (English)
张林; 蔡灵仓; 向士凯; 经福谦; 陈栋泉
2003-01-01
The relation between particle velocity Up, up to 4 km/s, and shock wave velocity Us in copper has been simulated with ab initio molecular dynamics. The simulated relationship without considering the correction of zero-point and finite temperature effects is Us = 4.23 + 1.53Up. After considering the correction the relation becomes Us = 4.08 + 1.53Up, which is consistent with the experimental result.
Ab initio molecular dynamics simulations of the Li4F4 cluster
Heidenreich, A.; Sauer, J.
1995-12-01
Molecular dynamics simulations have been performed directly on the ab initio potential energy surface of Li4F4, which was generated within the Hartree-Fock approximation using a Gaussian basis set (split valence contraction). Trajectories at different temperatures yield the temperature dependence of the infrared spectra and the photoelectron spectra. For the infrared spectra comparison is made with MD results using a shell model ion pair potential function.
i-PI: A Python interface for ab initio path integral molecular dynamics simulations
Ceriotti, Michele; Manolopoulos, David E
2014-01-01
Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high pressure water.
Study of atomic structure of liquid Hg-In alloys using ab-initio molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Sharma, Nalini; Ahluwalia, P. K. [Department of Physics, Himachal Pradesh University, Shimla(HP)-171005 (India); Thakur, Anil [Department of Physics, Govt. P. G. College Solan (HP)-173212 (India)
2015-05-15
Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Five liquid Hg-In mixtures (Hg{sub 10}In{sub 90}, Hg{sub 30}In{sub 70}, Hg{sub 50}In{sub 50}, Hg{sub 70}In{sub 30} and Hg{sub 90}In{sub 10}) at 299K are considered. The radial distribution function g(r) and structure factor S(q) of considered alloys are compared with respective experimental results for liquid Hg (l-Hg) and (l-In). The radial distribution function g(r) shows the presence of short range order in the systems considered. Smooth curves of Bhatia-Thornton partial structure factors factor shows the presence of liquid state in the considered alloys.
Low-temperature metallic liquid hydrogen: an ab-initio path-integral molecular dynamics perspective
Chen, Ji; Li, Xin-Zheng; Zhang, Qianfan; Probert, Matthew; Pickard, Chris; Needs, Richard; Michaelides, Angelos; Wang, Enge
2013-03-01
Experiments and computer simulations have shown that the melting temperature of solid hydrogen drops with pressure above about 65 GPa, suggesting that a low temperature liquid state might exist. It has also been suggested that this liquid state might be non-molecular and metallic, although evidence for such behaviour is lacking. Using a combination of ab initio path-integral molecular dynamics and the two-phase methods, we have simulated the melting of solid hydrogen under finite temperatures. We found an atomic solid phase from 500 to 800 GPa which melts at < 200 K. Beyond this and up to pressures of 1,200 GPa a metallic atomic liquid is stable at temperatures as low as 50 K. The quantum motion of the protons is critical to the low melting temperature in this system as ab initio simulations with classical nuclei lead to a considerably higher melting temperature of ~300 K across the entire pressure range considered.
Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo
Energy Technology Data Exchange (ETDEWEB)
Zen, Andrea, E-mail: a.zen@ucl.ac.uk [Dipartimento di Fisica, “La Sapienza” - Università di Roma, piazzale Aldo Moro 5, 00185 Rome (Italy); London Centre for Nanotechnology, University College London, London WC1E 6BT (United Kingdom); Luo, Ye, E-mail: xw111luoye@gmail.com; Mazzola, Guglielmo, E-mail: gmazzola@phys.ethz.ch; Sorella, Sandro, E-mail: sorella@sissa.it [SISSA–International School for Advanced Studies, Via Bonomea 26, 34136 Trieste (Italy); Democritos Simulation Center CNR–IOM Istituto Officina dei Materiali, 34151 Trieste (Italy); Guidoni, Leonardo, E-mail: leonardo.guidoni@univaq.it [Dipartimento di Fisica, “La Sapienza” - Università di Roma, piazzale Aldo Moro 5, 00185 Rome (Italy); Dipartimento di Scienze Fisiche e Chimiche, Università degli Studi dell’ Aquila, via Vetoio, 67100 L’ Aquila (Italy)
2015-04-14
Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article, we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in good agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous density functional theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab initio simulations of complex chemical systems.
Ab-initio molecular dynamics simulation of liquid water by Quantum Monte Carlo
Zen, Andrea; Mazzola, Guglielmo; Guidoni, Leonardo; Sorella, Sandro
2014-01-01
Despite liquid water is ubiquitous in chemical reactions at roots of life and climate on earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in excellent agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous Density Functional Theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab-initio simulations of complex chemical systems.
Kubota, Yoshiyuki; Ohnuma, Toshiharu; Bučko, Tomáš
2017-03-01
The reaction of carbon dioxide (CO2) with aqueous 2-aminoethanol (MEA) has been investigated using both blue moon ensemble and metadynamics approaches combined with ab initio molecular dynamics (AIMD) simulations. The AIMD simulations predicted the spontaneous deprotonation of the intermediate compound, MEA zwitterion, and they were used to study two possible routes for subsequent proton transfer reactions: the formation of the protonated MEA and the formation of MEA carbamic acid. The free-energy curve depicted by blue moon ensemble technique supported the favorable deprotonation of MEA zwitterion. The overall free-energy profile showed the favorable formation of the ionic products of MEA carbamate ion and protonated MEA.
Improved Ab Initio Molecular Dynamics by Minimal Biasing with Experimental Data
White, Andrew D; Hocky, Glen M; Voth, Gregory A
2016-01-01
Accounting for electrons and nuclei simultaneously is a key goal of computer simulation via ab initio molecular dynamics (AIMD). However, AIMD is often unable to accurately reproduce the properties of systems such as water due to inaccuracies in the underlying electronic density functionals, shortcomings that are often addressed by added empirical corrections and/or increasing the simulation temperature. We present here a maximum-entropy-based approach to directly incorporate limited experimental data via a minimal bias. The biased AIMD simulations of both water and of an excess proton in water are shown to give significantly improved properties for both the biased and unbiased observables.
Ab initio Path Integral Molecular Dynamics Based on Fragment Molecular Orbital Method
Fujita, Takatoshi; Watanabe, Hirofumi; Tanaka, Shigenori
2009-10-01
We have developed an ab initio path integral molecular dynamics method based on the fragment molecular orbital method. This “FMO-PIMD” method can treat both nuclei and electrons quantum mechanically, and is useful to simulate large hydrogen-bonded systems with high accuracy. After a benchmark calculation for water monomer, water trimer and glycine pentamer have been studied using the FMO-PIMD method to investigate nuclear quantum effects on structure and molecular interactions. The applicability of the present approach is demonstrated through a number of test calculations.
Directory of Open Access Journals (Sweden)
S. Tolosa
2013-01-01
Full Text Available A procedure for the theoretical study of chemical reactions in solution by means of molecular dynamics simulations of aqueous solution at infinite dilution is described using ab initio solute-solvent potentials and TIP3P water model to describe the interactions. The procedure is applied to the study of neutral hydrolysis of various molecules (HCONH2, HNCO, HCNHNH2, and HCOOCH3 via concerted and water-assisted mechanisms. We used the solvent as a reaction coordinate and the free energy curves for the calculation of the properties related with the reaction mechanism, namely, reaction and activation energies.
Xiao, H. Y.; Weber, W. J.; Zhang, Y.; Zu, X. T.; Li, S.
2015-01-01
The response of titanate pyrochlores (A2Ti2O7, A = Y, Gd and Sm) to electronic excitation is investigated utilizing an ab initio molecular dynamics method. All the titanate pyrochlores are found to undergo a crystalline-to-amorphous structural transition under a low concentration of electronic excitations. The transition temperature at which structural amorphization starts to occur depends on the concentration of electronic excitations. During the structural transition, O2-like molecules are formed, and this anion disorder further drives cation disorder that leads to an amorphous state. This study provides new insights into the mechanisms of amorphization in titanate pyrochlores under laser, electron and ion irradiations. PMID:25660219
Pham, Thi Nu; Ono, Shota; Ohno, Kaoru
2016-04-01
Doing ab initio molecular dynamics simulations, we demonstrate a possibility of hydrogenation of carbon monoxide producing methanol step by step. At first, the hydrogen atom reacts with the carbon monoxide molecule at the excited state forming the formyl radical. Formaldehyde was formed after adding one more hydrogen atom to the system. Finally, absorption of two hydrogen atoms to formaldehyde produces methanol molecule. This study is performed by using the all-electron mixed basis approach based on the time dependent density functional theory within the adiabatic local density approximation for an electronic ground-state configuration and the one-shot GW approximation for an electronic excited state configuration.
Timko, Jeff; Kuyucak, Serdar
2012-11-28
Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K(+) ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K(+) ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K(+) ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K(+) ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.
i-PI: A Python interface for ab initio path integral molecular dynamics simulations
Ceriotti, Michele; More, Joshua; Manolopoulos, David E.
2014-03-01
Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high-pressure water. Catalogue identifier: AERN_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERN_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 138626 No. of bytes in distributed program, including test data, etc.: 3128618 Distribution format: tar.gz Programming language: Python. Computer: Multiple architectures. Operating system: Linux, Mac OSX, Windows. RAM: Less than 256 Mb Classification: 7.7. External routines: NumPy Nature of problem: Bringing the latest developments in the modelling of nuclear quantum effects with path integral molecular dynamics to ab initio electronic structure programs with minimal implementational effort. Solution method: State-of-the-art path integral molecular dynamics techniques are implemented in a Python interface. Any electronic structure code can be patched to receive the atomic
Geng, Hua Y
2014-01-01
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model, the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4 fold for a two-level implementation, and can be increased to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibration...
Energy Technology Data Exchange (ETDEWEB)
Geng, Hua Y., E-mail: huay.geng@gmail.com [National Key Laboratory of Shock Wave and Detonation Physics, Institute of Fluid Physics, CAEP, P.O. Box 919-102, Mianyang, Sichuan, 621900 (China); Department of Chemistry and Chemical Biology, Cornell University, Baker Laboratory, Ithaca, NY 14853 (United States)
2015-02-15
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model—the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of r{sub s}=0.912.
Geng, Hua Y.
2015-02-01
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model-the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of rs = 0.912.
Ab initio molecular dynamics of solvation effects on reactivity at electrified interfaces
Herron, Jeffrey A.; Morikawa, Yoshitada; Mavrikakis, Manos
2016-08-01
Using ab initio molecular dynamics as implemented in periodic, self-consistent (generalized gradient approximation Perdew-Burke-Ernzerhof) density functional theory, we investigated the mechanism of methanol electrooxidation on Pt(111). We investigated the role of water solvation and electrode potential on the energetics of the first proton transfer step, methanol electrooxidation to methoxy (CH3O) or hydroxymethyl (CH2OH). The results show that solvation weakens the adsorption of methoxy to uncharged Pt(111), whereas the binding energies of methanol and hydroxymethyl are not significantly affected. The free energies of activation for breaking the C-H and O-H bonds in methanol were calculated through a Blue Moon Ensemble using constrained ab initio molecular dynamics. Calculated barriers for these elementary steps on unsolvated, uncharged Pt(111) are similar to results for climbing-image nudged elastic band calculations from the literature. Water solvation reduces the barriers for both C-H and O-H bond activation steps with respect to their vapor-phase values, although the effect is more pronounced for C-H bond activation, due to less disruption of the hydrogen bond network. The calculated activation energy barriers show that breaking the C-H bond of methanol is more facile than the O-H bond on solvated negatively biased or uncharged Pt(111). However, with positive bias, O-H bond activation is enhanced, becoming slightly more facile than C-H bond activation.
Marsalek, Ondrej
2015-01-01
Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ab initio ring polymer contraction (AI-RPC) scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive pro...
Xiong, L H; Yoo, H; Lou, H B; Wang, X D; Cao, Q P; Zhang, D X; Jiang, J Z; Xie, H L; Xiao, T Q; Jeon, S; Lee, G W
2015-01-28
X-ray diffraction and electrostatic levitation measurements, together with the ab initio molecular dynamics simulation of liquid Al(75)Cu(25) alloy have been performed from 800 to 1600 K. Experimental and ab initio molecular dynamics simulation results match well with each other. No abnormal changes were experimentally detected in the specific heat capacity over total hemispheric emissivity and density curves in the studied temperature range for a bulk liquid Al(75)Cu(25) alloy measured by the electrostatic levitation technique. The structure factors gained by the ab initio molecular dynamics simulation precisely coincide with the experimental data. The atomic structure analyzed by the Honeycutt-Andersen index and Voronoi tessellation methods shows that icosahedral-like atomic clusters prevail in the liquid Al(75)Cu(25) alloy and the atomic clusters evolve continuously. All results obtained here suggest that no liquid-liquid transition appears in the bulk liquid Al(75)Cu(25) alloy in the studied temperature range.
Indian Academy of Sciences (India)
A NASSOUR
2016-09-01
In the present paper, an empirical embedded atom method (EAM) potential for gold–silicon (Au–Si) is developed by fitting to ab initio force (the ‘force matching’ method) and experimental data. The force database is generated within ab initio molecular dynamics (AIMD). The database includes liquid phase at various temperatures. Classical molecular dynamics simulations are performed to examine structural, coordination numbers, structure factors and dynamic properties of Au$_{81}$Si$_{19}$ alloy, with the interaction described via EAM model. The results are in good agreement with AIMD simulations and experimental data.
Kawashima, Yukio; Tachikawa, Masanori
2013-05-01
Ab initio path integral molecular dynamics simulation was performed to understand the nuclear quantum effect on the hydrogen bond of hydrogen malonate anion. Static calculation predicted the proton transfer barrier as 0.12 kcal/mol. Conventional ab initio molecular dynamics simulation at 300 K found proton distribution with a double peak on the proton transfer coordinate. Inclusion of thermal effect alone elongates the hydrogen bond length, which increases the barrier height. Inclusion of nuclear quantum effect washes out this barrier, and distributes a single broad peak in the center. H/D isotope effect on the proton transfer is also discussed.
Structural properties of iron nitride on Cu(100): An ab-initio molecular dynamics study
Heryadi, Dodi
2011-01-01
Due to their potential applications in magnetic storage devices, iron nitrides have been a subject of numerous experimental and theoretical investigations. Thin films of iron nitride have been successfully grown on different substrates. To study the structural properties of a single monolayer film of FeN we have performed an ab-initio molecular dynamics simulation of its formation on a Cu(100) substrate. The iron nitride layer formed in our simulation shows a p4gm(2x2) reconstructed surface, in agreement with experimental results. In addition to its structural properties, we are also able to determine the magnetization of this thin film. Our results show that one monolayer of iron nitride on Cu(100) is ferromagnetic with a magnetic moment of 1.67 μ B. © 2011 Materials Research Society.
Ionescu, Andrei R; Whitfield, Dennis M; Zgierski, Marek Z; Nukada, Tomoo
2006-12-29
We present a constrained ab initio molecular dynamics method that allows the modeling of the conformational interconversions of glycopyranosyl oxacarbenium ions. The model was successfully tested by estimating the barriers to ring inversion for two 4-substituted tetrahydropyranosyl oxacarbenium ions. The model was further extended to predict the pathways that connect the (4)H(3) half-chair conformation of 2,3,4,6-tetra-O-methyl-d-glucopyranosyl cation to its inverted (5)S(1) conformation and the (4)H(3) half-chair conformation of 2,3,4,6-tetra-O-methyl-d-mannopyranosyl cation to its inverted (3)E conformation. The modeled interconversion pathways reconcile a large body of experimental work on the acid-catalyzed hydrolysis of glycosides and the mechanisms of a number of glucosidases and mannosidases.
A unified scheme for ab initio molecular orbital theory and path integral molecular dynamics
Shiga, Motoyuki; Tachikawa, Masanori; Miura, Shinichi
2001-11-01
We present a general approach for accurate calculation of chemical substances which treats both nuclei and electrons quantum mechanically, adopting ab initio molecular orbital theory for the electronic structure and path integral molecular dynamics for the nuclei. The present approach enables the evaluation of physical quantities dependent on the nuclear configuration as well as the electronic structure, within the framework of Born-Oppenheimer adiabatic approximation. As an application, we give the path integral formulation of electric response properties—dipole moment and polarizability, which characterize the changes both in electronic structure and nuclear configuration at a given temperature when uniform electrostatic field is present. We also demonstrate the calculation of a water molecule using the present approach and the result of temperature and isotope effects is discussed.
Brandt, Erik G; Agosta, Lorenzo; Lyubartsev, Alexander P
2016-07-21
Small-sized wet TiO2 nanoparticles have been investigated by ab initio molecular dynamics simulations. Chemical and physical adsorption of water on the TiO2-water interface was studied as a function of water content, ranging from dry nanoparticles to wet nanoparticles with monolayer coverage of water. The surface reactivity was shown to be a concave function of water content and driven by surface defects. The local coordination number at the defect was identified as the key factor to decide whether water adsorption proceeds through dissociation or physisorption on the surface. A consistent picture of TiO2 nanoparticle wetting at the microscopic level emerges, which corroborates existing experimental data and gives further insight into the molecular mechanisms behind nanoparticle wetting. These calculations will facilitate the engineering of metal oxide nanoparticles with a controlled catalytic water activity.
Hydrogen bond dynamics in liquid water: Ab initio molecular dynamics simulation
Energy Technology Data Exchange (ETDEWEB)
Kim, Cheolhee; Kim, Eunae [College of Pharmacy, Chosun University, Gwangju (Korea, Republic of); Yeom, Min Sun [Korea Institute of Science and Technology Information, Daejeon (Korea, Republic of)
2016-01-15
The effect of intermolecular interaction on the distribution of the harmonic vibrational frequencies of water molecules was investigated through ab initio molecular dynamics simulations based on the Born-Oppenheimer approach. For single water, the effect of the dynamics of the oxygen atom in single water and the simulation time step on the frequency distribution were examined. The distributions of the OH stretching and HOH bending vibrational frequencies of liquid water were compared to those of single water. The probability distributions of the change in OH bond length and the lifetime of the dangling OH bond were also obtained. The distribution of the frequencies was strongly affected by the long lifetime of the dangling OH bond, resulting in the formation of hydrogen bonds between water molecules.
Femtosecond Laser Processing of Germanium: An Ab Initio Molecular Dynamics Study
Ji, Pengfei
2016-01-01
An ab initio molecular dynamics study of femtosecond laser processing of germanium is presented in this paper. The method based on the finite temperature density functional theory is adopted to probe the structural change, thermal motion of the atoms, dynamic property of the velocity autocorrelation, and the vibrational density of states. Starting from a cubic system at room temperature (300 K) containing 64 germanium atoms with an ordered arrangement of 1.132 nm in each dimension, the femtosecond laser processing is simulated by imposing the Nose Hoover thermostat to the electronic subsystem lasting for ~100 fs and continuing with microcanonical ensemble simulation of ~200 fs. The simulation results show solid, liquid and gas phases of germanium under adjusted intensities of the femtosecond laser irradiation. We find the irradiated germanium distinguishes from the usual germanium crystal by analyzing their melting and dynamic properties.
Communication: Improved ab initio molecular dynamics by minimally biasing with experimental data
White, Andrew D.; Knight, Chris; Hocky, Glen M.; Voth, Gregory A.
2017-01-01
Accounting for electrons and nuclei simultaneously is a powerful capability of ab initio molecular dynamics (AIMD). However, AIMD is often unable to accurately reproduce properties of systems such as water due to inaccuracies in the underlying electronic density functionals. This shortcoming is often addressed by added empirical corrections and/or increasing the simulation temperature. We present here a maximum-entropy approach to directly incorporate limited experimental data via a minimal bias. Biased AIMD simulations of water and an excess proton in water are shown to give significantly improved properties both for observables which were biased to match experimental data and for unbiased observables. This approach also yields new physical insight into inaccuracies in the underlying density functional theory as utilized in the unbiased AIMD.
Ab-initio molecular dynamics study of lanthanides in liquid sodium
Li, Xiang; Samin, Adib; Zhang, Jinsuo; Unal, C.; Mariani, R. D.
2017-02-01
To mitigate the fuel cladding chemical interaction (FCCI) phenomena in liquid sodium cooled fast reactors, a fundamental understanding of the lanthanide (Ln) transport through liquid Nasbnd Cs filled pores in Usbnd Zr fuel is necessary. In this study, we investigate three abundant Ln fission products diffusion coefficients in liquid Na at multiple temperatures. By utilization of Ab-initio Molecular Dynamics, the Ln diffusivities are found to be in the magnitude order of liquid diffusion (10-5cm2 /s) and the temperature dependence of the diffusivity for different lanthanides in liquid sodium was explored. It is also observed that dilute concentration of Pr and Nd led to a significant change in Na diffusivity. The structural and electronic properties of Nasbnd Ln metallic systems have been investigated. The total coordination number shows dependence on both the temperature and the composition.
Decarboxylation of furfural on Pd(111): Ab initio molecular dynamics simulations
Xue, Wenhua; Dang, Hongli; Shields, Darwin; Liu, Yingdi; Jentoft, Friederike; Resasco, Daniel; Wang, Sanwu
2013-03-01
Furfural conversion over metal catalysts plays an important role in the studies of biomass-derived feedstocks. We report ab initio molecular dynamics simulations for the decarboxylation process of furfural on the palladium surface at finite temperatures. We observed and analyzed the atomic-scale dynamics of furfural on the Pd(111) surface and the fluctuations of the bondlengths between the atoms in furfural. We found that the dominant bonding structure is the parallel structure in which the furfural plane, while slightly distorted, is parallel to the Pd surface. Analysis of the bondlength fluctuations indicates that the C-H bond is the aldehyde group of a furfural molecule is likely to be broken first, while the C =O bond has a tendency to be isolated as CO. Our results show that the reaction of decarbonylation dominates, consistent with the experimental measurements. Supported by DOE (DE-SC0004600). Simulations and calculations were performed on XSEDE's and NERSC's supercomputers.
Ab Initio Molecular Dynamics Simulations on Structural Properties of Liquid In20Sn80
Institute of Scientific and Technical Information of China (English)
ZHAO Gang; LIU Chang-Song; ZHU Zhen-Gang
2005-01-01
@@ Ab initio molecular dynamics simulations on liquid In20Sn80 alloy are carried out at six different temperatures from 798 K to 1193 K. The temperature dependences of binding energy, volume, pair-correlation function and structurefactor are studied. The first-peak position of our calculated pair correlation function is in agreement with the experimental data. A shoulder is reproduced in the high wave number side of the first peak in our calculated structure factor, implying the existence of the residual directional bonds of Sn atoms in liquid In20Sn80 alloy. The first-peak height of our calculated structure factor and the coordination number of Sn atom decrease more sharply in the low-temperature region from 798K to 986K than that in the high-temperature region from 986K to 1193K, suggesting that a discontinuous structural change may occur at around 986K in liquid In20Sn80 alloy.
Boese, A D; Martin, J M L; Marx, D; Chandra, Amalendu; Martin, Jan M.L.; Marx, Dominik
2003-01-01
The ammonia dimer (NH3)2 has been investigated using high--level ab initio quantum chemistry methods and density functional theory (DFT). The structure and energetics of important isomers is obtained to unprecedented accuracy without resorting to experiment. The global minimum of eclipsed C_s symmetry is characterized by a significantly bent hydrogen bond which deviates from linearity by about 20 degrees. In addition, the so-called cyclic C_{2h} structure is extremely close in energy on an overall flat potential energy surface. It is demonstrated that none of the currently available (GGA, meta--GGA, and hybrid) density functionals satisfactorily describe the structure and relative energies of this nonlinear hydrogen bond. We present a novel density functional, HCTH/407+, designed to describe this sort of hydrogen bond quantitatively on the level of the dimer, contrary to e.g. the widely used BLYP functional. This improved functional is employed in Car-Parrinello ab initio molecular dynamics simulations of liq...
Ab initio molecular dynamics study of collective dynamics in liquid Tl: Thermo-viscoelastic analysis
Bryk, Taras; Demchuk, Taras
2017-08-01
We studied collective dynamics of pure liquid metal Tl using a combination of ab initio molecular dynamics (AIMD) simulations and a thermoviscoelastic model applied to calculations of dynamic eigenmodes and dispersion of collective excitations in particular. We found that for liquid Tl at ambient pressure the transverse current spectral functions obtained directly in ab initio simulations for wave numbers larger than first pseudo-Brillouin-zone boundary contain two low-and high-frequency peaks that is an evidence of emergence of the unusually high-frequency transverse modes as it was observed before in liquid Li at very high pressures. The thermo-viscoelastic dynamic model shows perfect reproduction of the simulation-derived longitudinal current autocorrelation functions, and the acoustic eigenmodes are in nice agreement with the peaks of the longitudinal current spectral functions up to the first pseudo-Brillouin-zone boundary. The deviation of the dynamic eigenmodes from peak positions at higher wave numbers gives evidence of L-T coupling effects.
Shiga, Motoyuki; Tachikawa, Masanori; Miura, Shinichi
2000-12-01
We present an accurate calculational scheme for many-body systems composed of electrons and nuclei, by path integral molecular dynamics technique combined with the ab initio molecular orbital theory. Based upon the scheme, the simulation of a water molecule at room temperature is demonstrated, applying all-electron calculation at the Hartree-Fock level of theory.
Silvestrelli, P.-L.; Alavi, A.; Parrinello, M.; Frenkel, D.
1997-01-01
The method of ab initio molecular dynamics, based on finite-temperature density-functional theory, is used to simulate laser heating of crystalline silicon. We found that a high concentration of excited electrons dramatically weakens the covalent bonding. As a result the system undergoes a melting t
Mehandzhiyski, Aleksandar Y; Riccardi, Enrico; van Erp, Titus S; Trinh, Thuat T; Grimes, Brian A
2015-08-20
The interaction between a carboxylate anion (deprotonated propanoic acid) and the divalent Mg(2+), Ca(2+), Sr(2+), Ba(2+) metal ions is studied via ab initio molecular dynamics. The main focus of the study is the selectivity of the carboxylate-metal ion interaction in aqueous solution. The interaction is modeled by explicitly accounting for the solvent molecules on a DFT level. The hydration energies of the metal ions along with their diffusion and mobility coefficients are determined and a trend correlated with their ionic radius is found. Subsequently, a series of 16 constrained molecular dynamics simulations for every ion is performed, and the interaction free energy is obtained from thermodynamic integration of the forces between the metal ion and the carboxylate ion. The results indicate that the magnesium ion interacts most strongly with the carboxylate, followed by calcium, strontium, and barium. Because the interaction free energy is not enough to explain the selectivity of the reaction observed experimentally, more detailed analysis is performed on the simulation trajectories to understand the steric changes in the reaction complex during dissociation. The solvent dynamics appear to play an important role during the dissociation of the complex and also in the observed selectivity behavior of the divalent ions.
Chen, Chen; Arntsen, Christopher; Voth, Gregory A.
2017-10-01
Incorporation of quantum mechanical electronic structure data is necessary to properly capture the physics of many chemical processes. Proton hopping in water, which involves rearrangement of chemical and hydrogen bonds, is one such example of an inherently quantum mechanical process. Standard ab initio molecular dynamics (AIMD) methods, however, do not yet accurately predict the structure of water and are therefore less than optimal for developing force fields. We have instead utilized a recently developed method which minimally biases AIMD simulations to match limited experimental data to develop novel multiscale reactive molecular dynamics (MS-RMD) force fields by using relative entropy minimization. In this paper, we present two new MS-RMD models using such a parameterization: one which employs water with harmonic internal vibrations and another which uses anharmonic water. We show that the newly developed MS-RMD models very closely reproduce the solvation structure of the hydrated excess proton in the target AIMD data. We also find that the use of anharmonic water increases proton hopping, thereby increasing the proton diffusion constant.
Sumner, Isaiah; Iyengar, Srinivasan S
2007-10-18
We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.
Marsalek, Ondrej; Markland, Thomas E
2016-02-07
Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.
Brandt, Erik G.; Agosta, Lorenzo; Lyubartsev, Alexander P.
2016-07-01
Small-sized wet TiO2 nanoparticles have been investigated by ab initio molecular dynamics simulations. Chemical and physical adsorption of water on the TiO2-water interface was studied as a function of water content, ranging from dry nanoparticles to wet nanoparticles with monolayer coverage of water. The surface reactivity was shown to be a concave function of water content and driven by surface defects. The local coordination number at the defect was identified as the key factor to decide whether water adsorption proceeds through dissociation or physisorption on the surface. A consistent picture of TiO2 nanoparticle wetting at the microscopic level emerges, which corroborates existing experimental data and gives further insight into the molecular mechanisms behind nanoparticle wetting. These calculations will facilitate the engineering of metal oxide nanoparticles with a controlled catalytic water activity.Small-sized wet TiO2 nanoparticles have been investigated by ab initio molecular dynamics simulations. Chemical and physical adsorption of water on the TiO2-water interface was studied as a function of water content, ranging from dry nanoparticles to wet nanoparticles with monolayer coverage of water. The surface reactivity was shown to be a concave function of water content and driven by surface defects. The local coordination number at the defect was identified as the key factor to decide whether water adsorption proceeds through dissociation or physisorption on the surface. A consistent picture of TiO2 nanoparticle wetting at the microscopic level emerges, which corroborates existing experimental data and gives further insight into the molecular mechanisms behind nanoparticle wetting. These calculations will facilitate the engineering of metal oxide nanoparticles with a controlled catalytic water activity. Electronic supplementary information (ESI) available: Simulation data on equilibration of energies and structures (root-mean-square-deviations and
Hayes, Robin L; Paddison, Stephen J; Tuckerman, Mark E
2011-06-16
Trifluoromethanesulfonic acid hydrates provide a well-defined system to study proton dissociation and transport in perfluorosulfonic acid membranes, typically used as the electrolyte in hydrogen fuel cells, in the limit of minimal water. The triflic acid pentahydrate crystal (CF(3)SO(3)H·5H(2)O) is sufficiently aqueous that it contains an extended three-dimensional water network. Despite it being extended, however, long-range proton transport along the network is structurally unfavorable and would require considerable rearrangement. Nevertheless, the triflic acid pentahydrate crystal system can provide a clear picture of the preferred locations of local protonic defects in the water network, which provides insights about related structures in the disordered, low-hydration environment of perfluorosulfonic acid membranes. Ab initio molecular dynamics simulations reveal that the proton defect is most likely to transfer to the closest water that has the expected presolvation and only contains water in its first solvation shell. Unlike the tetrahydrate of triflic acid (CF(3)SO(3)H·4H(2)O), there is no evidence of the proton preferentially transferring to a water molecule bridging two of the sulfonate groups. However, this could be an artifact of the crystal structure since the only such water molecule is separated from the proton by long O-O distances. Hydrogen bonding criteria, using the two-dimensional potential of mean force, are extracted. Radial distribution functions, free energy profiles, radii of gyration, and the root-mean-square displacement computed from ab initio path integral molecular dynamics simulations reveal that quantum effects do significantly extend the size of the protonic defect and increase the frequency of proton transfer events by nearly 15%. The calculated IR spectra confirm that the dominant protonic defect mostly exists as an Eigen cation but contains some Zundel ion characteristics. Chain lengths and ring sizes determined from the
Ab initio molecular dynamics of the reaction of quercetin with superoxide radical
Lespade, Laure
2016-08-01
Superoxide plays an important role in biology but in unregulated concentrations it is implicated in a lot of diseases such as cancer or atherosclerosis. Antioxidants like flavonoids are abundant in plant and are good scavengers of superoxide radical. The modeling of superoxide scavenging by flavonoids from the diet still remains a challenge. In this study, ab initio molecular dynamics of the reaction of the flavonoid quercetin toward superoxide radical has been carried out using Car-Parrinello density functional theory. The study has proven different reactant solvation by modifying the number of water molecules surrounding superoxide. The reaction consists in the gift of a hydrogen atom of one of the hydroxyl groups of quercetin to the radical. When it occurs, it is relatively fast, lower than 100 fs. Calculations show that it depends largely on the environment of the hydroxyl group giving its hydrogen atom, the geometry of the first water layer and the presence of a certain number of water molecules in the second layer, indicating a great influence of the solvent on the reactivity.
Energy Technology Data Exchange (ETDEWEB)
Fischer, Sean A.; Apra, Edoardo; Govind, Niranjan; Hess, Wayne P.; El-Khoury, Patrick Z.
2017-02-03
Recent developments in nanophotonics have paved the way for achieving significant advances in the realm of single molecule chemical detection, imaging, and dynamics. In particular, surface-enhanced Raman scattering (SERS) is a powerful analytical technique that is now routinely used to identify the chemical identity of single molecules. Understanding how nanoscale physical and chemical processes affect single molecule SERS spectra and selection rules is a challenging task, and is still actively debated. Herein, we explore underappreciated chemical phenomena in ultrasensitive SERS. We observe a fluctuating excited electronic state manifold, governed by the conformational dynamics of a molecule (4,4’-dimercaptostilbene, DMS) interacting with a metallic cluster (Ag20). This affects our simulated single molecule SERS spectra; the time trajectories of a molecule interacting with its unique local environment dictates the relative intensities of the observable Raman-active vibrational states. Ab initio molecular dynamics of a model Ag20-DMS system are used to illustrate both concepts in light of recent experimental results.
Direct ab initio molecular dynamics study of the two photodissociation channels of formic acid
Energy Technology Data Exchange (ETDEWEB)
Kurosaki, Yuzuru; Yokoyama, Keiichi; Teranishi, Yoshiaki
2005-01-31
A total of {approx}1200 trajectories have been integrated for the two photodissociation channels of formic acid, HCOOH {yields} H{sub 2}O + CO (1) and HCOOH {yields} CO{sub 2} + H{sub 2} (2), which occur with 248 and 193 nm photons, using the direct ab initio molecular dynamics method at the RMP2(full)/cc-pVDZ level of theory. It was found that the percentage of the energy distributed to a relative translational mode in reaction is much larger than that in reaction . This is mainly due to the difference in the geometry of transition state (TS); the H{sub 2}O geometry in the TS of reaction was predicted to significantly deviate from the equilibrium one, whereas the CO{sub 2} and H{sub 2} geometries in the TS of reaction were found to be more similar to their equilibrium ones. It was also found that the product diatomic molecules, CO and H{sub 2}, are both vibrationally and rotationally excited. The calculated relative population of the vibrationally excited CO for the 248 nm photodissociation was consistent with experiment.
Ab initio path-integral molecular dynamics and the quantum nature of hydrogen bonds
Yexin, Feng; Ji, Chen; Xin-Zheng, Li; Enge, Wang
2016-01-01
The hydrogen bond (HB) is an important type of intermolecular interaction, which is generally weak, ubiquitous, and essential to life on earth. The small mass of hydrogen means that many properties of HBs are quantum mechanical in nature. In recent years, because of the development of computer simulation methods and computational power, the influence of nuclear quantum effects (NQEs) on the structural and energetic properties of some hydrogen bonded systems has been intensively studied. Here, we present a review of these studies by focussing on the explanation of the principles underlying the simulation methods, i.e., the ab initio path-integral molecular dynamics. Its extension in combination with the thermodynamic integration method for the calculation of free energies will also be introduced. We use two examples to show how this influence of NQEs in realistic systems is simulated in practice. Project supported by the National Natural Science Foundation of China (Grant Nos. 11275008, 91021007, and 10974012) and the China Postdoctoral Science Foundation (Grant No. 2014M550005).
Shimamura, Kohei; Shimojo, Fuyuki; Nakano, Aiichiro; Tanaka, Shigenori
2016-12-01
NH3 is an essential molecule as a nitrogen source for prebiotic amino acid syntheses such as the Strecker reaction. Previous shock experiments demonstrated that meteorite impacts on ancient oceans would have provided a considerable amount of NH3 from atmospheric N2 and oceanic H2O through reduction by meteoritic iron. However, specific production mechanisms remain unclear, and impact velocities employed in the experiments were substantially lower than typical impact velocities of meteorites on the early Earth. Here, to investigate the issues from the atomistic viewpoint, we performed multi-scale shock technique-based ab initio molecular dynamics simulations. The results revealed a rapid production of NH3 within several picoseconds after the shock, indicating that shocks with greater impact velocities would provide further increase in the yield of NH3. Meanwhile, the picosecond-order production makes one expect that the important nitrogen source precursors of amino acids were obtained immediately after the impact. It was also observed that the reduction of N2 proceeded according to an associative mechanism, rather than a dissociative mechanism as in the Haber-Bosch process.
Simulating ionic thermal trasport by equilibrium ab-initio molecular dynamics
Marcolongo, Aris; Umari, Paolo; Baroni, Stefano
2014-03-01
The Green-Kubo approach to thermal transport is often considered to be incompatible with ab-initio molecular dynamics (AIMD) because a suitable quantum-mechanical definition of the heat current is not readily available, due to the ill-definedness of the microscopic energy density to which it is related by the continuity equation. We argue that a similar difficulty actually exists in classical mechanics as well, and we address the conditions that have to be fulfilled in order for the physically well defined transport coefficients to be independent of the ill defined microscopic energy density from which they derive. We then provide two alternative approaches to calculating thermal conductivites from equilibrium AIMD. The first is based on the Green-Kubo formula, supplemented with an expression for the energy current, which is a generalization of Thouless' expression for the adiabatic charge current. The second approach, which avoids the recourse to an energy current altogether, rests on an efficient and accurate extrapolation to infinite wavelengths of the energy-density time correlation functions. The two methods are compared on a simple classical test bed, and their implementation in AIMD is demonstrated with the calculation of the thermal conductivity of simple fluids.
Xu, Cong-Qiao; Lee, Mal-Soon; Wang, Yang-Gang; Cantu, David C; Li, Jun; Glezakou, Vassiliki-Alexandra; Rousseau, Roger
2017-02-28
The structure, composition, and atomic distribution of nanoalloys under operating conditions are of significant importance for their catalytic activity. In the present work, we use ab initio molecular dynamics simulations to understand the structural behavior of Au-Pd nanoalloys supported on rutile TiO2 under different conditions. We find that the Au-Pd structure is strongly dependent on the redox properties of the support, originating from strong metal-support interactions. Under reducing conditions, Pd atoms are inclined to move toward the metal/oxide interface, as indicated by a significant increase of Pd-Ti bonds. This could be attributed to the charge localization at the interface that leads to Coulomb attractions to positively charged Pd atoms. In contrast, under oxidizing conditions, Pd atoms would rather stay inside or on the exterior of the nanoparticle. Moreover, Pd atoms on the alloy surface can be stabilized by hydrogen adsorption, forming Pd-H bonds, which are stronger than Au-H bonds. Our work offers critical insights into the structure and redox properties of Au-Pd nanoalloy catalysts under working conditions.
Kritayakornupong, Chinapong; Vchirawongkwin, Viwat; Rode, Bernd M
2010-06-01
An ab initio quantum mechanical charge field (QMCF) molecular dynamics simulation has been performed to study the structural and dynamical properties of a dilute aqueous HCl solution. The solute molecule HCl and its surrounding water molecules were treated at Hartree-Fock level in conjunction with Dunning double-zeta plus polarization function basis sets. The simulation predicts an average H-Cl bond distance of 1.28 A, which is in good agreement with the experimental value. The H(HCl)...O(w) and Cl(HCl)...H(w) distances of 1.84 and 3.51 A were found for the first hydration shell. At the hydrogen site of HCl, a single water molecule is the most preferred coordination, whereas an average coordination number of 12 water molecules of the full first shell was observed for the chloride site. The hydrogen bonding at the hydrogen site of HCl is weakened by proton transfer reactions and an associated lability of ligand binding. Two proton transfer processes were observed in the QMCF MD simulation, demonstrating acid dissociation of HCl. A weak structure-making/breaking effect of HCl in water is recognized from the mean residence times of 2.1 and 0.8 ps for ligands in the neighborhood of Cl and H sites of HCl, respectively. Copyright 2009 Wiley Periodicals, Inc.
Hydration of the cyanide ion: an ab initio quantum mechanical charge field molecular dynamics study.
Moin, Syed Tarique; Hofer, Thomas S
2014-12-21
This paper presents an ab initio quantum mechanical charge field molecular dynamics simulation study of the cyanide anion (CN(-)) in aqueous solution where hydrogen bond formation plays a dominant role in the hydration process. Preferential orientation of water hydrogens compared to oxygen atoms was quantified in terms of radial, angular as well as coordination number distributions. All structural results indicate that the water hydrogens are attracted towards CN(-) atoms, thus contributing to the formation of the hydration layer. Moreover, a clear picture of the local arrangement of water molecules around the ellipsoidal CN(-) ion is provided via angular-radial distribution and spatial distribution functions. Apart from the structural analysis, the evaluation of water dynamics in terms of ligand mean residence times and H-bond correlation functions indicates the weak structure making capacity of the CN(-) ion. The similar values of H-bond lifetimes obtained for the NHwat and CHwat bonds indicate an isokinetic behaviour of these H-bonds, since there is a very small difference in the magnitude of the lifetimes. On the other hand, the H-bond lifetimes between water molecules of the hydration shell, and between solute and solvent evidence the slightly stable hydration of the CN(-). Overall, the H-bonding dominates in the hydration process of the cyanide anion enabling it to become soluble in the aqueous environment associated to chemical and biological processes.
Elastic Properties of CaSiO3 Perovskite from ab initio Molecular Dynamics
Directory of Open Access Journals (Sweden)
Shigeaki Ono
2013-10-01
Full Text Available Ab initio molecular dynamics simulations were performed to investigate the elasticity of cubic CaSiO3 perovskite at high pressure and temperature. All three independent elastic constants for cubic CaSiO3 perovskite, C11, C12, and C44, were calculated from the computation of stress generated by small strains. The elastic constants were used to estimate the moduli and seismic wave velocities at the high pressure and high temperature characteristic of the Earth’s interior. The dependence of temperature for sound wave velocities decreased as the pressure increased. There was little difference between the estimated compressional sound wave velocity (VP in cubic CaSiO3 perovskite and that in the Earth’s mantle, determined by seismological data. By contrast, a significant difference between the estimated shear sound wave velocity (VS and that in the Earth’s mantle was confirmed. The elastic properties of cubic CaSiO3 perovskite cannot explain the properties of the Earth’s lower mantle, indicating that the cubic CaSiO3 perovskite phase is a minor mineral in the Earth’s lower mantle.
Ab Initio Molecular Dynamics of Dimerization and Clustering in Alkali Metal Vapors.
Chaban, Vitaly V; Prezhdo, Oleg V
2016-06-30
Alkali metals are known to form dimers, trimers, and tetramers in their vapors. The mechanism and regularities of this phenomenon characterize the chemical behavior of the first group elements. We report ab initio molecular dynamics (AIMD) simulations of the alkali metal vapors and characterize their structural properties, including radial distribution functions and atomic cluster size distributions. AIMD confirms formation of Men, where n ranges from 2 to 4. High pressure sharply favors larger structures, whereas high temperature decreases their fraction. Heavier alkali metals maintain somewhat larger fractions of Me2, Me3, and Me4, relative to isolated atoms. A single atom is the most frequently observed structure in vapors, irrespective of the element and temperature. Due to technical difficulties of working with high temperatures and pressures in experiments, AIMD is the most affordable method of research. It provides valuable understanding of the chemical behavior of Li, Na, K, Rb, and Cs, which can lead to development of new chemical reactions involving these metals.
An ab initio molecular dynamics study of S{sub o} ketene fragmentation.
Energy Technology Data Exchange (ETDEWEB)
Forsythe, K.; Gray, S.; Klippenstein, S.; Hall, G.; Chemistry; Case Western Reserve Univ.; BNL
2001-08-01
The dynamical origins of product state distributions in the unimolecular dissociation of S{sub 0} ketene, CH{sub 2}CO ({tilde X}{sup 1}A{sub 1}) {yields} CH{sub 2}({tilde a} {sup 1}A{sub 1}) + CO, are studied with ab initio molecular dynamics. We focus on rotational distributions associated with ground vibrational state fragments. Trajectories are integrated between an inner, variational transition state (TS) and separated fragments in both the dissociative and associative directions. The average rotational energy in both CO and CH{sub 2} fragments decreases during the motion from the TS to separated fragments. However, the CO distribution remains slightly hotter than phase space theory (PST) predictions, whereas that for CH{sub 2} ends up significantly colder than PST, in good agreement with experiment. Our calculations do not, however, reproduce the experimentally observed correlations between CH{sub 2} and CO rotational states, in which the simultaneous formation of low rotational levels of each fragment is suppressed relative to PST. A limited search for nonstatistical behavior in the strong interaction region also fails to explain this discrepancy.
2015-01-01
Colloidal quantum dots (QDs) exhibit highly desirable size- and shape-dependent properties for applications from electronic devices to imaging. Indium phosphide QDs have emerged as a primary candidate to replace the more toxic CdSe QDs, but production of InP QDs with the desired properties lags behind other QD materials due to a poor understanding of how to tune the growth process. Using high-temperature ab initio molecular dynamics (AIMD) simulations, we report the first direct observation o...
Energy Technology Data Exchange (ETDEWEB)
Ganster, P
2004-10-15
A calcium aluminosilicate glass of molar composition 67 % SiO{sub 2} - 12 % Al{sub 2}O{sub 3} - 21 % CaO was modelled by classical and ab initio molecular dynamics. The size effect study in classical MD shows that the systems of 100 atoms are more ordered than the larger ones. These effects are mainly due to the 3-body terms in the empirical potentials. Nevertheless, these effects are small and the structures generated are in agreement with experimental data. In such kind of glass, we denote an aluminium avoidance and an excess of non bridging oxygens which can be compensated by tri coordinated oxygens. When the dynamics of systems of 100 and 200 atoms is followed by ab initio MD, some local arrangements occurs (bond length, angular distributions). Thus, more realistic vibrational properties are obtained in ab initio MD. The modelling of thin films shows that aluminium atoms extend to the most external part of the surface and they are all tri-coordinated. Calcium atoms are set in the sub layer part of the surface and they produce a depolymerization of the network. In classical MD, tri-coordinated aluminium atoms produce an important electric field above the surface. With non bridging oxygens, they constitute attractive sites for single water molecules. (author)
Energy Technology Data Exchange (ETDEWEB)
Pluharova, Eva; Baer, Marcel D.; Mundy, Christopher J.; Schmidt, Burkhard; Jungwirth, Pavel
2014-07-03
Understanding specific ion effects on proteins remains a considerable challenge. N-methylacetamide serves as a useful proxy for the protein backbone that can be well characterized both experimentally and theoretically. The spectroscopic signatures in the amide I band reflecting the strength of the interaction of alkali cations and alkali earth dications with the carbonyl group remain difficult to assign and controversial to interpret. Herein, we directly compute the IR shifts corresponding to the binding of either sodium or calcium to aqueous N-methylacetamide using ab initio molecular dynamics simulations. We show that the two cations interact with aqueous N-methylacetamide with different affinities and in different geometries. Since sodium exhibits a weak interaction with the carbonyl group, the resulting amide I band is similar to an unperturbed carbonyl group undergoing aqueous solvation. In contrast, the stronger calcium binding results in a clear IR shift with respect to N-methylacetamide in pure water. Support from the Czech Ministry of Education (grant LH12001) is gratefully acknowledged. EP thanks the International Max-Planck Research School for support and the Alternative Sponsored Fellowship program at Pacific Northwest National Laboratory (PNNL). PJ acknowledges the Praemium Academie award from the Academy of Sciences. Calculations of the free energy profiles were made possible through generous allocation of computer time from the North-German Supercomputing Alliance (HLRN). Calculations of vibrational spectra were performed in part using the computational resources in the National Energy Research Supercomputing Center (NERSC) at Lawrence Berkeley National Laboratory. This work was supported by National Science Foundation grant CHE-0431312. CJM is supported by the U.S. Department of Energy`s (DOE) Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. PNNL is operated for the Department of Energy by Battelle. MDB is
Suter, James L.; Kabalan, Lara; Khader, Mahmoud; Coveney, Peter V.
2015-11-01
Ab initio molecular dynamics simulations have been performed to gain an understanding of the interfacial microscopic structure and reactivity of fully hydrated clay edges. The models studied include both micropore and interlayer water. We identify acidic sites through dissociation mechanisms; the resulting ions can be stabilized by both micropore and interlayer water. We find clay edges possess a complex amphoteric behavior, which depends on the face under consideration and the location of isomorphic substitution. For the neutral (1 1 0) surface, we do not observe any dissociation on the timescale accessible. The edge terminating hydroxyl groups participate in a hydrogen bonded network of water molecules that spans the interlayer between periodic images of the clay framework. With isomorphic substitutions in the tetrahedral layer of the (1 1 0) clay edge, we find the adjacent exposed apical oxygen behaves as a Brönsted base and abstracts a proton from a nearby water molecule, which in turn removes a proton from an AlOH2 group. With isomorphic substitutions in the octahedral layer of the (1 1 0) clay edge the adjacent exposed apical oxygen atom does not abstract a proton from the water molecules, but increases the number of hydrogen bonded water molecules (from one to two). Acid treated clays are likely to have both sites protonated. The (0 1 0) surface does not have the same interfacial hydrogen bonding structure; it is much less stable and we observe dissociation of half the terminal SiOH groups (tbnd Sisbnd Osbnd H → tbnd Sisbnd O- + H+) in our models. The resulting anions are stabilized by solvation from both micropore and interlayer water molecules. This suggests that, when fully hydrated, the (0 1 0) surface can act as a Brönsted acid, even at neutral pH.
Investigating the quartz (1010)/water interface using classical and ab initio molecular dynamics.
Skelton, A A; Wesolowski, D J; Cummings, P T
2011-07-19
Two different terminations of the (1010) surface of quartz (α and β) interacting with water are simulated by classical (CMD) (using two different force fields) and ab initio molecular dynamics (AIMD) and compared with previously published X-ray reflectivity (XR) experiments. Radial distribution functions between hydroxyl and water show good agreement between AIMD and CMD using the ClayFF force field for both terminations. The Lopes et al. (Lopes, P. E. M.; Murashov, V.; Tazi, M.; Demchuk, E.; MacKerell, A. D. J. Phys. Chem. B2006, 110, 2782-2792) force field (LFF), however, underestimates the extent of hydroxyl-water hydrogen bonding. The β termination is found to contain hydroxyl-hydroxyl hydrogen bonds; the quartz surface hydroxyl hydrogens and oxygens that hydrogen bond with each other exhibit greatly reduced hydrogen bonding to water. Conversely, the hydroxyl hydrogen and oxygens that are not hydrogen bonded to other surface hydroxyls but are connected to those that are show a considerable amount of hydrogen bonding to water. The electron density distribution of an annealed surface of quartz (1010) obtained by XR is in qualitative agreement with electron densities calculated by CMD and AIMD. In all simulation methods, the interfacial water peak appears farther from the surface than observed by XR. Agreement among AIMD, LFF, and XR is observed for the relaxation of the near-surface atoms; however, ClayFF shows a larger discrepancy. Overall, results show that for both terminations of (1010), LFF treats the near-surface structure more accurately whereas ClayFF treats the interfacial water structure more accurately. It is shown that the number of hydroxyl and water hydrogen bonds to the bridging Si-O-Si oxygens connecting the surface silica groups to the rest of the crystal is much greater for the α than the β termination. It is suggested that this may play a role in the greater resistance to dissolution of the β termination than that of the α termination.
Zhao, Jing; Wang, Mei; Fu, Aiyun; Yang, Hongfang; Bu, Yuxiang
2015-08-03
We present an ab initio molecular dynamics (AIMD) simulation study into the transfer dynamics of an excess electron from its cavity-shaped hydrated electron state to a hydrated nucleobase (NB)-bound state. In contrast to the traditional view that electron localization at NBs (G/A/C/T), which is the first step for electron-induced DNA damage, is related only to dry or prehydrated electrons, and a fully hydrated electron no longer transfers to NBs, our AIMD simulations indicate that a fully hydrated electron can still transfer to NBs. We monitored the transfer dynamics of fully hydrated electrons towards hydrated NBs in aqueous solutions by using AIMD simulations and found that due to solution-structure fluctuation and attraction of NBs, a fully hydrated electron can transfer to a NB gradually over time. Concurrently, the hydrated electron cavity gradually reorganizes, distorts, and even breaks. The transfer could be completed in about 120-200 fs in four aqueous NB solutions, depending on the electron-binding ability of hydrated NBs and the structural fluctuation of the solution. The transferring electron resides in the π*-type lowest unoccupied molecular orbital of the NB, which leads to a hydrated NB anion. Clearly, the observed transfer of hydrated electrons can be attributed to the strong electron-binding ability of hydrated NBs over the hydrated electron cavity, which is the driving force, and the transfer dynamics is structure-fluctuation controlled. This work provides new insights into the evolution dynamics of hydrated electrons and provides some helpful information for understanding the DNA-damage mechanism in solution. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Electronic absorption and resonance Raman spectroscopy from ab initio quantum molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Ben-Nun, M.; Martinez, T.J.
1999-12-09
The absorption and resonance Raman excitation profiles of ethylene following {pi} {yields} {pi}* excitation and taking full account of anharmonicity and Duschinsky rotation effects are calculated from first principles molecular dynamics using the ab initio multiple spawning (AIMS) method and a correlation function approach. The AIMS method solves the nuclear and electronic Schroedinger equations simultaneously and it associates a unique nuclear wave function with each electronic state. The compound absorption spectrum has a full width at half maximum of 9,800 and 1,300 cm{sup {minus}1} (in agreement with the experimental value, 9,500 cm{sup {minus}1}) and a high-frequency structure spaced by 800 and 10 cm{sup {minus}1}, attributed to C{double{underscore}bond}C stretching. The resonance Raman excitation profile exhibits fundamental activity in all totally symmetric modes with the C{double{underscore}bond}C stretching mode being the most dominant. In addition, overtone activity is observed in the torsional motion, out-of-plane wagging motions and the out-of-plane rocking motions. The activity is consistent with the observation that the first excited state is twisted and one of the CH{sub 2} groups is pyramidalized. The coordinate dependence of the electronic transition dipole is investigated, and they find that it depends very strongly on the torsional coordinate and less so on the pyramidalization and C{double{underscore}bond}C stretching coordinates. However, within the approximations used in this paper this dependence does not influence the spectra significantly and the Condon approximation is quite accurate.
Diffusion within α-CuI studied using ab initio molecular dynamics simulations
Mohn, Chris E.; Stølen, Svein; Hull, Stephen
2009-08-01
The structure and dynamics of superionic α-CuI are studied in detail by means of ab initio Born-Oppenheimer molecular dynamics simulations. The extreme cation disorder and a soft immobile face centred cubic sublattice are evident from the highly diffuse atomic density profiles. The Cu-Cu pair distribution function and distribution of Cu-I-Cu bond angles possess distinct peaks at 2.6 Å and 60° respectively, which are markedly lower than the values expected from the average cationic density, pointing to the presence of pronounced short-range copper-copper correlations. Comparison with lattice static calculations shows that these correlations and the marked shift in the cationic density profile in the lang111rang directions are associated with a locally distorted cation sublattice, and that the movements within the tetrahedral cavities involve rapid jumps into and out of shallow basins on the system potential energy surface. On average, the iodines are surrounded by three coppers within their first coordination shell, with the fourth copper being located in a transition zone between two neighbouring iodine cavities. However, time-resolved analysis reveals that the local structure actually involves a mixture of threefold-, fourfold- and fivefold-coordinated iodines. Examination of the ionic trajectories shows that the copper ions jump rapidly to nearest neighbouring tetrahedral cavities (aligned in the lang100rang directions) following a markedly curved trajectory and often involving short-lived (~1 ps) interstitial positions. The nature of the correlated diffusion underlying the unusually high fraction of coppers with short residence time can be attributed to the presence of a large number of 'unsuccessful' jumps and the likelihood of cooperative motion of pairs of coppers. The calculated diffusion coefficient at 750 K, DCu = 2.8 × 10-5 cm2 s-1, is in excellent agreement with that found experimentally.
POLY-ANIONS IN LIQUID CSPB - AN AB-INITIO MOLECULAR-DYNAMICS SIMULATION
DEWIJS, GA; PASTORE, G; SELLONI, A; VANDERLUGT, W
1994-01-01
Most alkali-group-IV liquid alloys exhibit strong chemical effects leading to well-defined equiatomic compounds. This is generally explained by the survival of particular clusters of lead-''Zintl'' ions-in the liquid state. We report on an ab initio simulation of liquid CsPb, for which the chemical
An analysis of hydrated proton diffusion in ab initio molecular dynamics
Energy Technology Data Exchange (ETDEWEB)
Tse, Ying-Lung Steve; Voth, Gregory A., E-mail: gavoth@uchicago.edu [Department of Chemistry, James Franck Institute, and Computation Institute, University of Chicago, Chicago, Illinois 60637 (United States); Knight, Chris [Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439 (United States)
2015-01-07
A detailed understanding of the inherently multiscale proton transport process raises a number of scientifically challenging questions. For example, there remain many (partially addressed) questions on the molecular mechanism for long-range proton migration and the potential for the formation of long-lived traps giving rise to burst-and-rest proton dynamics. Using results from a sizeable collection of ab initio molecular dynamics (AIMD) simulations (totaling ∼2.7 ns) with various density functional approximations (Becke-Lee-Yang-Parr (BLYP), BLYP–D3, Hamprecht-Cohen-Tozer-Handy, B3LYP) and temperatures (300–330 K), equilibrium and dynamical properties of one excess proton and 128 water molecules are studied. Two features in particular (concerted hops and weak hydrogen-bond donors) are investigated to identify modes in the system that are strongly correlated with the onset of periods of burst-and-rest dynamics. The question of concerted hops seeks to identify those time scales over which long-range proton transport can be classified as a series of sequential water hopping events or as a near-simultaneous concerted process along compressed water wires. The coupling of the observed burst-and-rest dynamics with motions of a fourth neighboring water molecule (a weak hydrogen-bond donor) solvating the protonated water molecule is also investigated. The presence (absence) of hydrogen bonds involving this fourth water molecule before and after successful proton hopping events is found to be strongly correlated with periods of burst (rest) dynamics (and consistent with pre-solvation concepts). By analyzing several realizations of the AIMD trajectories on the 100-ps time scale, convergence of statistics can be assessed. For instance, it was observed that the probability for a fourth water molecule to approach the hydronium, if not already proximal at the beginning of the lifetime of the hydronium, is very low, indicative of the formation of stable void regions
An analysis of hydrated proton diffusion in ab initio molecular dynamics
Tse, Ying-Lung Steve; Knight, Chris; Voth, Gregory A.
2015-01-01
A detailed understanding of the inherently multiscale proton transport process raises a number of scientifically challenging questions. For example, there remain many (partially addressed) questions on the molecular mechanism for long-range proton migration and the potential for the formation of long-lived traps giving rise to burst-and-rest proton dynamics. Using results from a sizeable collection of ab initio molecular dynamics (AIMD) simulations (totaling ˜2.7 ns) with various density functional approximations (Becke-Lee-Yang-Parr (BLYP), BLYP-D3, Hamprecht-Cohen-Tozer-Handy, B3LYP) and temperatures (300-330 K), equilibrium and dynamical properties of one excess proton and 128 water molecules are studied. Two features in particular (concerted hops and weak hydrogen-bond donors) are investigated to identify modes in the system that are strongly correlated with the onset of periods of burst-and-rest dynamics. The question of concerted hops seeks to identify those time scales over which long-range proton transport can be classified as a series of sequential water hopping events or as a near-simultaneous concerted process along compressed water wires. The coupling of the observed burst-and-rest dynamics with motions of a fourth neighboring water molecule (a weak hydrogen-bond donor) solvating the protonated water molecule is also investigated. The presence (absence) of hydrogen bonds involving this fourth water molecule before and after successful proton hopping events is found to be strongly correlated with periods of burst (rest) dynamics (and consistent with pre-solvation concepts). By analyzing several realizations of the AIMD trajectories on the 100-ps time scale, convergence of statistics can be assessed. For instance, it was observed that the probability for a fourth water molecule to approach the hydronium, if not already proximal at the beginning of the lifetime of the hydronium, is very low, indicative of the formation of stable void regions. Furthermore
Directory of Open Access Journals (Sweden)
G.M. Bhuiyan
2012-10-01
Full Text Available Several static and dynamic properties of liquid Cu, Ag and Au at thermodynamic states near their respective melting points, have been evaluated by means of the orbital free ab-initio molecular dynamics simulation method. The calculated static structure shows good agreement with the available X-ray and neutron diffraction data. As for the dynamic properties, the calculated dynamic structure factors point to the existence of collective density excitations along with a positive dispersion for l-Cu and l-Ag. Several transport coefficients have been obtained which show a reasonable agreement with the available experimental data.
Lasoroski, Aurélie; Vuilleumier, Rodolphe; Pollet, Rodolphe
2014-07-07
The electronic relaxation of gadolinium complexes used as MRI contrast agents was studied theoretically by following the short time evolution of zero-field-splitting parameters. The statistical analysis of ab initio molecular dynamics trajectories provided a clear separation between static and transient contributions to the zero-field-splitting. For the latter, the correlation time was estimated at approximately 0.1 ps. The influence of the ligand was also probed by replacing one pendant arm of our reference macrocyclic complex by a bulkier phosphonate arm. In contrast to the transient contribution, the static zero-field-splitting was significantly influenced by this substitution.
Closser, Kristina D; Gessner, Oliver; Head-Gordon, Martin
2014-04-07
The dynamics resulting from electronic excitations of helium clusters were explored using ab initio molecular dynamics. The simulations were performed with configuration interaction singles and adiabatic classical dynamics coupled to a state-following algorithm. 100 different configurations of He7 were excited into the 2s and 2p manifold for a total of 2800 trajectories. While the most common outcome (90%) was complete fragmentation to 6 ground state atoms and 1 excited state atom, 3% of trajectories yielded bound, He2(*), and <0.5% yielded an excited helium trimer. The nature of the dynamics, kinetic energy release, and connections to experiments are discussed.
Bhuiyan, G M; González, D J; 10.5488/CMP.15.33604
2012-01-01
Several static and dynamic properties of liquid Cu, Ag and Au at thermodynamic states near their respective melting points, have been evaluated by means of the orbital free ab-initio molecular dynamics simulation method. The calculated static structure shows good agreement with the available X-ray and neutron diffraction data. As for the dynamic properties, the calculated dynamic structure factors point to the existence of collective density excitations along with a positive dispersion for l-Cu and l-Ag. Several transport coefficients have been obtained which show a reasonable agreement with the available experimental data.
Kakizaki, Akira; Takayanagi, Toshiyuki; Shiga, Motoyuki
2007-11-01
Path integral molecular dynamics simulations for the H6+ and D6+ cluster cations have been carried out in order to understand the floppy nature of their molecular structure due to quantum-mechanical fluctuation. A full-dimensional analytical potential energy surface for the ground electronic state of H6+ has been developed on the basis of accurate ab initio electronic structure calculations at the CCSD(T)/cc-pVTZ level. It is found that the outer H 2(D 2) nuclei rotate almost freely and that the probability density distributions of the central H 2(D 2) nuclei show strong spatial delocalization.
Whitfield, T. W.; Crain, J.; Martyna, G. J.
2006-03-01
In order to better understand the physical interactions that stabilize protein secondary structure, the neat liquid state of a peptidic fragment, N-methylacetamide (NMA), was studied using computer simulation. Three different descriptions of the molecular liquid were examined: an empirical force field treatment with classical nuclei, an empirical force field treatment with quantum mechanical nuclei, and an ab initio density functional theory (DFT) treatment. The DFT electronic structure was evaluated using the BLYP approximate functional and a plane wave basis set. The different physical effects probed by the three models, such as quantum dispersion, many-body polarization, and nontrivial charge distributions on the liquid properties, were compared. Much of the structural ordering in the liquid is characterized by hydrogen bonded chains of NMA molecules. Modest structural differences are present among the three models of liquid NMA. The average molecular dipole in the liquid under the ab initio treatment, however, is enhanced by 60% over the gas phase value.
Ab initio path integral molecular dynamics simulation study on the dihydrogen bond of NH4+⋯BeH2
Hayashi, Aiko; Shiga, Motoyuki; Tachikawa, Masanori
2005-07-01
An ab initio path integral molecular dynamics simulation has been performed to study the quantum and thermal effects of a dihydrogen bonded cation, NH4+⋯BeH2. In this system, an attractive interaction exists between two neighboring hydrogen atoms as N δ- H δ+ ⋯H δ- Be δ+ involving large-amplitude of vibration. Some properties playing a key role for this dihydrogen bonded system, such as the bond length, bond angle, and distribution of atomic charges, are investigated in detail by comparing the results of path integral and classical molecular dynamics with those of the equilibrium structure. It was found that the atomic charges of H δ+ and H δ- are decreased and the dihydrogen H δ+ ⋯H δ- bond length is expanded as the thermal and zero-point quantum effects.
Tachikawa, Hiroto
2006-01-12
Ionization processes of chlorobenzene-ammonia 1:1 complex (PhCl-NH3) have been investigated by means of full dimensional direct ab initio molecular dynamics (MD) method, static ab initio calculations, and density functional theory (DFT) calculations. The static ab initio and DFT calculations of neutral PhCl-NH3 complex showed that one of the hydrogen atoms of NH3 orients toward a carbon atom in the para-position of PhCl. The dynamics calculation for ionization of PhCl-NH3 indicated that two reaction channels are competitive with each other as product channels: one is an intramolecular SN2 reaction expressed by a reaction scheme [PhCl-NH3]+-->SN2 intermediate complex-->PhNH3++Cl, and the other is ortho-NH3 addition complex (ortho complex) in which NH3 attacks the ortho-carbon of PhCl+ and the trajectory leads to a bound complex expressed by (PhCl-NH3)+. The mechanism of the ionization of PhCl-NH3 is discussed on the basis of the theoretical results.
Pietrucci, Fabio; Andreoni, Wanda
2011-08-19
Social permutation invariant coordinates are introduced describing the bond network around a given atom. They originate from the largest eigenvalue and the corresponding eigenvector of the contact matrix, are invariant under permutation of identical atoms, and bear a clear signature of an order-disorder transition. Once combined with ab initio metadynamics, these coordinates are shown to be a powerful tool for the discovery of low-energy isomers of molecules and nanoclusters as well as for a blind exploration of isomerization, association, and dissociation reactions.
Vadali, Ramkumar V; Shi, Yan; Kumar, Sameer; Kale, Laxmikant V; Tuckerman, Mark E; Martyna, Glenn J
2004-12-01
Many systems of great importance in material science, chemistry, solid-state physics, and biophysics require forces generated from an electronic structure calculation, as opposed to an empirically derived force law to describe their properties adequately. The use of such forces as input to Newton's equations of motion forms the basis of the ab initio molecular dynamics method, which is able to treat the dynamics of chemical bond-breaking and -forming events. However, a very large number of electronic structure calculations must be performed to compute an ab initio molecular dynamics trajectory, making the efficiency as well as the accuracy of the electronic structure representation critical issues. One efficient and accurate electronic structure method is the generalized gradient approximation to the Kohn-Sham density functional theory implemented using a plane-wave basis set and atomic pseudopotentials. The marriage of the gradient-corrected density functional approach with molecular dynamics, as pioneered by Car and Parrinello (R. Car and M. Parrinello, Phys Rev Lett 1985, 55, 2471), has been demonstrated to be capable of elucidating the atomic scale structure and dynamics underlying many complex systems at finite temperature. However, despite the relative efficiency of this approach, it has not been possible to obtain parallel scaling of the technique beyond several hundred processors on moderately sized systems using standard approaches. Consequently, the time scales that can be accessed and the degree of phase space sampling are severely limited. To take advantage of next generation computer platforms with thousands of processors such as IBM's BlueGene, a novel scalable parallelization strategy for Car-Parrinello molecular dynamics is developed using the concept of processor virtualization as embodied by the Charm++ parallel programming system. Charm++ allows the diverse elements of a Car-Parrinello molecular dynamics calculation to be interleaved with low
John, Christopher; Spura, Thomas; Habershon, Scott; Kühne, Thomas D.
2016-04-01
We present a simple and accurate computational method which facilitates ab initio path-integral molecular dynamics simulations, where the quantum-mechanical nature of the nuclei is explicitly taken into account, at essentially no additional computational cost in comparison to the corresponding calculation using classical nuclei. The predictive power of the proposed quantum ring-polymer contraction method is demonstrated by computing various static and dynamic properties of liquid water at ambient conditions using density functional theory. This development will enable routine inclusion of nuclear quantum effects in ab initio molecular dynamics simulations of condensed-phase systems.
John, Chris; Habershon, Scott; Kühne, Thomas D
2015-01-01
We present a simple and accurate computational method, which facilitates ab-initio path-integral molecular dynamics simulations, where the quantum mechanical nature of the nuclei is explicitly taken into account, at essentially no additional computational cost in comparison to the corresponding calculation using classical nuclei. The predictive power of the proposed quantum ring-polymer contraction method is demonstrated by computing various static and dynamic properties of liquid water at ambient conditions. This development permits to routinely include nuclear quantum effects in ab-initio molecular dynamics simulations.
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Luo, Ye, E-mail: xw111luoye@gmail.com; Sorella, Sandro, E-mail: sorella@sissa.it [International School for Advanced Studies (SISSA), and CRS Democritos, CNR-INFM, Via Bonomea 265, I-34136 Trieste (Italy); Zen, Andrea, E-mail: zen.andrea.x@gmail.com [Dipartimento di Fisica, Università di Roma “La Sapienza,” Piazzale Aldo Moro 2, I-00185 Rome (Italy)
2014-11-21
We present a systematic study of a recently developed ab initio simulation scheme based on molecular dynamics and quantum Monte Carlo. In this approach, a damped Langevin molecular dynamics is employed by using a statistical evaluation of the forces acting on each atom by means of quantum Monte Carlo. This allows the use of an highly correlated wave function parametrized by several variational parameters and describing quite accurately the Born-Oppenheimer energy surface, as long as these parameters are determined at the minimum energy condition. However, in a statistical method both the minimization method and the evaluation of the atomic forces are affected by the statistical noise. In this work, we study systematically the accuracy and reliability of this scheme by targeting the vibrational frequencies of simple molecules such as the water monomer, hydrogen sulfide, sulfur dioxide, ammonia, and phosphine. We show that all sources of systematic errors can be controlled and reliable frequencies can be obtained with a reasonable computational effort. This work provides convincing evidence that this molecular dynamics scheme can be safely applied also to realistic systems containing several atoms.
Ab initio molecular dynamics study of hydrogen removal by ion-surface interactions
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Rosen, Johanna [Materials Chemistry, RWTH-Aachen, D-52056 Aachen (Germany); Larsson, Karin [Department of Materials Chemistry, Angstroem Laboratory, Uppsala University, Box 538, 751 21 Uppsala (Sweden); Schneider, Jochen M [Materials Chemistry, RWTH-Aachen, D-52056 Aachen (Germany)
2005-04-20
The energy dependence of surface reactions has been investigated through ab initio MD simulations for collisions between Al{sup 1+} and a gibbsite surface. No change in surface composition was observed for 0 eV initial kinetic energy of Al{sup 1+}. An increase in energy to 3.5 eV resulted in extended surface migration of hydrogen, subsequent H{sub 2} formation and desorption from the surface. These results may be understood based on thermodynamics and an increase in entropy upon H{sub 2} formation. They are of fundamental importance for an increased understanding of thin film growth through the correlation between ion energy and film composition. They may also indicate a pathway to affect impurity incorporation during film growth. (letter to the editor)
Binding of TNT to amplifying fluorescent polymers: an ab initio and molecular dynamics study.
Enlow, Mark A
2012-03-01
Molecular modeling techniques were employed to study the interaction of trinitrotoluene with an amplifying fluorescent polymer used in explosive sensor devices. The pentiptycene moiety present in these polymers appears to be the most energetically favorable binding site for trinitrotoluene. Surface features of the polymer suggest that the small cavity feature of the pentiptycene moiety may be more available for binding to analyte compounds due to steric crowding about the large cavity. Binding energies between model binding sites of the polymer and various analyte compounds were more rigorously estimated by semiempirical and ab initio techniques. Binding energies were found to be largest with trinitrotoluene and other nitroaromatic compounds. Electrostatic and π-stacking interactions between trinitrotoluene and the model host were investigated by studying a series of modified host compounds.
Lahnsteiner, Jonathan; Kresse, Georg; Kumar, Abhinav; Sarma, D. D.; Franchini, Cesare; Bokdam, Menno
2016-12-01
The high efficiency of lead organo-metal-halide perovskite solar cells has raised many questions about the role of the methylammonium (MA) molecules in the Pb-I framework. Experiments indicate that the MA molecules are able to "freely" spin around at room temperature even though they carry an intrinsic dipole moment. We have performed large supercell (2592 atoms) finite-temperature ab initio molecular dynamics calculations to study the correlation between the molecules in the framework. An underlying long-range antiferroelectric ordering of the molecular dipoles is observed. The dynamical correlation between neighboring molecules shows a maximum around room temperature in the mid-temperature phase. In this phase, the rotations are slow enough to (partially) couple to neighbors via the Pb-I cage. This results in a collective motion of neighboring molecules in which the cage acts as the mediator. At lower and higher temperatures, the motions are less correlated.
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Jakse, N.; Pasturel, A. [Sciences et Ingénierie des Matériaux et Procédés, UMR CNRS 5266, Grenoble INP, BP 75, 38402 Saint-Martin d’Hères Cedex (France)
2014-12-21
In the present work, the structural and dynamic properties of liquid and undercooled boron are investigated by means of ab initio molecular dynamics simulation. Our results show that both liquid and undercooled states present a well pronounced short-range order (SRO) mainly due to the formation of inverted umbrella structural units. Moreover, we observe the development of a medium-range order (MRO) in the undercooling regime related to the increase of inverted umbrella structural units and of their interconnection as the temperature decreases. We also evidence that this MRO leads to a partial crystallization in the β-rhombohedral crystal below T = 1900 K. Finally, we discuss the role played by the SRO and MRO in the nearly Arrhenius evolution of the diffusion and the non-Arrhenius temperature dependence of the shear viscosity, in agreement with the experiment.
Li, Peng; Niu, Wenxia; Gao, Tao; Wang, Hongyan
2014-10-01
The gas-phase reaction of an Np atom with H2O was investigated using density functional theory and ab initio molecular dynamics. The reaction mechanisms and the corresponding potential energy profiles for different possible spin states were analyzed. Three reaction channels were found in the mechanism study: the isomerization channel, the H2 elimination channel, and the H atom elimination channel. The latter two were observed in the dynamics simulation. It was found that the branching ratio of the title reaction depends on the initial kinetic energy along the transition vector. Product energy distributions for the reaction were evaluated by performing direct classical trajectory calculations on the lowest sextet potential energy surface. The results indicate that most of the available energy appears as the translational energy of the products. The overall results indicate that the H2 elimination channel with low kinetic energy is thermodynamically favored but competes with the H atom elimination channel with higher kinetic energy.
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Koizumi, Kenichi; Nobusada, Katsuyuki [Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki 444-8585 (Japan); Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Katsura, Kyoto 615-8520 (Japan); Boero, Mauro [Institut de Physique et Chimie des Matériaux de Strasbourg UMR 7504, University of Strasbourg and CNRS, 23 rue du Loess, F-67034 Strasbourg (France)
2015-12-31
Ab initio molecular dynamics simulations have been used to inspect the adsorption of O{sub 2} to a small gold-copper alloy cluster supported on graphene. The exposed Cu atom in this cluster acts as a crucial attractive site for the approaching of O{sub 2} and consequently widens the reaction channel for the adsorption process. Conversely, a pure Au cluster on the same graphene support is inactive for the O{sub 2} adsorption because the corresponding reaction channel for the adsorption is very narrow. These results clearly indicate that doping a different metal to the Au cluster is a way to enhance the oxygen adsorption and to promote catalytic reactions.
Feng, Ya-Juan; Huang, Teng; Wang, Chao; Liu, Yi-Rong; Jiang, Shuai; Miao, Shou-Kui; Chen, Jiao; Huang, Wei
2016-07-14
Molecular level insight into the interaction between volatile organic compounds (VOCs) and aerosols is crucial for improvement of atmospheric chemistry models. In this paper, the interaction between adsorbed toluene, one of the most significant VOCs in the urban atmosphere, and the aqueous surface of aerosols was studied by means of combined molecular dynamics simulations and ab initio quantum chemistry calculations. It is revealed that toluene can be stably adsorbed on the surface of aqueous droplets via hydroxyl-π hydrogen bonding between the H atoms of the water molecules and the C atoms in the aromatic ring. Further, significant modifications on the electrostatic potential map and frontier molecular orbital are induced by the solvation effect of surface water molecules, which would affect the reactivity and pathway of the atmospheric photooxidation of toluene. This study demonstrates that the surface interactions should be taken into consideration in the atmospheric chemical models on oxidation of aromatics.
Kolb, Brian; Guo, Hua
2016-07-01
Scattering and dissociative chemisorption of DCl on Au(111) are investigated using ab initio molecular dynamics with a slab model, in which the top two layers of Au are mobile. Substantial kinetic energy loss in the scattered DCl is found, but the amount of energy transfer is notably smaller than that observed in the experiment. On the other hand, the dissociative chemisorption probability reproduces the experimental trend with respect to the initial kinetic energy, but is about one order of magnitude larger than the reported initial sticking probability. While the theory-experiment agreement is significantly improved from the previous rigid surface model, the remaining discrepancies are still substantial, calling for further scrutiny in both theory and experiment.
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Samin, Adib; Li, Xiang; Zhang, Jinsuo [Nuclear Engineering Program, Department of Mechanical and Aerospace Engineering, The Ohio State University, 201 W 19th Avenue, Columbus, Ohio 43210 (United States); Mariani, R. D. [Idaho National Laboratory, Materials and Fuels Complex, Idaho Falls, Idaho 83415 (United States); Unal, Cetin [Los Alamos National Laboratory, P.O. Box 1663, Los Alamos, New Mexico 87545 (United States)
2015-12-21
For liquid-sodium-cooled fast nuclear reactor systems, it is crucial to understand the behavior of lanthanides and other potential fission products in liquid sodium or other liquid metal solutions such as liquid cesium-sodium. In this study, we focus on lanthanide behavior in liquid sodium. Using ab initio molecular dynamics, we found that the solubility of cerium in liquid sodium at 1000 K was less than 0.78 at. %, and the diffusion coefficient of cerium in liquid sodium was calculated to be 5.57 × 10{sup −9} m{sup 2}/s. Furthermore, it was found that cerium in small amounts may significantly alter the heat capacity of the liquid sodium system. Our results are consistent with the experimental results for similar materials under similar conditions.
Samin, Adib; Li, Xiang; Zhang, Jinsuo; Mariani, R. D.; Unal, Cetin
2015-12-01
For liquid-sodium-cooled fast nuclear reactor systems, it is crucial to understand the behavior of lanthanides and other potential fission products in liquid sodium or other liquid metal solutions such as liquid cesium-sodium. In this study, we focus on lanthanide behavior in liquid sodium. Using ab initio molecular dynamics, we found that the solubility of cerium in liquid sodium at 1000 K was less than 0.78 at. %, and the diffusion coefficient of cerium in liquid sodium was calculated to be 5.57 × 10-9 m2/s. Furthermore, it was found that cerium in small amounts may significantly alter the heat capacity of the liquid sodium system. Our results are consistent with the experimental results for similar materials under similar conditions.
Sun, Tao; Zhang, Dong-Bo; Wentzcovitch, Renata M.
2014-03-01
The stability of cubic CaSiO3 perovskite (CaPv) at high temperatures and pressures is investigated by vibrational normal-mode analysis. We compute power spectra of mode autocorrelation functions using a recently developed hybrid approach combining ab initio molecular dynamics with lattice dynamics. These power spectra, together with the probability distributions of atomic displacements, indicate that cubic CaPv is stabilized at T ˜600 K and P ˜ 26 GPa. We then utilize the concept of phonon quasiparticles to characterize the vibrational properties of cubic CaPv at high temperature and obtain anharmonic phonon dispersions through the whole Brillouin zone. Such temperature-dependent phonon dispersions pave the way for more accurate calculations of free-energy, thermodynamic, and thermoelastic properties of cubic CaPv at Earth's lower mantle conditions.
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Alemany, Manuel M. G. [Universidad de Santiago de Compostela; Longo, Roberto [Universidad de Santiago de Compostela; Gallego, Luis [Universidad de Santiago de Compostela; Gonzales, D. J. [Universidad de Valladolid; Gonzales, L. E. [Universidad de Valladolid; Tiago, Murilo L [ORNL; Chelikowsky, James [University of Texas, Austin
2007-01-01
We performed a comprehensive study of the static, dynamic and electronic properties of liquid Pb at T = 650 kelvins, density 0.0309 angstroms^{-3} by means of 216-particle ab initio molecular dynamics simulations based on a real-space implementation of pseudopotentials constructed within density-functional theory. The predicted results and available experimental data are very in good agreement, which confirms the adequacy of this technique to achieve a reliable description of the behavior of liquid metals, including their dynamic properties. Although some of the computed properties of liquid Pb are similar to those of simple liquid metals, others differ markedly. Our results show that an appropriate description of liquid Pb requires the inclusion of relativistic effects in the determination of the pseudopotentials of Pb.
Xue, Wenhua; Dang, Hongli; Liu, Yingdi; Jentoft, Friederike; Resasco, Daniel; Wang, Sanwu
2014-03-01
In the study of catalytic reactions of biomass, furfural conversion over metal catalysts with the presence of hydrogen has attracted wide attention. We report ab initio molecular dynamics simulations for furfural and hydrogen on the Pd(111) surface at finite temperatures. The simulations demonstrate that the presence of hydrogen is important in promoting furfural conversion. In particular, hydrogen molecules dissociate rapidly on the Pd(111) surface. As a result of such dissociation, atomic hydrogen participates in the reactions with furfural. The simulations also provide detailed information about the possible reactions of hydrogen with furfural. Supported by DOE (DE-SC0004600). This research used the supercomputer resources of the XSEDE, the NERSC Center, and the Tandy Supercomputing Center.
Self-Assembly and Dynamics of Organic 2D Molecular Sieves: Ab Initio and Molecular Dynamics Studies
St. John, Alexander; Wexler, Carlos
2015-03-01
Spontaneous molecular self-assembly is a promising route for bottom-up manufacturing of two-dimensional (2D) nanostructures with specific topologies on atomically flat surfaces. Of particular interest is the possibility of selective lock-and-key interaction of guest molecules inside cavities formed by complex self-assembled host structures. Our host structure is a monolayer consisting of interdigitated 1,3,5-tristyrylbenzene substituted by alkoxy peripheral chains containing n = 6, 8, 10, 12, or 14 carbon atoms (TSB3,5-C n) deposited on a highly ordered pyrolytic graphite (HOPG) surface. Using ab initio methods from quantum chemistry and molecular dynamics simulations, we construct and analyze the structure and functionality of the TSB3,5-C n monolayer as a molecular sieve. Supported by ACS-PRF 52696-ND5.
Stirling, András; Nair, Nisanth N; Lledós, Agustí; Ujaque, Gregori
2014-07-21
We present here a review of the mechanistic studies of the Wacker process stressing the long controversy about the key reaction steps. We give an overview of the previous experimental and theoretical studies on the topic. Then we describe the importance of the most recent Ab Initio Molecular Dynamics (AIMD) calculations in modelling organometallic reactivity in water. As a prototypical example of homogeneous catalytic reactions, the Wacker process poses serious challenges to modelling. The adequate description of the multiple role of the water solvent is very difficult by using static quantum chemical approaches including cluster and continuum solvent models. In contrast, such reaction systems are suitable for AIMD, and by combining with rare event sampling techniques, the method provides reaction mechanisms and the corresponding free energy profiles. The review also highlights how AIMD has helped to obtain a novel understanding of the mechanism and kinetics of the Wacker process.
Ko, Hsin-Yu; Distasio, Robert A., Jr.; Santra, Biswajit; Car, Roberto
2014-03-01
Pyridine has recently been investigated as a potentially effective material for use in artificial light harvesting.In this work, we propose the use of ab initio molecular dynamics (AIMD) to gain valuable physical insight into the artificial photosynthetic processes occurring in condensed-phase pyridine, the study of which has been limited to semi-empirical force fields to date.For this purpose, we introduce an accurate and efficient AIMD method, based on density functional theory (DFT) and a self-consistent pairwise description of van der Waals (vdW) interactions, for use in finite temperature and pressure (NPT) simulations on pyridine and several pyridine-like molecular crystals (PLMCs). Utilizing this approach, we demonstrate that vdW forces play a crucial role in the theoretical prediction of the structure and density of pyridine and PLMCs, and therefore must be accounted for in studies of these potential alternative energy materials. DOE: DE-SC0008626, NSF: DMS-1065894.
Plašienka, Dušan; Martoňák, Roman
2014-01-01
We present results of \\textit{ab initio} molecular dynamics study of a structural transformation occurring in hot liquid sulfur under high pressure, which corresponds to the chain-breakage phenomenon recently observed experimentally by Liu \\textit{et al.} [1] and to the electronic transition reported by Brazhkin \\textit{et al.} [2,3]. We performed an extensive \\textit{ab initio} study and confirmed the existence of one transformation separating two distinct liquid polymeric phases: one composed of short chain-like fragments and another one with very long chains. We have not observed additional transformations reported in Refs. [2,3] and in the recent theoretical study by Zhao and Mu [4] and our findings are in agreement with the most recent experiment [1]. We offer a structural description of this liquid-liquid transformation in terms of chain lengths, cross-linking and geometry and investigate several physical properties. We conclude that the transformation is accompanied by changes in configurational energy...
Matching a surface complexation model with ab initio molecular dynamics: montmorillonite case
Energy Technology Data Exchange (ETDEWEB)
Kulik, D.A.; Churakov, S.V. [Paul Scherrer Institute, Nuclear Energy and Safety Dpt., Lab. for Waste Management, CH-5232 Villigen PSI (Switzerland)
2005-07-01
Speciation modelling of sorption on mineral-water interfaces is performed with help of surface complexation models (SCM), suitable for diluted suspensions that seem to reach adsorption equilibrium within laboratory times. Electrostatic SCMs need several input parameters even for a relatively simple oxide mineral surface. Moreover, the electrolyte ion adsorption constants in triple layer (TL) or basic Stern (BS) models depend on the inner layer capacitance density Cl, but clear physical understanding of this parameter is missing so far. SCMs can fit acidimetric or metal titration data well at quite different combinations of input parameters, and this fact casts doubt on any interpretation of fitted parameter values in terms of microscopic physicochemical mechanisms. The problem is even deeper in SCMs for clay minerals like montmorillonite having at least two surface types: the edges exposing different (aluminol and silanol) functional groups, and the basal siloxane planes with permanent charge and ion exchange. A feasible way to overcome the caveat of SCMs is seen nowadays in relying on crystallographic data and ab initio calculations to restrict the EDL setup, species stoichiometries, and input parameter values when constructing the adsorption model. The aim of this contribution is to discuss how recent advances in sample surface characterization an d in quantum-chemistry calculations for pyrophyllite can help in putting together a multi-site-surface electrostatic SCM for montmorillonite implemented in GEM approach. The quality of macroscopic model fits is checked against the titration data. (authors)
Mechanism of GeSbTe phase change materials: an ab initio molecular dynamics study
Raty, Jean-Yves; Otjacques, Céline; Gaspard, Jean-Pierre; Bichara, Christophe
2008-03-01
Among phase change materials, Ge2Sb2Te5 (225) is one of the most successfully used in applications. Accepted models are based on EXAFS spectra and suppose a complete reorganization of bonds during amorphization, with Ge changing from sixfold to tetrahedral coordination. We perform ab initio MD simulations of the (225), (124) and (415) liquid alloys. We show that the crystalline, liquid and amorphous structure of these systems are similar, with very little sp3 hybridization around Ge atoms and a majority of p-sigma bonds. Using a set of quenched liquid configurations we reproduce the EXAFS measurements on the (225) composition and explain how the static Debye Waller factor due to the vacancies in the crystal phase leads to a cancellation of individual neighbors contribution to the EXAFS signal while in the amorphous, a larger coherence occurs, enhancing the EXAFS signal. The computed electrical conductivities of the three phases (cubic solid, liquid and amorphous) prove to be very different, accordingly with the experiment.
Walker, Brent; Michaelides, Angelos
2010-11-01
The impact of quantum nuclear effects on hydrogen (H-) bond strength has been inferred in earlier work from bond lengths obtained from path integral molecular dynamics (PIMD) simulations. To obtain a direct quantitative assessment of such effects, we use constrained-centroid PIMD simulations to calculate the free energy changes upon breaking the H-bonds in dimers of HF and water. Comparing ab initio simulations performed using PIMD and classical nucleus molecular dynamics (MD), we find smaller dissociation free energies with the PIMD method. Specifically, at 50 K, the H-bond in (HF)2 is about 30% weaker when quantum nuclear effects are included, while that in (H2O)2 is about 15% weaker. In a complementary set of simulations, we compare unconstrained PIMD and classical nucleus MD simulations to assess the influence of quantum nuclei on the structures of these systems. We find increased heavy atom distances, indicating weakening of the H-bond consistent with that observed by direct calculation of the free energies of dissociation.
Svoboda, Ondřej; Ončák, Milan; Slavíček, Petr
2011-10-01
We have applied ab initio based reflection principle to simulate photoelectron spectra of small water clusters, ranging from monomer to octamer. The role of quantum and thermal effects on the structure of the water photoelectron spectra is discussed within the ab initio path integral molecular dynamics (PIMD) framework. We have used the PIMD method with up to 40 beads to sample the ground state quantum distribution at temperature T = 180 K. We have thoroughly tested the performance of various density functionals (B3LYP, BHandHLYP, M06HF, BNL, LC-ωPBE, and CAM-B3LYP) for the ionization process description. The benchmarking based on a comparison of simulated photoelectron spectra to experimental data and high level equation-of-motion ionization potential coupled clusters with singles and doubles calculations has singled out the BHandHLYP and LC-ωPBE functionals as the most reliable ones for simulations of light induced processes in water. The good performance of the density functional theory functionals to model the water photoelectron spectra also reflects their ability to reliably describe open shell excited states. The width of the photoelectron spectrum converges quickly with the cluster size as it is controlled by specific interactions of local character. The peak position is, on the other hand, defined by long-range non-specific solvent effects; it therefore only slowly converges to the corresponding bulk value. We are able to reproduce the experimental valence photoelectron spectrum of liquid water within the combined model of the water octamer embedded in a polarizable dielectric continuum. We demonstrate that including the long-range polarization and the state-specific treatment of the solvent response are needed for a reliable liquid water ionization description.
A field-theoretic approach to linear scaling \\textit{ab-initio} molecular dynamics
Richters, Dorothee; Kühne, Thomas D
2012-01-01
We present a field-theoretic method suitable for linear scaling molecular dynamics simulations using forces from self-consistent electronic structure calculations. It is based on an exact decomposition of the grand canonical potential for independent fermions and does neither rely on the ability to localize the orbitals nor that the Hamilton operator is well-conditioned. Hence, this scheme enables highly accurate all-electron linear scaling calculations even for metallic systems. The inherent energy drift of Born-Oppenheimer molecular dynamics simulations, arising from an incomplete convergence of the self-consistent field cycle, is solved by means of a properly modified Langevin equation. The predictive power of this approach is illustrated using the example of liquid methane under extreme conditions.
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Miller, J.; Miaskiewicz, K. [Pacific Northwest Lab., Richland, WA (United States); Osman, R. [Mount Sinai School of Medicine, New York, NY (United States). Dept. of Physiology and Biophysics
1993-12-01
Studies of ring-saturated pyrimidine base lesions are used to illustrate an integrated modeling approach that combines quantum-chemical calculations with molecular dynamics simulation. Electronic-structure calculations on the lesions in Isolation reveal strong conformational preferences due to interactions between equatorial substituents to the pyrimidine ring. Large distortions of DNA should result when these interactions force the methyl group of thymine to assume an axial orientation, as is the case for thymine glycol but not for dihydrothymine. Molecular dynamics simulations of the dodecamer d(CGCGAATTCGCG){sub 2} with and without a ring-saturated thymine lesion at position T7 support this conclusion. Implications of these studies for recognition of thymine lesions by endonuclease III are also discussed.
Ab-initio molecular dynamics simulation on nano-system under external pressure
Institute of Scientific and Technical Information of China (English)
JI; Min; SUN; Deyan; GONG; Xingao
2004-01-01
A new constant-pressure molecular dynamics (MD) method is developed to simulate the dynamic behavior and structure transition of finite system under external pressure. In this method, no artificial parameter is introduced and the computation overheads are very small. As an application, a hard-soft transition of single wall carbon nanotube (SWCNT) under external pressure is found, which is in agreement with the experiments.
Energy Technology Data Exchange (ETDEWEB)
Parsons, A J; Ahmed, I; Rudd, C D [Division of Materials, Mechanics and Structures, Faculty of Engineering, University of Nottingham, Nottingham NG7 2RD (United Kingdom); Cuello, G J; Pellegrini, E; Richard, D; Johnson, M R, E-mail: andrew.parsons@nottingham.ac.uk [Institut Laue-Langevin, BP 156, 38042 Grenoble (France)
2010-12-08
Details of the microscopic structure of phosphate glasses destined for biomedical applications, which include sodium, magnesium and calcium cations, have been obtained from the static structure factor measured by means of neutron scattering. A complementary, molecular dynamics study has been performed on a range of phosphate glasses using density functional theory methods, which allow structural fluctuations, including bond breaking, in the liquid phase before quenching to the glass phase. Good agreement between experiment and simulation allows the molecular dynamics trajectories to be analysed in detail. In particular, attention is focused on the cross-linking of divalent cations in contrast with the structural aspects associated with monovalent cations. Magnesium cations are found equidistant and bridging between the phosphorus atoms of different phosphate chains, leading to a shorter phosphorus-phosphorus second neighbour distance (that is, a more compact packing of neighbouring phosphate chains) compared to the effect of sodium cations. Calcium cations show behaviour intermediate between those of magnesium and sodium. Molecular dynamics simulations give access to the cation mobility, which is lowest for magnesium, reflecting its structural, cross-linking role.
Sumner, Isaiah; Iyengar, Srinivasan S
2008-08-07
We discuss hybrid quantum-mechanics/molecular-mechanics (QM/MM) and quantum mechanics/quantum mechanics (QM/QM) generalizations to our recently developed quantum wavepacket ab initio molecular dynamics methodology for simultaneous dynamics of electrons and nuclei. The approach is a synergy between a quantum wavepacket dynamics, ab initio molecular dynamics, and the ONIOM scheme. We utilize this method to include nuclear quantum effects arising from a portion of the system along with a simultaneous description of the electronic structure. The generalizations provided here make the approach a potentially viable alternative for large systems. The quantum wavepacket dynamics is performed on a grid using a banded, sparse, and Toeplitz representation of the discrete free propagator, known as the "distributed approximating functional." Grid-based potential surfaces for wavepacket dynamics are constructed using an empirical valence bond generalization of ONIOM and further computational gains are achieved through the use of our recently introduced time-dependent deterministic sampling technique. The ab initio molecular dynamics is achieved using Born-Oppenheimer dynamics. All components of the methodology, namely, quantum dynamics and ONIOM molecular dynamics, are harnessed together using a time-dependent Hartree-like procedure. We benchmark the approach through the study of structural and vibrational properties of molecular, hydrogen bonded clusters inclusive of electronic, dynamical, temperature, and critical quantum nuclear effects. The vibrational properties are constructed through a velocity/flux correlation function formalism introduced by us in an earlier publication.
Perovskite Quantum Dots Modeled Using ab Initio and Replica Exchange Molecular Dynamics
Buin, Andrei
2015-06-18
© 2015 American Chemical Society. Organometal halide perovskites have recently attracted tremendous attention at both the experimental and theoretical levels. Much of this work has been dedicated to bulk material studies, yet recent experimental work has shown the formation of highly efficient quantum-confined nanocrystals with tunable band edges. Here we investigate perovskite quantum dots from theory, predicting an upper bound of the Bohr radius of 45 Å that agrees well with literature values. When the quantum dots are stoichiometric, they are trap-free and have nearly symmetric contributions to confinement from the valence and conduction bands. We further show that surface-associated conduction bandedge states in perovskite nanocrystals lie below the bulk states, which could explain the difference in Urbach tails between mesoporous and planar perovskite films. In addition to conventional molecular dynamics (MD), we implement an enhanced phase-space sampling algorithm, replica exchange molecular dynamics (REMD). We find that in simulation of methylammonium orientation and global minima, REMD outperforms conventional MD. To the best of our knowledge, this is the first REMD implementation for realistic-sized systems in the realm of DFT calculations.
Konstantinou, Konstantinos; Sushko, Peter V; Duffy, Dorothy M
2016-09-21
The nature of chemical bonding of molybdenum in high level nuclear waste glasses has been elucidated by ab initio molecular dynamics simulations. Two compositions, (SiO2)57.5-(B2O3)10-(Na2O)15-(CaO)15-(MoO3)2.5 and (SiO2)57.3-(B2O3)20-(Na2O)6.8-(Li2O)13.4-(MoO3)2.5, were considered in order to investigate the effect of ionic and covalent components on the glass structure and the formation of the crystallisation precursors (Na2MoO4 and CaMoO4). The coordination environments of Mo cations and the corresponding bond lengths calculated from our model are in excellent agreement with experimental observations. The analysis of the first coordination shell reveals two different types of molybdenum host matrix bonds in the lithium sodium borosilicate glass. Based on the structural data and the bond valence model, we demonstrate that the Mo cation can be found in a redox state and the molybdate tetrahedron can be connected with the borosilicate network in a way that inhibits the formation of crystalline molybdates. These results significantly extend our understanding of bonding in Mo-containing nuclear waste glasses and demonstrate that tailoring the glass composition to specific heavy metal constituents can facilitate incorporation of heavy metals at high concentrations.
Lee, Mal-Soon; Peter McGrail, B.; Rousseau, Roger; Glezakou, Vassiliki-Alexandra
2015-01-01
The boundary layer at solid-liquid interfaces is a unique reaction environment that poses significant scientific challenges to characterize and understand by experimentation alone. Using ab initio molecular dynamics (AIMD) methods, we report on the structure and dynamics of boundary layer formation, cation mobilization and carbonation under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar) on a prototypical anorthite (001) surface. At low coverage, water film formation is enthalpically favored, but entropically hindered. Simulated adsorption isotherms show that a water monolayer will form even at the low water concentrations of water-saturated scCO2. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies that readily form in the presence of a water monolayer. These results point to a carbonation mechanism that does not require prior carbonic acid formation in the bulk liquid. This work also highlights the modern capabilities of theoretical methods to address structure and reactivity at interfaces of high chemical complexity. PMID:26456362
Bučko, Tomáš; Šimko, František
2016-02-01
Ab initio molecular dynamics simulations in isobaric-isothermal ensemble have been performed to study the low- and the high-temperature crystalline and liquid phases of cryolite. The temperature induced transitions from the low-temperature solid (α) to the high-temperature solid phase (β) and from the phase β to the liquid phase have been simulated using a series of MD runs performed at gradually increasing temperature. The structure of crystalline and liquid phases is analysed in detail and our computational approach is shown to reliably reproduce the available experimental data for a wide range of temperatures. Relatively frequent reorientations of the AlF6 octahedra observed in our simulation of the phase β explain the thermal disorder in positions of the F- ions observed in X-ray diffraction experiments. The isolated AlF63-, AlF52-, AlF4-, as well as the bridged Al 2 Fm 6 - m ionic entities have been identified as the main constituents of cryolite melt. In accord with the previous high-temperature NMR and Raman spectroscopic experiments, the compound AlF5 2 - has been shown to be the most abundant Al-containing species formed in the melt. The characteristic vibrational frequencies for the AlFn 3 - n species in realistic environment have been determined and the computed values have been found to be in a good agreement with experiment.
Energy Technology Data Exchange (ETDEWEB)
Saalfrank, Peter [Institut für Chemie, Universität Potsdam, Karl-Liebknecht-Strasse 24-25, D-14476 Potsdam (Germany); Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián (Spain); Juaristi, J. I. [Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián (Spain); Centro de Física de Materiales CFM/MPC (CSIC-UPV/EHU), Paseo Manuel de Lardizabal 5, 20018 Donostia-San Sebastián (Spain); Departamento de Física de Materiales, Facultad de Químicas UPV/EHU, Apartado 1072, 20018 Donostia-San Sebastián (Spain); Alducin, M.; Muiño, R. Díez [Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián (Spain); Centro de Física de Materiales CFM/MPC (CSIC-UPV/EHU), Paseo Manuel de Lardizabal 5, 20018 Donostia-San Sebastián (Spain); Blanco-Rey, M. [Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián (Spain); Departamento de Física de Materiales, Facultad de Químicas UPV/EHU, Apartado 1072, 20018 Donostia-San Sebastián (Spain)
2014-12-21
Using density functional theory and Ab Initio Molecular Dynamics with Electronic Friction (AIMDEF), we study the adsorption and dissipative vibrational dynamics of hydrogen atoms chemisorbed on free-standing lead films of increasing thickness. Lead films are known for their oscillatory behaviour of certain properties with increasing thickness, e.g., energy and electron spillout change in discontinuous manner, due to quantum size effects [G. Materzanini, P. Saalfrank, and P. J. D. Lindan, Phys. Rev. B 63, 235405 (2001)]. Here, we demonstrate that oscillatory features arise also for hydrogen when chemisorbed on lead films. Besides stationary properties of the adsorbate, we concentrate on finite vibrational lifetimes of H-surface vibrations. As shown by AIMDEF, the damping via vibration-electron hole pair coupling dominates clearly over the vibration-phonon channel, in particular for high-frequency modes. Vibrational relaxation times are a characteristic function of layer thickness due to the oscillating behaviour of the embedding surface electronic density. Implications derived from AIMDEF for frictional many-atom dynamics, and physisorbed species will also be given.
Kritayakornupong, Chinapong; Vchirawongkwin, Viwat; Hofer, Thomas S; Rode, Bernd M
2008-09-25
The novel ab initio quantum mechanical charge field (QMCF) molecular dynamics simulation at the Hartree-Fock level has been employed to investigate hydration structure and dynamics of hydrogen fluoride in aqueous solution. The average H-F bond length of 0.93 A obtained from the QMCF MD simulation is in good agreement with the experimental data. The HHF...Ow distance of 1.62 A was evaluated for the first hydration shell, and 2.00 A was observed for the FHF...Hw distance. The stability of hydrogen bonding is more pronounced in the hydrogen site of hydrogen fluoride, with a single water molecule in this part of the first hydration shell. A wide range of coordination numbers between 3 and 9 with an average value of 5.6 was obtained for the fluorine site. The force constants of 819.1 and 5.9 N/m were obtained for the HHF-FHF and HHF...Ow interactions, respectively, proving the stability of the nondissociated form of hydrogen fluoride in aqueous solution. The mean residence times of 2.1 and 2.5 ps were determined for ligand exchange processes in the neighborhood of fluorine and hydrogen atoms of hydrogen fluoride, respectively, indicating a weak structure-making effect of hydrogen fluoride in water. The corresponding H-bond lifetimes attribute this effect to the H atom site of HF.
Moin, Syed Tarique; Lim, Len Herald V; Hofer, Thomas S; Randolf, Bernhard R; Rode, Bernd M
2011-04-18
An ab initio Quantum Mechanical Charge Field Molecular Dynamics Simulation (QMCF MD) was performed to investigate structure and dynamics behavior of hydrated sulfur dioxide (SO(2)) at the Hartree-Fock level of theory employing Dunning DZP basis sets for solute and solvent molecules. The intramolecular structural characteristics of SO(2), such as S═O bond lengths and O═S═O bond angle, are in good agreement with the data available from a number of different experiments. The structural features of the hydrated SO(2) were primarily evaluated in the form of S-O(wat) and O(SO(2))-H(wat) radial distribution functions (RDFs) which gave mean distances of 2.9 and 2.2 Å, respectively. The dynamical behavior characterizes the solute molecule to have structure making properties in aqueous solution or water aerosols, where the hydrated SO(2) can easily get oxidized to form a number of sulfur(VI) species, which are believed to play an important role in the atmospheric processes.
Weber, Hans; Schumacher, Mathias; Jóvári, Pál; Tsuchiya, Yoshimi; Skrotzki, Werner; Mazzarello, Riccardo; Kaban, Ivan
2017-08-01
GeTe is a prototypical phase-change material employed in data storage devices. In this work, the atomic structure of liquid GeTe is studied by x-ray and neutron diffraction in the temperature range from 1197 to 998 K. The dynamic viscosity is measured from 1273 to 953 K, which is 55 K below the solidification point, using an oscillating-cup viscometer. The density of liquid GeTe between 1293 and 973 K is determined by the high-energy γ -ray attenuation method. The experiments are complemented with ab initio molecular dynamics (AIMD) simulations based on density functional theory (DFT). Compatibility of the AIMD-DFT models with the diffraction data is proven by simultaneous fitting of all data sets in the frame of the reverse Monte Carlo simulation technique. It is shown that octahedral order dominates in liquid GeTe, although tetrahedral structures are also present. The viscosity of the equilibrium and weakly undercooled liquid GeTe obeys the Arrhenius law with a small activation energy of the order of 0.3 eV, which is indicative of a highly fragile liquid. The calculated density of states and electronic wave functions point to the existence of a pseudogap and localized electron states within the gap in the equilibrium liquid near the melting point as well as in the undercooled liquid.
Song, Bingyi; Jiang, Wenlong; Yang, Bin; Chen, Xiumin; Xu, Baoqiang; Kong, Lingxin; Liu, Dachun; Dai, Yongnian
2016-10-01
The possibility of the separation of Pb-Sb alloys by vacuum distillation was investigated theoretically. The results show that Pb and Sb can be separated by vacuum distillation. However, the experimental results show that vacuum distillation technique does not provide clear separation. According to the literature, Pb-Sb alloys belong to azeotropic compounds under some certain temperature; the experiment and computer simulation were carried out based on the exceptional condition so as to analyze the reason from the experiment and microstructure of Pb-Sb alloys perspective. The separation of Pb-Sb alloys by vacuum distillation was experimentally carried out to probe the azeotropic point. Also, the functions, such as partial radial distributions functions, the structure factor, mean square displacement, and the density of state, were calculated by ab-initio molecular dynamics for the representation of the structure and properties of Pb-Sb alloys with different composition of Sb. The experimental results indicate that there exists common volatilization for Pb-Sb alloys when Sb content is 16.5 wt pct. On the other hand, the calculation results show that there is an intense interaction between Pb and Sb when Sb content is 22 wt pct, which supports the experimental results although Sb content is slightly deviation.
Agosta, Lorenzo; Brandt, Erik G.; Lyubartsev, Alexander P.
2017-07-01
Ab initio molecular dynamics simulations are reported for water-embedded TiO2 surfaces to determine the diffusive and reactive behavior at full hydration. A three-domain model is developed for six surfaces [rutile (110), (100), and (001), and anatase (101), (100), and (001)] which describes waters as "hard" (irreversibly bound to the surface), "soft" (with reduced mobility but orientation freedom near the surface), or "bulk." The model explains previous experimental data and provides a detailed picture of water diffusion near TiO2 surfaces. Water reactivity is analyzed with a graph-theoretic approach that reveals a number of reaction pathways on TiO2 which occur at full hydration, in addition to direct water splitting. Hydronium (H3O+) is identified to be a key intermediate state, which facilitates water dissociation by proton hopping between intact and dissociated waters near the surfaces. These discoveries significantly improve the understanding of nanoscale water dynamics and reactivity at TiO2 interfaces under ambient conditions.
Indian Academy of Sciences (India)
QIONG WU; DONG XIANG; GUOLIN XIONG; WEIHUA ZHU; HEMING XIAO
2016-05-01
Ab initio molecular dynamics simulations were performed to study the initiation of decompositionand formation of first products of two molecular crystals pentaerythritol tetranitrate (PETN) and 5-nitro-2,4-dihydro-1,2,4-triazole-3-one (NTO) under thermal decomposition temperature (475 K for PETN and 531 Kfor NTO) coupled with different pressures (1-5 GPa). The pressure effects on the initial decomposition stepsand initially generated products on PETN and NTO were very different. PETN was triggered by C-H... O intermolecular hydrogen transfer. The initial decomposition mechanism was independent of the pressure. ForNTO, two different initial decomposition mechanisms were found. At 1, 2, and 3 GPa, it was triggered by NH....O intermolecular hydrogen transfer, while at 4 and 5 GPa, it was triggered by N-H.....N intermolecularhydrogen transfer. This indicates that the initial decomposition mechanism was dependent on the pressure.Our study may provide new insights into initial mechanisms and decomposition reactions of molecular crystalexplosives under thermal decomposition temperature coupled with different pressures with details at atomiclevel.
Mozafari, E.; Shulumba, N.; Steneteg, P.; Alling, B.; Abrikosov, Igor A.
2016-08-01
We present a theoretical scheme to calculate the elastic constants of magnetic materials in the high-temperature paramagnetic state. Our approach is based on a combination of disordered local moments picture and ab initio molecular dynamics (DLM-MD). Moreover, we investigate a possibility to enhance the efficiency of the simulations of elastic properties using the recently introduced method: symmetry imposed force constant temperature-dependent effective potential (SIFC-TDEP). We have chosen cubic paramagnetic CrN as a model system. This is done due to its technological importance and its demonstrated strong coupling between magnetic and lattice degrees of freedom. We have studied the temperature-dependent single-crystal and polycrystalline elastic constants of paramagentic CrN up to 1200 K. The obtained results at T = 300 K agree well with the experimental values of polycrystalline elastic constants as well as the Poisson ratio at room temperature. We observe that the Young's modulus is strongly dependent on temperature, decreasing by ˜14 % from T = 300 K to 1200 K. In addition we have studied the elastic anisotropy of CrN as a function of temperature and we observe that CrN becomes substantially more isotropic as the temperature increases. We demonstrate that the use of Birch law may lead to substantial errors for calculations of temperature induced changes of elastic moduli. The proposed methodology can be used for accurate predictions of mechanical properties of magnetic materials at temperatures above their magnetic order-disorder phase transition.
Tachikawa, Hiroto; Kawabata, Hiroshi
2008-06-19
The interaction between the fully reduced flavin-adenine dinucleotide (FADH (-)) and thymine dimer (T) 2 has been investigated by means of density functional theory (DFT) calculations. The charges of FADH (-) and (T) 2 were calculated to be -0.9 and -0.1, respectively, at the ground state. By photoirradiation, an electron transfer occurred from FADH (-) to (T) 2 at the first excited state. Next, the reaction dynamics of electron capture of (T) 2 have been investigated by means of the direct ab initio molecular dynamics (MD) method (HF/3-21G(d) and B3LYP/6-31G(d) levels) in order to elucidate the mechanism of the repair process of thymine dimer caused by the photoenzyme. The thymine dimer has two C-C single bonds between thymine rings (C 5-C 5' and C 6-C 6' bonds) at the neutral state, which is expressed by (T) 2. After the electron capture of (T) 2, the C 5-C 5' bond was gradually elongated and then it was preferentially broken. The time scale of the C-C bond breaking and formation of the intermediate with a single bond (T) 2 (-) was estimated to be 100-150 fs. The present calculations confirmed that the repair reaction of thymine dimer takes place efficiently via an electron-transfer process from the FADH (-) enzyme.
Distasio, Robert A., Jr.; Santra, Biswajit; Ko, Hsin-Yu; Car, Roberto
2014-03-01
In this work, we report highly accurate ab initio path-integral molecular dynamics (AI-PIMD) simulations on liquid water at ambient conditions utilizing the recently developed PBE0+vdW(SC) exchange-correlation functional, which accounts for exact exchange and a self-consistent pairwise treatment of van der Waals (vdW) or dispersion interactions, combined with nuclear quantum effects (via the colored-noise generalized Langevin equation). The importance of each of these effects in the theoretical prediction of the structure of liquid water will be demonstrated by a detailed comparative analysis of the predicted and experimental oxygen-oxygen (O-O), oxygen-hydrogen (O-H), and hydrogen-hydrogen (H-H) radial distribution functions as well as other structural properties. In addition, we will discuss the theoretically obtained proton momentum distribution, computed using the recently developed Feynman path formulation, in light of the experimental deep inelastic neutron scattering (DINS) measurements. DOE: DE-SC0008626, DOE: DE-SC0005180.
Ko, Hsin-Yu; Distasio, Robert A., Jr.; Santra, Biswajit; Car, Roberto
Molecular crystal structure prediction has posed a substantial challenge to first-principles methods and requires sophisticated electronic structure methods to determine the stabilities of nearly degenerate polymorphs. In this work, we demonstrate that the anharmonicity from van der Waals interactions is relevant to the finite-temperature structures of pyridine and pyridine-like molecular crystals. Using such an approach, we find that the equilibrium structures are well captured with classical ab initio molecular dynamics (AIMD), despite the presence of light atoms such as hydrogen. Employing path integral AIMD simulations, we demonstrate that the success of classical AIMD results from a separation of nuclear quantum effects between the intermolecular and intramolecular degrees of freedom. In this separation, the quasiclassical and anharmonic intermolecular degrees of freedom determine the equilibrium structure, while the quantum and harmonic intramolecular degrees of freedom are averaging to the correct intramolecular structure. This work has been supported by the Department of Energy under Grants No. DE-FG02-05ER46201 and DE-SC0008626.
Energy Technology Data Exchange (ETDEWEB)
Schiffmann, Florian; VandeVondele, Joost, E-mail: Joost.VandeVondele@mat.ethz.ch [Nanoscale Simulations, Department of Materials, ETH Zürich, Wolfgang-Pauli-Str. 27, CH-8093 Zürich (Switzerland)
2015-06-28
We present an improved preconditioning scheme for electronic structure calculations based on the orbital transformation method. First, a preconditioner is developed which includes information from the full Kohn-Sham matrix but avoids computationally demanding diagonalisation steps in its construction. This reduces the computational cost of its construction, eliminating a bottleneck in large scale simulations, while maintaining rapid convergence. In addition, a modified form of Hotelling’s iterative inversion is introduced to replace the exact inversion of the preconditioner matrix. This method is highly effective during molecular dynamics (MD), as the solution obtained in earlier MD steps is a suitable initial guess. Filtering small elements during sparse matrix multiplication leads to linear scaling inversion, while retaining robustness, already for relatively small systems. For system sizes ranging from a few hundred to a few thousand atoms, which are typical for many practical applications, the improvements to the algorithm lead to a 2-5 fold speedup per MD step.
Properties of molten Ge chalcogenides an ab initio molecular dynamics study
Raty, J Y; Bichara, C
2003-01-01
In this study, we perform first-principles molecular dynamics simulations of the eutectic alloy Ge sub 1 sub 5 Te sub 8 sub 5 at five different densities and temperatures. We obtain structures in agreement with the available diffraction data and obtain a new view of the molten Ge chalcogenides. We show that the anomalous volume contraction observed in the liquid 30 K above the eutectic temperature corresponds to a significant change of the Ge-Te partial structure factor. The detailed structural analysis shows that volume variations observed upon melting in Ge sub 1 sub 5 Te sub 8 sub 5 , as in liquid GeSe and GeTe, can be explained in terms of the competition between two types of local environment of the germanium atoms. A symmetrical coordination octahedron is entropically favoured at high temperature, while an asymmetrical octahedron resulting from the local manifestation of the Peierls distortion is electronically favoured at lower temperatures.
Ab Initio Path Integral Molecular Dynamics Simulation of Hydrogen in Silicon
Probert, M. I. J.; Glover, M. J.
2006-05-01
We report results of a first-principles theoretical study of an isolated neutral hydrogen atom in crystalline silicon. Spin-polarised density functional theory is used to treat the electrons, and the path-integral molecular dynamics method is used to describe the quantum properties of the nucleus at finite temperature. This is necessary as the hydrogen atom has sufficiently low mass that it exhibits significant nuclear quantum delocalisation and zero-point motion even at room temperature. Unlike post-hoc treatments, such as calculating a static potential energy surface, the path-integral treatment enables such effects to be included "on-the-fly". This is found to be significant, as a coupling is found between the structure of the host silicon lattice and the quantum delocalisation of the hydrogen defect.
Indian Academy of Sciences (India)
Arindam Bankura; Amalendu Chandra
2005-10-01
The hydration structure and translocation of an excess proton in hydrogen bonded water clusters of two different sizes are investigated by means of finite temperature quantum simulations. The simulations are performed by employing the method of Car–Parrinello molecular dynamics where the forces on the nuclei are obtained directly from `on the fly' quantum electronic structure calculations. Since no predefined interaction potentials are used in this scheme, it is ideally suited to study proton translocation processes which proceed through breaking and formation of chemical bonds. The coordination number of the hydrated proton and the index of oxygen to which the excess proton is attached are calculated along the simulation trajectories for both the clusters.
Chagarov, Evgueni Anatolievich
Chemical-mechanical polishing (CMP) is a widely accepted process in the semiconductor industry. Despite intense theoretical and experimental research on CMP, there is a serious lack of fundamental understanding of the physical-chemical processes of polishing. The present work is intended to investigate these fundamental processes on an atomistic level. To model CMP on the atomic scale, a model of the amorphous silica is prepared by applying Design of Experiments (DOE) techniques to systematically investigate molecular dynamics preparation. These simulations yield high-quality models of amorphous silica, which are in excellent agreement with experimental results and are defect-free. Molecular dynamics simulations are performed to investigate the mechanical deformation during CMP of silica for different geometries and relative velocities. The simulations clarify asperity shape evolution during the process of shear and reveal temperature distributions as a function of time. It is found that the ratio of radii of a particle and asperity strongly affects the amount of the material removed whereas the relative velocity has a weaker affect on it. During shear, a significant local temperature increase occurs. This temperature increase lasts for a short time (picoseconds), but it can have a major impact on the amount of material removed. It is found that there could be significant deposition of the material from the particle to the slab, which can fill surface trenches and thereby make the surface smoother. An analytic model is developed for describing the amount of material removed as a function of asperity and particle radii and relative velocity. Density-functional calculations of different surfaces of two silica polymorphs, alpha-quartz and beta-cristobalite, are performed. The surface energies are calculated as a function of oxygen partial pressure for several different surface reconstructions and terminations. The case of hydrogen passivation is investigated to
Partovi-Azar, Pouya
2015-01-01
We present a computational method to accurately calculate Raman spectra from first principles with an at least one order of magnitude higher efficiency. This scheme thus allows to routinely calculate finite-temperature Raman spectra "on-the-fly" by means of \\textit{ab-initio} molecular dynamics simulations. To demonstrate the predictive power of this approach we investigate the effect of hydrophobic and hydrophilic solutes in water solution on the infrared and Raman spectra.
Ab Initio Molecular Dynamics Study of Aqueous Solvation of Ethanol and Ethylene
Van Erp, T S; Erp, Titus S. van; Meijer, Evert Jan
2002-01-01
The structure and dynamics of aqueous solvation of ethanol and ethylene are studied by DFT-based Car-Parrinello molecular dynamics. We did not find an enhancement of the structure of the hydrogen bonded network of hydrating water molecules. Both ethanol and ethylene can easily be accommodated in the hydrogen-bonded network of water molecules without altering its structure. This is supports the conclusion from recent neutron diffraction experiments that there is no hydrophobic hydration around small hydrophobic groups. Analysis of the electronic charge distribution using Wannier functions shows that the dipole moment of ethanol increases from 1.8 D to 3.1 D upon solvation, while the apolar ethylene molecule attains an average dipole moment of 0.5 D. For ethylene, we identified configurations with $\\pi$-H bonded water molecules, that have rare four-fold hydrogen-bonded water coordination, yielding instantaneous dipole moments of ethylene of up to 1 D. The results provide valuable information for the improvement...
Non-equilibrium dynamics in disordered materials: Ab initio molecular dynamics simulations
Energy Technology Data Exchange (ETDEWEB)
Ohmura, Satoshi; Nagaya, Kiyonobu; Yao, Makoto [Department of Physics, Kyoto University, Kyoto 606-8502 (Japan); Shimojo, Fuyuki [Department of Physics, Kumamoto University, Kumamoto 860-8555 (Japan)
2015-08-17
The dynamic properties of liquid B{sub 2}O{sub 3} under pressure and highly-charged bromophenol molecule are studied by using molecular dynamics (MD) simulations based on density functional theory (DFT). Diffusion properties of covalent liquids under high pressure are very interesting in the sense that they show unexpected pressure dependence. It is found from our simulation that the magnitude relation of diffusion coefficients for boron and oxygen in liquid B{sub 2}O{sub 3} shows the anomalous pressure dependence. The simulation clarified the microscopic origin of the anomalous diffusion properties. Our simulation also reveals the dissociation mechanism in the coulomb explosion of the highly-charged bromophenol molecule. When the charge state n is 6, hydrogen atom in the hydroxyl group dissociates at times shorter than 20 fs while all hydrogen atoms dissociate when n is 8. After the hydrogen dissociation, the carbon ring breaks at about 100 fs. There is also a difference on the mechanism of the ring breaking depending on charge states, in which the ring breaks with expanding (n = 6) or shrink (n = 8)
Keith, J. Brandon; Fennick, Jacob R.; Junkermeier, Chad E.; Nelson, Daniel R.; Lewis, James P.
2009-03-01
FIREBALL is an ab initio technique for fast local orbital simulations of nanotechnological, solid state, and biological systems. We have implemented a convenient interface for new users and software architects in the platform-independent Java language to access FIREBALL's unique and powerful capabilities. The graphical user interface can be run directly from a web server or from within a larger framework such as the Computational Science and Engineering Online (CSE-Online) environment or the Distributed Analysis of Neutron Scattering Experiments (DANSE) framework. We demonstrate its use for high-throughput electronic structure calculations and a multi-100 atom quantum molecular dynamics (MD) simulation. Program summaryProgram title: FireballUI Catalogue identifier: AECF_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECF_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 279 784 No. of bytes in distributed program, including test data, etc.: 12 836 145 Distribution format: tar.gz Programming language: Java Computer: PC and workstation Operating system: The GUI will run under Windows, Mac and Linux. Executables for Mac and Linux are included in the package. RAM: 512 MB Word size: 32 or 64 bits Classification: 4.14 Nature of problem: The set up and running of many simulations (all of the same type), from the command line, is a slow process. But most research quality codes, including the ab initio tight-binding code FIREBALL, are designed to run from the command line. The desire is to have a method for quickly and efficiently setting up and running a host of simulations. Solution method: We have created a graphical user interface for use with the FIREBALL code. Once the user has created the files containing the atomic coordinates for each system that they are
Svoboda, Ondřej; Ončák, Milan; Slavíček, Petr
2011-10-01
We have performed large-scale simulations of UV absorption spectra of water clusters (monomer to octamer) using a combination of ab initio path-integral molecular dynamics with reflection principle. The aim of the present work is four-fold: (1) To explore the transition from isolated molecules to bulk water from the perspective of UV photoabsorption. (2) To investigate quantum nuclear and thermal effects on the shape of the water UV spectra. (3) To make an assessment of the density functional theory functionals to be used for water excited states. (4) To check the applicability of the QM/MM schemes for a description of the UV absorption. Within the path integral molecular dynamics (PIMD)/reflection principle approach both the thermal and quantum vibrational effects including anharmonicities are accounted for. We demonstrate that shape of the spectra is primarily controlled by the nuclear quantum effects. The excited states and transition characteristics of the water clusters were calculated with the time-dependent density functional theory and equation-of-motion coupled clusters singles and doubles methods. Based on our benchmark calculations considering the whole UV spectrum we argue that the BHandHLYP method performs best among the 6 functionals tested (B3LYP, BHandHLYP, BNL, CAM-B3LYP, LC-ωPBE, and M06HF). We observe a gradual blueshift of the maximum of the first absorption peak with the increasing cluster size. The UV absorption spectrum for the finite size clusters (i.e., the peak centers, peak widths, and photoabsorption cross section) essentially converges into the corresponding bulk water spectrum. The effect of distant molecules accounted for within the polarizable continuum model is shown to be almost negligible. Using the natural transition orbitals we demonstrate that the first absorption band is formed by localized excitations while the second band includes delocalized excited states. Consequently, the QM/MM electrostatic embedding scheme can only be
Ab initio molecular dynamics studies on effect of Zr on oxidation resistance of TiAlN coatings
Energy Technology Data Exchange (ETDEWEB)
Pi, Jingwu [State Key Lab of Powder Metallurgy, Central South University, Changsha,Hunan 410083 (China); Kong, Yi, E-mail: yikong@csu.edu.cn [State Key Lab of Powder Metallurgy, Central South University, Changsha,Hunan 410083 (China); Chen, Li [State Key Lab of Powder Metallurgy, Central South University, Changsha,Hunan 410083 (China); Zhuzhou Cemented Carbide Cutting Tools Co., Ltd., Zhuzhou, Hunan 412007 (China); Du, Yong [State Key Lab of Powder Metallurgy, Central South University, Changsha,Hunan 410083 (China)
2016-08-15
Highlights: • The lowest bonding energy sequence for dimers in the vacuum: Zr−O < Ti−O < Al−O. • The lowest bonding energy sequence for oxygen above the surface: Ti−O < Zr−O < Al−O. • At 300 K, the addition of Zr benefitting the formation of vacancy and TiO{sub 2}. • At 1123 K, the addition of Zr leading to a more stable surface. • Our findings explain that the oxidation resistance of TiAlZrN superior to TiAlN at 1123 K as well as TiAlZrN at 300 K. - Abstract: It was demonstrated experimentally that doping Zr into TiAlN coatings at room temperature will detriment its oxidation resistance. On the other hand, there are evidences that doping Zr into TiAlN at high temperature will improve coating's oxidation resistance. In the present work, we address the effect of Zr on the oxidation resistance of TiAlN by means of ab initio molecular dynamics simulations. The TiAlN and TiAlZrN (1 Zr atom replacing 1 Ti atom) surfaces covered with 4 oxygen atoms at 300 K and 1123 K were simulated. Based on the analysis of the atomic motion, bond formation after relaxation, and the charge density difference maps we find that at 300 K, the addition of Zr induces escape of Ti atoms from the surface, resulting in formation of surface vacancies and subsequently TiO{sub 2}. Comparison of metal-oxygen dimers in the vacuum and above the TiAlZrN surface further shows that the addition of Zr in the TiAlN surface will change the lowest bonding energy sequence from Zr−O < Ti−O < Al−O in the vacuum to Ti−O < Zr−O < Al−O above the TiAlZrN surface. From Molecular Dynamics simulations at 1123 K, it is find that no Ti vacancies were generated in the surface. Moreover, less charge is transferred from metal to N atoms and the bond lengths between Ti and O atoms become shorter at 1123 K as compared with 300 K, suggesting that the addition of Zr atom promotes the interaction of Ti and O at TiAlZrN surface at 1123 K, leading to a more stable surface. Our simulation
Laporte, Sara; Finocchi, Fabio; Paulatto, Lorenzo; Blanchard, Marc; Balan, Etienne; Guyot, François; Saitta, Antonino Marco
2015-08-21
We report a density-functional theory (DFT)-based study of the interface of bulk water with a prototypical oxide surface, MgO(001), and focus our study on the often-overlooked surface electric field. In particular, we observe that the bare MgO(001) surface, although charge-neutral and defectless, has an intense electric field on the Å scale. The MgO(001) surface covered with 1 water monolayer (1 ML) is investigated via a supercell accounting for the experimentally-observed (2 × 3) reconstruction, stable at ambient temperature, and in which two out of six water molecules are dissociated. This 1 ML-hydrated surface is also found to have a high, albeit short-ranged, normal component of the field. Finally, the oxide/water interface is studied via room-temperature ab initio molecular dynamics (AIMD) using 34 H2O molecules between two MgO(001) surfaces. To our best knowledge this is the first AIMD study of the MgO(001)/liquid water interface in which all atoms are treated using DFT and including several layers above the first adsorbed layer. We observe that the surface electric field, averaged over the AIMD trajectories, is still very strong on the fully-wet surface, peaking at about 3 V Å(-1). Even in the presence of bulk-like water, the structure of the first layer in contact with the surface remains similar to the (2 × 3)-reconstructed ice ad-layer on MgO(001). Moreover, we observe proton exchange within the first layer, and between the first and second layers - indeed, the O-O distances close to the surface are found to be distributed towards shorter distances, a property which has been shown to directly promote proton transfer.
Lee, Hee-Seung; Tuckerman, Mark E.
2007-04-01
Dynamical properties of liquid water were studied using Car-Parrinello [Phys. Rev. Lett. 55, 2471 (1985)] ab initio molecular dynamics (AIMD) simulations within the Kohn-Sham (KS) density functional theory employing the Becke-Lee-Yang-Parr exchange-correlation functional for the electronic structure. The KS orbitals were expanded in a discrete variable representation basis set, wherein the complete basis set limit can be easily reached and which, therefore, provides complete convergence of ionic forces. In order to minimize possible nonergodic behavior of the simulated water system in a constant energy (NVE) ensemble, a long equilibration run (30ps) preceded a 60ps long production run. The temperature drift during the entire 60ps trajectory was found to be minimal. The diffusion coefficient [0.055Å2/ps] obtained from the present work for 32 D2O molecules is a factor of 4 smaller than the most up to date experimental value, but significantly larger than those of other recent AIMD studies. Adjusting the experimental result so as to match the finite-sized system used in the present study brings the comparison between theory and experiment to within a factor of 3. More importantly, the system is not observed to become "glassy" as has been reported in previous AIMD studies. The computed infrared spectrum is in good agreement with experimental data, especially in the low frequency regime where the translational and librational motions of water are manifested. The long simulation length also made it possible to perform detailed studies of hydrogen bond dynamics. The relaxation dynamics of hydrogen bonds observed in the present AIMD simulation is slower than those of popular force fields, such as the TIP4P potential, but comparable to that of the TIP5P potential.
Vibrational properties of silica species in MgO-SiO2 glasses from ab initio molecular dynamics
Spiekermann, G.; Steele-MacInnis, M.; Kowalski, P. M.; Schmidt, C.; Jahn, S.
2012-04-01
Glasses and melts in the system MgO-SiO2 are analogs for magmas of the Earth's mantle. Therefore knowledge of the structure of these glasses and melts is important for understanding numerous geological processes. Raman spectroscopy is useful for probing the atomic-scale structure of glasses and melts. However, correct assignment of observed vibrational bands to specific structural and modal origins is challenging. We present the mode-projection technique to calculate vibrational subspectra for specific modal vibrations of several fundamental silica structures in silicate glasses. Structural subunits that we have studied include Q0 to Q4 tetrahedra, Si-O-Si bridging oxygen atoms for any degree of polymerization of the adjacent tetrahedra, the ethane-like symmetry of the dimer, and three- and four-fold rings. We apply this technique to ab initio molecular dynamics (MD) trajectories of MgO-SiO2 glasses at 1000 K. We found the tetrahedral symmetric stretch at 863 cm-1 for Q0, 885 cm-1 for Q1, a double peak of 960 cm-1 and 1037 cm-1 for Q2, 1032 cm-1 for Q3 and 1080 cm-1 for Q4. The bridging oxygen asymmetric stretch is at about 980 cm-1 for Q1-Q1, and it shifts to about 1100 cm-1 with increasing polymerization. This analysis has applications especially for understanding the structure of silica-poor glasses. For instance, two contradicting Raman spectroscopy studies of Mg2SiO4 glasses reported the most polymerized SiO4 tetrahedra in the glass structure to be either Q0 [1] or Q3 [2]. Our results indicate that the degree of polymerization is overestimated, if the Si-O-Si stretching modes are not considered in the interpretation of the measured Raman spectra. [1] Nasikas, N. K. and Chrissanthopoulos, A. and Bouropoulos, N. and Sen, S. and Papatheodorou, G. N., 2011, Chemistry of Materials 23, 3692-3697. [2] Kalampounias, A. G. and Nasikas, N. K. and Papatheodorou, G. N., 2009, Journal of Chemical Physics 131, 114513.
Energy Technology Data Exchange (ETDEWEB)
None, None
2016-01-01
The nature of chemical bonding of molybdenum in high level nuclear waste glasses has been elucidated by ab initio molecular dynamics simulations. Two compositions, (SiO2)57.5 – (B2O3)10 – (Na2O)15 – (CaO)15 – (MoO3)2.5 and (SiO2)57.3 – (B2O3)20 – (Na2O)6.8 – (Li2O)13.4 – (MoO3)2.5 , were considered in order to investigate the effect of ionic and covalent components on the glass structure and the formation of the crystallisation precursors (Na2MoO4 and CaMoO4). The coordination environments of Mo cations and the corresponding bond lengths calculated from our model are in excellent agreement with experimental observations. The analysis of the first coordination shell reveals two different types of molybdenum host matrix bonds in the lithium sodium borosilicate glass. Based on the structural data and the bond valence model, we demonstrate that the Mo cation can be found in a redox state and the molybdate tetrahedron can be connected with the borosilicate network in a way that inhibits the formation of crystalline molybdates. These results significantly extend our understanding of bonding in Mo-containing nuclear waste glasses and demonstrate that tailoring the glass composition to specific heavy metal constituents can facilitate incorporation of heavy metals at high concentrations. K.K. was supported through the Impact Studentship scheme at UCL co-funded by the IHI Corporation and UCL. P.V.S. thanks the Royal Society, which supported preliminary work on this project, and the Laboratory Directed Research and Development program at PNNL, a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy. Via our membership of the UK's HEC Materials Chemistry Consortium, which is funded by EPSRC (EP/L000202), this work used the ARCHER UK National Supercomputing Service (http://www.archer.ac.uk).
Kroes, Geert-Jan; Pavanello, Michele; Blanco-Rey, María; Alducin, Maite; Auerbach, Daniel J
2014-08-07
Energy loss from the translational motion of an atom or molecule impinging on a metal surface to the surface may determine whether the incident particle can trap on the surface, and whether it has enough energy left to react with another molecule present at the surface. Although this is relevant to heterogeneous catalysis, the relative extent to which energy loss of hot atoms takes place to phonons or electron-hole pair (ehp) excitation, and its dependence on the system's parameters, remain largely unknown. We address these questions for two systems that present an extreme case of the mass ratio of the incident atom to the surface atom, i.e., H + Cu(111) and H + Au(111), by presenting adiabatic ab initio molecular dynamics (AIMD) predictions of the energy loss and angular distributions for an incidence energy of 5 eV. The results are compared to the results of AIMDEFp calculations modeling energy loss to ehp excitation using an electronic friction ("EF") model applied to the AIMD trajectories, so that the energy loss to the electrons is calculated "post" ("p") the computation of the AIMD trajectory. The AIMD calculations predict average energy losses of 0.38 eV for Cu(111) and 0.13-0.14 eV for Au(111) for H-atoms that scatter from these surfaces without penetrating the surface. These energies closely correspond with energy losses predicted with Baule models, which is suggestive of structure scattering. The predicted adiabatic integral energy loss spectra (integrated over all final scattering angles) all display a lowest energy peak at an energy corresponding to approximately 80% of the average adiabatic energy loss for non-penetrative scattering. In the adiabatic limit, this suggests a way of determining the approximate average energy loss of non-penetratively scattered H-atoms from the integral energy loss spectrum of all scattered H-atoms. The AIMDEFp calculations predict that in each case the lowest energy loss peak should show additional energy loss in the
Campetella, M.; Bovi, D.; Caminiti, R.; Guidoni, L.; Bencivenni, L.; Gontrani, L.
2016-07-01
In this work we report an analysis of the bulk phase of 2-methoxyethylammonium nitrate based on ab initio molecular dynamics. The structural and dynamical features of the ionic liquid have been characterized and the computational findings have been compared with the experimental X-ray diffraction patterns, with infrared spectroscopy data, and with the results obtained from molecular dynamics simulations. The experimental infrared spectrum was interpreted with the support of calculated vibrational density of states as well as harmonic frequency calculations of selected gas phase clusters. Particular attention was addressed to the high frequency region of the cation (ω > 2000 cm-1), where the vibrational motions involve the NH3+ group responsible for hydrogen bond formation, and to the frequency range 1200-1400 cm-1 where the antisymmetric stretching mode (ν3) of nitrate is found. Its multiple absorption lines in the liquid arise from the removal of the degeneracy present in the D3h symmetry of the isolated ion. Our ab initio molecular dynamics leads to a rationalization of the frequency shifts and splittings, which are inextricably related to the structural modifications induced by a hydrogen bonding environment. The DFT calculations lead to an inhomogeneous environment.
Directory of Open Access Journals (Sweden)
del Rio B. G.
2017-01-01
Full Text Available We report results of an orbital-free ab initio molecular dynamics (OF-AIMD study of the free liquid surface (FLS of Sn at 1000 K and 600 K. A key ingredient in the OF-AIMD method is the local pseudopotential describing the ions-valence electrons interaction. We have used a force-matching method to derive a local pseudopotential suitable to account for the variation of the forces from the bulk to the FLS. We obtain very good results for structural properties, such as the reflectivity, including the characteristic shoulder it presents in x-ray experiments. Moreover we have been able to study ab initio for the first time the evolution in some dynamical properties as we move from the central region, where the system behaves like the bulk liquid, to the FLS.
del Rio, B. G.; González, L. E.
2017-08-01
We report results of an orbital-free ab initio molecular dynamics (OF-AIMD) study of the free liquid surface (FLS) of Sn at 1000 K and 600 K. A key ingredient in the OF-AIMD method is the local pseudopotential describing the ions-valence electrons interaction. We have used a force-matching method to derive a local pseudopotential suitable to account for the variation of the forces from the bulk to the FLS. We obtain very good results for structural properties, such as the reflectivity, including the characteristic shoulder it presents in x-ray experiments. Moreover we have been able to study ab initio for the first time the evolution in some dynamical properties as we move from the central region, where the system behaves like the bulk liquid, to the FLS.
Kessler, Jan; Spura, Thomas; Karhan, Kristof; Partovi-Azar, Pouya; Hassanali, Ali A; Kühne, Thomas D
2015-01-01
The structure and dynamics of the water/vapor interface is revisited by means of path-integral and second-generation Car-Parrinello ab-initio molecular dynamics simulations in conjunction with an instantaneous surface definition [A. P. Willard and D. Chandler, J. Phys. Chem. B 114, 1954 (2010)]. In agreement with previous studies, we find that one of the OH bonds of the water molecules in the topmost layer is pointing out of the water into the vapor phase, while the orientation of the underlying layer is reversed. Therebetween, an additional water layer is detected, where the molecules are aligned parallel to the instantaneous water surface.
Tachikawa, Hiroto
2005-01-01
Direct ab initio molecular dynamics (MD) calculations have been carried out for the reaction of cyclopropenyl chloride with halide ion (F–) (F– + (CH)3Cl → F(CH)3 + Cl–) in gas phase. Both SN2 and SN2′ channels were found as product channels. These channels are strongly dependent on the collision angle of F– to the target (CH)3Cl molecule. The collision at one of the carbon atoms of the C=C double bond leads to the SN2′ reaction channel; whereas the collision at the methylene carbon atom lead...
Directory of Open Access Journals (Sweden)
Niall J. English
2015-08-01
Full Text Available Equilibrium Born-Oppenheimer molecular dynamics simulations have been performed in the canonical ensemble to investigate the structural properties of liquid water and ice Ih (hexagonal ice at 298 and 273 K, respectively, using a state-of-the-art non-local correlation functional, whilst size effects have been examined explicitly in the case of liquid water. This has led to improved agreement with experiments for pair distribution functions, in addition to molecular dipole moments, vis-à-vis previous flavours of ab-initio molecular dynamics simulation of water, highlighting the importance of appropriate dispersion. Intramolecular geometry has also been examined, in addition to hydrogen-bonding interactions; it was found that an improved description of dispersion via non-local correlation helps to reduce over-structuring associated with the Perdew-Becke-Ernzerhof (PBE and other commonly-used functionals.
Amokrane, S.; Ayadim, A.; Levrel, L.
2015-11-01
We consider the question of the amorphization of metallic alloys by melt quenching, as predicted by molecular dynamics simulations with semi-empirical potentials. The parametrization of the potentials is discussed on the example of the ternary Cu-Ti-Zr transition metals alloy, using the ab-initio simulation as a reference. The pair structure in the amorphous state is computed from a potential of the Stillinger-Weber form. The transferability of the parameters during the quench is investigated using two parametrizations: from solid state data, as usual and from a new parametrization on the liquid structure. When the adjustment is made on the pair structure of the liquid, a satisfactory transferability is found between the pure components and their alloys. The liquid structure predicted in this way agrees well with experiment, in contrast with the one obtained using the adjustment on the solid. The final structure, after quenches down to the amorphous state, determined with the new set of parameters is shown to be very close to the ab-initio one, the latter being in excellent agreement with recent X-rays diffraction experiments. The corresponding critical temperature of the glass transition is estimated from the behavior of the heat capacity. Discussion on the consistency between the structures predicted using semi-empirical potentials and ab-initio simulation, and comparison of different experimental data underlines the question of the dependence of the final structure on the thermodynamic path followed to reach the amorphous state.
Novko, Dino; Lončarić, Ivor; Blanco-Rey, María; Juaristi, J. Iñaki; Alducin, Maite
2017-08-01
We study surface temperature effects on the adsorption and relaxation of N atoms on Ag(111). To this aim, we perform ab initio molecular dynamics simulations with electronic friction, in which the surface is coupled to a thermostat that fixes the desired surface temperature. Simulations performed at 80 and 700 K show that the surface temperature has minor effects on magnitudes such as the initial adsorption probability, the relaxation rate of the adsorbing N, and the energy lost in electronic excitations. Slight differences are identified in the adsorption paths with the appearance of subsurface absorption events at 700 K that are not observed at 80 K. Furthermore, we perform additional simulations without a thermostat in order to examine the validity of commonly used ab initio molecular dynamics simulations in which no heat dissipation from the simulation cell is allowed. Our results show that such a methodology may not suffice to simulate the low-temperature regime since the surface becomes unphysically heated within a few picoseconds upon adsorption of the N atom. However, neither in this unfavorable case are the magnitudes defining the dynamics of the adsorbates at the same time scale significantly modified from those obtained at constant surface temperature.
Oguri, Tomoya; Shimamura, Kohei; Shibuta, Yasushi; Shimojo, Fuyuki; Yamaguchi, Shu
2014-03-01
Dissociation of ethanol on a nickel cluster is investigated by ab initio molecular dynamics simulation to reveal the bond dissociation mechanism of carbon source molecules during carbon nanotube synthesis. C-C bonds in only CHxCO fragments are dissociated on the nickel cluster, whereas there is no preferential structure among the fragments for C-O bond dissociation. The dissociation preference is uncorrelated with the bond dissociation energy of corresponding bonds in freestanding molecules but is correlated with the energy difference between fragment molecules before and after dissociation on the nickel surface. Moreover, carbon-chain formation occurs after C-C bond dissociation in a continuous simulation. What determines the chirality of CNTs? What happens at the dissociation stage of carbon source molecules? Regarding the former question, many researchers have pointed out the good epitaxial relationship between a graphite network and a close-packed facet (i.e., fcc(1 1 1) or hcp(0 0 0 1)) of transition metals [17-19]. Therefore, the correlation between the chirality of CNTs and the angle of the step edge on metal (or metal carbide) surfaces has been closely investigated [20-22]. In association with this geometric matching, the epitaxial growth of graphene on Cu(1 1 1) and Ni(1 1 1) surfaces has recently been achieved via CCVD technique [23-25], which is a promising technique for the synthesis of large-area and monolayer graphene.Regarding the latter question, it is empirically known that the yield and quality of CNT products strongly depend on the choice of carbon source molecules and additives. For example, it is well known that the use of ethanol as carbon source molecules yields a large amount of SWNTs without amorphous carbons (called the alcohol CCVD (ACCVD) technique) compared with the CCVD process using hydrocarbons [4]. Moreover, the addition of a small amount of water dramatically enhances the activity and lifetime of the catalytic metal (called the
Imandi, Venkataramana; Nair, Nisanth N.
2016-09-01
The absence of isotope scrambling observed by Henry and coworkers in the Wacker oxidation of deuterated allylic alcohol was used by them as support for the inner-sphere mechanism hydroxypalladation mechanism. One of the assumptions used to interpret their experimental data was that allyl alcohol oxidation takes place through non-cyclic intermediate routes as in the case of ethene. Here we verify this assumption through ab initio metadynamics simulations of the Wacker oxidation of allyl alcohol in explicit solvent. Importance of our results in interpreting the isotope scrambling experiments is discussed.
Taioli, Simone; Garberoglio, Giovanni; Simonucci, Stefano; a Beccara, Silvio; Aversa, Lucrezia; Nardi, Marco; Verucchi, Roberto; Iannotta, Salvatore; Dapor, Maurizio; Alfè, Dario
2013-01-28
In this work, we investigate the processes leading to the room-temperature growth of silicon carbide thin films by supersonic molecular beam epitaxy technique. We present experimental data showing that the collision of fullerene on a silicon surface induces strong chemical-physical perturbations and, for sufficient velocity, disruption of molecular bonds, and cage breaking with formation of nanostructures with different stoichiometric character. We show that in these out-of-equilibrium conditions, it is necessary to go beyond the standard implementations of density functional theory, as ab initio methods based on the Born-Oppenheimer approximation fail to capture the excited-state dynamics. In particular, we analyse the Si-C(60) collision within the non-adiabatic nuclear dynamics framework, where stochastic hops occur between adiabatic surfaces calculated with time-dependent density functional theory. This theoretical description of the C(60) impact on the Si surface is in good agreement with our experimental findings.
Hayashi, Aiko; Shiga, Motoyuki; Tachikawa, Masanori
2006-11-01
In order to investigate the H /D isotope effect on a dihydrogen bonded cation system, we have studied NH4+⋯BeH2 and its isotopomers by ab initio path integral molecular dynamics. It is found that the dihydrogen bond can be exchanged by NH4+ rotation. The deuterated isotopomer (ND4+⋯BeD2; DD) can exchange the dihydrogen bond more easily than other isotopomers such as (NH4+⋯BeH2; HH). This unusual isotope effect is ascribed to the "quantum localization" which occurs when the effective energy barrier for the rotational mode becomes higher by the zero point energy of other modes. We also found that the binding energy of dihydrogen bonds for DD species is the smallest among the isotopomers.
Energy Technology Data Exchange (ETDEWEB)
E. Bohm A. Bhatele L. V. Kale M. E. Tuckerman S. Kumar J. A. Gunnels G. J. Martyna; Bohm, E. [Thomas M. Siebel Center, Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States). Dept of Computer Science; Bhatele, A. [Thomas M. Siebel Center, Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States). Dept of Computer Science; Kale, L. V. [Thomas M. Siebel Center, Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States). Dept of Computer Science; Tuckerman, M. E. [New York Univ., NY (United States). Dept. of Chemistry and Courant Institute of Mathematical Sciences; Kumar, S. [IBM T. J. Watson Research Center, Yorktown Heights, NY (United States). IBM Research Division; Gunnels, J. A. [IBM T. J. Watson Research Center, Yorktown Heights, NY (United States). IBM Research Division; Martyna, G. J. [IBM T. J. Watson Research Center, Yorktown Heights, NY (United States). IBM Research Division
2008-01-01
Important scientific problems can be treated via ab initio-based molecular modeling approaches, wherein atomic forces are derived from an energy Junction that explicitly considers the electrons. The Car-Parrinello ab initio molecular dynamics (CPAIMD) method is widely used to study small systems containing on the order of 10 to 103 atoms. However, the impact of CPAIMD has been limited until recently because of difficulties inherent to scaling the technique beyond processor numbers about equal to the number of electronic states. CPAIMD computations involve a large number of interdependent phases with high interprocessor communication overhead. These phases require the evaluation of various transforms and non-square matrix multiplications that require large interprocessor data movement when efficiently parallelized. Using the Charm++ parallel programming language and runtime system, the phases are discretized into a large number of virtual processors, which are, in turn, mapped flexibly onto physical processors, thereby allowing interleaving of work. Algorithmic and IBM Blue Gene/L(tm) system-specific optimizations are employed to scale the CPAIMD method to at least 30 times the number of electronic states in small systems consisting of 24 to 768 atoms (32 to 1,024 electronic states) in order to demonstrate fine-grained parallelism. The largest systems studied scaled well across the entire machine (20,480 nodes).
Ab initio molecular dynamics simulations of ion–solid interactions in Gd2Zr2O7 and Gd2Ti2O7
Energy Technology Data Exchange (ETDEWEB)
Wang, X. J.; Xiao, H. Y.; Zu, X. T.; Zhang, Y.; Weber, W. J.
2013-01-01
The development of ab initio molecular dynamics (AIMD) method has made it a powerful tool in describing ion-solid interactions in materials, with identification determination of threshold displacement energies with ab initio accuracy, and prediction of new mechanism for defect generation and new defective states that are different from classical molecular dynamics (MD) simulations. In the present work, this method is employed to study the low energy recoil events in Gd2Zr2O7 and Gd2Ti2O7. The weighted average threshold displacement energies in Gd2Zr2O7 are determined to be 38.8 eV for Gd, 41.4 eV for Zr, 18.6 eV for O48f, and 15.6 eV for O8b, which are smaller than the respective values of 41.8, >53.8, 22.6 and 16.2 eV in Gd2Ti2O7. It reveals that all the ions in Gd2Zr2O7 are more easily displaced than those in Gd2Ti2O7, and anion order-disorder are more likely to be involved in the displacement events than cation disordering. The average charge transfer from the primary knock-on atom to its neighbors is estimated to be ~0.15, ~0.11-0.27 and ~0.1-0.13 |e| for Gd, Zr (or Ti), and O, respectively. Negligence of the charge transfer in the interatomic potentials may result in the larger threshold displacement energies in classical MD.
Ab initio molecular dynamics simulations of ion–solid interactions in Gd2Zr2O7 and Gd2Ti2O7
Energy Technology Data Exchange (ETDEWEB)
Wang, X. J.; Xiao, Haiyan Y.; Zu, Xiaotao; Zhang, Yanwen; Weber, William J.
2012-12-21
The development of the ab initio molecular dynamics (AIMD) method has made it a powerful tool in describing ion–solid interactions in materials, with the determination of threshold displacement energies with ab initio accuracy, and prediction of a new mechanism for defect generation and new defective states that are different from classical molecular dynamics (MD) simulations. In the present work, this method is employed to study the low energy recoil events in Gd2Zr2O7 and Gd2Ti2O7. The weighted average threshold displacement energies in Gd2Zr2O7 are determined to be 38.8 eV for Gd, 41.4 eV for Zr, 18.6 eV for O48f, and 15.6 eV for O8b, which are smaller than the respective values of 41.8, >53.8, 22.6 and 16.2 eV in Gd2Ti2O7. It reveals that all the ions in Gd2Zr2O7 are more easily displaced than those in Gd2Ti2O7, and anion order–disorder is more likely to be involved in the displacement events than cation disordering. The average charge transfer from the primary knock-on atom to its neighbors is estimated to be [similar]0.15, [similar]0.11 to 0.27 and [similar]0.1 to 0.13 |e| for Gd, Zr (or Ti), and O, respectively. Neglecting the charge transfer in the interatomic potentials may result in the larger threshold displacement energies in classical MD.
Scherrer, Arne; Vuilleumier, Rodolphe; Sebastiani, Daniel
2016-08-28
We report the first fully ab initio calculation of dynamical vibrational circular dichroism spectra in the liquid phase using nuclear velocity perturbation theory (NVPT) derived electronic currents. Our approach is rigorous and general and thus capable of treating weak interactions of chiral molecules as, e.g., chirality transfer from a chiral molecule to an achiral solvent. We use an implementation of the NVPT that is projected along the dynamics to obtain the current and magnetic dipole moments required for accurate intensities. The gauge problem in the liquid phase is resolved in a twofold approach. The electronic expectation values are evaluated in a distributed origin gauge, employing maximally localized Wannier orbitals. In a second step, the gauge invariant spectrum is obtained in terms of a scaled molecular moments, which allows to systematically include solvent effects while keeping a significant signal-to-noise ratio. We give a thorough analysis and discussion of this choice of gauge for the liquid phase. At low temperatures, we recover the established double harmonic approximation. The methodology is applied to chiral molecules ((S)-d2-oxirane and (R)-propylene-oxide) in the gas phase and in solution. We find an excellent agreement with the theoretical and experimental references, including the emergence of signals due to chirality transfer from the solute to the (achiral) solvent.
Scherrer, Arne; Vuilleumier, Rodolphe; Sebastiani, Daniel
2016-08-01
We report the first fully ab initio calculation of dynamical vibrational circular dichroism spectra in the liquid phase using nuclear velocity perturbation theory (NVPT) derived electronic currents. Our approach is rigorous and general and thus capable of treating weak interactions of chiral molecules as, e.g., chirality transfer from a chiral molecule to an achiral solvent. We use an implementation of the NVPT that is projected along the dynamics to obtain the current and magnetic dipole moments required for accurate intensities. The gauge problem in the liquid phase is resolved in a twofold approach. The electronic expectation values are evaluated in a distributed origin gauge, employing maximally localized Wannier orbitals. In a second step, the gauge invariant spectrum is obtained in terms of a scaled molecular moments, which allows to systematically include solvent effects while keeping a significant signal-to-noise ratio. We give a thorough analysis and discussion of this choice of gauge for the liquid phase. At low temperatures, we recover the established double harmonic approximation. The methodology is applied to chiral molecules ((S)-d2-oxirane and (R)-propylene-oxide) in the gas phase and in solution. We find an excellent agreement with the theoretical and experimental references, including the emergence of signals due to chirality transfer from the solute to the (achiral) solvent.
Canaval, Lorenz R; Hadisaputra, Saprizal; Hofer, Thomas S
2015-07-07
Ab initio QMCF-MD simulations of aqueous 18-crown-6 (18C6) and strontium(II)-18-crown-6 (18C6-Sr) were performed to gather insight into their hydration properties. Strongly different characteristics were found for the two solutes in terms of structure and dynamics such as H-bonding. They, however, have in common that their backbone shows high flexibility in aqueous medium, adopting structures significantly differing from idealized gas phase geometries. In particular, planar oxyethylene units stable in the picosecond range occurred in 18C6, while the strontium complex readily exhibits a bent structure. Detailed analysis of this high flexibility was done via two dimensional root mean square deviation plots as well as the evolution of dihedral angles and angles within the simulation trajectory. The vibrational spectra obtained from the QMCF-MD simulations are in excellent agreement with experimental data and show a pronounced blueshift upon complexation of the strontium(II) ion in 18C6.
Mei, Yuan; Etschmann, Barbara; Liu, Weihua; Sherman, David M.; Testemale, Denis; Brugger, Joël
2016-04-01
Chlorine and sulfur are the main elements involved in the complexing of metals in ore-forming fluids. The nature and thermodynamic properties of the Zn(II)-Cl complexes have been investigated by previous experimental and theoretical studies and are now well established up to high temperatures (600 °C). In contrast, the role of bisulfide complexes for zinc speciation in sulfur-bearing fluids remains poorly known, and a better understanding of Zn(II)-HS complexation is required for modeling zinc transport in magmatic and metamorphic fluids and for optimizing the hydrometallurgical processing of sulfide ores. We have conducted ab initio molecular dynamics (MD) simulations to calculate the speciation of Zn(II)-HS complexes from ambient to hydrothermal-magmatic conditions (25-600 °C, up to 2000 bar). These theoretical calculations were complemented by X-ray absorption spectroscopy (XAS) measurements of Zn(II) in HS--rich solutions at 200-500 °C and 600-1000 bar. The speciation and geometrical properties predicted by the ab initio MD simulations and the in situ XAS data are in excellent agreement. Upon heating from room temperature to 250 °C, Zn(II) speciation in HS--rich solutions shows a transition from the sixfold octahedral hexaaquo complex [Zn(H2O)6]2+ to fourfold tetrahedral [Zn(HS)n(H2O)4-n]2-n complexes (n = 1-4). Ab initio MD simulations also show that at temperatures > 250 °C, the threefold trigonal-planar [Zn(HS)3]- complex becomes increasingly stable, and predominates in S-rich solutions; in contrast, chloro-complexes display a tetrahedral geometry at 25-500 °C, while trigonal planar ZnCl3- predominates at temperatures > 500 °C. The stability constants of Zn(II)-HS complexes were calculated by thermodynamic integration of constrained ab initio MD simulations at 200, 350 and 600 °C. The stability constants generated from this study predict that zinc can be transported by HS- at high temperature in reduced, neutral to alkaline solutions, while Zn
Vchirawongkwin, Viwat; Kritayakornupong, Chinapong; Tongraar, Anan; Rode, Bernd M
2012-10-14
Hydration structure and dynamics of an aqueous Sc(III) solution were characterized by means of an extended ab initio quantum mechanical/molecular dynamical (QM/MM) molecular dynamics simulation at Hartree-Fock level. A monocapped trigonal prismatic structure composed of seven water molecules surrounding scandium(III) ion was proposed by the QM/MM simulation including the quantum mechanical effects for the first and second hydration shells. The mean Sc(III)-O bond length of 2.14 Å was identified for six prism water molecules with one capping water located at around 2.26 Å, reproducing well the X-ray diffraction data. The Sc(III)-O stretching frequency of 432 cm(-1) corresponding to a force constant of 130 N m(-1), evaluated from the enlarged QM/MM simulation, is in good agreement with the experimentally determined value of 430 cm(-1) (128 N m(-1)). Various water exchange processes in the second hydration shell of the hydrated Sc(III) ion predict a mean ligand residence time of 7.3 ps.
Accurate path integral molecular dynamics simulation of ab-initio water at near-zero added cost
Elton, Daniel; Fritz, Michelle; Soler, José; Fernandez-Serra, Marivi
It is now established that nuclear quantum motion plays an important role in determining water's structure and dynamics. These effects are important to consider when evaluating DFT functionals and attempting to develop better ones for water. The standard way of treating nuclear quantum effects, path integral molecular dynamics (PIMD), multiplies the number of energy/force calculations by the number of beads, which is typically 32. Here we introduce a method whereby PIMD can be incorporated into a DFT molecular dynamics simulation at virtually zero cost. The method is based on the cluster (many body) expansion of the energy. We first subtract the DFT monomer energies, using a custom DFT-based monomer potential energy surface. The evolution of the PIMD beads is then performed using only the more-accurate Partridge-Schwenke monomer energy surface. The DFT calculations are done using the centroid positions. Various bead thermostats can be employed to speed up the sampling of the quantum ensemble. The method bears some resemblance to multiple timestep algorithms and other schemes used to speed up PIMD with classical force fields. We show that our method correctly captures some of key effects of nuclear quantum motion on both the structure and dynamics of water. We acknowledge support from DOE Award No. DE-FG02-09ER16052 (D.E.) and DOE Early Career Award No. DE-SC0003871 (M.V.F.S.).
Nattino, Francesco; Galparsoro, Oihana; Costanzo, Francesca; Díez Muiño, Ricardo; Alducin, Maite; Kroes, Geert-Jan
2016-06-01
Accurately modeling surface temperature and surface motion effects is necessary to study molecule-surface reactions in which the energy dissipation to surface phonons can largely affect the observables of interest. We present here a critical comparison of two methods that allow to model such effects, namely, the ab initio molecular dynamics (AIMD) method and the generalized Langevin oscillator (GLO) model, using the dissociation of N2 on W(110) as a benchmark. AIMD is highly accurate as the surface atoms are explicitly part of the dynamics, but this advantage comes with a large computational cost. The GLO model is much more computationally convenient, but accounts for lattice motion effects in a very approximate way. Results show that, despite its simplicity, the GLO model is able to capture the physics of the system to a large extent, returning dissociation probabilities which are in better agreement with AIMD than static-surface results. Furthermore, the GLO model and the AIMD method predict very similar energy transfer to the lattice degrees of freedom in the non-reactive events, and similar dissociation dynamics.
Dietrick, Scott M; Iyengar, Srinivasan S
2012-12-11
A method of analysis is introduced to probe the spectral features obtained from ab initio molecular dynamics simulations. Here, the instantaneous mass-weighted velocities are projected onto irreducible representations constructed from discrete time translation groups comprising operations that invoke the time-domain symmetries (or periodic phase space orbits) reflected in the spectra. The projected velocities are decomposed using singular value decomposition (SVD) to construct a set of "modes" pertaining to a given frequency domain. These modes now include all anharmonicities, as sampled during the dynamics simulations. In this approach, the underlying motions are probed in a manner invariant with respect to coordinate transformations, operations being performed along the time axis rather than coordinate axes, making the analysis independent of choice of reference frame. The method is used to probe the underlying motions responsible for the doublet at ∼1000 cm(-1) in the vibrational spectrum of the H5O2(+), Zundel cation. The associated analysis results are confirmed by projecting the Fourier transformed velocities onto the harmonic normal mode coordinates and a set of mass-weighted, symmetrized Jacobi coordinates. It is found that the two peaks of the doublet are described and differentiated by their respective contributions from the proton transfer, water-water stretch, and water wag coordinates, as these are defined. Temperature dependent effects are also briefly noted.
Tummanapelli, Anil Kumar; Vasudevan, Sukumaran
2015-03-01
Estimation of the dissociation constant, or pKa, of weak acids continues to be a central goal in theoretical chemistry. Here we show that ab initio Car-Parrinello molecular dynamics simulations in conjunction with metadynamics calculations of the free energy profile of the dissociation reaction can provide reasonable estimates of the successive pKa values of polyprotic acids. We use the distance-dependent coordination number of the protons bound to the hydroxyl oxygen of the carboxylic group as the collective variable to explore the free energy profile of the dissociation process. Water molecules, sufficient to complete three hydration shells surrounding the acid molecule, were included explicitly in the computation procedure. Two distinct minima corresponding to the dissociated and un-dissociated states of the acid are observed and the difference in their free energy values provides the estimate for pKa, the acid dissociation constant. We show that the method predicts the pKa value of benzoic acid in good agreement with experiment and then show using phthalic acid (benzene dicarboxylic acid) as a test system that both the first and second pKa values as well, as the subtle difference in their values for different isomers can be predicted in reasonable agreement with experimental data.
Tummanapelli, Anil Kumar; Vasudevan, Sukumaran
2014-11-26
The theoretical estimation of the dissociation constant, or pKa, of weak acids continues to be a challenging field. Here, we show that ab initio Car-Parrinello molecular dynamics simulations in conjunction with metadynamics calculations of the free-energy profile of the dissociation reaction provide reasonable estimates of the pKa value. Water molecules, sufficient to complete the three hydration shells surrounding the acid molecule, were included explicitly in the computation procedure. The free-energy profiles exhibit two distinct minima corresponding to the dissociated and neutral states of the acid, and the difference in their values provides the estimate for pKa. We show for a series of organic acids that CPMD simulations in conjunction with metadynamics can provide reasonable estimates of pKa values. The acids investigated were aliphatic carboxylic acids, chlorine-substituted carboxylic acids, cis- and trans-butenedioic acid, and the isomers of hydroxybenzoic acid. These systems were chosen to highlight that the procedure could correctly account for the influence of the inductive effect as well as hydrogen bonding on pKa values of weak organic acids. In both situations, the CPMD metadynamics procedure faithfully reproduces the experimentally observed trend and the magnitudes of the pKa values.
Energy Technology Data Exchange (ETDEWEB)
Nattino, Francesco, E-mail: f.nattino@chem.leidenuniv.nl; Genova, Alessandro; Guijt, Marieke; Kroes, Geert-Jan [Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, P.O. Box 9502, 2300 RA Leiden (Netherlands); Muzas, Alberto S.; Díaz, Cristina [Departamento de Química Módulo 13, Universitad Autónoma de Madrid, 28049 Madrid (Spain); Auerbach, Daniel J. [Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, P.O. Box 9502, 2300 RA Leiden (Netherlands); Max Planck Institute for Biophysical Chemistry, Göttingen (Germany)
2014-09-28
Obtaining quantitative agreement between theory and experiment for dissociative adsorption of hydrogen on and associative desorption of hydrogen from Cu(111) remains challenging. Particularly troubling is the fact that theory gives values for the high energy limit to the dissociative adsorption probability that is as much as two times larger than experiment. In the present work we approach this discrepancy in three ways. First, we carry out a new analysis of the raw experimental data for D{sub 2} associatively desorbing from Cu(111). We also perform new ab initio molecular dynamics (AIMD) calculations that include effects of surface atom motion. Finally, we simulate time-of-flight (TOF) spectra from the theoretical reaction probability curves and we directly compare them to the raw experimental data. The results show that the use of more flexible functional forms for fitting the raw TOF spectra gives fits that are in slightly better agreement with the raw data and in considerably better agreement with theory, even though the theoretical reaction probabilities still achieve higher values at high energies. The mean absolute error (MAE) for the energy E{sub 0} at which the reaction probability equals half the experimental saturation value is now lower than 1 kcal/mol, the limit that defines chemical accuracy, while a MAE of 1.5 kcal/mol was previously obtained. The new AIMD results are only slightly different from the previous static surface results and in slightly better agreement with experiment.
Xu, Gui-Liang; Sheng, Tian; Chong, Lina; Ma, Tianyuan; Sun, Cheng-Jun; Zuo, Xiaobing; Liu, Di-Jia; Ren, Yang; Zhang, Xiaoyi; Liu, Yuzi; Heald, Steve M; Sun, Shi-Gang; Chen, Zonghai; Amine, Khalil
2017-02-08
Sodium-ion batteries (SIBs) have been considered as one of the promising power source candidates for the stationary storage industries owing to the much lower cost of sodium than lithium. It is well-known that the electrode materials largely determine the energy density of the battery systems. However, recent discoveries on the electrode materials showed that most of them present distinct lithium and sodium storage performance, which is not yet well understood. In this work, we performed a comparative understanding on the structural changes of porous cobalt oxide during its electrochemical lithiation and sodiation process by in operando synchrotron small angel X-ray scattering, X-ray diffraction, and X-ray absorption spectroscopy. It was found that compared to the lithiation process, the porous cobalt oxide undergoes less pore structure changes, oxidation state, and local structure changes as well as crystal structure evolution during its sodiation process, which is attributed to the intrinsic low sodiation activity of cobalt oxide as evidenced by ab initio molecular dynamics simulations. Moreover, it was indicated that the sodiation activity of metal sulfides is higher than that of metal oxides, indicating a better candidate for SIBs. Such understanding is crucial for future design and improvement of high-performance electrode materials for SIBs.
Energy Technology Data Exchange (ETDEWEB)
Fang, X W; Ding, Z J [Hefei National Laboratory for Physical Sciences at Microscale and Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China); Wang, C Z; Yao, Y X; Ho, K M, E-mail: wangcz@ameslab.gov, E-mail: zjding@ustc.edu.cn [Ames Laboratory-US Department of Energy and Department of Physics, Iowa State University, Ames, IA 50011 (United States)
2011-06-15
An ab initio molecular dynamics (MD) simulation is performed to investigate the structural evolution in Al{sub 90}Sm{sub 10} liquid from 1500 to 900 K. Development of Al{sub 11}Sm{sub 3} local order upon rapid cooling is suggested by the Honeycutt-Anderson (HA) index analysis and the appearance of a predominant Sm-Sm-Sm bond angle around 90{sup 0} when the liquid approaches the melting point ({approx}920 K). Direct structural evidence of Al{sub 11}Sm{sub 3} fragments at 900 K is obtained using an atomic cluster alignment method developed recently. Meanwhile, development of strong icosahedral short range order (ISRO) and a non-negligible amount of fcc-type clusters around Al in the system are also observed. These results suggest that fcc Al and Al{sub 11}Sm{sub 3} crystalline phases would compete strongly with the formation of an amorphous phase that exhibits ISRO in the diffusionless solidification limit upon rapid quenching.
Energy Technology Data Exchange (ETDEWEB)
Fischer, Sean A.; Ueltschi, Tyler W.; El-Khoury, Patrick Z.; Mifflin, Amanda L.; Hess, Wayne P.; Wang, Hongfei; Cramer, Christopher J.; Govind, Niranjan
2016-03-03
Carbon-hydrogen (C-H) vibration modes serve as key probes in the chemical iden- tication of hydrocarbons and in vibrational sum-frequency generation (SFG) spec- *troscopy of hydrocarbons at the liquid/gas interface. Their assignments pose a chal- lenge from a theoretical viewpoint. In this work, we present a detailed study of the C-H stretching region of dimethyl sulfoxide (DMSO) using a new Gaussian basis set- based ab initio molecular dynamics (AIMD) module that we have implemented in the NWChem computational chemistry program. By combining AIMD simulations and static normal mode analysis, we interpret experimental infrared and Raman spectra and explore the role of anharmonic effects in this system. Our anharmonic normal mode analysis of the in-phase and out-of-phase symmetric C-H stretching modes chal- lenges the previous experimental assignment of the shoulder in the symmetric C-H stretching peak as an overtone or Fermi resonance. In addition, our AIMD simulations also show signicant broadening of the in-phase symmetric C-H stretching resonance, which suggests that the experimentally observed shoulder is due to thermal broadening of the symmetric stretching resonance.
Lim, Len Herald V; Bhattacharjee, Anirban; Asam, S Sikander; Hofer, Thomas S; Randolf, Bernhard R; Rode, Bernd M
2010-03-01
An ab initio quantum mechanical charge field molecular dynamics (QMCF MD) simulation was performed to investigate the behavior of the Sb(3+) ion in aqueous solution. The simulation reveals a significant influence of the residual valence shell electron density on the solvation structure and dynamics of Sb(3+). A strong hemidirectional behavior of the ligand binding pattern is observed for the first hydration shell extending up to the second hydration layer. The apparent domain partitioned structural behavior was probed by solvent reorientational kinetics and three-body distribution functions. The three-dimensional hydration space was conveniently segmented such that domains having different properties were properly resolved. The approach afforded a fair isolation of localized solvent structural and dynamical motifs that Sb(3+) seems to induce to a remarkable degree. Most intriguing is the apparent impact of the lone pair electrons on the second hydration shell, which offers insight into the mechanistic aspects of hydrogen bonding networks in water. Such electronic effects observed in the hydration of Sb(3+) can only be studied by applying a suitable quantum mechanical treatment including first and second hydration shell as provided by the QMCF ansatz.
Direct ab initio molecular dynamics study on a microsolvated SN2 reaction of OH-(H2O) with CH3Cl
Tachikawa, Hiroto
2006-10-01
Reaction dynamics for a microsolvated SN2 reaction OH-(H2O)+CH3Cl have been investigated by means of the direct ab initio molecular dynamics method. The relative center-of-mass collision energies were chosen as 10, 15, and 25kcal/mol. Three reaction channels were found as products. These are (1) a channel leading to complete dissociation (the products are CH3OH+Cl-+H2O: denoted by channel I), (2) a solvation channel (the products are Cl-(H2O)+CH3OH: channel II), and (3) a complex formation channel (the products are CH3OH ⋯H2O+Cl-: channel III). The branching ratios for the three channels were drastically changed as a function of center-of-mass collision energy. The ratio of complete dissociation channel (channel I) increased with increasing collision energy, whereas that of channel III decreased. The solvation channel (channel II) was minor at all collision energies. The selectivity of the reaction channels and the mechanism are discussed on the basis of the theoretical results.
Ko, Hsin-Yu; Santra, Biswajit; Distasio, Robert A., Jr.; Wu, Xifan; Car, Roberto
Hybrid functionals are known to alleviate the self-interaction error in density functional theory (DFT) and provide a more accurate description of the electronic structure of molecules and materials. However, hybrid DFT in the condensed-phase has a prohibitively high associated computational cost which limits their applicability to large systems of interest. In this work, we present a general-purpose order(N) implementation of hybrid DFT in the condensed-phase using Maximally localized Wannier function; this implementation is optimized for massively parallel computing architectures. This algorithm is used to perform large-scale ab initio molecular dynamics simulations of liquid water, ice, and aqueous ionic solutions. We have performed simulations in the isothermal-isobaric ensemble to quantify the effects of exact exchange on the equilibrium density properties of water at different thermodynamic conditions. We find that the anomalous density difference between ice I h and liquid water at ambient conditions as well as the enthalpy differences between ice I h, II, and III phases at the experimental triple point (238 K and 20 Kbar) are significantly improved using hybrid DFT over previous estimates using the lower rungs of DFT This work has been supported by the Department of Energy under Grants No. DE-FG02-05ER46201 and DE-SC0008626.
Directory of Open Access Journals (Sweden)
V.O. Kharchenko
2015-06-01
Full Text Available Within this paper we have the studied structural and electronic properties of zirconium crystal with vacancies from the first principles. We have defined the optimal values for the lattice constants. The corresponding densities of states and energetic spectrum were calculated. These results gave a possibility to define the Fermi structure of the zirconium crystal with vacancies. In the framework of the molecular dynamics simulations we have studied the dynamics of the ensemble of periodically located vacancies in the zirconium crystal with an increase in temperature. We have analyzed the reconstruction of atomic structure and change in the total volume of the crystal with the temperature growth. The dependencies of the volume expansion coefficient for the pure zirconium without vacancies end zirconium crystal with different vacancies concentration on the temperature were studied.
Zhao, G.; Yan, J. L.; Yu, Y. J.; Ding, M. C.; Zhao, X. G.; Wang, H. Y.
2017-01-01
The relationship between structural order and water-like anomalies in tetrahedral liquids is still open. Here, first-principle molecular dynamics are performed to study it in metastable liquid Si. It is found that in T-P phase diagram, there indeed exists a structural anomaly region, which encloses density anomaly but not diffusivity anomaly. This is consistent with that of SW Si and BKS SiO2 but different from that of SPC/E water. Two-body excess entropy anomaly can neither capture the diffusivity, structural, and density anomalies, as it can in a two-scale potential fluid. In structural anomaly region, tetrahedrality order qtetra (measuring the extent to which an atom and its four nearest neighbours adopt tetrahedral arrangement) and translational order ttrans (measuring the tendency of two atoms to adopt preferential separation) are not perfectly correlated, which is different from that in SW Si and renders it impossible to use the isotaxis line to quantify the degree of structural order needed for water-like anomalies to occur. Along the isotherm of critical temperature Tc, ttrans/qtetra is approximately linear with pressure. With decreasing pressure along the isotherm below Tc, ttrans/qtetra departs downward from the line, while it is the opposite case above Tc.
Thermal effects on CH$_3$NH$_3$PbI$_3$ perovskite from ab-initio molecular dynamics simulations
Carignano, Marcelo A; Hutter, Jürg
2014-01-01
We present a molecular dynamics simulation study of CH$_3$NH$_3$PbI$_3$ based on forces calculated from density functional theory. The simulation were performed on model systems having 8 and 27 unit cells, and for a total simulation time of 40 ps in each case. Analysis of the finite size effects, in particular the mobility of the organic component, suggests that the smaller system is over correlated through the long range electrostatic interaction. In the larger system this finite size artifact is relaxed producing a more reliable description of the anisotropic rotational behavior of the methyl ammonium molecules. The thermal effects on the optical properties of the system were also analyzed. The HOMO-LUMO energy gap fluctuates around its central value with a standard deviation of approximately 0.1 eV. The projected density of states consistently place the Fermi level on the $p$ orbitals of the I atoms, and the lowest virtual state on $p$ orbitals of the Pb atoms throughout the whole simulation trajectory.
Zhao, G.; Yan, J. L.; Yu, Y. J.; Ding, M. C.; Zhao, X. G.; Wang, H. Y.
2017-01-01
The relationship between structural order and water-like anomalies in tetrahedral liquids is still open. Here, first-principle molecular dynamics are performed to study it in metastable liquid Si. It is found that in T-P phase diagram, there indeed exists a structural anomaly region, which encloses density anomaly but not diffusivity anomaly. This is consistent with that of SW Si and BKS SiO2 but different from that of SPC/E water. Two-body excess entropy anomaly can neither capture the diffusivity, structural, and density anomalies, as it can in a two-scale potential fluid. In structural anomaly region, tetrahedrality order qtetra (measuring the extent to which an atom and its four nearest neighbours adopt tetrahedral arrangement) and translational order ttrans (measuring the tendency of two atoms to adopt preferential separation) are not perfectly correlated, which is different from that in SW Si and renders it impossible to use the isotaxis line to quantify the degree of structural order needed for water-like anomalies to occur. Along the isotherm of critical temperature Tc, ttrans/qtetra is approximately linear with pressure. With decreasing pressure along the isotherm below Tc, ttrans/qtetra departs downward from the line, while it is the opposite case above Tc. PMID:28054595
Martins-Costa, Marilia T C; García-Prieto, Francisco F; Ruiz-López, Manuel F
2015-02-14
Understanding the influence of solute-solvent interactions on chemical reactivity has been a subject of intense research in the last few decades. Theoretical studies have focused on bulk solvation phenomena and a variety of models and methods have been developed that are now widely used by both theoreticians and experimentalists. Much less attention has been paid, however, to processes that occur at liquid interfaces despite the important role such interfaces play in chemistry and biology. In this study, we have carried out sequential molecular dynamics simulations and quantum mechanical calculations to analyse the influence of the air-water interface on the reactivity of formaldehyde, acetaldehyde and benzaldehyde, three simple aldehydes of atmospheric interest. The calculated free-energy profiles exhibit a minimum at the interface, where the average reactivity indices may display large solvation effects. The study emphasizes the role of solvation dynamics, which are responsible for large fluctuations of some molecular properties. We also show that the photolysis rate constant of benzaldehyde in the range 290-308 nm increases by one order of magnitude at the surface of a water droplet, from 2.7 × 10(-5) s(-1) in the gas phase to 2.8 × 10(-4) s(-1) at the air-water interface, and we discuss the potential impact of this result on the chemistry of the troposphere. Experimental data in this domain are still scarce and computer simulations like those presented in this work may provide some insights that can be useful to design new experiments.
Li, Junjie; Li, Xiaohu; Iyengar, Srinivasan S
2014-06-10
We discuss a multiconfigurational treatment of the "on-the-fly" electronic structure within the quantum wavepacket ab initio molecular dynamics (QWAIMD) method for coupled treatment of quantum nuclear effects with electronic structural effects. Here, multiple single-particle electronic density matrices are simultaneously propagated with a quantum nuclear wavepacket and other classical nuclear degrees of freedom. The multiple density matrices are coupled through a nonorthogonal configuration interaction (NOCI) procedure to construct the instantaneous potential surface. An adaptive-mesh-guided set of basis functions composed of Gaussian primitives are used to simplify the electronic structure calculations. Specifically, with the replacement of the atom-centered basis functions positioned on the centers of the quantum-mechanically treated nuclei by a mesh-guided band of basis functions, the two-electron integrals used to compute the electronic structure potential surface become independent of the quantum nuclear variable and hence reusable along the entire Cartesian grid representing the quantum nuclear coordinates. This reduces the computational complexity involved in obtaining a potential surface and facilitates the interpretation of the individual density matrices as representative diabatic states. The parametric nuclear position dependence of the diabatic states is evaluated at the initial time-step using a Shannon-entropy-based sampling function that depends on an approximation to the quantum nuclear wavepacket and the potential surface. This development is meant as a precursor to an on-the-fly fully multireference electronic structure procedure embedded, on-the-fly, within a quantum nuclear dynamics formalism. We benchmark the current development by computing structural, dynamic, and spectroscopic features for a series of bihalide hydrogen-bonded systems: FHF(-), ClHCl(-), BrHBr(-), and BrHCl(-). We find that the donor-acceptor structural features are in good
Firaha, Dzmitry S; Thomas, Martin; Hollóczki, Oldamur; Korth, Martin; Kirchner, Barbara
2016-11-28
In this study, we aim at understanding the influence of dispersion correction on the ab initio molecular dynamics simulations of ionic liquid (IL) systems. We investigated a large bulk system of the 1-butyl-3-methylimidazolium triflate IL and a small cluster system of ethylamine in ethylammonium nitrate both under periodic boundary conditions. The large system displays several changes upon neglect of dispersion correction, the most striking one is the surprising decrease of the well-known microheterogeneity which is accompanied by an increase of side chain hydrogen atom-anion interplay. For the diffusion coefficient, we observe a correction towards experimental behavior in terms of the cation becoming faster than the anion with dispersion correction. Changes in the electronic structure upon dispersion correction are reflected in larger/smaller dipole moments for anions/cations also seen in the calculated IR spectrum. The energetics of different ion pair dimer subsystems (polar and non-polar) are in accordance with the analysis of the trajectories: A detailed balance in the ionic liquid system determines its particular behavior. While the overall interaction terms for dispersion-corrected calculations are higher, the decrease in microheterogeneity upon inclusion of dispersion interaction becomes obvious due to the relation between all contributions to polar-polar terms. For the small system, we clearly observe the well known behavior that the hybrid functionals show higher reaction barriers than the pure generalized gradient approximation (GGA) functionals. The correction of dispersion reduces the discrepancies in some cases. Accounting for the number of jumps, we observe that dispersion correction reduces the discrepancies from 50% to less than 10%.
Firaha, Dzmitry S.; Thomas, Martin; Hollóczki, Oldamur; Korth, Martin; Kirchner, Barbara
2016-11-01
In this study, we aim at understanding the influence of dispersion correction on the ab initio molecular dynamics simulations of ionic liquid (IL) systems. We investigated a large bulk system of the 1-butyl-3-methylimidazolium triflate IL and a small cluster system of ethylamine in ethylammonium nitrate both under periodic boundary conditions. The large system displays several changes upon neglect of dispersion correction, the most striking one is the surprising decrease of the well-known microheterogeneity which is accompanied by an increase of side chain hydrogen atom-anion interplay. For the diffusion coefficient, we observe a correction towards experimental behavior in terms of the cation becoming faster than the anion with dispersion correction. Changes in the electronic structure upon dispersion correction are reflected in larger/smaller dipole moments for anions/cations also seen in the calculated IR spectrum. The energetics of different ion pair dimer subsystems (polar and non-polar) are in accordance with the analysis of the trajectories: A detailed balance in the ionic liquid system determines its particular behavior. While the overall interaction terms for dispersion-corrected calculations are higher, the decrease in microheterogeneity upon inclusion of dispersion interaction becomes obvious due to the relation between all contributions to polar-polar terms. For the small system, we clearly observe the well known behavior that the hybrid functionals show higher reaction barriers than the pure generalized gradient approximation (GGA) functionals. The correction of dispersion reduces the discrepancies in some cases. Accounting for the number of jumps, we observe that dispersion correction reduces the discrepancies from 50% to less than 10%.
Liu, Peng; Johansson, Viktor; Trilaksana, Herri; Rosdahl, Jan; Andersson, Gunther G; Kloo, Lars
2017-06-14
The organization of dye molecules in the dye layer adsorbed on the semiconductor substrate in dye-sensitized solar cells has been studied using a combination of theoretical methods and experimental techniques. The model system is based on the simple D-π-A dye L0, which has been chemically modified by substituting the acceptor group CN with Br (L0Br) to offer better X-ray contrast. Experimental EXAFS data based on the Br K-edge backscattering show no obvious difference between dye-sensitized titania powder and titania film samples, thus allowing model systems to be based on powder slurries. Ab initio molecular dynamic (aiMD) calculations have been performed to extract less biased information from the experimental EXASF data. Using the aiMD calculation as input, the EXAFS structural models can be generated a priori that match the experimental data. Our study shows that the L0Br dye adsorbs in the trans-L0Br configuration and that adsorption involves both a proximity to other L0Br dye molecules and the titanium atoms in the TiO2 substrate. These results indicate direct coordination of the dye molecules to the TiO2 surface in contrast to previous results on metal-organic dyes. The molecular coverage of L0Br on mesoporous TiO2 was also estimated using NICIS spectroscopy. The NICISS results emphasized that the L0Br dye on nanoporous titania mainly forms monolayers with a small contribution of multilayer coverage.
Pinto de Magalhães, Halua; Brennwald, Matthias S; Kipfer, Rolf
2017-03-22
Atmospheric noble gases are routinely used as natural tracers to analyze gas transfer processes in aquatic systems. Their isotopic ratios can be employed to discriminate between different physical transport mechanisms by comparison to the unfractionated atmospheric isotope composition. In many applications of aquatic systems molecular diffusion was thought to cause a mass dependent fractionation of noble gases and their isotopes according to the square root ratio of their masses. However, recent experiments focusing on isotopic fractionation within a single element challenged this broadly accepted assumption. The determined fractionation factors of Ne, Ar, Kr and Xe isotopes revealed that only Ar follows the prediction of the so-called square root relation, whereas within the Ne, Kr and Xe elements no mass-dependence was found. The reason for this unexpected divergence of Ar is not yet understood. The aim of our computational exercise is to establish the molecular-resolved mechanisms behind molecular diffusion of noble gases in water. We make the hypothesis that weak intermolecular interactions are relevant for the dynamical properties of noble gases dissolved in water. Therefore, we used ab initio molecular dynamics to explicitly account for the electronic degrees of freedom. Depending on the size and polarizability of the hydrophobic particles such as noble gases, their motion in dense and polar liquids like water is subject to different diffusive regimes: the inter-cavity hopping mechanism of small particles (He, Ne) breaks down if a critical particle size achieved. For the case of large particles (Kr, Xe), the motion through the water solvent is governed by mass-independent viscous friction leading to hydrodynamical diffusion. Finally, Ar falls in between the two diffusive regimes, where particle dispersion is propagated at the molecular collision time scale of the surrounding water molecules.
Energy Technology Data Exchange (ETDEWEB)
Amokrane, S.; Ayadim, A.; Levrel, L. [Groupe “Physique des Liquides et Milieux Complexes,” Faculté des Sciences et Technologie, Université Paris-Est (Créteil), 61 av. du Général de Gaulle, 94010 Créteil Cedex (France)
2015-11-21
We consider the question of the amorphization of metallic alloys by melt quenching, as predicted by molecular dynamics simulations with semi-empirical potentials. The parametrization of the potentials is discussed on the example of the ternary Cu-Ti-Zr transition metals alloy, using the ab-initio simulation as a reference. The pair structure in the amorphous state is computed from a potential of the Stillinger-Weber form. The transferability of the parameters during the quench is investigated using two parametrizations: from solid state data, as usual and from a new parametrization on the liquid structure. When the adjustment is made on the pair structure of the liquid, a satisfactory transferability is found between the pure components and their alloys. The liquid structure predicted in this way agrees well with experiment, in contrast with the one obtained using the adjustment on the solid. The final structure, after quenches down to the amorphous state, determined with the new set of parameters is shown to be very close to the ab-initio one, the latter being in excellent agreement with recent X-rays diffraction experiments. The corresponding critical temperature of the glass transition is estimated from the behavior of the heat capacity. Discussion on the consistency between the structures predicted using semi-empirical potentials and ab-initio simulation, and comparison of different experimental data underlines the question of the dependence of the final structure on the thermodynamic path followed to reach the amorphous state.
Bhargava, B L; Balasubramanian, S
2007-05-03
Ab initio molecular dynamics (AIMD) studies have been carried out on liquid 1-n-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF6]) and its mixture with CO2 using the Car-Parrinello molecular dynamics (CPMD) method. Results from AIMD and empirical potential molecular dynamics (MD) have been compared and were found to differ in some respects. With a strong resemblance to the crystal, the AIMD simulated neat liquid exhibits many cation-anion hydrogen bonds, a feature that is almost absent in the MD results. The anions were observed to be strongly polarized in the condensed phase. The addition of CO2 increased the probability of this hydrogen bond formation. CO2 molecules in the vicinity of the ions of [bmim][PF6] exhibit larger deviations from linearity in their instantaneous configurations. The polar environment of the liquid induces a dipole moment in CO2, lifting the degeneracy of its bending mode. The calculated splitting in the vibrational mode compares well with infrared spectroscopic data. The solvation of CO2 in [bmim][PF6] is primarily facilitated by the anion, as seen from the radial and spatial distribution functions. CO2 molecules were found to be aligned tangential to the PF6 spheres with their most probable location being the octahedral voids of the anion. The structural data obtained from AIMD simulations can serve as a benchmark to refine interaction potentials for this important room-temperature ionic liquid.
2017-01-01
A critical step toward the rational design of new catalysts that achieve selective and efficient reduction of CO2 to specific hydrocarbons and oxygenates is to determine the detailed reaction mechanism including kinetics and product selectivity as a function of pH and applied potential for known systems. To accomplish this, we apply ab initio molecular metadynamics simulations (AIMμD) for the water/Cu(100) system with five layers of the explicit solvent under a potential of −0.59 V [reversible hydrogen electrode (RHE)] at pH 7 and compare with experiment. From these free-energy calculations, we determined the kinetics and pathways for major products (ethylene and methane) and minor products (ethanol, glyoxal, glycolaldehyde, ethylene glycol, acetaldehyde, ethane, and methanol). For an applied potential (U) greater than −0.6 V (RHE) ethylene, the major product, is produced via the Eley–Rideal (ER) mechanism using H2O + e–. The rate-determining step (RDS) is C–C coupling of two CO, with ΔG‡ = 0.69 eV. For an applied potential less than −0.60 V (RHE), the rate of ethylene formation decreases, mainly due to the loss of CO surface sites, which are replaced by H*. The reappearance of C2H4 along with CH4 at U less than −0.85 V arises from *CHO formation produced via an ER process of H* with nonadsorbed CO (a unique result). This *CHO is the common intermediate for the formation of both CH4 and C2H4. These results suggest that, to obtain hydrocarbon products selectively and efficiency at pH 7, we need to increase the CO concentration by changing the solvent or alloying the surface. PMID:28167767
Energy Technology Data Exchange (ETDEWEB)
Wang, Yaocen; Takeuchi, Akira; Makino, Akihiro [Institute for Material Research, Tohoku University, Sendai 980-8577 (Japan); Liang, Yunye [New Industry Creation Hatchery Center, Tohoku University, Sendai 980-8579 (Japan); Kawazoe, Yoshiyuki [New Industry Creation Hatchery Center, Tohoku University, Sendai 980-8579 (Japan); Kutateladze Institute of Thermophysics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk (Russian Federation)
2014-05-07
Iron-based amorphous and nano-crystalline alloys have attracted a growing interest due to their potential in the application of magnetic coil production. However, fundamental understanding of the nano-crystallization mechanisms and magnetic features in the amorphous structure are still lack of knowledge. In the present work, we performed ab initio molecular dynamics simulation to clarify the ionic and electronic structure in atomic scale, and to derive the origin of the good magnetic property of Fe{sub 85}Si{sub 2}B{sub 8}P{sub 4}Cu{sub 1} amorphous alloy. The simulation gave a direct evidence of the Cu-P bonding preference in the amorphous alloy, which may promote nucleation in nano-crystallization process. On the other hand, the electron transfer and the band/orbital features in the amorphous alloy suggests that alloying elements with large electronegativity and the potential to expand Fe disordered matrix are preferred for enhancing the magnetization.
Ohta, Ayumi; Kobayashi, Osamu; Danielache, Sebastian O.; Nanbu, Shinkoh
2017-03-01
The ultra-fast photoisomerization reactions between 1,3-cyclohexadiene (CHD) and 1,3,5-cis-hexatriene (HT) in both hexane and ethanol solvents were revealed by nonadiabatic ab initio molecular dynamics (AI-MD) with a particle-mesh Ewald summation method and our Own N-layered Integrated molecular Orbital and molecular Mechanics model (PME-ONIOM) scheme. Zhu-Nakamura version trajectory surface hopping method (ZN-TSH) was employed to treat the ultra-fast nonadiabatic decaying process. The results for hexane and ethanol simulations reasonably agree with experimental data. The high nonpolar-nonpolar affinity between CHD and the solvent was observed in hexane solvent, which definitely affected the excited state lifetimes, the product branching ratio of CHD:HT, and solute (CHD) dynamics. In ethanol solvent, however, the CHD solute was isomerized in the solvent cage caused by the first solvation shell. The photochemical dynamics in ethanol solvent results in the similar property to the process appeared in vacuo (isolated CHD dynamics).
On the hierarchical parallelization of ab initio simulations
Ruiz-Barragan, Sergi; Shiga, Motoyuki
2016-01-01
A hierarchical parallelization has been implemented in a new unified code PIMD-SMASH for ab initio simulation where the replicas and the Born-Oppenheimer forces are parallelized. It is demonstrated that ab initio path integral molecular dynamics simulations can be carried out very efficiently for systems up to a few tens of water molecules. The code was then used to study a Diels-Alder reaction of cyclopentadiene and butenone by ab initio string method. A reduction in the reaction energy barrier is found in the presence of hydrogen-bonded water, in accordance with experiment.
Recent achievements in ab initio modelling of liquid water
Khaliullin, Rustam Z
2013-01-01
The application of newly developed first-principle modeling techniques to liquid water deepens our understanding of the microscopic origins of its unusual macroscopic properties and behaviour. Here, we review two novel ab initio computational methods: second-generation Car-Parrinello molecular dynamics and decomposition analysis based on absolutely localized molecular orbitals. We show that these two methods in combination not only enable ab initio molecular dynamics simulations on previously inaccessible time and length scales, but also provide unprecedented insights into the nature of hydrogen bonding between water molecules. We discuss recent applications of these methods to water clusters and bulk water.
Javadian, Soheila; Taghavi, Fariba; Yari, Faramarz; Hashemianzadeh, Seyed Majid
2012-09-01
In this study, the mechanism of the temperature-dependent phase transition of confined water inside a (9,9) single-walled carbon nanotube (SWCNT) was studied using the hierarchical multi-scale modeling techniques of molecular dynamics (MD) and density functional theory (DFT). The MD calculations verify the formation of hexagonal ice nanotubes at the phase transition temperature T(c)=275K by a sharp change in the location of the oxygen atoms inside the SWCNT. Natural bond orbital (NBO) analysis provides evidence of considerable intermolecular charge transfer during the phase transition and verifies that the ice nanotube contains two different forms of hydrogen bonding due to confinement. Nuclear quadrupole resonance (NQR) and nuclear magnetic resonance (NMR) analyses were used to demonstrate the fundamental influence of intermolecular hydrogen bonding interactions on the formation and electronic structure of ice nanotubes. In addition, the NQR analysis revealed that the rearrangement of nano-confined water molecules during the phase transition could be detected directly by the orientation of ¹⁷O atom EFG tensor components related to the molecular frame axes. The effects of nanoscale confinements in ice nanotubes and water clusters were analyzed by experimentally observable NMR and NQR parameters. These findings showed a close relationship between the phase behavior and orientation of the electronic structure in nanoscale structures and demonstrate the usefulness of NBO and NQR parameters for detecting phase transition phenomena in nanoscale confining environments.
Ducati, Lucas C; Marchenko, Alex; Autschbach, Jochen
2016-11-21
The influence of solvent (water) coordination and dynamics on the electronic structure and nuclear magnetic resonance (NMR) indirect spin-spin coupling (J-coupling) constants in a series of Tl-Pt bonded complexes is investigated using Kohn-Sham (KS) Car-Parrinello molecular dynamics (CPMD) and relativistic hybrid KS NMR calculations with and without coordination to water. Coordination of the Tl center by water molecules has a dramatic impact on (1)J(Tl-Pt) and other J-coupling constants. It is shown that a previous computational study of the same complexes using static optimized structures and nonhybrid functionals was correct about the important role of the solvent but obtained reasonable agreement with experimental NMR data because of a cancellation of substantial errors. For example, the CPMD trajectories show that on average the inner coordination shell of Tl is not saturated, as previously assumed, which leads to poor agreement with experiment when the J-coupling constants are averaged over the CPMD trajectories using NMR calculations with nonhybrid functionals. The combination of CPMD with hybrid KS NMR calculations provides a much more realistic computational model that reproduces the large magnitudes of (1)J(Tl-Pt) and the correct trends for other coupling constants. An analysis of (1)J(Tl-Pt) in terms of localized orbitals shows that the presence of coordinating water molecules increases the capacity for covalent interactions between Tl and Pt. There is pronounced multicenter bonding along the metal-metal axis of the complexes.
Fedorova, Irina V.; Krestyaninov, Michael A.; Safonova, Lyubov P.
2016-09-01
Car-Parrinello molecular dynamics simulations of phosphoric acid (H3PO4)-N,N-dimethylformamide (DMF) mixtures over the whole composition range have been carried out. It has been found that the neutral molecules are the dominant species in this system. The concentration dependences of the average number of H-bonds per proton acceptor atom in P=O and C=O groups as well as per proton donor atom in DMFH+ ions towards phosphate species have been discussed. The H-bonding between components in all investigated mixtures of H3PO4 and DMF is possible. A significant fraction of the protonated DMF forms appears at phosphoric acid mole fraction higher than 0.37, indicating a high probability of proton transfer from phosphate species to oxygen atoms in C=O groups. The intermolecular proton transfer between phosphate species themselves is mainly observed when xH3PO4 > 0.19. Satisfactory agreement with available experimental data for structural characteristics of the investigated system was obtained.
Wang, Junsheng
2010-11-16
The nucleation of solid Al from the melt by TiB2 is well established and is believed to involve the formation of Al3Ti. Since the atomic-scale mechanisms involved are not fully understood, we look to computer simulation to provide insight. As there is an absence of suitable potentials for all of this complex system we have performed large-scale density-functional-theory molecular dynamics simulations of the nucleation of solid Al from the melt on TiB2 and Al3Ti substrates at undercoolings of around 2 K. Using periodic boundary conditions, we find limited ordering and no signs of incipient growth in the liquid Al close to the B-terminated surface of TiB2. By contrast, we see fcc-like ordering near the Ti-terminated surface, with growth being frustrated by the lattice mismatch between bulk Al and the TiB2 substrate. The Al interatomic distances at the Ti-terminated surface are similar to distances found in Al3Ti; we suggest that the layer encasing TiB2 observed experimentally may be strained Al on a Ti-terminated surface rather than Al3Ti. For the Al3Ti substrate, fcc-like structures are observed on both sides which extend rapidly into the melt. Periodic boundaries introduce unphysical stresses which we removed by introducing a vacuum region to separate the liquid from the solid at one of the interfaces. We see ordering in the Al on both the B-terminated (0001) surface of TiB2, and on Al3Ti(112), with the ordering able to be stronger on the Al3Ti substrate. However, we cannot draw strong conclusions as these simulations need more time to allow long-ranged fluctuations in the liquid Al to dampen out. The huge computational cost restricted the range and duration of simulations that was possible.
Al89La6Ni5非晶合金的第一性原理分子动力学模拟%Ab initio molecular dynamics simulation of Al89 La6 Ni5 metallic glass
Institute of Scientific and Technical Information of China (English)
田华
2014-01-01
Ab initio molecular dynamics simulation of Al89 La6 Ni5 alloy were performed at descending tempera-tures to discuss the evolution of short-range order ( SRO) with temperature,the pair correlation functions,coor-dination polyhedron ( clusters) have been analyzed.This work suggests the SRO of atoms is near densely packed in the glassy state.With temperature decreasing to glassy state, the SRO of Al atoms changes slightly, while the environment around La and Al atoms has obviously variation.Thus it can be inferred, by La addition, the envi-ronments of Ni atoms changed, resulting in improved glass forming ability for the Al-La-Ni alloys.The result provides strong evidence for the existence of Al–Ni covalent bonds, analysis of electronic structures further re-vealed that the interaction between Al-p and Ni-d electrons near Fermi level is responsible for the enhanced Al-Ni bonding.%采用第一性原理分子动力学（ AIMD）方法模拟 Al89 La6 Ni5合金的退火过程，结合双体相关函数和配位多面体（团簇）分布分析了体系短程有序结构随温度的演化。结构分析表明，非晶态 Al89 La6 Ni5原子短程有序结构近似密堆排列；在非晶形成过程中，Al 原子周围短程有序结构几乎没有发生变化，而 La 和 Ni原子周围环境发生明显改变，由此推测，La 原子的加入改变了 Ni 原子周围的短程有序结构，因而增加了Al－La－Ni 体系的非晶形成能力；Al 原子和Ni原子间存在Al－Ni共价键作用，电子态密度的计算说明，费米面附近Al－p和Ni－d 之间电子的相互作用是Al－Ni原子间形成局域共价键的原因。
Discovering chemistry with an ab initio nanoreactor
Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.
2014-12-01
Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provide detailed physical insight. Although theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor—a highly accelerated first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor, we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, which provide new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery, in addition to its traditional role of interpreting experimental findings.
Hydrogen Desorption from Mg Hydride: An Ab Initio Study
Directory of Open Access Journals (Sweden)
Simone Giusepponi
2012-07-01
Full Text Available Hydrogen desorption from hydride matrix is still an open field of research. By means of accurate first-principle molecular dynamics (MD simulations an Mg–MgH2 interface is selected, studied and characterized. Electronic structure calculations are used to determine the equilibrium properties and the behavior of the surfaces in terms of structural deformations and total energy considerations. Furthermore, extensive ab-initio molecular dynamics simulations are performed at several temperatures to characterize the desorption process at the interface. The numerical model successfully reproduces the experimental desorption temperature for the hydride.
Pu, Maoping; Privalov, Timofei
2014-12-01
With the help of state-of-the-art ab initio molecular dynamics methods, we investigated the reaction pathway of the {tBu3 P + H2 + B(C6 F5 )3 } system at the mesoscopic level. It is shown that: i) the onset of H2 activation is at much larger boron⋅⋅⋅phosphorus distances than previously thought; ii) the system evolves to the product in a roaming-like fashion because of quasi-periodic nuclear motion along the asymmetric normal mode of P⋅⋅⋅HH⋅⋅⋅B fragment; iii) transient configurations of a certain type are present despite structural interference from the solvent; iv) transient-state configurations with sub-picosecond lifetime have potentially interesting infrared activity in the organic solvent (toluene) as well as in the gas phase. The presented results should be helpful for future experimental and theoretical studies of frustrated Lewis pair (FLP) activity.
Phonocatalysis. An ab initio simulation experiment
Directory of Open Access Journals (Sweden)
Kwangnam Kim
2016-06-01
Full Text Available Using simulations, we postulate and show that heterocatalysis on large-bandgap semiconductors can be controlled by substrate phonons, i.e., phonocatalysis. With ab initio calculations, including molecular dynamic simulations, the chemisorbed dissociation of XeF6 on h-BN surface leads to formation of XeF4 and two surface F/h-BN bonds. The reaction pathway and energies are evaluated, and the sorption and reaction emitted/absorbed phonons are identified through spectral analysis of the surface atomic motion. Due to large bandgap, the atomic vibration (phonon energy transfer channels dominate and among them is the match between the F/h-BN covalent bond stretching and the optical phonons. We show that the chemisorbed dissociation (the pathway activation ascent requires absorption of large-energy optical phonons. Then using progressively heavier isotopes of B and N atoms, we show that limiting these high-energy optical phonons inhibits the chemisorbed dissociation, i.e., controllable phonocatalysis.
Dietrick, Scott M; Pacheco, Alexander B; Phatak, Prasad; Stevens, Philip S; Iyengar, Srinivasan S
2012-01-12
The effect of water on the stability and vibrational states of a hydroxy-isoprene adduct is probed through the introduction of 1-15 water molecules. It is found that when a static nuclear harmonic approximation is invoked there is a substantial red-shift of the alcohol O-H stretch (of the order of 800 cm(-1)) as a result of introduction of water. When potential energy surface sampling and associated anharmonicities are introduced through finite temperature ab initio dynamics, this hydroxy-isoprene OH stretch strongly couples with all the water vibrational modes as well as the hydroxy-isoprene OH bend modes. A new computational technique is introduced to probe the coupling between these modes. The method involves a two-dimensional, time-frequency analysis of the finite temperature vibrational properties. Such an analysis not only provides information about the modes that are coupled as a result of finite-temperature analysis, but also the temporal evolution of such coupling.
Energy Technology Data Exchange (ETDEWEB)
Bernard, St
1998-12-31
The quest for metallic hydrogen is a major goal for both theoretical and experimental condensed matter physics. Hydrogen and deuterium have been compressed up to 200 GPa in diamond anvil cells, without any clear evidence for a metallic behaviour. Loubeyere has recently suggested that hydrogen could metallize, at pressures within experimental range, in a new Van der Waals compound: Ar(H{sub 2}){sub 2} which is characterized at ambient pressure by an open and anisotropic sublattice of hydrogen molecules, stabilized by an argon skeleton. This thesis deals with a detailed ab initio investigation, by Car-Parrinello molecular dynamics methods, of the evolution under pressure of this compound. In a last chapter, we go to much higher pressures and temperatures, in order to compare orbital and orbital free ab initio methods for the dense hydrogen plasma. (author) 109 refs.
Limitations of Ab Initio Predictions of Peptide Binding to MHC Class II Molecules
DEFF Research Database (Denmark)
Zhang, Hao; Lund, Ole; Nielsen, Morten
2010-01-01
potentials derived from the analysis of known protein structures; energetic evaluation of different peptide snapshots in a molecular dynamics simulation; and direct analysis of contacts made in known 3D structures of peptide:MHC complexes. These methods are ab initio in that they require structural data...
Ab-initio modeling of an anion $C_{60}^-$ pseudopotential for fullerene-based compounds
Vrubel, I I; Ivanov, V K
2015-01-01
A pseudopotential of $C_{60}^-$ has been constructed from ab-initio quantum-mechanical calculations. Since the obtained pseudopotential can be easily fitted by rather simple analytical approximation it can be effectively used both in classical and quantum molecular dynamics of fullerene-based compounds.
Virtual synthesis of crystals using ab initio MD: Case study on LiFePO4
Mishra, S. B.; Nanda, B. R. K.
2017-05-01
Molecular dynamics simulation technique is fairly successful in studying the structural aspects and dynamics of fluids. Here we study the ability of ab initio molecular dynamics (ab initio MD) to carry out virtual experiments to synthesize new crystalline materials and to predict their structures. For this purpose the olivine phosphate LiFePO4 (LFPO) is used as an example. As transition metal oxides in general are stabilized with layered geometry, we carried out ab initio MD simulations over a hypothetical layered configuration consisting of alternate LiPO2 and FeO2 layers. With intermittent steps of electron minimization, the resulted equilibrium lattice consist of PO4 tetrahedra and distorted Fe-O complexes similar to the one observed in the experimental lattice.
Ab initio valence calculations in chemistry
Cook, D B
1974-01-01
Ab Initio Valence Calculations in Chemistry describes the theory and practice of ab initio valence calculations in chemistry and applies the ideas to a specific example, linear BeH2. Topics covered include the Schrödinger equation and the orbital approximation to atomic orbitals; molecular orbital and valence bond methods; practical molecular wave functions; and molecular integrals. Open shell systems, molecular symmetry, and localized descriptions of electronic structure are also discussed. This book is comprised of 13 chapters and begins by introducing the reader to the use of the Schrödinge
Webber, J Beau W; Anderson, Ross; Strange, John H; Tohidi, Bahman
2007-05-01
The Gibbs-Thomson effect modifies the pressure and temperature at which clathrates occur, hence altering the depth at which they occur in the seabed. Nuclear magnetic resonance (NMR) measurements as a function of temperature are being conducted for water/ice/hydrate systems in a range of pore geometries, including templated SBA-15 silicas, controlled pore glasses and sol-gel silicas. Rotator-phase plastic ice is shown to be present in confined geometry, and bulk tetrahydrofuran hydrate is also shown to probably have a rotator phase. A novel NMR cryoporometry protocol, which probes both melting and freezing events while avoiding the usual problem of supercooling for the freezing event, has been developed. This enables a detailed probing of the system for a given pore size and geometry and the exploration of differences between hydrate formation and dissociation processes inside pores. These process differences have an important effect on the environment, as they impact on the ability of a marine hydrate system to re-form once warmed above a critical temperature. Ab initio quantum-mechanical molecular dynamics calculations are also being employed to probe the dynamics of liquids in pores at nanometric dimensions.
Ab Initio Calculation on Self-Assembled Base-Functionalized Single-Walled Carbon Nanotubes
Institute of Scientific and Technical Information of China (English)
SONG Chen; XIA Yue-Yuan; ZHAO Ming-Wen; LIU Xiang-Dong; LI Ji-Ling; LI Li-Juan; LI Feng; HUANG Bo-Da
2006-01-01
@@ We perform ab initio calculations on the self-assembled base-functionalized single-walled carbon nanotubes (SWNTs) which exhibit the quasi-1D ‘ladder’ structure. The optimized configuration in the ab initio calculation is very similar to that obtainedfrom molecular dynamics simulation. We also calculate the electronic structures of the self-assembled base-functionalized SWNTs that exhibit distinct difference from the single-branch base-functionalized SWNT with a localized state lying just below the Fermi level, which may result from the coupling interaction between the bases accompanied by the self-assembly behaviour.
Reciprocity Theorems for Ab Initio Force Calculations
Wei, C; Mele, E J; Rappe, A M; Lewis, Steven P.; Rappe, Andrew M.
1996-01-01
We present a method for calculating ab initio interatomic forces which scales quadratically with the size of the system and provides a physically transparent representation of the force in terms of the spatial variation of the electronic charge density. The method is based on a reciprocity theorem for evaluating an effective potential acting on a charged ion in the core of each atom. We illustrate the method with calculations for diatomic molecules.
Discovering chemistry with an ab initio nanoreactor
Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.
2014-01-01
Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerat...
Ab initio dynamics of the cytochrome P450 hydroxylation reaction
Energy Technology Data Exchange (ETDEWEB)
Elenewski, Justin E.; Hackett, John C, E-mail: jchackett@vcu.edu [Department of Physiology and Biophysics and The Massey Cancer Center, School of Medicine, Virginia Commonwealth University, 401 College Street, Richmond, Virginia 23219-1540 (United States)
2015-02-14
The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis.
Institute of Scientific and Technical Information of China (English)
危洪清; 龙志林; 许福; 张平; 唐翌
2014-01-01
Local structural changes from liquid to amorphous state in three Cu45Zr55-xAlx (x = 3, 7, 12) ternary metallic glasses have been investigated by the ab initio molecular dynamics simulation. The atomic structure of the glasses has been analyzed by means of bond-type index method in Honeycutt-Andersen and Voronoi tessellation method. Al-centered icosahedral clusters are identified as the basic local structural units and these Al-centered stable clusters play a key role in the structural heterogeneity and glass-forming ability of the Cu-Zr-Al bulk metallic glasses.%利用第一性原理分子动力学模拟对Cu45Zr55-xAlx (x=3,7,12)块体非晶合金熔体在快速冷却为玻璃态过程中原子结构的演变进行了系统的研究。结果显示,以Al为中心的二十面体是合金熔体在液-固转变过程中最稳定的原子团簇结构,可视为该合金系中的基本结构单元；以Al为中心的稳定团簇的数量和在空间中的组成形式决定了该合金微观结构的非均匀性和原子扩散能力的大小,这也是影响合金宏观力学性能和玻璃形成能力的关键因素。
Highly scalable Ab initio genomic motif identification
Marchand, Benoit
2011-01-01
We present results of scaling an ab initio motif family identification system, Dragon Motif Finder (DMF), to 65,536 processor cores of IBM Blue Gene/P. DMF seeks groups of mutually similar polynucleotide patterns within a set of genomic sequences and builds various motif families from them. Such information is of relevance to many problems in life sciences. Prior attempts to scale such ab initio motif-finding algorithms achieved limited success. We solve the scalability issues using a combination of mixed-mode MPI-OpenMP parallel programming, master-slave work assignment, multi-level workload distribution, multi-level MPI collectives, and serial optimizations. While the scalability of our algorithm was excellent (94% parallel efficiency on 65,536 cores relative to 256 cores on a modest-size problem), the final speedup with respect to the original serial code exceeded 250,000 when serial optimizations are included. This enabled us to carry out many large-scale ab initio motiffinding simulations in a few hours while the original serial code would have needed decades of execution time. Copyright 2011 ACM.
Ab initio Bogoliubov coupled cluster theory
Signoracci, Angelo; Hagen, Gaute; Duguet, Thomas
2014-09-01
Coupled cluster (CC) theory has become a standard method in nuclear theory for realistic ab initio calculations of medium mass nuclei, but remains limited by its requirement of a Slater determinant reference state which reasonably approximates the nuclear system of interest. Extensions of the method, such as equation-of-motion CC, permit the calculation of nuclei with one or two nucleons added or removed from a doubly magic core, yet still only a few dozen nuclei are accessible with modern computational restrictions. In order to extend the applicability of ab initio methods to open-shell systems, the superfluid nature of nuclei must be taken into account. By utilizing Bogoliubov algebra and employing spontaneous symmetry breaking with respect to particle number conservation, superfluid systems can be treated by a single reference state. An ab initio theory to include correlations on top of a Bogoliubov reference state has been developed in the guise of standard CC theory. The formalism and first results of this Bogoliubov coupled cluster theory will be presented to demonstrate the applicability of the method.
Melting of sodium under high pressure. An ab-initio study
Energy Technology Data Exchange (ETDEWEB)
González, D. J.; González, L. E. [Departamento de Física Teórica, Atómica y Optica, Universidad de Valladolid, 47011 Valladolid (Spain)
2015-08-17
We report ab-initio molecular dynamics simulations of dense liquid/solid sodium for a pressure range from 0 to 100 GPa. The simulations have been performed with the orbital free ab-initio molecular dynamics method which, by using the electron density as the basic variable, allows to perform simulations with large samples and for long runs. The calculated melting curve shows a maximum at a pressure ≈ 30 GPa and it is followed by a long, steep decrease. These features are in good agreement with the experimental data. For various pressures along the melting curve, we have calculated several liquid static properties (pair distribution functions, static structure factors and short-range order parameters) in order to analyze the structural effects of pressure.
Operator evolution for ab initio nuclear theory
Schuster, Micah D; Johnson, Calvin W; Jurgenson, Eric D; Navratil, Petr
2014-01-01
The past two decades have seen a revolution in ab initio calculations of nuclear properties. One key element has been the development of a rigorous effective interaction theory, applying unitary transformations to soften the nuclear Hamiltonian and hence accelerate the convergence as a function of the model space size. For consistency, however, one ought to apply the same transformation to other operators when calculating transitions and mean values from the eigenstates of the renormalized Hamiltonian. Working in a translationally-invariant harmonic oscillator basis for the two- and three-nucleon systems, we evolve the Hamiltonian, square-radius and total dipole strength operators by the similarity renormalization group (SRG). The inclusion of up to three-body matrix elements in the 4He nucleus all but completely restores the invariance of the expectation values under the transformation. We also consider a Gaussian operator with adjustable range and find at short ranges an increased contribution from such ind...
Discovering chemistry with an ab initio nanoreactor
Martinez, Todd
Traditional approaches for modeling chemical reaction networks such as those involved in combustion have focused on identifying individual reactions and using theoretical approaches to explore the underlying mechanisms. Recent advances involving graphical processing units (GPUs), commodity products developed for the videogaming industry, have made it possible to consider a distinct approach wherein one attempts to discover chemical reactions and mechanisms. We provide a brief summary of these developments and then discuss the concept behind the ``ab initio nanoreactor'' which explores the space of possible chemical reactions and molecular species for a given stoichiometry. The nanoreactor concept is exemplified with an example to the Urey-Miller reaction network which has been previously advanced as a potential model for prebiotic chemistry. We briefly discuss some of the future directions envisioned for the development of this nanoreactor concept.
Ab initio alpha-alpha scattering
Elhatisari, Serdar; Rupak, Gautam; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A; Luu, Thomas; Meißner, Ulf-G
2015-01-01
Processes involving alpha particles and alpha-like nuclei comprise a major part of stellar nucleosynthesis and hypothesized mechanisms for thermonuclear supernovae. In an effort towards understanding alpha processes from first principles, we describe in this letter the first ab initio calculation of alpha-alpha scattering. We use lattice effective field theory to describe the low-energy interactions of nucleons and apply a technique called the adiabatic projection method to reduce the eight-body system to an effective two-cluster system. We find good agreement between lattice results and experimental phase shifts for S-wave and D-wave scattering. The computational scaling with particle number suggests that alpha processes involving heavier nuclei are also within reach in the near future.
An ab initio study of hydroxylated graphane
Buonocore, Francesco; Capasso, Andrea; Lisi, Nicola
2017-09-01
Graphene-based derivatives with covalent functionalization and well-defined stoichiometry are highly desirable in view of their application as functional surfaces. Here, we have evaluated by ab initio calculations the energy of formation and the phase diagram of hydroxylated graphane structures, i.e., fully functionalized graphene derivatives coordinated with -H and -OH groups. We compared these structures to different hydrogenated and non-hydrogenated graphene oxide derivatives, with high level of epoxide and hydroxyl groups functionalization. Based on our calculations, stable phases of hydroxylated graphane with low and high contents of hydrogen are demonstrated for high oxygen and hydrogen partial pressure, respectively. Stable phases of graphene oxide with a mixed carbon hybridization are also found. Notably, the synthesis of hydroxylated graphane has been recently reported in the literature.
Giant magnetoresistance An ab-initio description
Binder, J
2000-01-01
A new theoretical concept to study the microscopic origin of Giant Magnetoresistance (GMR) from first principles is presented. The method is based on ab-initio electronic structure calculations within the spin density functional theory using a Screened KORRINGA-KOHNROSTOKER method. Scattering at impurity atoms in the multilayers is described by means of a GREEN's-function method. The scattering potentials are calculated self-consistently. The transport properties are treated quasi-classically solving the BOLTZMANN equation including the electronic structure of the layered system and the anisotropic scattering. The solution of the BOLTZMANN equation is performed iteratively taking into account both scattering out and scattering in terms (vertex corrections). The method is applied to Co/Cu and Fe/Cr multilayers. Trends of scattering cross sections, residual resistivities and GMR ratios are discussed for various transition metal impurities at different positions in the Co/Cu or Fe/Cr multilayers. Furthermore the...
Ji, Pengfei
2016-01-01
By combining ab initio quantum mechanics calculation and Drude model, electron temperature and lattice temperature dependent electron thermal conductivity is calculated and implemented into a multiscale model of laser material interaction, which couples the classical molecular dynamics and two-temperature model. The results indicated that the electron thermal conductivity obtained from ab initio calculation leads to faster thermal diffusion than that using the electron thermal conductivity from empirical determination, which further induces deeper melting region, larger number of density waves travelling inside the copper film and more various speeds of atomic clusters ablated from the irradiated film surface.
Melting curves of metals by ab initio calculations
Minakov, Dmitry; Levashov, Pavel
2015-06-01
In this work we used several ab initio approaches to reproduce melting curves and discussed their abilities, advantages and drawbacks. We used quasiharmonic appoximation and Lindemann criterion to build melting curves in wide region of pressures. This approach allows to calculate the total free energy of electrons and phonons, so it is possible to obtain all thermodynamic properties in the crystalline state. We also used quantum molecular dynamics simulations to investigate melting at various pressures. We explored the size-effect of the heat until it melts (HUM) method in detail. Special attention was paid to resolve the boundaries of the melting region on density. All calculations were performed for aluminum, copper and gold. Results were in good agreement with available experimental data. Also we studied the influence of electronic temperature on melting curves. It turned out that the melting temperature increased with the rise of electron temperature at normal density and had non-monotonic behavior at higher densities. This work is supported by the Ministry of Education and Science of the Russian Federation (Project No. 3.522.2014/K).
An efficient approach to ab initio Monte Carlo simulation.
Leiding, Jeff; Coe, Joshua D
2014-01-21
We present a Nested Markov chain Monte Carlo (NMC) scheme for building equilibrium averages based on accurate potentials such as density functional theory. Metropolis sampling of a reference system, defined by an inexpensive but approximate potential, was used to substantially decorrelate configurations at which the potential of interest was evaluated, thereby dramatically reducing the number needed to build ensemble averages at a given level of precision. The efficiency of this procedure was maximized on-the-fly through variation of the reference system thermodynamic state (characterized here by its inverse temperature β(0)), which was otherwise unconstrained. Local density approximation results are presented for shocked states of argon at pressures from 4 to 60 GPa, where-depending on the quality of the reference system potential-acceptance probabilities were enhanced by factors of 1.2-28 relative to unoptimized NMC. The optimization procedure compensated strongly for reference potential shortcomings, as evidenced by significantly higher speedups when using a reference potential of lower quality. The efficiency of optimized NMC is shown to be competitive with that of standard ab initio molecular dynamics in the canonical ensemble.
Rational design of electrolyte components by ab initio calculations
Energy Technology Data Exchange (ETDEWEB)
Johansson, Patrik; Jacobsson, Per [Department of Applied Physics, Chalmers University of Technology, SE-412 96 Goeteborg (Sweden)
2006-02-28
This paper is a small review of the use of computer simulations and especially the use of standard quantum-mechanical ab initio electronic structure calculations to rationally design and investigate different choices of chemicals/systems for lithium battery electrolytes. Covered systems and strategies to enhance the performance of electrolytes will range from assisting the interpretation of vibrational spectroscopy experiments over development of potentials for molecular dynamics simulations, to the design of new lithium salts and the lithium ion coordination in liquid, polymer, and gel polymer electrolytes. Examples of studied properties include the vibrational spectra of anions and ion pairs to characterize the nature and extent of the interactions present, the lithium ion affinities of anions, important for the salt solvation and the ability to provide a high concentration of charge carriers, the HOMO energies of the anions to estimate the stability versus oxidation, the anion volumes that correlate to the anion mobility, the lithium ion coordination and dynamics to reveal the limiting steps of lithium ion transport, etc. (author)
The Hydration Structure of Carbon Monoxide by Ab Initio Methods
Awoonor-Williams, Ernest
2016-01-01
The solvation of carbon monoxide (CO) in liquid water is important for understanding its toxicological effects and biochemical roles. In this paper, we use ab initio molecular dynamics (AIMD) and CCSD(T)-F12 calculations to assess the accuracy of the Straub and Karplus molecular mechanical (MM) model for CO(aq). The CCSD(T)-F12 CO--H2O potential energy surfaces show that the most stable structure corresponds to water donating a hydrogen bond to the C center. The MM-calculated surface it incorrectly predicts that the O atom is a stronger hydrogen bond acceptor than the C atom. The AIMD simulations indicate that CO is solvated like a hydrophobic solute, with very limited hydrogen bonding with water. The MM model tends to overestimate the degree of hydrogen bonding and overestimates the atomic radius of the C atom. The calculated Gibbs energy of hydration is in good agreement with experiment (9.3 kJ/mol calc. vs 10.7 kJ/mol exptl.). The calculated diffusivity of CO(aq) in TIP3P-model water was 5.19 x 10-5 cm2/s ...
Local Environment Distribution in Ab Initio Liquid Water
Santra, Biswajit; Distasio, Robert A., Jr.; Car, Roberto
2013-03-01
We have analyzed the distribution of local environments in liquid water at ambient conditions and its inherent potential energy surface (IPES) based on state-of-the-art ab initio molecular dynamics simulations performed on 128 molecules implementing hybrid PBE0 exchange [PRB 79, 085102 (2009)] and van der Waals (vdW) interactions [PRL 102, 073005 (2009)]. The local environments of molecules are characterized in terms of the local structure index (LSI) [JCP 104, 7671 (1996)] which is able to distinguish high- and low-density molecular environments. In agreement with simulations based on model potentials, we find that the distribution of LSI is unimodal at ambient conditions and bimodal in the IPES, consistent with the existence of polymorphism in amorphous phases of water. At ambient conditions spatial LSI fluctuations extend up to ~7 Å and their dynamical correlation decays on a time scale of ~3 ps, as found for density fluctuations in a recent study [PRL 106, 037801 (2011)]. DOE: DE-SC0008626, DOE: DE-SC0005180, NSF: CHE-0956500
Energy Technology Data Exchange (ETDEWEB)
Matsushita, Y., E-mail: kurita@cs.tut.ac.jp; Murakawa, T., E-mail: kurita@cs.tut.ac.jp; Shimamura, K., E-mail: kurita@cs.tut.ac.jp; Oishi, M., E-mail: kurita@cs.tut.ac.jp; Ohyama, T., E-mail: kurita@cs.tut.ac.jp; Kurita, N., E-mail: kurita@cs.tut.ac.jp [Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580 (Japan)
2015-02-27
The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA.
Ab initio calculation of the Hoyle state
Epelbaum, Evgeny; Lee, Dean; Meißner, Ulf-G
2011-01-01
The Hoyle state plays a crucial role in the hydrogen burning of stars heavier than our sun and in the production of carbon and other elements necessary for life. This excited state of the carbon-12 nucleus was postulated by Hoyle^{1} as a necessary ingredient for the fusion of three alpha particles to produce carbon at stellar temperatures. Although the Hoyle state was seen experimentally more than a half century ago^{2,3}, nuclear theorists have not yet uncovered the nature of this state from first principles. In this letter we report the first ab initio calculation of the low-lying states of carbon-12 using supercomputer lattice simulations and a theoretical framework known as effective field theory. In addition to the ground state and excited spin-2 state, we find a resonance at -85(3) MeV with all of properties of the Hoyle state and in agreement with the experimentally observed energy. These lattice simulations provide insight into the structure of this unique state and new clues as to the amount of fine...
Ab initio phase diagram of iridium
Burakovsky, L.; Burakovsky, N.; Cawkwell, M. J.; Preston, D. L.; Errandonea, D.; Simak, S. I.
2016-09-01
The phase diagram of iridium is investigated using the Z methodology. The Z methodology is a technique for phase diagram studies that combines the direct Z method for the computation of melting curves and the inverse Z method for the calculation of solid-solid phase boundaries. In the direct Z method, the solid phases along the melting curve are determined by comparing the solid-liquid equilibrium boundaries of candidate crystal structures. The inverse Z method involves quenching the liquid into the most stable solid phase at various temperatures and pressures to locate a solid-solid boundary. Although excellent agreement with the available experimental data (to ≲65 GPa) is found for the equation of state (EOS) of Ir, it is the third-order Birch-Murnaghan EOS with B0'=5 rather than the more widely accepted B0'=4 that describes our ab initio data to higher pressure (P ) . Our results suggest the existence of a random-stacking hexagonal close-packed structure of iridium at high P . We offer an explanation for the 14-layer hexagonal structure observed in experiments by Cerenius and Dubrovinsky.
Ab initio phonon scattering by dislocations
Wang, Tao; Carrete, Jesús; van Roekeghem, Ambroise; Mingo, Natalio; Madsen, Georg K. H.
2017-06-01
Heat management in thermoelectric and power devices as well as in random access memories poses a grand challenge and can make the difference between a working and an abandoned device design. Despite the prevalence of dislocations in all these technologies, the modeling of their thermal resistance is based on 50-year-old analytical approximations, whose simplicity was driven by practical limitations rather than physical insight. We introduce an efficient ab initio approach based on Green's functions computed by two-dimensional reciprocal space integration. By combining elasticity theory and density functional theory, we calculate the scattering strength of a 90∘ misfit edge dislocation in Si. Because of the breakdown of the Born approximation, earlier literature models fail, even qualitatively. We find that a dislocation density larger than 109cm-2 is necessary to substantially influence thermal conductivity at room temperature and above. We quantify how much of the reduction of thermal conductivity measured in nanograined samples can be explained by realistic dislocation concentrations.
Ab initio materials physics and microscopic electrodynamics of media
2016-01-01
We argue that the amazing progress of first-principles materials physics necessitates a revision of the Standard Approach to electrodynamics of media. We hence subject this Standard Approach to a thorough critique, which shows both its inherent conceptual problems and its practical inapplicability to modern ab initio calculations. We then go on to show that the common practice in ab initio materials physics has overcome these difficulties by taking a different, microscopic approach to electro...
Ab initio studies of ionization potentials of hydrated hydroxide and hydronium
Swartz, Charles W
2013-01-01
The ionization potential distributions of hydrated hydroxide and hydronium are computed with many-body approach for electron excitations with configurations generated by {\\it ab initio} molecular dynamics. The experimental features are well reproduced and found to be closely related to the molecular excitations. In the stable configurations, the ionization potential is mainly perturbed by water molecules within the first solvation shell. On the other hand, electron excitation is delocalized on both proton receiving and donating complex during proton transfer, which shifts the excitation energies and broadens the spectra for both hydrated ions.
Ab-initio simulation of photoinduced transformation of small rings in amorphous silica
Bernasconi, D. Donadio M.
2004-01-01
We have studied the photoinduced transformation of small rings (3-membered) in amorphous silica by Car-Parrinello simulations. The process of ring opening leading to the formation of a couple of paramagnetic centers, namely an E' and a non-bridging-oxygen hole center (NBOHC), has been proposed experimentally to occur in silica exposed to F2 laser irradiation (at 7.9 eV). By using a new scheme for the simulation of rare events in ab-initio molecular dynamics (Iannuzzi, Laio and Parrinello, Phy...
Ab-initio study of several static and dynamic properties of liquid palladium and platinum
Directory of Open Access Journals (Sweden)
González L. E.
2017-01-01
Full Text Available We report a study on several static and dynamic properties of liquid Pd and Pt metals at thermodynamic conditions near their respective triple points. The calculations have been carried out by an ab initio molecular dynamics simulation technique. Results are reported for several static structural magnitudes which are compared with the available X-ray diffraction. As for the dynamic properties, results have been obtained for both single and collective dynamical magnitudes as well as for some transport coeffcients which are compared with the corresponding experimental data.
Orbital free ab initio study of static and dynamic properties of some liquid transition metals
Directory of Open Access Journals (Sweden)
Bhuiyan G. M.
2017-01-01
Full Text Available Several static and dynamic properties of liquid transition metals Cr, Mn and Co are studied for the first time using the orbital free ab-initio molecular dynamics simulation (OF-AIMD. This method is based on the density functional theory (DFT which accounts for the electronic energy of the system whereas the interionic forces are derived from the electronic energy via the Hellman-Feynman theorem. The external energy functional is treated with a local pseudopotential. Results are reported for static structure factors, isothermal compressibility, diffusion coeffcients, sound velocity and viscosity and comparison is performed with the available experimental data and other theoretical calculations.
Surface Tension of Ab Initio Liquid Water at the Water-Air Interface
Nagata, Yuki; Bonn, Mischa; Kühne, Thomas D
2016-01-01
We report calculations of the surface tension of the water-air interface using ab initio molecular dynamics (AIMD) simulations. We investigate the simulation cell size dependence of the surface tension of water from force field molecular dynamics (MD) simulations, which show that the calculated surface tension increases with increasing simulation cell size, thereby illustrating that a correction for finite size effects is required for the small system used in the AIMD simulation. The AIMD simulations reveal that the double-{\\xi} basis set overestimates the experimentally measured surface tension due to the Pulay stress, while the triple and quadruple-{\\xi} basis sets give similar results. We further demonstrate that the van der Waals corrections critically affect the surface tension. AIMD simulations without the van der Waals correction substantially underestimate the surface tension, while van der Waals correction with the Grimme's D2 technique results in the value for the surface tension that is too high. T...
Ab Initio Studies of Stratospheric Ozone Depletion Chemistry
Lee, Timothy J.; Head-Gordon, Martin; Langhoff, Stephen R. (Technical Monitor)
1995-01-01
An overview of the current understanding of ozone depletion chemistry, particularly with regards the formation of the so-called Antarctic ozone hole, will be presented together with an outline as to how ab initio quantum chemistry can be used to further our understanding of stratospheric chemistry. The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of fluorine, chlorine, bromine and nitrogen oxide species will be demonstrated by presentation of some example studies. The ab initio results will be shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the theoretical results are shown to fill in the gaps and to resolve experimental controversies. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of halogen oxide species will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of experimental studies.
Renison, C Alicia; Fernandes, Kyle D; Naidoo, Kevin J
2015-07-05
This article describes an extension of the quantum supercharger library (QSL) to perform quantum mechanical (QM) gradient and optimization calculations as well as hybrid QM and molecular mechanical (QM/MM) molecular dynamics simulations. The integral derivatives are, after the two-electron integrals, the most computationally expensive part of the aforementioned calculations/simulations. Algorithms are presented for accelerating the one- and two-electron integral derivatives on a graphical processing unit (GPU). It is shown that a Hartree-Fock ab initio gradient calculation is up to 9.3X faster on a single GPU compared with a single central processing unit running an optimized serial version of GAMESS-UK, which uses the efficient Schlegel method for s- and l-orbitals. Benchmark QM and QM/MM molecular dynamics simulations are performed on cellobiose in vacuo and in a 39 Å water sphere (45 QM atoms and 24843 point charges, respectively) using the 6-31G basis set. The QSL can perform 9.7 ps/day of ab initio QM dynamics and 6.4 ps/day of QM/MM dynamics on a single GPU in full double precision. © 2015 Wiley Periodicals, Inc.
Ab initio study of the structural properties of acetonitrile-water mixtures
Chen, Jinfan; Sit, Patrick H.-L.
2015-08-01
Structural properties of acetonitrile and acetonitrile-water mixtures are studied using Density Functional Theory (DFT) and ab initio molecular dynamics simulations. Stable molecular clusters consisted of several water and acetonitrile molecules are identified to provide microscopic understanding of the interaction among water and acetonitrile molecules. Ab initio molecular dynamics simulations are performed to study the liquid structure at the finite temperature. Three mixing compositions in which the mole fraction of acetonitrile equals 0.109, 0.5 and 0.891 are studied. These compositions correspond to three distinct structural regimes. At the 0.109 and 0.891 mole fraction of acetonitrile, the majority species are mostly connected among themselves and the minority species are either isolated or forming small clusters without disrupting the network of the majority species. At the 0.5 mole fraction of acetonitrile, large water and acetonitrile clusters persist throughout the simulation, exhibiting the microheterogeneous behavior in acetonitrile-water mixtures in the mid-range mixing ratio.
Experimental and ab initio investigations on textured Li–Mn–O spinel thin film cathodes
Energy Technology Data Exchange (ETDEWEB)
Fischer, J., E-mail: Julian.Fischer@kit.edu [Karlsruhe Institute of Technology (KIT), Institute for Applied Materials (IAM), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen (Germany); Music, D. [RWTH Aachen University, Materials Chemistry, Kopernikusstrasse 10, 52074 Aachen (Germany); Bergfeldt, T.; Ziebert, C.; Ulrich, S.; Seifert, H.J. [Karlsruhe Institute of Technology (KIT), Institute for Applied Materials (IAM), Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen (Germany)
2014-12-01
This paper describes the tailored preparation of nearly identical lithium–manganese–oxide thin film cathodes with different global grain orientations. The thin films were synthesized by rf magnetron sputtering from a LiMn{sub 2}O{sub 4}-target in a pure argon plasma. Under appropriate processing conditions, thin films with a cubic spinel structure and a nearly similar density and surface topography but different grain orientation, i.e. (111)- and (440)-textured films, were achieved. The chemical composition was determined by inductively coupled plasma optical emission spectroscopy and carrier gas hot extraction. The constitution- and microstructure were evaluated by X-ray diffraction and Raman spectroscopy. The surface morphology and roughness were investigated by scanning electron and atomic force microscopy. The differently textured films represent an ideal model system for studying potential effects of grain orientation on the lithium ion diffusion and electrochemical behavior in LiMn{sub 2}O{sub 4}-based thin films. They are nearly identical in their chemical composition, atomic bonding behavior, surface-roughness, morphology and thickness. Our initial ab initio molecular dynamics data indicate that Li ion transport is faster in (111)-textured structure than in (440)-textured one. - Highlights: • Thin film model system of differently textured cubic Li–Mn–O spinels. • Investigation of the Li–Mn–O thin film mass density by X-ray reflectivity. • Ab initio molecular dynamics simulation on Li ion diffusion in LiMn{sub 2}O{sub 4}.
Use of ab initio quantum chemical methods in battery technology
Energy Technology Data Exchange (ETDEWEB)
Deiss, E. [Paul Scherrer Inst. (PSI), Villigen (Switzerland)
1997-06-01
Ab initio quantum chemistry can nowadays predict physical and chemical properties of molecules and solids. An attempt should be made to use this tool more widely for predicting technologically favourable materials. To demonstrate the use of ab initio quantum chemistry in battery technology, the theoretical energy density (energy per volume of active electrode material) and specific energy (energy per mass of active electrode material) of a rechargeable lithium-ion battery consisting of a graphite electrode and a nickel oxide electrode has been calculated with this method. (author) 1 fig., 1 tab., 7 refs.
P-V Relation for Mercuric Calcogenides: Ab Initio Method
Directory of Open Access Journals (Sweden)
G. Misra
2011-01-01
Full Text Available Mercuric Calcogenides found many applications in electronic and optical devices as semiconducting materials. An equation of state provides useful information about the relationship between pressure (P, volume (V and temperature (T that helps to understand the behaviour of materials under the effect of high pressure and high temperature. The present paper sheds light on the electronic structure of Mercuric Calcogenides by simulating its electronic properties through ab initio method. This ab initio method is extended to derive the equation of state for Mercuric Calcogenides. The present equation of state has also been tested for the prediction of End Point. The computed results compare well with Quantum statistical data.
Gas phase ion chemistry of coumarins: ab initio calculations used to ...
African Journals Online (AJOL)
Gas phase ion chemistry of coumarins: ab initio calculations used to justify ... and quadrupole mass spectrometer (qMS) coupled to a gas chromatograph is ... Ab Initio calculations, Electron ionization, Positive chemical ionization, Negative ...
Resonance and Aromaticity : An Ab Initio Valence Bond Approach
Rashid, Zahid; van Lenthe, Joop H.; Havenith, Remco W. A.
2012-01-01
Resonance energy is one of the criteria to measure aromaticity. The effect of the use of different orbital models is investigated in the calculated resonance energies of cyclic conjugated hydrocarbons within the framework of the ab initio Valence Bond Self-Consistent Field (VBSCF) method. The VB wav
Ab initio calculations and modelling of atomic cluster structure
DEFF Research Database (Denmark)
Solov'yov, Ilia; Lyalin, Andrey G.; Greiner, Walter
2004-01-01
The optimized structure and electronic properties of small sodium and magnesium clusters have been investigated using it ab initio theoretical methods based on density-functional theory and post-Hartree-Fock many-body perturbation theory accounting for all electrons in the system. A new theoretical...
Ab initio study of alanine polypeptide chain twisting
DEFF Research Database (Denmark)
Solov'yov, Ilia; Yakubovich, Alexander V.; Solov'yov, Andrey V.
2006-01-01
chains. These particular degrees of freedom are essential for the characterization of the proteins folding process. Calculations have been carried out within the ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined...
Relaxation of Small Molecules: an ab initio Study
Institute of Scientific and Technical Information of China (English)
CAO Yi-Gang; JIAO Zheng-Kuan; A. Antons; K. Schroeder; S. Blügel2
2002-01-01
Using an ab initio total energy and force method, we have relaxed several group IV and group V elementalclusters, in detail the arsenic and antimony dimers, silicon, phosphorus, arsenic and antimony tetramers. The obtainedbond lengths and cohesive energies are more accurate than other calculating methods, and in excellent agreement withthe experimental results.
Ab initio interatomic potentials and the thermodynamic properties of fluids
Vlasiuk, Maryna; Sadus, Richard J.
2017-07-01
Monte Carlo simulations with accurate ab initio interatomic potentials are used to investigate the key thermodynamic properties of argon and krypton in both vapor and liquid phases. Data are reported for the isochoric and isobaric heat capacities, the Joule-Thomson coefficient, and the speed of sound calculated using various two-body interatomic potentials and different combinations of two-body plus three-body terms. The results are compared to either experimental or reference data at state points between the triple and critical points. Using accurate two-body ab initio potentials, combined with three-body interaction terms such as the Axilrod-Teller-Muto and Marcelli-Wang-Sadus potentials, yields systematic improvements to the accuracy of thermodynamic predictions. The effect of three-body interactions is to lower the isochoric and isobaric heat capacities and increase both the Joule-Thomson coefficient and speed of sound. The Marcelli-Wang-Sadus potential is a computationally inexpensive way to utilize accurate two-body ab initio potentials for the prediction of thermodynamic properties. In particular, it provides a very effective way of extending two-body ab initio potentials to liquid phase properties.
Ab-Initio Theory of Charge Transport in Organic Crystals
Hannewald, K.; Bobbert, P. A.
2005-06-01
A theory of charge transport in organic crystals is presented. Using a Holstein-Peierls model, an explicit expression for the charge-carrier mobilities as a function of temperature is obtained. Calculating all material parameters from ab initio calculations, the theory is applied to oligo-acene crystals and a brief comparison to experiment is given.
Structural flexibility of DABCO. Ab initio and DFT benchmark study
Nizovtsev, Anton S.; Ryzhikov, Maxim R.; Kozlova, Svetlana G.
2017-01-01
The energy and structural parameters of 1,4-diazabicyclo[2.2.2]octane (DABCO) obtained by various DFT methods are examined versus ab initio and experimental data. The features of twisting potentials of DABCO and closely-related species (1-azabicyclo[2.2.2]octane and bicyclo[2.2.2]octane) are discussed in light of computational schemes applied.
Energy Technology Data Exchange (ETDEWEB)
Liu, Hanchao; Wang, Yimin; Bowman, Joel M. [Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322 (United States)
2015-05-21
The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H{sub 2}O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previous spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0–4000 cm{sup −1} is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.
Liu, Hanchao; Wang, Yimin; Bowman, Joel M
2015-05-21
The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H2O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previous spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0-4000 cm(-1) is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.
Ab initio calculation of the electronic absorption spectrum of liquid water
Energy Technology Data Exchange (ETDEWEB)
Martiniano, Hugo F. M. C.; Galamba, Nuno [Grupo de Física Matemática da Universidade de Lisboa, Av. Professor Gama Pinto 2, 1649-003 Lisboa (Portugal); Cabral, Benedito J. Costa, E-mail: ben@cii.fc.ul.pt [Grupo de Física Matemática da Universidade de Lisboa, Av. Professor Gama Pinto 2, 1649-003 Lisboa (Portugal); Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa (Portugal); Instituto de Física da Universidade de São Paulo, CP 66318, 05314-970 São Paulo, SP (Brazil)
2014-04-28
The electronic absorption spectrum of liquid water was investigated by coupling a one-body energy decomposition scheme to configurations generated by classical and Born-Oppenheimer Molecular Dynamics (BOMD). A Frenkel exciton Hamiltonian formalism was adopted and the excitation energies in the liquid phase were calculated with the equation of motion coupled cluster with single and double excitations method. Molecular dynamics configurations were generated by different approaches. Classical MD were carried out with the TIP4P-Ew and AMOEBA force fields. The BLYP and BLYP-D3 exchange-correlation functionals were used in BOMD. Theoretical and experimental results for the electronic absorption spectrum of liquid water are in good agreement. Emphasis is placed on the relationship between the structure of liquid water predicted by the different models and the electronic absorption spectrum. The theoretical gas to liquid phase blue-shift of the peak positions of the electronic absorption spectrum is in good agreement with experiment. The overall shift is determined by a competition between the O–H stretching of the water monomer in liquid water that leads to a red-shift and polarization effects that induce a blue-shift. The results illustrate the importance of coupling many-body energy decomposition schemes to molecular dynamics configurations to carry out ab initio calculations of the electronic properties in liquid phase.
Energy Technology Data Exchange (ETDEWEB)
Ventelon, L. [CEA Saclay, Dept. des Materiaux pour le Nucleaire (DEN/DANS/DMN/SRMP), 91 - Gif-sur-Yvette (France)
2008-07-01
In the framework of the multi scale simulation of metals and alloys plasticity, the aim of this study is to develop a methodology of ab initio dislocations study and to apply it to the [111] screw dislocation in the bc iron. (A.L.B.)
Two-step spin-switchable tetranuclear Fe(II) molecular solid: Ab initio theory and predictions
Maldonado, Pablo; Kanungo, Sudipta; Saha-Dasgupta, Tanusri; Oppeneer, Peter M.
2013-07-01
Using density functional theory supplemented with on-site Coulomb U interaction in combination with ab initio molecular dynamics simulations, we investigate the spin-crossover (SCO) properties of a Fe(II) based cyanide-bridged square molecular system, [FeII4(μ-CN)4(bpy)4(tpa)2](PF6)4 (where bpy = 2,2'-bipyridine and tpa = tris(2-pyridylmethyl)amine], exhibiting a two-step SCO transition. The ab initio calculated SCO temperatures are found to show remarkably good agreement with experimentally measured spin conversion temperatures [M. Nihei , Angew. Chem., Int. Ed.1433-785110.1002/anie.200502216 44, 6484 (2005)]. Our theoretical study predicts further chemo switching of the spin state by introduction of guest molecules such as CO2, CS2, and H2O into the porous topology of the system, which would add another dimensionality to this interesting material.
Campetella, Marco; Bodo, Enrico; Montagna, Maria; De Santis, Serena; Gontrani, Lorenzo
2016-03-01
We have explored by means of ab initio molecular dynamics the homologue series of 11 different ionic liquids based on the combination of the cholinium cation with deprotonated amino acid anions. We present a structural analysis of the liquid states of these compounds as revealed by accurate ab initio computations of the forces. We highlight the persistent structural motifs that see the ionic couple as the basic building block of the liquid whereby a strong hydrogen bonding network substantially determines the short range structural behavior of the bulk state. Other minor docking features of the interaction network are also discovered and described. Special cases along the series such as Cysteine and Phenylalanine are discussed in the view of their peculiar properties due to zwitterion formation and additional long-range structural organization.
Structure and dynamics of liquid Zn: an analysis of ab-initio simulations
Directory of Open Access Journals (Sweden)
del Rio B. G.
2017-01-01
Full Text Available The static and dynamic properties of liquid Zn have been studied using an ab initio molecular dynamics method. Results are reported for the thermodynamic states at 723K near which inelastic neutron and x-ray scattering data are available. The calculated static structure shows very good agreement with experimental measurements, including an asymmetric main peak. The dynamic structure reveals the existence of propagating density fluctuations, and the associated dispersion relation has also been calculated. The possible coupling between longitudinal and transverse excitation modes has been investigated by looking at specific signatures in two wavevector regions: the first one is located around the position of the main peak of the structure factor, qp, as suggested by the recently reported appearance of high frequency transverse waves in several liquid metals under high pressures; the second region is around qp/2, as suggested by inelastic scattering experiments for liquid Zn and other metals.
Structural phase transition of CdTe: an ab initio study.
Alptekin, Sebahaddin
2013-01-01
A constant pressure ab initio MD technique and density functional theory with a generalized gradient approximation (GGA) was used to study the pressure-induced phase transition in zinc-blende CdTe. We found that CdTe undergoes a structural first-order phase transition to [Formula: see text] (binary β-tin) tetragonal structure in the constant pressure molecular dynamics simulation at 20 GPa. When the pressure was increased to 50 GPa, the phase of tetragonal structure converted to a new Imm2 orthorhombic structure. These phase transformations were also calculated by using the enthalpy calculations. Transition phases, lattice parameters and bulk properties we attained are comparable with experimental and theoretical data.
Pressure-induced phase transition in wurtzite ZnTe: an ab initio study.
Alptekin, Sebahaddin
2012-03-01
A constant pressure ab initio MD technique and density functional theory with a generalized gradient approximation (GGA) was used to study the pressure-induced phase transition in wurtzite ZnTe. A first-order phase transition from the wurtzite structure to a Cmcm structure was successfully observed in a constant-pressure molecular dynamics simulation. This phase transformation was also analyzed using enthalpy calculations. We also investigated the stability of wurtzite (WZ) and zinc-blende (ZB) phases from energy-volume calculations, and found that both structures show quite similar equations of state and transform into a Cmcm structure at 16 GPa using enthalpy calculations, in agreement with experimental observations. The transition phase, lattice parameters and bulk properties we obtained are comparable with experimental and theoretical data.
Mundy, Christopher J; Curioni, Alessandro; Goldman, Nir; Will Kuo, I-F; Reed, Evan J; Fried, Laurence E; Ianuzzi, Marcella
2008-05-14
We report herein ab initio molecular dynamics simulations of graphite under shock compression in conjunction with the multiscale shock technique. Our simulations reveal that a novel short-lived layered diamond intermediate is formed within a few hundred of femtoseconds upon shock loading at a shock velocity of 12 kms (longitudinal stress>130 GPa), followed by formation of cubic diamond. The layered diamond state differs from the experimentally observed hexagonal diamond intermediate found at lower pressures and previous hydrostatic calculations in that a rapid buckling of the graphitic planes produces a mixture of hexagonal and cubic diamond (layered diamond). Direct calculation of the x-ray absorption spectra in our simulations reveals that the electronic structure of the final state closely resembles that of compressed cubic diamond.
Ab initio multiple spawning dynamics using multi-state second-order perturbation theory.
Tao, Hongli; Levine, Benjamin G; Martínez, Todd J
2009-12-10
We have implemented multi-state second-order perturbation theory (MS-CASPT2) in the ab initio multiple spawning (AIMS) method for first-principles molecular dynamics including nonadiabatic effects. The nonadiabatic couplings between states are calculated numerically using an efficient method which requires only two extra energy calculations per time step. As a representative example, we carry out AIMS-MSPT2 calculations of the excited state dynamics of ethylene. Two distinct types of conical intersections, previously denoted as the twisted-pyramidalized and ethylidene intersections, are responsible for ultrafast population transfer from the excited state to the ground state. Although these two pathways have been observed in prior dynamics simulations, we show here that the branching ratio is affected by dynamic correlation with the twisted-pyramidalized intersection overweighting the ethylidene-like intersection during the decay process at the AIMS-MSPT2 level of description.
Ab initio determination of effective electron-phonon coupling factor in copper
Ji, Pengfei; Zhang, Yuwen
2016-04-01
The electron temperature Te dependent electron density of states g (ε), Fermi-Dirac distribution f (ε), and electron-phonon spectral function α2 F (Ω) are computed as prerequisites before achieving effective electron-phonon coupling factor Ge-ph. The obtained Ge-ph is implemented into a molecular dynamics (MD) and two-temperature model (TTM) coupled simulation of femtosecond laser heating. By monitoring temperature evolutions of electron and lattice subsystems, the result utilizing Ge-ph from ab initio calculation shows a faster decrease of Te and increase of Tl than those using Ge-ph from phenomenological treatment. The approach of calculating Ge-ph and its implementation into MD-TTM simulation is applicable to other metals.
Ab initio determination of effective electron-phonon coupling factor in copper
Ji, Pengfei
2016-01-01
The electron temperature T_e dependent electron density of states g({\\epsilon}), Fermi-Dirac distribution f({\\epsilon}), and electron-phonon spectral function {\\alpha}^2 F({\\Omega}) are computed as prerequisites before achieving effective electron-phonon coupling factor. The obtained is implemented into a molecular dynamics (MD) and two-temperature model (TTM) coupled simulation of femtosecond laser heating. By monitoring temperature evolutions of electron and lattice subsystems, the result utilizing G_(e-ph) from ab initio calculation, shows a faster decrease of T_e and increase of T_l than those using G_(e-ph) from phenomenological treatment. The approach of calculating G_(e-ph) and its implementation into MD-TTM simulation is applicable to other metals.
Impact of oxygen on the 300-K isotherm of Laser Megajoule ablator using ab initio simulation
Colin-Lalu, P.; Recoules, V.; Salin, G.; Huser, G.
2015-11-01
The ablator material for inertial confinement fusion (ICF) capsules on the Laser Mégajoule is a glow-discharge polymer (GDP) plastic. Its equation of state (EOS) is of primary importance for the design of such capsules, since it has direct consequences on shock timing and is essential to mitigate hydrodynamic instabilities. Using ab initio molecular dynamics (AIMD), we have investigated the 300-K isotherm of amorphous CH1.37O0.08 plastic, whose structure is close to GDP plastic. The 300-K isotherm, which is often used as a cold curve within tabular EOS, is an important contribution of the EOS in the multimegabar pressure range. AIMD results are compared to analytic models within tabular EOS, pointing out large discrepancies. In addition, we show that the effect of oxygen decreases 300-K isotherm pressure by 10%-15%. The implication of these observations is the ability to improve ICF target performance, which is essential to achieve fusion ignition.
HCO+ dissociation in a strong laser field: An ab initio classical trajectory study
Lee, Suk Kyoung; Li, Wen; Bernhard Schlegel, H.
2012-05-01
We have investigated the photodissociation of HCO+ in a strong field with a wavelength of 10 μm using ab initio molecular dynamics. Classical trajectories were calculated at three field intensities. At 2.9 × 1014 W/cm2 and phase ϕ = 0, protons have two distinct dissociation times, mainly due to the reorientation of HCO+ relative to the field direction prior to dissociation. The kinetic energy distribution at this intensity agrees with Wardlaw's wagging tail model, suggesting that dissociation occurs through barrier-suppression. At 1.7 × 1014 and 8.8 × 1013 W/cm2, barrier suppression is incomplete and the maximum kinetic energy is less than predicted by the wagging tail model.
AB INITIO Modeling of Thermomechanical Properties of Mo-Based Alloys for Fossil Energy Conversion
Energy Technology Data Exchange (ETDEWEB)
Ching, Wai-Yim
2013-12-31
In this final scientific/technical report covering the period of 3.5 years started on July 1, 2011, we report the accomplishments on the study of thermo-mechanical properties of Mo-based intermetallic compounds under NETL support. These include computational method development, physical properties investigation of Mo-based compounds and alloys. The main focus is on the mechanical and thermo mechanical properties at high temperature since these are the most crucial properties for their potential applications. In particular, recent development of applying ab initio molecular dynamic (AIMD) simulations to the T1 (Mo{sub 5}Si{sub 3}) and T2 (Mo{sub 5}SiB{sub 2}) phases are highlighted for alloy design in further improving their properties.
An ab initio approach to free-energy reconstruction using logarithmic mean force dynamics.
Nakamura, Makoto; Obata, Masao; Morishita, Tetsuya; Oda, Tatsuki
2014-05-14
We present an ab initio approach for evaluating a free energy profile along a reaction coordinate by combining logarithmic mean force dynamics (LogMFD) and first-principles molecular dynamics. The mean force, which is the derivative of the free energy with respect to the reaction coordinate, is estimated using density functional theory (DFT) in the present approach, which is expected to provide an accurate free energy profile along the reaction coordinate. We apply this new method, first-principles LogMFD (FP-LogMFD), to a glycine dipeptide molecule and reconstruct one- and two-dimensional free energy profiles in the framework of DFT. The resultant free energy profile is compared with that obtained by the thermodynamic integration method and by the previous LogMFD calculation using an empirical force-field, showing that FP-LogMFD is a promising method to calculate free energy without empirical force-fields.
Ab initio study on the dynamics of furfural at the liquid-solid interfaces
Dang, Hongli; Xue, Wenhua; Shields, Darwin; Liu, Yingdi; Jentoft, Friederike; Resasco, Daniel; Wang, Sanwu
2013-03-01
Catalytic biomass conversion sometimes occurs at the liquid-solid interfaces. We report ab initio molecular dynamics simulations at finite temperatures for the catalytic reactions involving furfural at the water-Pd and water-Cu interfaces. We found that, during the dynamic process, the furan ring of furfural prefers to be parallel to the Pd surface and the aldehyde group tends to be away from the Pd surface. On the other hand, at the water-Cu(111) interface, furfural prefers to be tilted to the Cu surface while the aldehyde group is bonded to the surface. In both cases, interaction of liquid water and furfural is identified. The difference of dynamic process of furfural at the two interfaces suggests different catalytic reaction mechanisms for the conversion of furfural, consistent with the experimental investigations. Supported by DOE (DE-SC0004600). Simulations and calculations were performed on XSED's and NERSC's supercomputers
The density matrix renormalization group for ab initio quantum chemistry
Wouters, Sebastian
2014-01-01
During the past 15 years, the density matrix renormalization group (DMRG) has become increasingly important for ab initio quantum chemistry. Its underlying wavefunction ansatz, the matrix product state (MPS), is a low-rank decomposition of the full configuration interaction tensor. The virtual dimension of the MPS, the rank of the decomposition, controls the size of the corner of the many-body Hilbert space that can be reached with the ansatz. This parameter can be systematically increased until numerical convergence is reached. The MPS ansatz naturally captures exponentially decaying correlation functions. Therefore DMRG works extremely well for noncritical one-dimensional systems. The active orbital spaces in quantum chemistry are however often far from one-dimensional, and relatively large virtual dimensions are required to use DMRG for ab initio quantum chemistry (QC-DMRG). The QC-DMRG algorithm, its computational cost, and its properties are discussed. Two important aspects to reduce the computational co...
Spin-orbit decomposition of ab initio wavefunctions
Johnson, Calvin W
2014-01-01
Although the modern shell-model picture of atomic nuclei is built from single-particle orbits with good total angular momentum $j$, leading to $j$-$j$ coupling, phenomenological models suggested decades ago that for $0p$-shell nuclides a simpler picture can be realized via coupling of total spin $S$ and total orbital angular momentum $L$. I revisit this idea with large-basis, no-core shell model (NCSM) calculations using modern \\textit{ab initio} two-body interactions, and dissect the resulting wavefunctions into their component $L$- and $S$-components. Remarkably, there is broad agreement with calculations using the phenomenological Cohen-Kurath forces, despite a gap of nearly fifty years and six orders of magnitude in basis dimensions. I suggest $L$-$S$ may be a useful tool for analyzing \\textit{ab initio} wavefunctions of light nuclei, for example in the case of rotational bands.
Spin-orbit decomposition of ab initio nuclear wave functions
Johnson, Calvin W.
2015-03-01
Although the modern shell-model picture of atomic nuclei is built from single-particle orbits with good total angular momentum j , leading to j -j coupling, decades ago phenomenological models suggested that a simpler picture for 0 p -shell nuclides can be realized via coupling of the total spin S and total orbital angular momentum L . I revisit this idea with large-basis, no-core shell-model calculations using modern ab initio two-body interactions and dissect the resulting wave functions into their component L - and S -components. Remarkably, there is broad agreement with calculations using the phenomenological Cohen-Kurath forces, despite a gap of nearly 50 years and six orders of magnitude in basis dimensions. I suggest that L -S decomposition may be a useful tool for analyzing ab initio wave functions of light nuclei, for example, in the case of rotational bands.
High Level Ab Initio Kinetics as a Tool for Astrochemistry
Klippenstein, Stephen
2015-05-01
We will survey the application of ab initio theoretical kinetics to reactions of importance to astrochemistry. Illustrative examples will be taken from our calculations for (i) interstellar chemistry, (ii) Titan's atmospheric chemistry, and (iii) the chemistry of extrasolar giant planets. The accuracy of various aspects of the calculations will be summarized including (i) the underlying ab initio electronic structure calculations, (ii) the treatment of the high pressure recombination process, and (iii) the treatment of the pressure dependence of the kinetics. The applications will consider the chemistry of phosphorous on giant planets, the kinetics of water dimerization, the chemistry of nitrogen on Titan's atmosphere, as well as various reactions of interstellar chemistry interest such as the recombination of OH with H, and O(3P) reacting with C2H5, CH2, and CCS. Chemical Sciences and Engineering Division.
Toward the Ab-initio Description of Medium Mass Nuclei
Barbieri, C; Soma, V; Duguet, T; Navratil, P
2012-01-01
As ab-initio calculations of atomic nuclei enter the A=40-100 mass range, a great challenge is how to approach the vast majority of open-shell (degenerate) isotopes. We add realistic three-nucleon interactions to the state of the art many-body Green's function theory of closed-shells, and find that physics of neutron driplines is reproduced with very good quality. Further, we introduce the Gorkov formalism to extend ab-initio theory to semi-magic, fully open-shell, isotopes. Proof-of-principle calculations for Ca-44 and Ni-74 confirm that this approach is indeed feasible. Combining these two advances (open-shells and three-nucleon interactions) requires longer, technical, work but it is otherwise within reach.
Ab initio theories for light nuclei and neutron stars
Gezerlis, Alexandros
2016-09-01
In this talk I will touch upon several features of modern ab initio low-energy nuclear theory. I will start by discussing what ``ab initio'' means in this context. Specifically, I will spend some time going over nucleon-nucleon and three-nucleon interactions and their connections with the underlying theory of Quantum Chromodynamics. I will then show how these interactions are used to describe light nuclei using essentially exact few-body methods. I will then discuss heavier systems, especially those of astrophysical relevance, as well as the methods used to tackle them. This work was supported by the Natural Sciences and Engineering Research Council (NSERC) of Canada and the Canada Foundation for Innovation (CFI).
Ab Initio Studies of Metal Hexaboride Materials
Schmidt, Kevin M.
Metal hexaborides are refractory ceramics with several qualities relevant to materials design, such as low work functions, high hardness, low thermal expansion coefficients, and high melting points, among many other properties of interest for industrial applications. Thermal and mechanical stability is a common feature provided by the covalently-bonded network boron atoms, and electronic properties can vary significantly with the resident metal. While these materials are currently employed as electron emitters and abrasives, promising uses of these materials also include catalytic applications for chemical dissociation reactions of various molecules such as hydrogen, water and carbon monoxide, for example. However, these extensions require a thorough understanding of particular mechanical and electronic properties. This dissertation is a collection of studies focused on understanding the behavior of metal hexaboride materials using computational modeling methods to investigate materials properties of these from both classical and quantum mechanical points of view. Classical modeling is performed using molecular dynamics methods with interatomic potentials obtained from density functional theory (DFT) calculations. Atomic mean-square displacements from the quasi-harmonic approximation and lattice energetic data are produced with DFT for developing the potentials. A generalized method was also developed for the inversion of cohesive energy curves of crystalline materials; pairwise interatomic potentials are extracted using detailed geometrical descriptions of the atomic interactions and a list of atomic displacements and degeneracies. The surface structure of metal hexaborides is studied with DFT using several model geometries to describe the terminal cation layouts, and these provide a basis for further studies on metal hexaboride interactions with hydrogen. The surface electronic structure calculations show that segregated regions of metal and boron
Study of Nuclear Clustering from an Ab Initio Perspective
Kravvaris, Konstantinos; Volya, Alexander
2017-08-01
We put forward a new ab initio approach that seamlessly bridges the structure, clustering, and reactions aspects of the nuclear quantum many-body problem. The configuration interaction technique combined with the resonating group method based on a harmonic oscillator basis allows us to treat the reaction and multiclustering dynamics in a translationally invariant way and preserve the Pauli principle. Our presentation includes studies of Be,108 and an exploration of 3 α clustering in 12C.
Ab initio calculation of tight-binding parameters
Energy Technology Data Exchange (ETDEWEB)
McMahan, A.K.; Klepeis, J.E.
1997-12-01
We calculate ab initio values of tight-binding parameters for the f- electron metal Ce and various phases of Si, from local-density functional one-electron Hamiltonian and overlap matrix elements. Our approach allows us to unambiguously test the validity of the common minimal basis and two-center approximations as well as to determine the degree of transferability of both nonorthogonal and orthogonal hopping parameters in the cases considered.
Uniaxial Phase Transition in Si : Ab initio Calculations
Cheng, C.
2002-01-01
Based on a previously proposed thermodynamic analysis, we study the relative stabilities of five Si phases under uniaxial compression using ab initio methods. The five phases are diamond, beta-tin, sh, sc, and hcp structures. The possible phase-transition patterns were investigated by considering the phase transitions between any two chosen phases of the five phases. By analyzing the different conributions to the relative pahse stability, we identified the most important factors in reducing t...
Ab Initio-Based Predictions of Hydrocarbon Combustion Chemistry
2015-07-15
144306 (2010)] and the cubic -‐ spline -‐fitted PES reported by Xu, Xie, Zhang, Lin, and Guo...SUBTITLE 13. SUPPLEMENTARY NOTES 12. DISTRIBUTION AVAILIBILITY STATEMENT 6. AUTHORS 7. PERFORMING ORGANIZATION NAMES AND ADDRESSES 15. SUBJECT TERMS b ...accurate global PESs and for direct dynamics simulations using interpolating moving least squares (IMLS) that guarantee high fidelity to ab initio data. A
GAUSSIAN 76: An ab initio Molecular Orbital Program
Binkley, J. S.; Whiteside, R.; Hariharan, P. C.; Seeger, R.; Hehre, W. J.; Lathan, W. A.; Newton, M. D.; Ditchfield, R.; Pople, J. A.
1978-01-01
Gaussian 76 is a general-purpose computer program for ab initio Hartree-Fock molecular orbital calculations. It can handle basis sets involving s, p and d-type Gaussian functions. Certain standard sets (STO-3G, 4-31G, 6-31G*, etc.) are stored internally for easy use. Closed shell (RHF) or unrestricted open shell (UHF) wave functions can be obtained. Facilities are provided for geometry optimization to potential minima and for limited potential surface scans.
Nuclear forces and ab initio calculations of atomic nuclei
Meißner, Ulf-G.
2014-01-01
Nuclear forces and the nuclear many-body problem have been some of Gerry Brown's main topics in his so productive life as a theoretical physicist. In this talk, I outline how Gerry's work laid the foundations of the modern theory of nuclear forces and ab initio calculations of atomic nuclei. I also present some recent developments obtained in the framework of nuclear lattice simulations.
Thermochemical data for CVD modeling from ab initio calculations
Energy Technology Data Exchange (ETDEWEB)
Ho, P. [Sandia National Labs., Albuquerque, NM (United States); Melius, C.F. [Sandia National Labs., Livermore, CA (United States)
1993-12-31
Ab initio electronic-structure calculations are combined with empirical bond-additivity corrections to yield thermochemical properties of gas-phase molecules. A self-consistent set of heats of formation for molecules in the Si-H, Si-H-Cl, Si-H-F, Si-N-H and Si-N-H-F systems is presented, along with preliminary values for some Si-O-C-H species.
Ab initio simulations of phase stability and martensitic transitions in NiTi
Haskins, Justin B.; Thompson, Alexander E.; Lawson, John W.
2016-12-01
For NiTi-based alloys, the shape memory effect is governed by a transition from a low-temperature martensite phase to a high-temperature austenite phase. Despite considerable experimental and computational work, basic questions regarding the stability of the phases and the martensitic phase transition remain unclear even for the simple case of binary, equiatomic NiTi. We perform ab initio molecular dynamics simulations to describe the temperature-dependent behavior of NiTi and resolve several of these outstanding issues. Structural correlation functions and finite temperature phonon spectra are evaluated to determine phase stability. We show that finite temperature, entropic effects stabilize the experimentally observed martensite (B19') and austenite (B2) phases while destabilizing the theoretically predicted (B33) phase. Free energy computations based on ab initio thermodynamic integration confirm these results and permit estimates of the transition temperature between the phases. In addition to the martensitic phase transition, we predict a new transition between the B33 and B19' phases. The role of defects in suppressing phase transformation temperatures is discussed.
Ab Initio Simulations of Temperature Dependent Phase Stability and Martensitic Transitions in NiTi
Haskins, Justin B.; Thompson, Alexander E.; Lawson, John W.
2016-01-01
For NiTi based alloys, the shape memory effect is governed by a transition from a low-temperature martensite phase to a high-temperature austenite phase. Despite considerable experimental and computational work, basic questions regarding the stability of the phases and the martensitic phase transition remain unclear even for the simple case of binary, equiatomic NiTi. We perform ab initio molecular dynamics simulations to describe the temperature-dependent behavior of NiTi and resolve several of these outstanding issues. Structural correlation functions and finite temperature phonon spectra are evaluated to determine phase stability. In particular, we show that finite temperature, entropic effects stabilize the experimentally observed martensite (B19') and austenite (B2) phases while destabilizing the theoretically predicted (B33) phase. Free energy computations based on ab initio thermodynamic integration confirm these results and permit estimates of the transition temperature between the phases. In addition to the martensitic phase transition, we predict a new transition between the B33 and B19' phases. The role of defects in suppressing these phase transformations is discussed.
Ab initio calculations of the optical properties of crystalline and liquid InSb
Energy Technology Data Exchange (ETDEWEB)
Sano, Haruyuki, E-mail: h-sano@ishikawa-nct.ac.jp [National Institute of Technology, Ishikawa College, Kitacyujo, Tsubata, Ishikawa 929-0392 (Japan); Mizutani, Goro [School of Materials Science, Japan Advanced Institute of Science and Technology, Tatsunokuchi, Ishikawa 923-1292 (Japan)
2015-11-15
Ab initio calculations of the electronic and optical properties of InSb were performed for both the crystalline and liquid states. Two sets of atomic structure models for liquid InSb at 900 K were obtained by ab initio molecular dynamics simulations. To reduce the effect of structural peculiarities in the liquid models, an averaging of the two sets of the calculated electronic and optical properties corresponding to the two liquid models was performed. The calculated results indicate that, owing to the phase transition from crystal to liquid, the density of states around the Fermi level increases. As a result, the energy band gap opening near the Fermi level disappears. Consequently, the optical properties change from semiconductor to metallic behavior. Namely, owing to the melting of InSb, the interband transition peaks disappear and a Drude-like dispersion is observed in the optical dielectric functions. The optical absorption at a photon energy of 3.06 eV, which is used in Blu-ray Disc systems, increases owing to the melting of InSb. This increase in optical absorption is proposed to result from the increased optical transitions below 2 eV.
Ab Initio Nuclear Structure and Reaction Calculations for Rare Isotopes
Energy Technology Data Exchange (ETDEWEB)
Draayer, Jerry P. [Louisiana State Univ., Baton Rouge, LA (United States)
2014-09-28
We have developed a novel ab initio symmetry-adapted no-core shell model (SA-NCSM), which has opened the intermediate-mass region for ab initio investigations, thereby providing an opportunity for first-principle symmetry-guided applications to nuclear structure and reactions for nuclear isotopes from the lightest p-shell systems to intermediate-mass nuclei. This includes short-lived proton-rich nuclei on the path of X-ray burst nucleosynthesis and rare neutron-rich isotopes to be produced by the Facility for Rare Isotope Beams (FRIB). We have provided ab initio descriptions of high accuracy for low-lying (including collectivity-driven) states of isotopes of Li, He, Be, C, O, Ne, Mg, Al, and Si, and studied related strong- and weak-interaction driven reactions that are important, in astrophysics, for further understanding stellar evolution, X-ray bursts and triggering of s, p, and rp processes, and in applied physics, for electron and neutrino-nucleus scattering experiments as well as for fusion ignition at the National Ignition Facility (NIF).
Ab initio and experimental studies of glow-discharge polymer used in laser mégajoule capsules
Colin-Lalu, P.; Recoules, V.; Salin, G.; Huser, G.
2017-01-01
The equations of state tables used in Inertial Confinement Fusion Capsule design tools are highly dependent on the cold curve in the multimegabar pressure range. Original ab initio molecular dynamic simulations were performed to get accurate cold curves of glow-discharge polymer (GDP) plastics. Furthermore the effect of oxygen absorption by GDP structure is studied on the cold curve, as well as its impact on the Hugoniot curves. Results are compared with the Hugoniot experimental data obtained in a recent experiment at the LULI2000 laser facility in France. This study leads to improve the equation of states knowledge of ablator materials, which is of primary importance for NIF and LMJ experiments.
Ji, Pengfei; Zhang, Yuwen
2016-03-01
On the basis of ab initio quantum mechanics (QM) calculation, the obtained electron heat capacity is implemented into energy equation of electron subsystem in two temperature model (TTM). Upon laser irradiation on the copper film, energy transfer from the electron subsystem to the lattice subsystem is modeled by including the electron-phonon coupling factor in molecular dynamics (MD) and TTM coupled simulation. The results show temperature and thermal melting difference between the QM-MD-TTM integrated simulation and pure MD-TTM coupled simulation. The successful construction of the QM-MD-TTM integrated simulation provides a general way that is accessible to other metals in laser heating.
Ji, Pengfei
2016-01-01
On the basis of ab initio quantum mechanics (QM) calculation, the obtained electron heat capacity is implemented into energy equation of electron subsystem in two temperature model (TTM). Upon laser irradiation on the copper film, energy transfer from the electron subsystem to the lattice subsystem is modeled by including the electron-phonon coupling factor in molecular dynamics (MD) and TTM coupled simulation. The results show temperature and thermal melting difference between the QM-MD-TTM integrated simulation and pure MD-TTM coupled simulation. The successful construction of the QM-MD-TTM integrated simulation provide a general way that is accessible to other metals in laser heating.
Pollet, Rodolphe; Bonnet, Célia S; Retailleau, Pascal; Durand, Philippe; Tóth, Éva
2017-03-27
The proton-exchange process between water and a carbamate has been studied experimentally and theoretically in a lanthanide-based paramagnetic chemical exchange saturation transfer agent endowed with potential multimodality detection capabilities (optical imaging, or T1 MRI for the Gd(III) analogue). In addition to an in-depth structural analysis by a combined approach (using X-ray crystallography, NMR, and molecular dynamics), our ab initio simulation in aqueous solution sheds light on the reaction mechanism for this proton exchange, which involves structural Grotthuss diffusion.
Ghosh, Debashree; Golan, Amir; Takahashi, Lynelle K; Krylov, Anna I; Ahmed, Musahid
2012-01-05
The ionization energy of gas-phase deoxyribose was determined using tunable vacuum ultraviolet synchrotron radiation coupled to an effusive thermal source. Adiabatic and vertical ionization energies of the ground and first four excited states of α-pyranose, the structure that dominates in the gas phase, were calculated using high-level electronic structure methods. An appearance energy of 9.1(±0.05) eV was recorded, which agrees reasonably well with a theoretical value of 8.8 eV for the adiabatic ionization energy. A clear picture of the dissociative photoionization dynamics of deoxyribose emerges from the fragmentation pattern recorded using mass spectrometry and from ab initio molecular dynamics calculations. The experimental threshold 9.4 (±0.05) eV for neutral water elimination upon ionization is captured well in the calculations, and qualitative insights are provided by molecular orbital analysis and molecular dynamics snapshots along the reaction coordinate.
Morse-Smale Analysis of Ion Diffusion in Ab Initio Battery Materials Simulations
Energy Technology Data Exchange (ETDEWEB)
Gyulassy, Attila [Univ. of Utah, Salt Lake City, UT (United States); Knoll, Aaron [Univ. of Utah, Salt Lake City, UT (United States); Lau, Kah Chun [Argonne National Lab. (ANL), Argonne, IL (United States); Wang, Bei [Univ. of Utah, Salt Lake City, UT (United States); Bremer, Peer-Timo [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Papka, Michael [Argonne National Lab. (ANL), Argonne, IL (United States); Curtiss, Larry A [Argonne National Lab. (ANL), Argonne, IL (United States); Pascucci, Valerio [Univ. of Utah, Salt Lake City, UT (United States)
2017-06-03
Ab initio molecular dynamics (AIMD) simulations are increasingly useful in modeling, optimizing and synthesizing materials in energy sciences. In solving Schrödinger’s equation, they generate the electronic structure of the simulated atoms as a scalar field. However, methods for analyzing these volume data are not yet common in molecular visualization. The Morse-Smale complex is a proven, versatile tool for topological analysis of scalar fields. In this paper, we apply the discrete Morse-Smale complex to analysis of first-principles battery materials simulations. We consider a carbon nanosphere structure used in battery materials research, and employ Morse-Smale decomposition to determine the possible lithium ion diffusion paths within that structure. Our approach is novel in that it uses the wavefunction itself as opposed distance fields, and that we analyze the 1-skeleton of the Morse-Smale complex to reconstruct our diffusion paths. Furthermore, it is the first application where specific motifs in the graph structure of the complete 1-skeleton define features, namely carbon rings with specific valence. We compare our analysis of DFT data with that of a distance field approximation, and discuss implications on larger classical molecular dynamics simulations.
Energy Technology Data Exchange (ETDEWEB)
Lucas, G
2006-10-15
The behaviour of silicon carbide under irradiation has been studied using classical and ab initio simulations, focusing on the nano scale elementary processes. First, we have been interested in the calculation of threshold displacement energies, which are difficult to determine both experimentally and theoretically, and also the associated Frenkel pairs. In the framework of this thesis, we have carried out simulations in classical and ab initio molecular dynamics. For the classical approach, two types of potentials have been used: the Tersoff potential, which led to non satisfactory results, and a new one which has been developed during this thesis. This potential allows a better modelling of SiC under irradiation than most of the empirical potentials available for SiC. It is based on the EDIP potential, initially developed to describe defects in silicon, that we have generalized to SiC. For the ab initio approach, the feasibility of the calculations has been validated and average energies of 19 eV for the C and 38 eV for the Si sublattices have been determined, close to the values empirically used in the fusion community. The results obtained with the new potential EDIP are globally in agreement with those values. Finally, the elementary processes involved in the crystal recovery have been studied by calculating the stability of the created Frenkel pairs and determining possible recombination mechanisms with the nudged elastic band method. (author)
Benchmarks of the ab initio FCI, MCSM and NCFC methods
Abe, T; Otsuka, T; Shimizu, N; Utsuno, Y; Vary, J P
2012-01-01
We report ab initio no-core solutions for properties of light nuclei with three different approaches in order to assess the accuracy and convergence rates of each method. Full Configuration Interaction (FCI), Monte Carlo Shell Model (MCSM) and No Core Full Configuration (NCFC) approaches are solved separately for the ground state energy and other properties of seven light nuclei using the realistic JISP16 nucleon-nucleon interaction. The results are consistent among the different approaches. The methods differ significantly in how the required computational resources scale with increasing particle number for a given accuracy.
Ab initio modeling of small proteins by iterative TASSER simulations
Directory of Open Access Journals (Sweden)
Zhang Yang
2007-05-01
Full Text Available Abstract Background Predicting 3-dimensional protein structures from amino-acid sequences is an important unsolved problem in computational structural biology. The problem becomes relatively easier if close homologous proteins have been solved, as high-resolution models can be built by aligning target sequences to the solved homologous structures. However, for sequences without similar folds in the Protein Data Bank (PDB library, the models have to be predicted from scratch. Progress in the ab initio structure modeling is slow. The aim of this study was to extend the TASSER (threading/assembly/refinement method for the ab initio modeling and examine systemically its ability to fold small single-domain proteins. Results We developed I-TASSER by iteratively implementing the TASSER method, which is used in the folding test of three benchmarks of small proteins. First, data on 16 small proteins (α-root mean square deviation (RMSD of 3.8Å, with 6 of them having a Cα-RMSD α-RMSD α-RMSD of the I-TASSER models was 3.9Å, whereas it was 5.9Å using TOUCHSTONE-II software. Finally, 20 non-homologous small proteins (α-RMSD of 3.9Å was obtained for the third benchmark, with seven cases having a Cα-RMSD Conclusion Our simulation results show that I-TASSER can consistently predict the correct folds and sometimes high-resolution models for small single-domain proteins. Compared with other ab initio modeling methods such as ROSETTA and TOUCHSTONE II, the average performance of I-TASSER is either much better or is similar within a lower computational time. These data, together with the significant performance of automated I-TASSER server (the Zhang-Server in the 'free modeling' section of the recent Critical Assessment of Structure Prediction (CASP7 experiment, demonstrate new progresses in automated ab initio model generation. The I-TASSER server is freely available for academic users http://zhang.bioinformatics.ku.edu/I-TASSER.
Ab initio study of phase equilibria in TiCx
DEFF Research Database (Denmark)
Korzhavyi, P.A.; Pourovskii, L.V.; Hugosson, H.W.
2002-01-01
The phase diagram for the vacancy-ordered structures in the substoichiometric TiCx (x = 0.5-1.0) has been established from Monte Carlo simulations with the long-range pair and multisite effective interactions obtained from ab initio calculations. Three ordered superstructures of vacancies (Ti2C, Ti......3C2, and Ti6C5) are found to be ground state configurations. Their stability has been verified by full-potential total energy calculations of the fully relaxed structures....
Accelerating Ab Initio Nuclear Physics Calculations with GPUs
Potter, Hugh; Maris, Pieter; Sosonkina, Masha; Vary, James; Binder, Sven; Calci, Angelo; Langhammer, Joachim; Roth, Robert; Çatalyürek, Ümit; Saule, Erik
2014-01-01
This paper describes some applications of GPU acceleration in ab initio nuclear structure calculations. Specifically, we discuss GPU acceleration of the software package MFDn, a parallel nuclear structure eigensolver. We modify the matrix construction stage to run partly on the GPU. On the Titan supercomputer at the Oak Ridge Leadership Computing Facility, this produces a speedup of approximately 2.2x - 2.7x for the matrix construction stage and 1.2x - 1.4x for the entire run.
Ab initio electronic properties of dual phosphorus monolayers in silicon
DEFF Research Database (Denmark)
Drumm, Daniel W.; Per, Manolo C.; Budi, Akin
2014-01-01
In the midst of the epitaxial circuitry revolution in silicon technology, we look ahead to the next paradigm shift: effective use of the third dimension - in particular, its combination with epitaxial technology. We perform ab initio calculations of atomically thin epitaxial bilayers in silicon......, investigating the fundamental electronic properties of monolayer pairs. Quantitative band splittings and the electronic density are presented, along with effects of the layers’ relative alignment and comments on disordered systems, and for the first time, the effective electronic widths of such device...
Spin-orbit decomposition of ab initio wavefunctions
Johnson, Calvin W.
2014-01-01
Although the modern shell-model picture of atomic nuclei is built from single-particle orbits with good total angular momentum $j$, leading to $j$-$j$ coupling, phenomenological models suggested decades ago that for $0p$-shell nuclides a simpler picture can be realized via coupling of total spin $S$ and total orbital angular momentum $L$. I revisit this idea with large-basis, no-core shell model (NCSM) calculations using modern \\textit{ab initio} two-body interactions, and dissect the resulti...
Tailoring magnetoresistance at the atomic level: An ab initio study
Tao, Kun
2012-01-05
The possibility of manipulating the tunneling magnetoresistance (TMR) of antiferromagnetic nanostructures is predicted in the framework of ab initio calculations. By the example of a junction composed of an antiferromagnetic dimer and a spin-polarized scanning tunneling microscopy tip we show that the TMR can be tuned and even reversed in sign by lateral and vertical movements of the tip. Moreover, our finite-bias calculations demonstrate that the magnitude and the sign of the TMR can also be tuned by an external voltage. © 2012 American Physical Society.
Ab initio structure determination via powder X-ray diffraction
Indian Academy of Sciences (India)
Digamber G Porob; T N Guru Row
2001-10-01
Structure determination by powder X-ray diffraction data has gone through a recent surge since it has become important to get to the structural information of materials which do not yield good quality single crystals. Although the method of structure completion when once the starting model is provided is facile through the Rietveld refinement technique, the structure solution ab initio os still not push-button technology. In this article a survey of the recent development in this area is provided with an illustration of the structure determination of -NaBi3V2O10.
Ab-initio study of transition metal hydrides
Energy Technology Data Exchange (ETDEWEB)
Sharma, Ramesh [Dept. of Physics, Feroze Gandhi Insititute of Engineering and Technology, Raebareli-229001 (India); Shukla, Seema, E-mail: sharma.yamini62@gmail.com; Dwivedi, Shalini, E-mail: sharma.yamini62@gmail.com; Sharma, Yamini, E-mail: sharma.yamini62@gmail.com [Theoretical Condensed Matter Physics Laboratory, Dept. of Physics Feroze Gandhi College, Raebareli-229001 (India)
2014-04-24
We have performed ab initio self consistent calculations based on Full potential linearized augmented plane wave (FP-LAPW) method to investigate the optical and thermal properties of yttrium hydrides. From the band structure and density of states, the optical absorption spectra and specific heats have been calculated. The band structure of Yttrium metal changes dramatically due to hybridization of Y sp orbitals with H s orbitals and there is a net charge transfer from metal to hydrogen site. The electrical resistivity and specific heats of yttrium hydrides are lowered but the thermal conductivity is slightly enhanced due to increase in scattering from hydrogen sites.
Morphing ab initio potential energy curve of beryllium monohydride
Špirko, Vladimír
2016-12-01
Effective (mass-dependent) potential energy curves of the ground electronic states of 9BeH, 9BeD, and 9BeT are constructed by morphing a very accurate MR-ACPF ab initio potential of Koput (2011) within the framework of the reduced potential energy curve approach of Jenč (1983). The morphing is performed by fitting the RPC parameters to available experimental ro-vibrational data. The resulting potential energy curves provide a fairly quantitative reproduction of the fitted data. This allows for a reliable prediction of the so-far unobserved molecular states in terms of only a small number of fitting parameters.
Knyazev, D V
2014-01-01
This work is devoted to the investigation of transport and optical properties of liquid aluminum in the two-temperature case. At first optical properties, static electrical and thermal conductivities were obtained in the \\textit{ab initio} calculation. The \\textit{ab initio} calculation is based on the quantum molecular dynamics, density functional theory and the Kubo-Greenwood formula. The semiempirical approximation was constructed based on the results of the \\textit{ab initio} caculation. The approximation yields the dependences $\\sigma_{1_\\mathrm{DC}}\\propto1/T_i^{0.25}$ and $K\\propto T_e/T_i^{0.25}$ for the static electrical conductivity and thermal conductivity, respectively. The approximation is valid for liquid aluminum at $\\rho=2.70$~g/cm$^3$, 3~kK~$\\leq T_i\\leq T_e\\leq20$~kK. Our results are well described by the Drude model with the effective relaxation time $\\tau\\propto T_i^{-0.25}$. We have compared our results with a number of other models. They are all reduced in the low-temperature limit to th...
Energy Technology Data Exchange (ETDEWEB)
Bernard, S.; Jollet, F.; Jomard, G.; Siberchicot, B.; Torrent, M.; Zerah, G.; Amadon, B.; Bouchet, J.; Richard, N.; Robert, G. [CEA Bruyeres-le-Chatel, 91 (France)
2005-07-01
The determination of equations of states of heavy metals through ab initio calculation, i.e. without any adjustable parameter, allows to access to pressure and temperature thermodynamic conditions sometimes inaccessible to experiment. To perform such calculations, density functional theory (DFT) is a good starting point: when electronic densities are homogeneous enough, the local density approximation (LDA) remarkably accounts for thermodynamic properties of heavy metals, such as tantalum, or the light actinides, as well for static properties - equilibrium volume, elastic constants - as for dynamical quantities like phonon spectra. For heavier elements, like neptunium or plutonium, relativistic effects and strong electronic interactions must be taken into account, which requires more sophisticated theoretical approaches. (authors)
Unified ab initio approaches to nuclear structure and reactions
Navratil, Petr; Hupin, Guillaume; Romero-Redondo, Carolina; Calci, Angelo
2016-01-01
The description of nuclei starting from the constituent nucleons and the realistic interactions among them has been a long-standing goal in nuclear physics. In addition to the complex nature of the nuclear forces, with two-, three- and possibly higher many-nucleon components, one faces the quantum-mechanical many-nucleon problem governed by an interplay between bound and continuum states. In recent years, significant progress has been made in {\\em ab initio} nuclear structure and reaction calculations based on input from QCD-employing Hamiltonians constructed within chiral effective field theory. After a brief overview of the field, we focus on ab initio many-body approaches - built upon the No-Core Shell Model - that are capable of simultaneously describing both bound and scattering nuclear states, and present results for resonances in light nuclei, reactions important for astrophysics and fusion research. In particular, we review recent calculations of resonances in the $^6$He halo nucleus, of five- and six...
Finite Elements in Ab Initio Electronic-Structure Calulations
Pask, J. E.; Sterne, P. A.
Over the course of the past two decades, the density functional theory (DFT) (see e.g., [1]) of Hohenberg, Kohn, and Sham has proven to be an accurate and reliable basis for the understanding and prediction of a wide range of materials properties from first principles (ab initio), with no experimental input or empirical parameters. However, the solution of the Kohn-Sham equations of DFT is a formidable task and this has limited the range of physical systems which can be investigated by such rigorous, quantum mechanical means. In order to extend the interpretive and predictive power of such quantum mechanical theories further into the domain of "real materials", involving nonstoichiometric deviations, defects, grain boundaries, surfaces, interfaces, and the like; robust and efficient methods for the solution of the associated quantum mechanical equations are critical. The finite-element (FE) method (see e.g., [2]) is a general method for the solution of partial differential and integral equations which has found wide application in diverse fields ranging from particle physics to civil engineering. Here, we discuss its application to large-scale ab initio electronic-structure calculations.
Ab initio calculations of reactions of light nuclei
Hupin, Guillaume; Quaglioni, Sofia; Navrátil, Petr
2017-09-01
An ab initio (i.e., from first principles) theoretical framework capable of providing a unified description of the structure and low-energy reaction properties of light nuclei is desirable as a support tool for accurate evaluations of crucial reaction data for nuclear astrophysics, fusion-energy research, and other applications. We present an efficient many-body approach to nuclear bound and scattering states alike, known as the ab initio no-core shell model with continuum. In this approach, square-integrable energy eigenstates of the A-nucleon system are coupled to (A-A)+A target-plus-projectile wave functions in the spirit of the resonating group method to obtain an efficient description of the many-body nuclear dynamics both at short and medium distances and at long ranges. We show that predictive results for nucleon and deuterium scattering on 4He nuclei can be obtained from the direct solution of the Schröedinger equation with modern nuclear potentials.
Ab Initio Thermodynamic Model for Magnesium Carbonates and Hydrates
Energy Technology Data Exchange (ETDEWEB)
Chaka, Anne M.; Felmy, Andrew R.
2014-03-28
An ab initio thermodynamic framework for predicting properties of hydrated magnesium carbonate minerals has been developed using density-functional theory linked to macroscopic thermodynamics through the experimental chemical potentials for MgO, water, and CO2. Including semiempirical dispersion via the Grimme method and small corrections to the generalized gradient approximation of Perdew, Burke, and Ernzerhof for the heat of formation yields a model with quantitative agreement for the benchmark minerals brucite, magnesite, nesquehonite, and hydromagnesite. The model shows how small differences in experimental conditions determine whether nesquehonite, hydromagnesite, or magnesite is the result of laboratory synthesis from carbonation of brucite, and what transformations are expected to occur on geological time scales. Because of the reliance on parameter-free first principles methods, the model is reliably extensible to experimental conditions not readily accessible to experiment and to any mineral composition for which the structure is known or can be hypothesized, including structures containing defects, substitutions, or transitional structures during solid state transformations induced by temperature changes or processes such as water, CO2, or O2 diffusion. Demonstrated applications of the ab initio thermodynamic framework include an independent means to evaluate differences in thermodynamic data for lansfordite, predicting the properties of Mg analogs of Ca-based hydrated carbonates monohydrocalcite and ikaite which have not been observed in nature, and an estimation of the thermodynamics of barringtonite from the stoichiometry and a single experimental observation.
Ab initio thermodynamic model for magnesium carbonates and hydrates.
Chaka, Anne M; Felmy, Andrew R
2014-09-04
An ab initio thermodynamic framework for predicting properties of hydrated magnesium carbonate minerals has been developed using density-functional theory linked to macroscopic thermodynamics through the experimental chemical potentials for MgO, water, and CO2. Including semiempirical dispersion via the Grimme method and small corrections to the generalized gradient approximation of Perdew, Burke, and Ernzerhof for the heat of formation yields a model with quantitative agreement for the benchmark minerals brucite, magnesite, nesquehonite, and hydromagnesite. The model shows how small differences in experimental conditions determine whether nesquehonite, hydromagnesite, or magnesite is the result of laboratory synthesis from carbonation of brucite, and what transformations are expected to occur on geological time scales. Because of the reliance on parameter-free first-principles methods, the model is reliably extensible to experimental conditions not readily accessible to experiment and to any mineral composition for which the structure is known or can be hypothesized, including structures containing defects, substitutions, or transitional structures during solid state transformations induced by temperature changes or processes such as water, CO2, or O2 diffusion. Demonstrated applications of the ab initio thermodynamic framework include an independent means to evaluate differences in thermodynamic data for lansfordite, predicting the properties of Mg analogues of Ca-based hydrated carbonates monohydrocalcite and ikaite, which have not been observed in nature, and an estimation of the thermodynamics of barringtonite from the stoichiometry and a single experimental observation.
Ab-initio simulations of materials using VASP: Density-functional theory and beyond.
Hafner, Jürgen
2008-10-01
During the past decade, computer simulations based on a quantum-mechanical description of the interactions between electrons and between electrons and atomic nuclei have developed an increasingly important impact on solid-state physics and chemistry and on materials science-promoting not only a deeper understanding, but also the possibility to contribute significantly to materials design for future technologies. This development is based on two important columns: (i) The improved description of electronic many-body effects within density-functional theory (DFT) and the upcoming post-DFT methods. (ii) The implementation of the new functionals and many-body techniques within highly efficient, stable, and versatile computer codes, which allow to exploit the potential of modern computer architectures. In this review, I discuss the implementation of various DFT functionals [local-density approximation (LDA), generalized gradient approximation (GGA), meta-GGA, hybrid functional mixing DFT, and exact (Hartree-Fock) exchange] and post-DFT approaches [DFT + U for strong electronic correlations in narrow bands, many-body perturbation theory (GW) for quasiparticle spectra, dynamical correlation effects via the adiabatic-connection fluctuation-dissipation theorem (AC-FDT)] in the Vienna ab initio simulation package VASP. VASP is a plane-wave all-electron code using the projector-augmented wave method to describe the electron-core interaction. The code uses fast iterative techniques for the diagonalization of the DFT Hamiltonian and allows to perform total-energy calculations and structural optimizations for systems with thousands of atoms and ab initio molecular dynamics simulations for ensembles with a few hundred atoms extending over several tens of ps. Applications in many different areas (structure and phase stability, mechanical and dynamical properties, liquids, glasses and quasicrystals, magnetism and magnetic nanostructures, semiconductors and insulators, surfaces
Agrawal, P M; Malshe, M; Narulkar, R; Raff, L M; Hagan, M; Bukkapatnum, S; Komanduri, R
2009-02-05
Previous methods proposed for obtaining analytic potential-energy surfaces (PES) from ab initio electronic structure calculations are not self-starting. They generally require that the sampling of configuration space important in the reaction dynamics of the process being investigated be initiated by using chemical intuition or a previously developed semiempirical potential-energy surface. When the system under investigation contains four or more atoms undergoing three- and four-center reactions in addition to bond scission processes, obtaining a sufficiently converged initial sampling can be very difficult due to the extremely large volume of configuration space that is important in the reaction dynamics. It is shown that by combining direct dynamics (DD) with previously reported molecular dynamics (MD), novelty sampling (NS), and neural network (NN) methods, an analytical surface suitable for MD computations for large systems may be obtained. Application of the method to the investigation of N-O bond scission and cis-trans isomerization reactions of HONO followed by comparison of the resulting neural network potential-energy surface to one obtained by using a semiempirical potential to initiate the sampling shows that the two potential surfaces are the same within the fitting accuracy of the surfaces. It is concluded that the combination of direct dynamics, molecular dynamics, novelty sampling, and neural network fitting provides a self-starting, robust, and accurate DD/MD/NS/NN method for the execution of first-principles, ab initio, molecular dynamics studies in systems containing four or more atoms which are undergoing simultaneous two-, three-, and four-center reactions.
Realization of prediction of materials properties by ab initio computer simulation
Indian Academy of Sciences (India)
Yoshiyuki Kawazoe
2003-01-01
Ab initio treatment is becoming realistic to predict physical, chemical, and even mechanical properties of academically and industrially interesting materials. There is, however, some limitation in size and time of the system up to the order of several hundred atoms and ∼ 1 pico second, even if we use the fastest supercomputer efficiently. Therefore, it is very difficult to simulate realistic materials with grain boundaries and important reactions like diffusion in materials. To improve this situation, two ways have been invented. One way is to upgrade approximations to match the necessary levels according to inhomogeneous electron gas theory beyond the present day standard, i.e. local density approximation (LDA). The reason is simply that the system we are interested in is composed of many particles interacting with Coulomb forces governed by quantum mechanics. (Complete knowledge is available, and only what we should do is to make better approximations to explain the phenomena!). Another is to extract the necessary parameters from the ab initio calculations on systems with limited number of atoms, and apply these results into cluster variation, direct, or any other sophisticated methods based on classical concepts such as statistical mechanics. In this paper, several typical examples recently worked out by our research group are introduced to indicate that these methodologies are actually possible to be successfully used to predict materials properties before experiments based on the present day state-of-art supercomputing systems. It includes scientific visualization of the results of ab initio molecular dynamics simulation on atom insertion process to C60 and to carbon nanotube, tight-binding calculation of single electron conductance properties in nanotube to create nano-scale diode virtually by computer, which will be a base of future nanoscale electric device in nanometer size, Li + H reaction without Born–Oppenheimer approximation, structural phase
Ab initio study of alanine polypeptide chains twisting
Solovyov, I A; Solovyov, A V; Yakubovitch, A V; Greiner, Walter; Solov'yov, Andrey V.; Solov'yov, Ilia A.; Yakubovitch, Alexander V.
2005-01-01
We have investigated the potential energy surfaces for alanine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles Phi and Psi, which are widely used for the characterization of the polypeptide chains. These particular degrees of freedom are essential for the characterization of proteins folding process. Calculations have been carried out within ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined stable conformations and calculated the energy barriers for transitions between them. Using a thermodynamic approach, we have estimated the times of characteristic transitions between these conformations. The results of our calculations have been compared with those obtained by other theoretical methods and with the available experimental data extracted from the Protein Data Base. This comparison demonstrates a reasonable corres...
A Review on Ab Initio Approaches for Multielectron Dynamics
Ishikawa, Kenichi L
2015-01-01
In parallel with the evolution of femtosecond and attosecond laser as well as free-electron laser technology, a variety of theoretical methods have been developed to describe the behavior of atoms, molecules, clusters, and solids under the action of those laser pulses. Here we review major ab initio wave-function-based numerical approaches to simulate multielectron dynamics in atoms and molecules driven by intense long-wavelength and/or ultrashort short-wavelength laser pulses. Direct solution of the time-dependent Schr\\"odinger equation (TDSE), though its applicability is limited to He, ${\\rm H}_2$, and Li, can provide an exact description and has been greatly contributing to the understanding of dynamical electron-electron correlation. Multiconfiguration self-consistent-field (MCSCF) approach offers a flexible framework from which a variety of methods can be derived to treat both atoms and molecules, with possibility to systematically control the accuracy. The equations of motion of configuration interactio...
An Efficient Approach to Ab Initio Monte Carlo Simulation
Leiding, Jeff
2013-01-01
We present a Nested Markov Chain Monte Carlo (NMC) scheme for building equilibrium averages based on accurate potentials such as density functional theory. Metropolis sampling of a reference system, defined by an inexpensive but approximate potential, is used to substantially decorrelate configurations at which the potential of interest is evaluated, thereby dramatically reducing the number needed to build ensemble averages at a given level of precision. The efficiency of this procedure is maximized on-the-fly through variation of the reference system thermodynamic state (characterized here by its inverse temperature \\beta^0), which is otherwise unconstrained. Local density approximation (LDA) results are presented for shocked states in argon at pressures from 4 to 60 GPa. Depending on the quality of the reference potential, the acceptance probability is enhanced by factors of 1.2-28 relative to unoptimized NMC sampling, and the procedure's efficiency is found to be competitive with that of standard ab initio...
High-throughput ab-initio dilute solute diffusion database
Wu, Henry; Mayeshiba, Tam; Morgan, Dane
2016-07-01
We demonstrate automated generation of diffusion databases from high-throughput density functional theory (DFT) calculations. A total of more than 230 dilute solute diffusion systems in Mg, Al, Cu, Ni, Pd, and Pt host lattices have been determined using multi-frequency diffusion models. We apply a correction method for solute diffusion in alloys using experimental and simulated values of host self-diffusivity. We find good agreement with experimental solute diffusion data, obtaining a weighted activation barrier RMS error of 0.176 eV when excluding magnetic solutes in non-magnetic alloys. The compiled database is the largest collection of consistently calculated ab-initio solute diffusion data in the world.
Ab initio quantum dynamics using coupled-cluster.
Kvaal, Simen
2012-05-21
The curse of dimensionality (COD) limits the current state-of-the-art ab initio propagation methods for non-relativistic quantum mechanics to relatively few particles. For stationary structure calculations, the coupled-cluster (CC) method overcomes the COD in the sense that the method scales polynomially with the number of particles while still being size-consistent and extensive. We generalize the CC method to the time domain while allowing the single-particle functions to vary in an adaptive fashion as well, thereby creating a highly flexible, polynomially scaling approximation to the time-dependent Schrödinger equation. The method inherits size-consistency and extensivity from the CC method. The method is dubbed orbital-adaptive time-dependent coupled-cluster, and is a hierarchy of approximations to the now standard multi-configurational time-dependent Hartree method for fermions. A numerical experiment is also given.
Interatomic Coulombic decay widths of helium trimer: Ab initio calculations
Energy Technology Data Exchange (ETDEWEB)
Kolorenč, Přemysl, E-mail: kolorenc@mbox.troja.mff.cuni.cz [Charles University in Prague, Faculty of Mathematics and Physics, Institute of Theoretical Physics, V Holešovičkách 2, 180 00 Prague (Czech Republic); Sisourat, Nicolas [Sorbonne Universités, UPMC Univ Paris 06, UMR 7614, Laboratoire de Chimie Physique Matière et Rayonnement, F-75005 Paris (France); CNRS, UMR 7614, Laboratoire de Chimie Physique Matière et Rayonnement, F-75005 Paris (France)
2015-12-14
We report on an extensive study of interatomic Coulombic decay (ICD) widths in helium trimer computed using a fully ab initio method based on the Fano theory of resonances. Algebraic diagrammatic construction for one-particle Green’s function is utilized for the solution of the many-electron problem. An advanced and universal approach to partitioning of the configuration space into discrete states and continuum subspaces is described and employed. Total decay widths are presented for all ICD-active states of the trimer characterized by one-site ionization and additional excitation of an electron into the second shell. Selected partial decay widths are analyzed in detail, showing how three-body effects can qualitatively change the character of certain relaxation transitions. Previously unreported type of three-electron decay processes is identified in one class of the metastable states.
Ab initio dynamical exchange interactions in frustrated antiferromagnets
Simoni, Jacopo; Stamenova, Maria; Sanvito, Stefano
2017-08-01
The ultrafast response to an optical pulse excitation of the spin-spin exchange interaction in transition metal antiferromagnets is studied within the framework of the time-dependent spin-density functional theory. We propose a formulation for the full dynamical exchange interaction, which is nonlocal in space, and it is derived starting from ab initio arguments. Then, we investigate the effect of the laser pulse on the onset of the dynamical process. It is found that we can distinguish two types of excitations, both activated immediately after the action of the laser pulse. While the first one can be associated to a Stoner-like excitation and involves the transfer of spin from one site to another, the second one is related to the ultrafast modification of a Heisenberg-like exchange interaction and can trigger the formation of spin waves in the first few hundred femtoseconds of the time evolution.
Ab initio investigation of the mechanical properties of copper
Institute of Scientific and Technical Information of China (English)
Liu Yue-Lin; Gui Li-Jiang; Jin Shuo
2012-01-01
Employing the ab initio total energy method based on the density functional theory with the generalized gradient approximation,we have systematically investigated the theoretical mechanical properties of copper (Cu).The theoretical tensile strengths are calculated to be 25.3 GPa,5.9 GPa,and 37.6 GPa for the fcc Cu single crystal in the [001],[110],and [111] directions,respectively.Among the three directions,the [110] direction is the weakest one due to the occurrence of structure transition at the lower strain and the weakest interaction of atoms between the (110) planes,while the [111] direction is the strongest direction because of the strongest interaction of atoms between the (111) planes.In terms of the elastic constants of Cu single crystal,we also estimate some mechanical quantities of polycrystalline Cu,including bulk modulus B,shear modulus G,Young's modulus Ep,and Poisson's ratio v.
Ab initio and kinetic modeling studies of formic acid oxidation
DEFF Research Database (Denmark)
Marshall, Paul; Glarborg, Peter
2015-01-01
A detailed chemical kinetic model for oxidation of formic acid (HOCHO) in flames has been developed, based on theoretical work and data from literature. Ab initio calculations were used to obtain rate coefficients for reactions of HOCHO with H, O, and HO2. Modeling predictions with the mechanism...... as the fate of HOCO, determines the oxidation rate of formic acid. At lower temperatures HO2, formed from HOCO + O2, is an important chain carrier and modeling predictions become sensitive to the HOCHO + HO2 reaction. © 2014 The Combustion Institute....... on calculations with the kinetic model. Formic acid is consumed mainly by reaction with OH, yielding OCHO, which dissociates rapidly to CO2 + H, and HOCO, which may dissociate to CO + OH or CO2 + H, or react with H, OH, or O2 to form more stable products. The branching fraction of the HOCHO + OH reaction, as well...
Ab initio study of II-(VI){sub 2} dichalcogenides
Energy Technology Data Exchange (ETDEWEB)
Olsson, P; Vidal, J; Lincot, D, E-mail: polsson@kth.se [Institut de R and D sur l' energie photovoltaique (IRDEP), UMR 7174-EDF-CNRS-ENSCP, 6 quai Watier, 78401 Chatou Cedex (France)
2011-10-12
The structural stabilities of the (Zn,Cd)(S,Se,Te){sub 2} dichalcogenides have been determined ab initio. These compounds are shown to be stable in the pyrite phase, in agreement with available experiments. Structural parameters for the ZnTe{sub 2} pyrite semiconductor compound proposed here are presented. The opto-electronic properties of these dichalcogenide compounds have been calculated using quasiparticle GW theory. Bandgaps, band structures and effective masses are proposed as well as absorption coefficients and refraction indices. The compounds are all indirect semiconductors with very flat conduction band dispersion and high absorption coefficients. The work functions and surface properties are predicted. The Te and Se based compounds could be of interest as absorber materials in photovoltaic applications. (paper)
Ab initio quantum dynamics using coupled-cluster
Kvaal, Simen
2012-01-01
The curse of dimensionality (COD) limits the current state-of-the-art {\\it ab initio} propagation methods for non-relativistic quantum mechanics to relatively few particles. For stationary structure calculations, the coupled-cluster (CC) method overcomes the COD in the sense that the method scales polynomially with the number of particles while still being size-consistent and extensive. We generalize the CC method to the time domain while allowing the single-particle functions to vary in an adaptive fashion as well, thereby creating a highly flexible, polynomially scaling approximation to the time-dependent Schr\\"odinger equation. The method inherits size-consistency and extensivity from the CC method. The method is dubbed orbital-adaptive time-dependent coupled-cluster (OATDCC), and is a hierarchy of approximations to the now standard multi-configurational time-dependent Hartree method for fermions. A numerical experiment is also given.
Quantum plasmonics: from jellium models to ab initio calculations
Directory of Open Access Journals (Sweden)
Varas Alejandro
2016-08-01
Full Text Available Light-matter interaction in plasmonic nanostructures is often treated within the realm of classical optics. However, recent experimental findings show the need to go beyond the classical models to explain and predict the plasmonic response at the nanoscale. A prototypical system is a nanoparticle dimer, extensively studied using both classical and quantum prescriptions. However, only very recently, fully ab initio time-dependent density functional theory (TDDFT calculations of the optical response of these dimers have been carried out. Here, we review the recent work on the impact of the atomic structure on the optical properties of such systems. We show that TDDFT can be an invaluable tool to simulate the time evolution of plasmonic modes, providing fundamental understanding into the underlying microscopical mechanisms.
The ab-initio density matrix renormalization group in practice.
Olivares-Amaya, Roberto; Hu, Weifeng; Nakatani, Naoki; Sharma, Sandeep; Yang, Jun; Chan, Garnet Kin-Lic
2015-01-21
The ab-initio density matrix renormalization group (DMRG) is a tool that can be applied to a wide variety of interesting problems in quantum chemistry. Here, we examine the density matrix renormalization group from the vantage point of the quantum chemistry user. What kinds of problems is the DMRG well-suited to? What are the largest systems that can be treated at practical cost? What sort of accuracies can be obtained, and how do we reason about the computational difficulty in different molecules? By examining a diverse benchmark set of molecules: π-electron systems, benchmark main-group and transition metal dimers, and the Mn-oxo-salen and Fe-porphine organometallic compounds, we provide some answers to these questions, and show how the density matrix renormalization group is used in practice.
Ab initio study of the transition-metal carbene cations
Institute of Scientific and Technical Information of China (English)
李吉海; 冯大诚; 冯圣玉
1999-01-01
The geometries and bonding characteristics of the first-row transition-metal carbene cations MCH2+ were investigated by ab initio molecular orbital theory （HF/LANL2DZ）. All of MCH2+ are coplanar. In the closed shell structures the C bonds to M with double bonds; while in the open shell structures the partial double bonds are formed, because one of the σ and π orbitals is singly occupied. It is mainly the π-type overlap between the 2px orbital of C and 4px, 3dxz, orbitals of M+ that forms the π orbitals. The dissociation energies of C—M bond appear in periodic trend from Sc to Cu. Most of the calculated bond dissociation energies are close to the experimental ones.
Ab initio electronic structure and optical conductivity of bismuth tellurohalides
Schwalbe, Sebastian; Starke, Ronald; Schober, Giulio A H; Kortus, Jens
2016-01-01
We investigate the electronic structure, dielectric and optical properties of bismuth tellurohalides BiTeX (X = I, Cl, Br) by means of all-electron density functional theory. In particular, we present the ab initio conductivities and dielectric tensors calculated over a wide frequency range, and compare our results with the recent measurements by Akrap et al. , Makhnev et al. , and Rusinov et al. . We show how the low-frequency branch of the optical conductivity can be used to identify characteristic intra- and interband transitions between the Rashba spin-split bands in all three bismuth tellurohalides. We further calculate the refractive indices and dielectric constants, which in turn are systematically compared to previous predictions and measurements. We expect that our quantitative analysis will contribute to the general assessment of bulk Rashba materials for their potential use in spintronics devices.
Suwattanasophon, Chonticha; Wolschann, Peter; Faller, Roland
2016-01-01
Increased cholesterol levels are associated with multiple pathological conditions. In this work, molecular dynamics simulations were applied to observe the influence of membrane cholesterol levels on a voltage-gated sodium channel. Different lipid compositions are modeled around the channel to obtain information about the possible effects by which cholesterol influences NavAb channels. Cholesterol was normally not directly interacting with either the closed or inactivated conformation. Cholesterol increased lipid packing implying that it plays a crucial role in restricting lipid movement in the region around 1 nm of the channel in a 1-palmitoyl-2-oeleoyl phosphatidylcholine matrix. Our results provide the first computational indication of an indirect modulation of NavAb channels by membrane cholesterol.
360⁰ -View of Quantum Theory and Ab Initio Simulation at Extreme Conditions: 2014 Sanibel Symposium
Energy Technology Data Exchange (ETDEWEB)
Cheng, Hai-Ping [Univ. of Florida, Gainesville, FL (United States)
2016-09-02
The Sanibel Symposium 2014 was held February 16-21, 2014, at the King and Prince, St. Simons Island, GA. It was successful in bringing condensed-matter physicists and quantum chemists together productively to drive the emergence of those specialties. The Symposium had a significant role in preparing a whole generation of quantum theorists. The 54th Sanibel meeting looked to the future in two ways. We had 360⁰-View sessions to honor the exceptional contributions of Rodney Bartlett (70), Bill Butler (70), Yngve Öhrn (80), Fritz Schaefer (70), and Malcolm Stocks (70). The work of these five has greatly impacted several generations of quantum chemists and condensed matter physicists. The “360⁰” is the sum of their ages. More significantly, it symbolizes a panoramic view of critical developments and accomplishments in theoretical and computational chemistry and physics oriented toward the future. Thus, two of the eight 360⁰-View sessions focused specifically on younger scientists. The 360⁰-View program was the major component of the 2014 Sanibel meeting. Another four sessions included a sub-symposium on ab initio Simulations at Extreme Conditions, with focus on getting past the barriers of present-day Born-Oppenheimer molecular dynamics by advances in finite-temperature density functional theory, orbital-free DFT, and new all-numerical approaches.
del Rio, B. G.; González, L. E.
2017-06-01
We perform ab initio molecular dynamics simulations of liquid Zn near the melting point in order to study the longitudinal and transverse dynamic properties of the system. We find two propagating excitations in both of them in a wide range of wave vectors. This is in agreement with some experimental observations of the dynamic structure factor in the region around half the position of the main peak. Moreover, the two-mode structure in the transverse and longitudinal current correlation functions had also been previously observed in high pressure liquid metallic systems. We perform a theoretical analysis in order to investigate the possible origin of such two components by resorting to mode-coupling theories. They are found to describe qualitatively the appearance of two modes in the dynamics, but their relative intensities are not quantitatively reproduced. We suggest some possible improvements of the theory through the analysis of the structure of the memory functions. We also analyze the single-particle dynamics embedded in the velocity autocorrelation function, and explain its characteristics through mode-coupling concepts.
Carbon and proton Overhauser DNP from MD simulations and ab initio calculations: TEMPOL in acetone.
Küçük, Sami Emre; Biktagirov, Timur; Sezer, Deniz
2015-10-14
A computational analysis of the Overhauser effect is reported for the proton, methyl carbon, and carbonyl carbon nuclei of liquid acetone doped with the nitroxide radical TEMPOL. A practical methodology for calculating the dynamic nuclear polarization (DNP) coupling factors by accounting for both dipole-dipole and Fermi-contact interactions is presented. The contribution to the dipolar spectral density function of nuclear spins that are not too far from TEMPOL is computed through classical molecular dynamics (MD) simulations, whereas the contribution of distant spins is included analytically. Fermi contacts are obtained by subjecting a few molecules from every MD snapshot to ab initio quantum mechanical calculations. Scalar interaction is found to be an essential part of the (13)C Overhauser DNP. While mostly detrimental to the carbonyl carbon of acetone it is predicted to result in large enhancements of the methyl carbon signal at magnetic fields of 9 T and beyond. In contrast, scalar coupling is shown to be negligible for the protons of acetone. The additional influence of proton polarization on the carbon DNP (three-spin effect) is also analyzed computationally. Its effect, however, is concluded to be practically insignificant for liquid acetone.
Zeng, Xiancheng; Hu, Hao; Hu, Xiangqian; Cohen, Aron J; Yang, Weitao
2008-03-28
Electron transfer (ET) reactions are one of the most important processes in chemistry and biology. Because of the quantum nature of the processes and the complicated roles of the solvent, theoretical study of ET processes is challenging. To simulate ET processes at the electronic level, we have developed an efficient density functional theory (DFT) quantum mechanical (QM)/molecular mechanical (MM) approach that uses the fractional number of electrons as the order parameter to calculate the redox free energy of ET reactions in solution. We applied this method to study the ET reactions of the aqueous metal complexes Fe(H(2)O)(6)(2+/3+) and Ru(H(2)O)(6)(2+/3+). The calculated oxidation potentials, 5.82 eV for Fe(II/III) and 5.14 eV for Ru(II/III), agree well with the experimental data, 5.50 and 4.96 eV, for iron and ruthenium, respectively. Furthermore, we have constructed the diabatic free energy surfaces from histogram analysis based on the molecular dynamics trajectories. The resulting reorganization energy and the diabatic activation energy also show good agreement with experimental data. Our calculations show that using the fractional number of electrons (FNE) as the order parameter in the thermodynamic integration process leads to efficient sampling and validate the ab initio QM/MM approach in the calculation of redox free energies.
van der Linden, Marx Gomes; Ferreira, Diogo César; de Oliveira, Leandro Cristante; Onuchic, José N; de Araújo, Antônio F Pereira
2014-07-01
The three-dimensional structure of proteins is determined by their linear amino acid sequences but decipherment of the underlying protein folding code has remained elusive. Recent studies have suggested that burials, as expressed by atomic distances to the molecular center, are sufficiently informative for structural determination while potentially obtainable from sequences. Here we provide direct evidence for this distinctive role of burials in the folding code, demonstrating that burial propensities estimated from local sequence can indeed be used to fold globular proteins in ab initio simulations. We have used a statistical scheme based on a Hidden Markov Model (HMM) to classify all heavy atoms of a protein into a small number of burial atomic types depending on sequence context. Molecular dynamics simulations were then performed with a potential that forces all atoms of each type towards their predicted burial level, while simple geometric constraints were imposed on covalent structure and hydrogen bond formation. The correct folded conformation was obtained and distinguished in simulations that started from extended chains for a selection of structures comprising all three folding classes and high burial prediction quality. These results demonstrate that atomic burials can act as informational intermediates between sequence and structure, providing a new conceptual framework for improving structural prediction and understanding the fundamentals of protein folding.
360⁰ -View of Quantum Theory and Ab Initio Simulation at Extreme Conditions: 2014 Sanibel Symposium
Energy Technology Data Exchange (ETDEWEB)
Cheng, Hai-Ping [Univ. of Florida, Gainesville, FL (United States)
2016-09-02
The Sanibel Symposium 2014 was held February 16-21 2014 at the King and Prince, St. Simons Island, GA. It was successful in bringing condensed-matter physicists and quantum chemists together productively to drive the emergence of those specialties. The Symposium had a significant role in preparing a whole generation of quantum theorists. The 54th Sanibel meeting looked to the future in two ways. We had 360⁰-View sessions to honor the exceptional contributions of Rodney Bartlett (70), Bill Butler (70), Yngve Öhrn (80), Fritz Schaefer (70), and Malcolm Stocks (70). The work of these five has greatly impacted several generations of quantum chemists and condensed matter physicists. The “360⁰” is the sum of their ages. More significantly, it symbolizes a panoramic view of critical developments and accomplishments in theoretical and computational chemistry and physics oriented toward the future. Thus, two of the eight 360⁰-View sessions focused specifically on younger scientists. The 360⁰-View program was the major component of the 2014 Sanibel meeting. Another four sessions included a sub-symposium on ab initio Simulations at Extreme Conditions, with focus on getting past the barriers of present-day Born-Oppenheimer molecular dynamics by advances in finite-temperature density functional theory, orbital-free DFT, and new all-numerical approaches.
Ab-initio optimization of the crystal structure ksi and ksi* in Al- Mn-Pd
Energy Technology Data Exchange (ETDEWEB)
Sanatana Bonilla, Alejandro [Universitaet Stuttgart (Germany). Institut fuer Theoretische und Angewandte Physik; Grupo de Sistemas Complejos, Universidad Antonio, Bogota (Colombia); Engel, Michael [Univ. of Michigan, Ann Arbor (United States); Trebin, Hans-Rainer [Universitaet Stuttgart (Germany). Institut fuer Theoretische und Angewandte Physik; Mihalkovic, Marek [Inst. of Physics, Slovak Academy of Sciences Bratslava (Slovakia)
2010-07-01
A structural model is given for two approximants, {xi} and {xi}{sup *}, of the decagonal Al-Mn-Pd phase. Both structures were shown to be completely described by two sorts of interpenetrating clusters, namely ''Distorted Bergman Cluster'' (DBC) and by ''Pseudo Mackay Cluster'' (PMC). On the basis of these two atomic clusters the two phases can be characterized as some simple periodic tiling of assembly of the column clusters projected onto the plane perpendicular to the 1.6 nm stacking axis. From crystallographic studies the skeleton of heavy atoms was fully described, whereas the inner shell from PMC was poorly detailed. The structural models have been investigated using ab initio and molecular dynamics numerical methods. For this study, suitable improved pair potentials were used in order to determine the ideal cluster structure and the interactions between adjacent clusters. Plausibility of the suggested structures was tested using competing crystalline phases obtained through convex hull calculations and allowing us to suggest a reliable atomic model for the inner shell of the PMC. 3.
X-ray absorption of liquid water studied by advanced ab initio methods
Sun, Zhaoru; Wang, Jianping; Kang, Wei; Car, Roberto; Wu, Xifan
Oxygen K-edge X-ray absorption spectra (XAS) provide a sensitive local probe of the H-bond structure of liquid water. Based on the static COHSEX approach, we computed the XAS spectra of liquid water from molecular structures generated by ab initio molecular dynamics (AIMD) simulations using a van der Waals (vdW) inclusive hybrid functional (PBE0) that gives ambient water structure in quantitative agreement with experiment [JCP 141, 084502 (2014)]. We find that good agreement between experimental and theoretical XAS requires both improved molecular modeling and excitation treatment. In our simulation the over-structured H-bond network resulting from GGA-AIMD is systematically reduced as the directional H-bond strength is lowered by the mitigated self-interaction error in PBE0 and the increased population of interstitial water molecules promoted by vdW interactions. The better H-bond structure in turn gives improved XAS spectra. Moreover, we find that the orbitals obtained from the self-consistent diagonalization of the self-energy are crucial in obtaining spectra that compare well with experiment. Doe SciDAC: DE-SC0008626 and DE-SC0008726.
The Structure, Density, and Local Environment Distribution in Ab Initio Liquid Water
Santra, Biswajit; Distasio, Robert A., Jr.; Wu, Xifan; Car, Roberto
2014-03-01
We have performed extensive ab initio molecular dynamics (AIMD) simulations of liquid water at ambient conditions in the canonical (NVT) and isothermal-isobaric (NPT) ensembles to understand the individual and collective importance of exact exchange, van der Waals interactions, and nuclear quantum effects on the structural properties of liquid water. AIMD simulations which include these effects result in oxygen-oxygen radial distribution functions which are in excellent agreement with experiments and a liquid water structure having an equilibrium density within 1% of the experimental value of 1 g/cm3. A detailed analysis of the distribution of local structure in ambient liquid water has revealed that the inherent potential energy surface is bimodal with respect to high- and low-density molecular environments, consistent with the existence of polymorphism in the amorphous phases of water. With these findings in mind, the methodology presented herein overcomes the well-known limitations of semi-local density functional theory (GGA-DFT) providing a detailed and accurate microscopic description of ambient liquid water. DOE: DE-SC0008626, DOE: DE-SC0005180, NSF: CHE-0956500.
Emergence of rotational bands in ab initio no-core configuration interaction calculations
Caprio, M A; Vary, J P; Smith, R
2015-01-01
Rotational bands have been observed to emerge in ab initio no-core configuration interaction (NCCI) calculations for p-shell nuclei, as evidenced by rotational patterns for excitation energies, electromagnetic moments, and electromagnetic transitions. We investigate the ab initio emergence of nuclear rotation in the Be isotopes, focusing on 9Be for illustration, and make use of basis extrapolation methods to obtain ab initio predictions of rotational band parameters for comparison with experiment. We find robust signatures for rotational motion, which reproduce both qualitative and quantitative features of the experimentally observed bands.
Heats of Segregation of BCC Binaries from ab Initio and Quantum Approximate Calculations
Good, Brian S.
2004-01-01
We compare dilute-limit heats of segregation for selected BCC transition metal binaries computed using ab initio and quantum approximate energy methods. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent LMTO-based parameters. Quantum approximate segregation energies are computed with and without atomistic relaxation, while the ab initio calculations are performed without relaxation. Results are discussed within the context of a segregation model driven by strain and bond-breaking effects. We compare our results with full-potential quantum calculations and with available experimental results.
Ab initio calculation of the potential bubble nucleus 34Si
Duguet, T.; Somà, V.; Lecluse, S.; Barbieri, C.; Navrátil, P.
2017-03-01
Background: The possibility that an unconventional depletion (referred to as a "bubble") occurs in the center of the charge density distribution of certain nuclei due to a purely quantum mechanical effect has attracted theoretical and experimental attention in recent years. Based on a mean-field rationale, a correlation between the occurrence of such a semibubble and an anomalously weak splitting between low angular-momentum spin-orbit partners has been further conjectured. Energy density functional and valence-space shell model calculations have been performed to identify and characterize the best candidates, among which 34Si appears as a particularly interesting case. While the experimental determination of the charge density distribution of the unstable 34Si is currently out of reach, (d ,p ) experiments on this nucleus have been performed recently to test the correlation between the presence of a bubble and an anomalously weak 1 /2--3 /2- splitting in the spectrum of 35Si as compared to 37S. Purpose: We study the potential bubble structure of 34Si on the basis of the state-of-the-art ab initio self-consistent Green's function many-body method. Methods: We perform the first ab initio calculations of 34Si and 36S. In addition to binding energies, the first observables of interest are the charge density distribution and the charge root-mean-square radius for which experimental data exist in 36S. The next observable of interest is the low-lying spectroscopy of 35Si and 37S obtained from (d ,p ) experiments along with the spectroscopy of 33Al and 35P obtained from knock-out experiments. The interpretation in terms of the evolution of the underlying shell structure is also provided. The study is repeated using several chiral effective field theory Hamiltonians as a way to test the robustness of the results with respect to input internucleon interactions. The convergence of the results with respect to the truncation of the many-body expansion, i.e., with respect to
Espinosa-Garcia, Joaquin; Rangel, Cipriano; Suleimanov, Yury V
2017-07-26
We have developed an analytical full-dimensional potential energy surface, named PES-2017, for the gas-phase hydrogen abstraction reaction between the cyano radical and methane. This surface is fitted using high-level ab initio information as input. Using the PES-2017 surface, a kinetics study was performed via two theoretical approaches: variational transition-state theory with multidimensional tunnelling (VTST-MT) and ring polymer molecular dynamics (RPMD). The results are compared with the experimental data. In the whole temperature range analysed, 300-1500 K, both theories agree within a factor of kinetic isotope effects are important, reproducing the scarce experimental evidence. The good agreement with the ab initio information used in the fitting process (self-consistency test) and with the kinetic behaviour in a wide temperature range gives confidence and strength to the new surface.
Wang, Zi; Bevan, Kirk H.
2016-01-01
In the present work, we study the effects of the electronic relaxation of semicore levels on polaron activation energies and dynamics. Within the framework of adiabatic ab initio theory, we utilize both static transition state theory and molecular dynamics methods for an in-depth study of polaronic hopping in delithiated LiFePO4 (FePO4). Our results show that electronic relaxation of semicore states is significant in FePO4, resulting in a lower activation barrier and kinetics that is one to two orders faster compared to the result of calculations that do not incorporate semicore states. In general, the results suggest that the relaxation of states far below the Fermi energy could dramatically impact the ab initio polaronic barrier estimates for many transition metal oxides and phosphates.
Ab initio molecular crystal structures, spectra, and phase diagrams.
Hirata, So; Gilliard, Kandis; He, Xiao; Li, Jinjin; Sode, Olaseni
2014-09-16
Conspectus Molecular crystals are chemists' solids in the sense that their structures and properties can be understood in terms of those of the constituent molecules merely perturbed by a crystalline environment. They form a large and important class of solids including ices of atmospheric species, drugs, explosives, and even some organic optoelectronic materials and supramolecular assemblies. Recently, surprisingly simple yet extremely efficient, versatile, easily implemented, and systematically accurate electronic structure methods for molecular crystals have been developed. The methods, collectively referred to as the embedded-fragment scheme, divide a crystal into monomers and overlapping dimers and apply modern molecular electronic structure methods and software to these fragments of the crystal that are embedded in a self-consistently determined crystalline electrostatic field. They enable facile applications of accurate but otherwise prohibitively expensive ab initio molecular orbital theories such as Møller-Plesset perturbation and coupled-cluster theories to a broad range of properties of solids such as internal energies, enthalpies, structures, equation of state, phonon dispersion curves and density of states, infrared and Raman spectra (including band intensities and sometimes anharmonic effects), inelastic neutron scattering spectra, heat capacities, Gibbs energies, and phase diagrams, while accounting for many-body electrostatic (namely, induction or polarization) effects as well as two-body exchange and dispersion interactions from first principles. They can fundamentally alter the role of computing in the studies of molecular crystals in the same way ab initio molecular orbital theories have transformed research practices in gas-phase physical chemistry and synthetic chemistry in the last half century. In this Account, after a brief summary of formalisms and algorithms, we discuss applications of these methods performed in our group as compelling
Metal cluster fission: jellium model and Molecular dynamics simulations
DEFF Research Database (Denmark)
Lyalin, Andrey G.; Obolensky, Oleg I.; Solov'yov, Ilia;
2004-01-01
Fission of doubly charged sodium clusters is studied using the open-shell two-center deformed jellium model approximation and it ab initio molecular dynamic approach accounting for all electrons in the system. Results of calculations of fission reactions Na_10^2+ --> Na_7^+ + Na_3^+ and Na_18^2+ ...
Energy Technology Data Exchange (ETDEWEB)
González-Cataldo, F. [Grupo de NanoMateriales, Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago (Chile); Wilson, Hugh F.; Militzer, B., E-mail: fgonzalez@lpmd.cl [Department of Earth and Planetary Science, University of California Berkeley, Berkeley, CA 94720 (United States)
2014-05-20
By combining density functional molecular dynamics simulations with a thermodynamic integration technique, we determine the free energy of metallic hydrogen and silica, SiO{sub 2}, at megabar pressures and thousands of degrees Kelvin. Our ab initio solubility calculations show that silica dissolves into fluid hydrogen above 5000 K for pressures from 10 and 40 Mbars, which has implications for the evolution of rocky cores in giant gas planets like Jupiter, Saturn, and a substantial fraction of known extrasolar planets. Our findings underline the necessity of considering the erosion and redistribution of core materials in giant planet evolution models, but they also demonstrate that hot metallic hydrogen is a good solvent at megabar pressures, which has implications for high-pressure experiments.
del Rio, Beatriz G.; González, David J.; González, Luis E.
2016-10-01
Several static and dynamic properties of bulk liquid Ag at a thermodynamic state near its triple point have been calculated by means of ab initio molecular dynamics simulations. The calculated static structure shows a very good agreement with the available experimental data. The dynamical structure reveals propagating excitations whose dispersion at long wavelengths is compatible with the experimental sound velocity. Results are also reported for other transport coefficients. Additional simulations have also been performed so as to study the structure of the free liquid surface. The calculated longitudinal ionic density profile shows an oscillatory behaviour, whose properties are analyzed through macroscopic and microscopic methods. The intrinsic X-ray reflectivity of the surface is predicted to show a layering peak associated to the interlayer distance.
DEFF Research Database (Denmark)
Møgelhøj, Andreas; Kelkkanen, Kari André; Wikfeldt, K Thor
2011-01-01
The structure of liquid water at ambient conditions is studied in ab initio molecular dynamics simulations in the NVE ensemble using van der Waals (vdW) density-functional theory, i.e., using the new exchange-correlation functionals optPBE-vdW and vdW-DF2, where the latter has softer nonlocal...... shows some resemblance with experiment for high-density water ( Soper , A. K. and Ricci , M. A. Phys. Rev. Lett. 2000 , 84 , 2881 ), but not directly with experiment for ambient water. Considering the accuracy of the new functionals for interaction energies, we investigate whether the simulation...... protocol could cause the deviation. An O-O PCF consisting of a linear combination of 70% from vdW-DF2 and 30% from low-density liquid water, as extrapolated from experiments, reproduces near-quantitatively the experimental O-O PCF for ambient water. This suggests the possibility that the new functionals...
Short-range order in ab initio computer generated amorphous and liquid Cu–Zr alloys: A new approach
Energy Technology Data Exchange (ETDEWEB)
Galván-Colín, Jonathan, E-mail: jgcolin@ciencias.unam.mx [Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Apartado Postal 70-360, México, D.F. 04510, México (Mexico); Valladares, Ariel A., E-mail: valladar@unam.mx [Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Apartado Postal 70-360, México, D.F. 04510, México (Mexico); Valladares, Renela M.; Valladares, Alexander [Facultad de Ciencias, Universidad Nacional Autónoma de México, Apartado Postal 70-542, México, D.F. 04510, México (Mexico)
2015-10-15
Using ab initio molecular dynamics and a new approach based on the undermelt-quench method we generated amorphous and liquid samples of Cu{sub x}Zr{sub 100−x} (x=64, 50, 36) alloys. We characterized the topology of our resulting structures by means of the pair distribution function and the bond-angle distribution; a coordination number distribution was also calculated. Our results for both amorphous and liquids agree well with experiment. Dependence of short-range order with the concentration is reported. We found that icosahedron-like geometry plays a major role whenever the alloys are Cu-rich or Zr-rich disregarding if the samples are amorphous or liquid. The validation of these results, in turn would let us calculate other properties so far disregarded in the literature.
DEFF Research Database (Denmark)
Wolf, T. J. A.; Kuhlman, Thomas Scheby; Schalk, O.
2014-01-01
Time-resolved photoelectron spectroscopy and ab initio multiple spawning were applied to the ultrafast non-adiabatic dynamics of hexamethylcyclopentadiene. The high level of agreement between experiment and theory associates wavepacket motion with a distinct degree of freedom....
Hydrogen adsorption on boron doped graphene: an {\\it ab initio} study
Miwa, R. H.; Martins, T B; Fazzio, A.
2007-01-01
The electronic and structural properties of (i) boron doped graphene sheets, and (ii) the chemisorption processes of hydrogen adatoms on the boron doped graphene sheets have been examined by {\\it ab initio} total energy calculations.
Energy Technology Data Exchange (ETDEWEB)
Churakov, S.V
2005-03-01
Pyrophyllite, Al{sub 2}[Si{sub 4}O{sub 10}](OH){sub 2}, is the simplest structural prototype for 2:1 dioctahedral phyllosilicate. Because the net electric charge in pyrophyllite is zero, it is the best candidate for investigating the non electrostatic contribution to sorption and transport phenomena in clays. Using ab-initio simulations, we have investigated the reactivity and structure of the water-solid interface on the basal plane and edge sites of pyrophyllite. The calculations predict slightly hydrophobic behaviour of the basal plane. For the high water coverage (100), (110) and (-110), lateral facets have a lower energy than for the (010), (130) and (-130) surfaces. Analysis of the surface reactivity reveals that the =Al-OH groups are most easily protonated on the (010), (130) and (-130) facets. The =Al-O-Si= sites will be protonated on the (100), (130), (110), (-110) and (-130) surfaces. The =Al-OH{sub 2} complexes are more easily de-protonated than the =Si-OH and =Al-OH sites. A spontaneous, reversible exchange of the protons between the solution and the edge sites has been observed in ab-initio molecular dynamics simulations at 300 K. Such near-surface proton diffusion may result in a significant contribution to the diffusion coefficients measured in neutron scattering experiments. (author)
Ab initio simulations of pseudomorphic silicene and germanene bidimensional heterostructures
Debernardi, Alberto; Marchetti, Luigi
2016-06-01
Among the novel two-dimensional (2D) materials, silicene and germanene, which are two honeycomb crystal structures composed of a monolayer of Si and Ge, respectively, have attracted the attention of material scientists because they combine the advantages of the new 2D ultimate-scaled electronics with their compatibility with industrial processes presently based on Si and Ge. We envisage pseudomorphic lateral heterostructures based on ribbons of silicene and germanene, which are the 2D analogs of conventional 3D Si/Ge superlattices and quantum wells. In spite of the considerable lattice mismatch (˜4 % ) between free-standing silicene and germanene, our ab initio simulations predict that, considering striped 2D lateral heterostructures made by alternating silicene and germanene ribbons of constant width, the silicene/germanene junction remains pseudomorphic—i.e., it maintains lattice-matched edges—up to critical ribbon widths that can reach some tens of nanometers. Such critical widths are one order of magnitude larger than the critical thickness measured in 3D pseudomorphic Si/Ge heterostructures and the resolution of state-of-the-art lithography, thus enabling the possibility of lithography patterned silicene/germanene junctions. We computed how the strain produced by the pseudomorphic growth modifies the crystal structure and electronic bands of the ribbons, providing a mechanism for band-structure engineering. Our results pave the way for lithography patterned lateral heterostructures that can serve as the building blocks of novel 2D electronics.
Ab initio studies of niobium defects in uranium
Energy Technology Data Exchange (ETDEWEB)
Xiang, S; Huang, H; Hsiung, L
2007-06-01
Uranium (U), with the addition of small amount of niobium (Nb), is stainless. The Nb is fully miscible with the high temperature phase of U and tends to segregate upon cooling below 647 C. The starting point of segregation is the configuration of Nb substitutional or interstitial defects. Using density-functional-theory based ab initio calculations, the authors find that the formation energy of a single vacancy is 1.08 eV, that of Nb substitution is 0.59 eV, that of Nb interstitial at octahedral site is 1.58 eV, and that of Nb interstitial at tetrahedral site is 2.35 eV; all with reference to a reservoir of {gamma} phase U and pure Nb. The formation energy of Nb defects correlates with the local perturbation of electron distribution; higher formation energy to larger perturbation. Based on this study, Nb atoms thermodynamically prefer to occupy substitutional sites in {gamma} phase U, and they prefer to be in individual substitutional defects than clusters.
Engineering Room-temperature Superconductors Via ab-initio Calculations
Gulian, Mamikon; Melkonyan, Gurgen; Gulian, Armen
The BCS, or bosonic model of superconductivity, as Little and Ginzburg have first argued, can bring in superconductivity at room temperatures in the case of high-enough frequency of bosonic mode. It was further elucidated by Kirzhnitset al., that the condition for existence of high-temperature superconductivity is closely related to negative values of the real part of the dielectric function at finite values of the reciprocal lattice vectors. In view of these findings, the task is to calculate the dielectric function for real materials. Then the poles of this function will indicate the existence of bosonic excitations which can serve as a "glue" for Cooper pairing, and if the frequency is high enough, and the dielectric matrix is simultaneously negative, this material is a good candidate for very high-Tc superconductivity. Thus, our approach is to elaborate a methodology of ab-initio calculation of the dielectric function of various materials, and then point out appropriate candidates. We used the powerful codes (TDDF with the DP package in conjunction with ABINIT) for computing dielectric responses at finite values of the wave vectors in the reciprocal lattice space. Though our report is concerned with the particular problem of superconductivity, the application range of the data processing methodology is much wider. The ability to compute the dielectric function of existing and still non-existing (though being predicted!) materials will have many more repercussions not only in fundamental sciences but also in technology and industry.
Ab-initio calculations for dilute magnetic semiconductors
Energy Technology Data Exchange (ETDEWEB)
Belhadji, Brahim
2008-03-03
This thesis focusses on ab-initio calculations for the electronic structure and the magnetic properties of dilute magnetic semiconductors (DMS). In particular we aim at the understanding of the complex exchange interactions in these systems. Our calculations are based on density functional theory, being ideally suited for a description of the material specific properties of the considered DMS. Moreover we use the KKR Green function method in connection with the coherent potential approximation (CPA), which allows to include the random substitutional disorder in a mean field-like approximation for the electronic structure. Finally we calculate the exchange coupling constants J{sub ij} between two impurities in a CPA medium by using the Lichtenstein formula and from this calculate the Curie temperature by a numerically exact Monte Carlo method. Based on this analysis we found and investigated four different exchange mechanisms being of importance in DMS systems: Double exchange, p-d exchange, antiferromagnetic superexchanges, and ferromagnetic superexchange. A second topic we have investigated in this thesis is the pressure dependence of the exchange interactions and the Curie temperatures in (Ga,Mn)As and (In,Mn)As, using the LDA and the LDA+U approximations. Exact calculations of T{sub C} by Monte Carlo simulations show a somehow different behavior. (orig.)
Ab initio modelling of boron related defects in amorphous silicon
Energy Technology Data Exchange (ETDEWEB)
Oliveira, Tiago A.; Torres, Vitor J.B. [Department of Physics, University of Aveiro, Campus Santiago, 3810-193 Aveiro (Portugal)
2012-10-15
We have modeled boron related point defects in amorphous silicon, using an ab initio method, the Density functional theory-pseudopotential code Aimpro. The boron atoms were embedded in 64 atom amorphous silicon cubic supercells. The calculations were performed using boron defects in 15 different supercells. These supercells were developed using a modified Wooten-Winer-Weaire bond switching mechanism. In average, the properties of the 15 supercells agree with the observed radial and bond angle distributions, as well the electronic and vibrational density of states and Raman spectra. In amorphous silicon it has been very hard to find real self-interstitials, since for almost all the tested configurations, the amorphous lattice relaxes overall. We found that substitutional boron prefers to be 4-fold coordinated. We find also an intrinsic hole-trap in the non-doped amorphous lattice, which may explain the low efficiency of boron doping. The local vibrational modes are, in average, higher than the correspondent crystalline values (copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)
Ab initio calculation of the potential bubble nucleus $^{34}$Si
Duguet, T; Lecluse, S; Barbieri, C; Navrátil, P
2016-01-01
The possibility that an unconventional depletion in the center of the charge density distribution of certain nuclei occurs due to a purely quantum mechanical effect has attracted theoretical and experimental attention in recent years. We report on ab initio self-consistent Green's function calculations of one of such candidates, $^{34}$Si, together with its Z+2 neighbour $^{36}$S. Binding energies, rms radii and density distributions of the two nuclei as well as low-lying spectroscopy of $^{35}$Si, $^{37}$S, $^{33}$Al and $^{35}$P are discussed. The interpretation of one-nucleon removal and addition spectra in terms of the evolution of the underlying shell structure is also provided. The study is repeated using several chiral effective field theory Hamiltonians as a way to test the robustness of the results with respect to input inter-nucleon interactions. The prediction regarding the (non-)existence of the bubble structure in $^{34}$Si varies significantly with the nuclear Hamiltonian used. However, demandin...
Ab initio evaluations of the He solubility in liquid Li
Energy Technology Data Exchange (ETDEWEB)
Sedano, Luis A. [EURATOM-CIEMAT Assoc., Materials for Fusion Program, Bd. 43 P0.04, Avda. Complutense 22, 28040 Madrid (Spain)]. E-mail: luis.sedano@ciemat.es; Hassanein, Ahmed [Argonne Nat. Lab, 9700 South Class Av., Argonne, IL (United States)]. E-mail: hassanein@anl.gov; Sanz, Javier [ETSII-UNED, c/Juan del Rosal, 12, 28040 Madrid (E) (Spain)]. E-mail: jsanz@ind.UNED.es
2005-11-15
Modified embedding atom methods (MEAM) are developed to have predictions of the partial molar heat of solution (-H{sub s}) by direct simulation of metal cohesion, He-metal and He-He interaction. Transitions from crystalline Li to configurations, having the liquid Li structure's factors (h-bar (q)), are simulated ab initio. Once h-bar (q) reproduced, He atoms are added, one by one, to the Li system. Parallel lines for each case, with slopes clearly independent on the number of He atoms in the system, are obtained for energy versus pressure at given temperatures. Average differences between two adjacent parallels at zero pressure, once kinetic energy of the system discounted, represents the energy gained by an He atom when added to the Li system, related to the solution energy -H{sub s}. The molar excess entropy of gas in solution (S-bar {sub l}{sup ex}) is previously evaluated following diverse fundamental approaches: a 'thermodynamic liquid-hole' (TL-H) model for alkali liquids and a statistical-mechanics (Neff and McQuarrie's) model (SMM). Between 600 and 900 deg. C, a typical range of interest for the use of Li in fusion technology, the computed values for the (He) Henry's constant in Li range from 8x10{sup -14} to 10{sup -13} at. fr. Pa{sup -1}.
Ab initio predictions of the symmetry energy and recent constraints
Sammarruca, Francesca
2017-01-01
The symmetry energy plays a crucial role in the structure and the dynamics of neutron-rich systems, including the formation of neutron skins, the location of neutron drip lines, as well as intriguing correlations with the structure of compact stars. With experimental efforts in progress or being planned to shed light on the less known aspects of the nuclear chart, microscopic predictions based on ab initio approaches are very important. In recent years, chiral effective field theory has become popular because of its firm connection with quantum chromodynamics and its systematic approach to the development of nuclear forces. Predictions of the symmetry energy obtained from modern chiral interactions will be discussed in the light of recent empirical constraints extracted from heavy ion collisions at 400 MeV per nucleon at GSI. Applications of our equations of state to neutron-rich systems will also be discussed, with particular emphasis on neutron skins, which are sensitive to the density dependence of the symmetry energy.
Ab initio modeling of decomposition in iron based alloys
Gorbatov, O. I.; Gornostyrev, Yu. N.; Korzhavyi, P. A.; Ruban, A. V.
2016-12-01
This paper reviews recent progress in the field of ab initio based simulations of structure and properties of Fe-based alloys. We focus on thermodynamics of these alloys, their decomposition kinetics, and microstructure formation taking into account disorder of magnetic moments with temperature. We review modern theoretical tools which allow a consistent description of the electronic structure and energetics of random alloys with local magnetic moments that become totally or partially disordered when temperature increases. This approach gives a basis for an accurate finite-temperature description of alloys by calculating all the relevant contributions to the Gibbs energy from first-principles, including a configurational part as well as terms due to electronic, vibrational, and magnetic excitations. Applications of these theoretical approaches to the calculations of thermodynamics parameters at elevated temperatures (solution energies and effective interatomic interactions) are discussed including atomistic modeling of decomposition/clustering in Fe-based alloys. It provides a solid basis for understanding experimental data and for developing new steels for modern applications. The precipitation in Fe-Cu based alloys, the decomposition in Fe-Cr, and the short-range order formation in iron alloys with s-p elements are considered as examples.
Ab initio transport across bismuth selenide surface barriers
Narayan, Awadhesh
2014-11-24
© 2014 American Physical Society. We investigate the effect of potential barriers in the form of step edges on the scattering properties of Bi2Se3(111) topological surface states by means of large-scale ab initio transport simulations. Our results demonstrate the suppression of perfect backscattering, while all other scattering processes, which do not entail a complete spin and momentum reversal, are allowed. Furthermore, we find that the spin of the surface state develops an out-of-plane component as it traverses the barrier. Our calculations reveal the existence of quasibound states in the vicinity of the surface barriers, which appear in the form of an enhanced density of states in the energy window corresponding to the topological state. For double barriers we demonstrate the formation of quantum well states. To complement our first-principles results we construct a two-dimensional low-energy effective model and illustrate its shortcomings. Our findings are discussed in the context of a number of recent experimental works.
Ab initio calculations of the absorption spectrum of chalcone
Oumi, Manabu; Maurice, David; Head-Gordon, Martin
1999-03-01
The excitation energies and excited states of trans-chalcone ( trans-( s-cis)-1,3-diphenylpropenone), and several related molecules ( trans-( s-cis)-3-phenylpropenal, s-cis-1-phenylpropenone, propenal, trans-( s-cis)-1-(4-hydroxyphenyl)-3-phenylpropenone, trans-( s-cis)3-(4-hydroxyphenyl)-1-phenylpropenone) have been calculated using single reference ab initio molecular orbital methods, and characterized by attachment-detachment density analysis. The results suggest assignments for the lowest three electronic transitions observed experimentally for trans-( s-cis)-chalcone in solution. The extent of localization of the electronic transitions is established by calculations on the excited states of trans-( s-cis)-3-phenylpropenal, s-cis-1-phenylpropenone and propenal, as well as analysis of the chalcone calculations. Contrary to some previous work, none of these excitations are strongly delocalized over the entire molecule. Calculated substituent shifts for the hydroxy chalcones are in qualitative agreement with experimental data, and support the localized interpretation of the main π→ π* transition.
Ab initio thermodynamic results for warm dense matter
Bonitz, Michael
2016-10-01
Warm dense matter (WDM) - an exotic state where electrons are quantum degenerate and ions may be strongly correlated - is ubiquitous in dense astrophysical plasmas and highly compressed laboratory systems including inertial fusion. Accurate theoretical predictions require precision thermodynamic data for the electron gas at high density and finite temperature around the Fermi temperature. First such data have been obtained by restricted path integral Monte Carlo (restricted PIMC) simulations and transformed into analytical fits for the free energy. Such results are also key input for novel finite temperature density functional theory. However, the RPIMC data of Ref. 1 are limited to moderate densities, and even there turned out to be surprisingly inaccurate, which is a consequence of the fermion sign problem. These problems were recently overcome by the development of alternative QMC approaches in Kiel (configuration PIMC and permutation blocking PIMC) and Imperial College (Density matrix QMC). The three methods have their strengths and limitations in complementary parameter regions and provide highly accurate thermodynamic data for the electronic contributions in WDM. While the original results were obtained for small particle numbers, recently accurate finite size corrections were derived allowing to compute ab initio thermodynamic data with an unprecedented accuracy of better than 0.3 percent. This provides the final step for the use as benchmark data for experiments and models of Warm dense matter. Co-authors: T. Schoof, S. Groth, T. Dornheim, F. D. Malone, M. Foulkes, and T. Sjostroem, Funded by: DFG via SFB-TR24 and project BO1366-10.
Local structure analysis in ab initio liquid water
Santra, Biswajit; DiStasio, Robert A., Jr.; Martelli, Fausto; Car, Roberto
2015-09-01
Within the framework of density functional theory, the inclusion of exact exchange and non-local van der Waals/dispersion (vdW) interactions is crucial for predicting a microscopic structure of ambient liquid water that quantitatively agrees with experiment. In this work, we have used the local structure index (LSI) order parameter to analyse the local structure in such highly accurate ab initio liquid water. At ambient conditions, the LSI probability distribution, P(I ), was unimodal with most water molecules characterised by more disordered high-density-like local environments. With thermal excitations removed, the resultant bimodal P(I ) in the inherent potential energy surface (IPES) exhibited a 3:1 ratio between high-density- and low-density-like molecules, with the latter forming small connected clusters amid the predominant population. By considering the spatial correlations and hydrogen bond network topologies among water molecules with the same LSI identities, we demonstrate that the signatures of the experimentally observed low- and high-density amorphous phases of ice are present in the IPES of ambient liquid water. Analysis of the LSI autocorrelation function uncovered a persistence time of ∼ 4 ps - a finding consistent with the fact that natural thermal fluctuations are responsible for transitions between these distinct yet transient local aqueous environments in ambient liquid water.
Balan, Etienne; Lazzeri, M.; Mauri, F.; Calas, G.
2007-01-01
We review here some recent applications of ab initio calculations to the modelling of spectroscopic and energetic properties of minerals, which are key components of lateritic soils or govern their geochemical properties. Quantum mechanical ab initio calculations are based on density functional theory and density functional perturbation theory. Among the minerals investigated, zircon is a typical resistant primary mineral. Its resistance to weathering is at the origin of the peculiar geochemi...
An ab initio Non-Equilibrium Green Function Approach to Charge Transport: Dithiolethine
Institute of Scientific and Technical Information of China (English)
Alexander Schnurpfeil; SONG Bo; Martin Albrecht
2006-01-01
@@ We present a novel ab initio non-equilibrium approach to calculate the current across a molecular junction. The method rests on a wavefunction-based full ab initio description of the central region of the junction combined with a tight binding approximation for the electrodes in the frame of the Keldysh Green function formalism. Our procedure is demonstrated for a dithiolethine molecule located between silver electrodes. The main conducting channel is identified and the full current-voltage characteristic is calculated.
Mills, Jeffrey D; Ben-Nun, Michal; Rollin, Kyle; Bromley, Michael W J; Li, Jiabo; Hinde, Robert J; Winstead, Carl L; Sheehy, Jeffrey A; Boatz, Jerry A; Langhoff, Peter W
2016-08-25
Continuing attention has addressed incorportation of the electronically dynamical attributes of biomolecules in the largely static first-generation molecular-mechanical force fields commonly employed in molecular-dynamics simulations. We describe here a universal quantum-mechanical approach to calculations of the electronic energy surfaces of both small molecules and large aggregates on a common basis which can include such electronic attributes, and which also seems well-suited to adaptation in ab initio molecular-dynamics applications. In contrast to the more familiar orbital-product-based methodologies employed in traditional small-molecule computational quantum chemistry, the present approach is based on an "ex-post-facto" method in which Hamiltonian matrices are evaluated prior to wave function antisymmetrization, implemented here in the support of a Hilbert space of orthonormal products of many-electron atomic spectral eigenstates familiar from the van der Waals theory of long-range interactions. The general theory in its various forms incorporates the early semiempirical atoms- and diatomics-in-molecules approaches of Moffitt, Ellison, Tully, Kuntz, and others in a comprehensive mathematical setting, and generalizes the developments of Eisenschitz, London, Claverie, and others addressing electron permutation symmetry adaptation issues, completing these early attempts to treat van der Waals and chemical forces on a common basis. Exact expressions are obtained for molecular Hamiltonian matrices and for associated energy eigenvalues as sums of separate atomic and interaction-energy terms, similar in this respect to the forms of classical force fields. The latter representation is seen to also provide a long-missing general definition of the energies of individual atoms and of their interactions within molecules and matter free from subjective additional constraints. A computer code suite is described for calculations of the many-electron atomic eigenspectra and
Gao, Ai-Hua; Wang, Mei-Shan
2017-03-01
The photoisomerization mechanisms of N-salicilydenemethylfurylamine upon excitation to the first singlet state are investigated by means of surface-hopping dynamics simulations based on the Zhu-Nakamura theory. Due to different orientations of the methyl-furyl part with respect to the salicylaldimine part and different orientations of hydroxy group with respect to the benzene ring, various stable structures are obtained in the optimization. The enol isomer, S0-ENOL-5a, is the most stable conformer. An ultrafast excited-state intramolecular proton transfer is observed after photoexcitation of the most stable enol conformer and then the molecule reaches the excited-state minimum. After the internal conversion around a conical intersection, the system relaxes to either the cis-keto or trans-keto region in the ground state. The potential energy profiles of the ground and the first excited singlet state are also calculated. According to full-dimensional nonadiabatic dynamics simulations and potential energy profiles, the trans-keto and cis-keto photoproducts can be responsible for the photochromic effect of N-salicilydenemethylfurylamine.
Xie, Sheng-Yi; Li, Xian-Bin; Tian, Wei Quan; Wang, Dan; Chen, Nian-Ke; Han, Dong; Sun, Hong-Bo
2014-09-15
The reduction of graphene oxide can be used as a simple way to produce graphene on a large scale. However, the numerous edges produced by the oxidation of graphite seriously degrade the quality of the graphene and its carrier transport property. In this work, the reduction of oxygen-passivated graphene edges and the subsequent linking of separated graphene sheets by calcium are investigated by using first-principles calculations. The calculations show that calcium can effectively remove the oxygen groups from two adjacent edges. The joining point of the edges serves as the starting point of the reduction and facilitates the reaction. Once the oxygen groups are removed, the crack is sutured. If the joining point is lacking, it becomes difficult to zip the separated fragments. A general electron-reduction model and a random atom-reduction model are suggested for these two situations. The present study sheds light on the reduction of graphene-oxide edges by using reactive metals to give large-sized graphene through a simple chemical reaction.
Cosmic-Ray Modulation: an Ab Initio Approach
Engelbrecht, N. E.; Burger, R. A.
2014-10-01
A better understanding of cosmic-ray modulation in the heliosphere can only be gained through a proper understanding of the effects of turbulence on the diffusion and drift of cosmic rays. We present an ab initio model for cosmic-ray modulation, incorporating for the first time the results yielded by a two-component turbulence transport model. This model is solved for periods of minimum solar activity, utilizing boundary values chosen so that model results are in fair to good agreement with spacecraft observations of turbulence quantities, not only in the solar ecliptic plane but also along the out-of-ecliptic trajectory of the Ulysses spacecraft. These results are employed as inputs for modelled slab and 2D turbulence energy spectra. The latter spectrum is chosen based on physical considerations, with a drop-off at the very lowest wavenumbers commencing at the 2D outerscale. There currently exist no models or observations for this quantity, and it is the only free parameter in this study. The modelled turbulence spectra are used as inputs for parallel mean free path expressions based on those derived from quasi-linear theory and perpendicular mean free paths from extended nonlinear guiding center theory. Furthermore, the effects of turbulence on cosmic-ray drifts are modelled in a self-consistent way, employing a recently developed model for drift along the wavy current sheet. The resulting diffusion coefficients and drift expressions are applied to the study of galactic cosmic-ray protons and antiprotons using a three-dimensional, steady-state cosmic-ray modulation code, and sample solutions in fair agreement with multiple spacecraft observations are presented.
Lithium Insertion In Silicon Nanowires: An ab Initio Study
Zhang, Qianfan
2010-09-08
The ultrahigh specific lithium ion storage capacity of Si nanowires (SiNWs) has been demonstrated recently and has opened up exciting opportunities for energy storage. However, a systematic theoretical study on lithium insertion in SiNWs remains a challenge, and as a result, understanding of the fundamental interaction and microscopic dynamics during lithium insertion is still lacking. This paper focuses on the study of single Li atom insertion into SiNWs with different sizes and axis orientations by using full ab initio calculations. We show that the binding energy of interstitial Li increases as the SiNW diameter grows. The binding energies at different insertion sites, which can be classified as surface, intermediate, and core sites, are quite different. We find that surface sites are energetically the most favorable insertion positions and that intermediate sites are the most unfavorable insertion positions. Compared with the other growth directions, the [110] SiNWs with different diameters always present the highest binding energies on various insertion locations, which indicates that [110] SiNWs are more favorable by Li doping. Furthermore, we study Li diffusion inside SiNWs. The results show that the Li surface diffusion has a much higher chance to occur than the surface to core diffusion, which is consistent with the experimental observation that the Li insertion in SiNWs is layer by layer from surface to inner region. After overcoming a large barrier crossing surface-to-intermediate region, the diffusion toward center has a higher possibility to occur than the inverse process. © 2010 American Chemical Society.
Efficient conformational space exploration in ab initio protein folding simulation.
Ullah, Ahammed; Ahmed, Nasif; Pappu, Subrata Dey; Shatabda, Swakkhar; Ullah, A Z M Dayem; Rahman, M Sohel
2015-08-01
Ab initio protein folding simulation largely depends on knowledge-based energy functions that are derived from known protein structures using statistical methods. These knowledge-based energy functions provide us with a good approximation of real protein energetics. However, these energy functions are not very informative for search algorithms and fail to distinguish the types of amino acid interactions that contribute largely to the energy function from those that do not. As a result, search algorithms frequently get trapped into the local minima. On the other hand, the hydrophobic-polar (HP) model considers hydrophobic interactions only. The simplified nature of HP energy function makes it limited only to a low-resolution model. In this paper, we present a strategy to derive a non-uniform scaled version of the real 20×20 pairwise energy function. The non-uniform scaling helps tackle the difficulty faced by a real energy function, whereas the integration of 20×20 pairwise information overcomes the limitations faced by the HP energy function. Here, we have applied a derived energy function with a genetic algorithm on discrete lattices. On a standard set of benchmark protein sequences, our approach significantly outperforms the state-of-the-art methods for similar models. Our approach has been able to explore regions of the conformational space which all the previous methods have failed to explore. Effectiveness of the derived energy function is presented by showing qualitative differences and similarities of the sampled structures to the native structures. Number of objective function evaluation in a single run of the algorithm is used as a comparison metric to demonstrate efficiency.
Resonance and aromaticity: an ab initio valence bond approach.
Rashid, Zahid; van Lenthe, Joop H; Havenith, Remco W A
2012-05-17
Resonance energy is one of the criteria to measure aromaticity. The effect of the use of different orbital models is investigated in the calculated resonance energies of cyclic conjugated hydrocarbons within the framework of the ab initio Valence Bond Self-Consistent Field (VBSCF) method. The VB wave function for each system was constructed using a linear combination of the VB structures (spin functions), which closely resemble the Kekulé valence structures, and two types of orbitals, that is, strictly atomic (local) and delocalized atomic (delocal) p-orbitals, were used to describe the π-system. It is found that the Pauling-Wheland's resonance energy with nonorthogonal structures decreases, while the same with orthogonalized structures and the total mean resonance energy (the sum of the weighted off-diagonal contributions in the Hamiltonian matrix of orthogonalized structures) increase when delocal orbitals are used as compared to local p-orbitals. Analysis of the interactions between the different structures of a system shows that the resonance in the 6π electrons conjugated circuits have the largest contributions to the resonance energy. The VBSCF calculations also show that the extra stability of phenanthrene, a kinked benzenoid, as compared to its linear counterpart, anthracene, is a consequence of the resonance in the π-system rather than the H-H interaction in the bay region as suggested previously. Finally, the empirical parameters for the resonance interactions between different 4n+2 or 4n π electrons conjugated circuits, used in Randić's conjugated circuits theory or Herdon's semi-emprical VB approach, are quantified. These parameters have to be scaled by the structure coefficients (weights) of the contributing structures.
Ab initio calculations of ^12C and neutron drops
Pieper, Steven C.
2009-10-01
Ab initio calculations of nuclei, which treat a nucleus as a system of A nucleons interacting by realistic two- and three-nucleon forces, have made tremendous progress in the last 15 years. This is a result of better Hamiltonians, rapidly increasing computer power, and new or improved many-body methods. Three methods are principally being used: Green's function Monte Carlo (GFMC), no-core shell model, and coupled cluster. In the limit of large computer resources, all three methods produce exact eigenvalues of a given nuclear Hamiltonian. With DOE SciDAC and INCITE support, all three methods are using the largest computers available today. Under the UNEDF SciDAC grant, the Argonne GFMC program was modified to efficiently use more than 2000 processors. E. Lusk (Argonne), R.M. Butler (Middle Tennessee State U.) and I have developed an Asynchronous Dynamic Load-Balancing (ADLB) library. In addition all the cores in a node are used via OpenMP as one ADLB/MPI client. In this way we obtain very good scalability up to 30,000 processors on Argonne's IBM Blue Gene/P. Two systems of particular interest that require this computer power are ^12C and neutron drops. V.R. Pandharipande (UIUC, deceased), J. Carlson (LANL), R.B. Wiringa (Argonne), and I have developed new trial wave functions that explicitly contain the three-alpha particle structure of ^12C. These are being used with the Argonne V18 and Illinois-7 potentials which reproduce the energies of 51 states in 3energy-density functionals.
An investigation of ab initio shell-model interactions derived by no-core shell model
Wang, XiaoBao; Dong, GuoXiang; Li, QingFeng; Shen, CaiWan; Yu, ShaoYing
2016-09-01
The microscopic shell-model effective interactions are mainly based on the many-body perturbation theory (MBPT), the first work of which can be traced to Brown and Kuo's first attempt in 1966, derived from the Hamada-Johnston nucleon-nucleon potential. However, the convergence of the MBPT is still unclear. On the other hand, ab initio theories, such as Green's function Monte Carlo (GFMC), no-core shell model (NCSM), and coupled-cluster theory with single and double excitations (CCSD), have made many progress in recent years. However, due to the increasing demanding of computing resources, these ab initio applications are usually limited to nuclei with mass up to A = 16. Recently, people have realized the ab initio construction of valence-space effective interactions, which is obtained through a second-time renormalization, or to be more exactly, projecting the full-manybody Hamiltonian into core, one-body, and two-body cluster parts. In this paper, we present the investigation of such ab initio shell-model interactions, by the recent derived sd-shell effective interactions based on effective J-matrix Inverse Scattering Potential (JISP) and chiral effective-field theory (EFT) through NCSM. In this work, we have seen the similarity between the ab initio shellmodel interactions and the interactions obtained by MBPT or by empirical fitting. Without the inclusion of three-body (3-bd) force, the ab initio shell-model interactions still share similar defects with the microscopic interactions by MBPT, i.e., T = 1 channel is more attractive while T = 0 channel is more repulsive than empirical interactions. The progress to include more many-body correlations and 3-bd force is still badly needed, to see whether such efforts of ab initio shell-model interactions can reach similar precision as the interactions fitted to experimental data.
Modeling hybrid perovskites by molecular dynamics.
Mattoni, Alessandro; Filippetti, Alessio; Caddeo, Claudia
2017-02-01
The topical review describes the recent progress in the modeling of hybrid perovskites by molecular dynamics simulations. Hybrid perovskites and in particular methylammonium lead halide (MAPI) have a tremendous technological relevance representing the fastest-advancing solar material to date. They also represent the paradigm of an organic-inorganic crystalline material with some conceptual peculiarities: an inorganic semiconductor for what concerns the electronic and absorption properties with a hybrid and solution processable organic-inorganic body. After briefly explaining the basic concepts of ab initio and classical molecular dynamics, the model potential recently developed for hybrid perovskites is described together with its physical motivation as a simple ionic model able to reproduce the main dynamical properties of the material. Advantages and limits of the two strategies (either ab initio or classical) are discussed in comparison with the time and length scales (from pico to microsecond scale) necessary to comprehensively study the relevant properties of hybrid perovskites from molecular reorientations to electrocaloric effects. The state-of-the-art of the molecular dynamics modeling of hybrid perovskites is reviewed by focusing on a selection of showcase applications of methylammonium lead halide: molecular cations disorder; temperature evolution of vibrations; thermally activated defects diffusion; thermal transport. We finally discuss the perspectives in the modeling of hybrid perovskites by molecular dynamics.
Modeling hybrid perovskites by molecular dynamics
Mattoni, Alessandro; Filippetti, Alessio; Caddeo, Claudia
2017-02-01
The topical review describes the recent progress in the modeling of hybrid perovskites by molecular dynamics simulations. Hybrid perovskites and in particular methylammonium lead halide (MAPI) have a tremendous technological relevance representing the fastest-advancing solar material to date. They also represent the paradigm of an organic-inorganic crystalline material with some conceptual peculiarities: an inorganic semiconductor for what concerns the electronic and absorption properties with a hybrid and solution processable organic-inorganic body. After briefly explaining the basic concepts of ab initio and classical molecular dynamics, the model potential recently developed for hybrid perovskites is described together with its physical motivation as a simple ionic model able to reproduce the main dynamical properties of the material. Advantages and limits of the two strategies (either ab initio or classical) are discussed in comparison with the time and length scales (from pico to microsecond scale) necessary to comprehensively study the relevant properties of hybrid perovskites from molecular reorientations to electrocaloric effects. The state-of-the-art of the molecular dynamics modeling of hybrid perovskites is reviewed by focusing on a selection of showcase applications of methylammonium lead halide: molecular cations disorder; temperature evolution of vibrations; thermally activated defects diffusion; thermal transport. We finally discuss the perspectives in the modeling of hybrid perovskites by molecular dynamics.
An ab initio study of plutonium oxides surfaces; Etude ab initio des surfaces d'oxydes de Pu
Energy Technology Data Exchange (ETDEWEB)
Jomard, G.; Bottin, F.; Amadon, B
2007-07-01
By means of first-principles calculations, we have studied the atomic structure as well as the thermodynamic stability of various plutonium dioxide surfaces in function of their environment (in terms of oxygen partial pressure and temperature). All these simulations have been performed with the ABINIT code. It is well known that DFT fails to describe correctly plutonium-based materials since 5f electrons in such systems are strongly correlated. In order to go beyond DFT, we have treated PuO{sub 2} and {beta}-Pu{sub 2}O{sub 3} in a DFT+U framework. We show that the couple of parameters (U,J) that works well for pure Pu is also well designed for describing ground state (GS) properties of these two oxides. The major improvement with respect with DFT is that we are able to predict an insulating GS in agreement with experiments. The presence of a gap in the DOS (Density of States) of plutonium oxides should play a significant role in the predicted surface reactivity. However, performing DFT+U calculations on surfaces of plutonium oxide from scratch was too ambitious. That is why we decided, as a first step, to study the stability of the (100), (110) and (111) surfaces of PuO{sub 2} in a DFT-GGA framework. For each of these orientations, we considered various terminations. These ab initio results have been introduced in a thermodynamic model which allows us to predict the relative stability of the different terminations as a function of temperature and oxygen partial pressure (p{sub O{sub 2}}). We conclude that at room temperature and for p{sub O{sub 2}}{approx}10 atm., the polar O{sub 2}-(100) termination is favoured. The stabilization of such a polar stoichiometric surface is surprising and should be confirmed by DFT+U calculations before any final conclusion. (authors)
Transferable ab Initio Dipole Moment for Water: Three Applications to Bulk Water.
Liu, Hanchao; Wang, Yimin; Bowman, Joel M
2016-03-03
We recently reported a second-generation, ab initio dipole moment surface (DMS) for water and applied it successfully to the IR spectrum of liquid water at 300 K. Here the transferability of this DMS is demonstrated in three applications. One is the distribution of monomer dipole moments, considering two definitions, and effective atomic charges of liquid water at 300 K and also for a model of ice Ih at 0 K. The second one is a calculation of the dielectric constant of liquid water at 280, 300, 320, 340, 360 K, and the third one is correcting the intensities of the IR spectrum of liquid water at 300 K, obtained using the q-TIP4P/F potential, bringing them into much improved agreement with experiment. For the purpose of obtaining statistical ensembles we use molecular dynamics simulations with the TIP4P+E3B water model developed by Skinner and co-workers. The average monomer dipole moments for 300 K water and 0 K ice Ih are 2.94 and 3.54 D, respectively, in good agreement with literature values. Effective monomer charge distributions are derived from the monomer dipoles and give average values of -1.02 e for O and 0.51 e for H in liquid water, which are also in agreement with values reported from experiment. The calculated dielectric constant of liquid water at the above five temperatures is compared to experiment and is roughly 10-15% lower than experiment.
The role of metals in amyloid aggregation - Experiments and ab initio simulations
Minicozzi, V.; Morante, S.; Rossi, G. C.; Stellato, F.; Christian, N.; Jansen, K.
With a combination of modern spectroscopic techniques and numerical first principle simulations it is possible to investigate the physico-chemical basis of the beta-amyloid aggregation phenomenon, which is suspected to be at the basis of the development of the Alzheimer disease. On the experimental side, in fact, X-ray absorption spectroscopy can be successfully used to determine the atomic structure around the metal binding site in samples where beta-amyloid peptides are complexed with either Cu2+ or Zn2+ ions. Exploiting spectroscopic information obtained on a selected set of fragments of the natural Abeta-peptide, the residues that along the sequence are coordinated to the metal are identified. Although copper data can be consistently interpreted assuming that oligopeptides encompassing the minimal 1-16 amino acidic sequence display a metal coordination mode which involves three Histidines (His6, His13, and His14), in complexes with zinc a four Histidines coordination mode is seen to be preferred. Lacking a fourth Histidine in the Abeta1-16 fragment, this geometrical arrangement hints to a Zn2+ promoted inter-peptide aggregation mode. On the theoretical side, first principle ab initio molecular dynamics simulations of the Car-Parrinello type, which have proved to be of invaluable help in understanding the microscopic mechanisms of chemical bonding both in solid-state physics and structural biophysics, have been employed in an effort to give a microscopic basis and find a phenomenological interpretation of the body of available experimental data on Abeta-peptides-metal complexes. Using medium size PC-clusters as well as larger parallel platforms, it is possible to deal with systems comprising 300-500 atoms and 1,000-2,000 electrons for simulation times as long as 2-3 ps. We present structural results that nicely compare with NMR and XAS data.
Electron Transport through Polyene Junctions in between Carbon Nanotubes: an Ab Initio Realization
Chen, Yiing-Rei; Chen, Kai-Yu; Dou, Kun-Peng; Tai, Jung-Shen; Lee, Hsin-Han; Kaun, Chao-Cheng
With both ab initio and tight-binding model calculations, we study a system of polyene bridged armchair carbon nanotube electrodes, considering one-polyene and two-polyene cases, to address aspects of quantum transport through junctions with multiple conjugated molecules. The ab initio results of the two-polyene cases not only show the interference effect in transmission, but also the sensitive dependence of such effect on the combination of relative contact sites, which agrees nicely with the tight-binding model. Moreover, we show that the discrepancy mainly brought by ab initio relaxation provides an insight into the influence upon transmission spectra, from the junction's geometry, bonding and effective potential. This work was supported by the Ministry of Science and Technology of the Republic of China under Grant Nos. 99-2112-M-003-012-MY2 and 103-2622-E-002-031, and the National Center for Theoretical Sciences of Taiwan.
Density-matrix based determination of low-energy model Hamiltonians from ab initio wavefunctions.
Changlani, Hitesh J; Zheng, Huihuo; Wagner, Lucas K
2015-09-14
We propose a way of obtaining effective low energy Hubbard-like model Hamiltonians from ab initio quantum Monte Carlo calculations for molecular and extended systems. The Hamiltonian parameters are fit to best match the ab initio two-body density matrices and energies of the ground and excited states, and thus we refer to the method as ab initio density matrix based downfolding. For benzene (a finite system), we find good agreement with experimentally available energy gaps without using any experimental inputs. For graphene, a two dimensional solid (extended system) with periodic boundary conditions, we find the effective on-site Hubbard U(∗)/t to be 1.3 ± 0.2, comparable to a recent estimate based on the constrained random phase approximation. For molecules, such parameterizations enable calculation of excited states that are usually not accessible within ground state approaches. For solids, the effective Hamiltonian enables large-scale calculations using techniques designed for lattice models.
Chan, Garnet Kin-Lic; Nakatani, Naoki; Li, Zhendong; White, Steven R
2016-01-01
Current descriptions of the ab initio DMRG algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab-initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational par...
Energy Technology Data Exchange (ETDEWEB)
Keegan, Ronan M. [STFC Rutherford Appleton Laboratory, Didcot OX11 0FA (United Kingdom); Bibby, Jaclyn; Thomas, Jens [University of Liverpool, Liverpool L69 7ZB (United Kingdom); Xu, Dong [Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037 (United States); Zhang, Yang [University of Michigan, Ann Arbor, MI 48109 (United States); Mayans, Olga [University of Liverpool, Liverpool L69 7ZB (United Kingdom); Winn, Martyn D. [Science and Technology Facilities Council Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Rigden, Daniel J., E-mail: drigden@liv.ac.uk [University of Liverpool, Liverpool L69 7ZB (United Kingdom); STFC Rutherford Appleton Laboratory, Didcot OX11 0FA (United Kingdom)
2015-02-01
Two ab initio modelling programs solve complementary sets of targets, enhancing the success of AMPLE with small proteins. AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected.
Electrical resistivity of NaPb compound-forming liquid alloy using ab initio pseudopotentials
Indian Academy of Sciences (India)
Anil Thakur; N S Negi; P K Ahluwalla
2005-08-01
The study of electrical resistivity of compound-forming liquid alloy, NaPb, is presented as a function of concentration. Hard sphere diameters of Na and Pb are obtained through the interionic pair potentials evaluated using Troullier and Martins ab initio pseudopotential, which have been used to calculate the partial structure factors (). Considering the liquid alloy to be a ternary mixture, Ziman formula, modified for complex formation has been used for calculating resistivity of binary liquid alloys. Form factors are calculated using ab initio pseudopotentials. The results suggest that Ziman formalism, when used with ab initio pseudopotentials, are quite successful in explaining the electrical resistivity data of compound-forming binary liquid alloys.
Keegan, Ronan M; Bibby, Jaclyn; Thomas, Jens; Xu, Dong; Zhang, Yang; Mayans, Olga; Winn, Martyn D; Rigden, Daniel J
2015-02-01
AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected.
Atomic carbon chains as spin-transmitters: An ab initio transport study
DEFF Research Database (Denmark)
Fürst, Joachim Alexander; Brandbyge, Mads; Jauho, Antti-Pekka
2010-01-01
An atomic carbon chain joining two graphene flakes was recently realized in a ground-breaking experiment by Jin et al. (Phys. Rev. Lett., 102 (2009) 205501). We present ab initio results for the electron transport properties of such chains and demonstrate complete spin-polarization of the transmi......An atomic carbon chain joining two graphene flakes was recently realized in a ground-breaking experiment by Jin et al. (Phys. Rev. Lett., 102 (2009) 205501). We present ab initio results for the electron transport properties of such chains and demonstrate complete spin...
Ab initio quantum-enhanced optical phase estimation using real-time feedback control
DEFF Research Database (Denmark)
Berni, Adriano; Gehring, Tobias; Nielsen, Bo Melholt
2015-01-01
as demonstrated in a variety of different optical systems(3-8). Most of these accounts, however, deal with the measurement of a very small shift of an already known phase, which is in stark contrast to ab initio phase estimation where the initial phase is unknown(9-12). Here, we report on the realization...... of a quantum-enhanced and fully deterministic ab initio phase estimation protocol based on real-time feedback control. Using robust squeezed states of light combined with a real-time Bayesian adaptive estimation algorithm, we demonstrate deterministic phase estimation with a precision beyond the quantum shot...
Ab initio I-V characteristics of short C-20 chains
DEFF Research Database (Denmark)
Roland, C.; Larade, B.; Taylor, Jeremy Philip
2002-01-01
We have calculated the I-V characteristics of short chains of C-20 molecular cages between Al and Au leads with an ab initio formalism. The results indicate that a linear chain of such molecules acts primarily as metallic nanowires. The transmission, however, depends sensitively both on the orien......We have calculated the I-V characteristics of short chains of C-20 molecular cages between Al and Au leads with an ab initio formalism. The results indicate that a linear chain of such molecules acts primarily as metallic nanowires. The transmission, however, depends sensitively both...
Lopuszynski, Michal; Majewski, Jacek A.
2007-01-01
We present theoretical studies for the third-order elastic constants $C_{ijk}$ in zinc-blende nitrides AlN, GaN, and InN. Our predictions for these compounds are based on detailed ab initio calculations of strain-energy and strain-stress relations in the framework of the density functional theory. To judge the computational accuracy, we compare the ab initio calculated results for $C_{ijk}$ with experimental data available for Si and GaAs. We also underline the relation of the third-order ela...
An ab initio study on single electron transfer between ClO2 and phenol
Institute of Scientific and Technical Information of China (English)
崔崇威; 黄君礼
2004-01-01
The SET mechanism between chlorine dioxide (ClO2 ) and phenol was studied by using ab initio method at 4-31G* level. Geometries of the reactants, intermediate and products of the reaction were optimized and the single point energy calculations of the species were performed. The relative structure data of the reactants, intermediate and products are given. The SET mechanism between ClO2 and phenol was confirmed by ab initio calculations. The reaction is exothermic about 200. 88 k J/mol.
Ab initio theory of charge-carrier conduction in ultrapure organic crystals
Hannewald, K.; Bobbert, P. A.
2004-08-01
We present an ab initio description of charge-carrier mobilities in organic molecular crystals of high purity. Our approach is based on Holstein's original concept of small-polaron bands but generalized with respect to the inclusion of nonlocal electron-phonon coupling. By means of an explicit expression for the mobilities as a function of temperature in combination with ab initio calculations of the material parameters, we demonstrate the predictive power of our theory by applying it to naphthalene. The results show a good qualitative agreement with experiment and provide insight into the difference between electron and hole mobilities as well as their peculiar algebraic and anisotropic temperature dependencies.
Castro-Palacios, Juan Carlos; Rubayo-Soneira, Jesús; Ishii, Keisaku; Yamashita, Koichi
2007-04-01
The intermolecular potentials for the NO(X 2Pi)-Kr and NO(A 2Sigma+)-Kr systems have been calculated using highly accurate ab initio calculations. The spin-restricted coupled cluster method for the ground 1 2A' state [NO(X 2Pi)-Kr] and the multireference singles and doubles configuration interaction method for the excited 2 2A' state [NO(A 2Sigma+)-Kr], respectively, were used. The potential energy surfaces (PESs) show two linear wells and one that is almost in the perpendicular position. An analytical representation of the PESs has been constructed for the triatomic systems and used to carry out molecular dynamics (MD) simulations of the NO-doped krypton matrix response after excitation of NO. MD results are shown comparatively for three sets of potentials: (1) anisotropic ab initio potentials [NO molecule direction fixed during the dynamics and considered as a point (its center of mass)], (2) isotropic ab initio potentials (isotropic part in a Legendre polynomial expansion of the PESs), and (3) fitted Kr-NO potentials to the spectroscopic data. An important finding of this work is that the anisotropic and isotropic ab initio potentials calculated for the Kr-NO triatomic system are not suitable for describing the dynamics of structural relaxation upon Rydberg excitation of a NO impurity in the crystal. However, the isotropic ab initio potential in the ground state almost overlaps the published experimental potential, being almost independent of the angle asymmetry. This fact is also manifested in the radial distribution function around NO. However, in the case of the excited state the isotropic ab initio potential differs from the fitted potentials, which indicates that the Kr-NO interaction in the matrix is quite different because of the presence of the surrounding Kr atoms acting on the NO molecule. MD simulations for isotropic potentials reasonably reproduce the experimental observables for the femtosecond response and the bubble size but do not match
KAMINSKI, GEORGE A.; STERN, HARRY A.; BERNE, B. J.; FRIESNER, RICHARD A.; CAO, YIXIANG X.; MURPHY, ROBERT B.; ZHOU, RUHONG; HALGREN, THOMAS A.
2014-01-01
We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic-size systems. Employing high-level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using the fast and reliable quantum mechanical methods supplies robust fitting data for the resulting parameter sets. As a result, gas-phase many-body effects for dipeptides are captured within the average RMSD of 0.22 kcal/mol from their ab initio values, and conformational energies for the di- and tetrapeptides are reproduced within the average RMSD of 0.43 kcal/mol from their quantum mechanical counterparts. The latter is achieved in part because of application of a novel torsional fitting technique recently developed in our group, which has already been used to greatly improve accuracy of the peptide conformational equilibrium prediction with the OPLS-AA force field.1 Finally, we have employed the newly developed first-generation model in computing gas-phase conformations of real proteins, as well as in molecular dynamics studies of the systems. The results show that, although the overall accuracy is no better than what can be achieved with a fixed-charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields. It can be considered as a solid basis for building a more accurate and complete second-generation model. PMID:12395421
Ab initio Defect Energetics in LaBO3 Perovskite Solid Oxide Fuel Cell Materials
DEFF Research Database (Denmark)
Lee, Yueh-Lin; Morgan, Dane; Kleis, Jesper;
2009-01-01
Perovskite materials of the form ABO3 are a promising family of compounds for use in solid oxide fuel cell (SOFC) cathodes. Study of the physics of these compounds under SOFC conditions with ab initio methods is particularly challenging due to high temperatures, exchange of oxygen with O2 gas...
Ab initio and work function and surface energy anisotropy of LaB6
Uijttewaal, M. A.; de Wijs, G. A.; de Groot, R. A.
2006-01-01
Lanthanum hexaboride is one of the cathode materials most used in high-power electronics technology, but the many experimental results do not provide a consistent picture of the surface properties. Therefore, we report the first ab initio calculations of the work functions and surface energies of
van Setten, M.J.; de Wijs, G.A.; Popa, V.A.; Popa, V.A.; Brocks, G.
2005-01-01
Magnesium alanate Mg(AlH4)2 has recently raised interest as a potential material for hydrogen storage. We apply ab initio calculations to characterize structural, electronic and energetic properties of Mg(AlH4)2. Density functional theory calculations within the generalized gradient approximation
DEFF Research Database (Denmark)
Abild-Pedersen, Frank; Nørskov, Jens Kehlet; Rostrup-Nielsen, Jens;
2006-01-01
Mechanisms and energetics of graphene growth catalyzed by nickel nanoclusters were studied using ab initio density functional theory calculations. It is demonstrated that nickel step-edge sites act as the preferential growth centers for graphene layers on the nickel surface. Carbon is transported...
Ab initio study of energy-level alignments in polymer-dye blends
Pasveer, W.F.; Bobbert, P.A.; Michels, M.A.J.; Langeveld-Voss, B.M.W.; Schoo, H.F.M.; Bastiaansen, J.J.A.M.
2003-01-01
Polymers with a small amount of dye blended in offer an attractive possibility to change the color of the emitted light by changing the dye. We present ab initio calculations within density-functional theory of the HOMO/ LUMO energies for dipyrrolomethane dyes, polyphenylenevinylene and polyfluorene
DEFF Research Database (Denmark)
Cybulski, Hubert; Fernandez, Berta; Henriksen, Christian
2012-01-01
We evaluate the phenylacetylene-argon intermolecular potential energy surface by fitting a representative number of ab initio interaction energies to an analytic function. These energies are calculated at a grid of intermolecular geometries, using the CCSD(T) method and the aug-cc-pVDZ basis set ...
Ab Initio Investigations of the C2F4S Isomers and of Their Interconversions
DEFF Research Database (Denmark)
Shim, Irene; Vallano-Lorenzo, Sandra; Lisbona-Martin, Pilar
2003-01-01
The transition states and the activation energies for the unobserved isomerization reactions between the three possible C2F4S isomers with divalent sulfur, trifluorothioacetyl fluoride 1, tetrafluorothiirane 2, and trifluoroethenesulfenyl fluoride 3, have been determined by ab initio Hartree-Fock...
Ab initio electronic-structure calculations on the Nb/Zr multilayer system
Leuken, H. v.; Czyżyk, M.T.; Springelkamp, F.; Groot, R.A. de
1990-01-01
Ab initio electronic-structure calculations are performed for the Nb/Zr metallic multilayer system in the coherent bcc structure and in the incoherent bcc/hcp structure, observed for small and larger modulation wavelengths, respectively. A new calculational scheme, the localized-spherical-wave
Dispersion Interactions between Rare Gas Atoms: Testing the London Equation Using ab Initio Methods
Halpern, Arthur M.
2011-01-01
A computational chemistry experiment is described in which students can use advanced ab initio quantum mechanical methods to test the ability of the London equation to account quantitatively for the attractive (dispersion) interactions between rare gas atoms. Using readily available electronic structure applications, students can calculate the…
An ab initio Valence Bond Study on Cyclopenta-Fused Naphthalenes and Fluoranthenes
Havenith, R.W.A.; van Lenthe, J.H.; Jenneskens, L.W.
2005-01-01
To probe the effect of external cyclopenta-fusion on a naphthalene core, ab initio valence bond (VB) calculations have been performed, using strictly atomic benzene p-orbitals and p-orbitals that are allowed to delocalize, on naphthalene (1), acenaphthylene (2), pyracylene (3), cyclopenta[b,c]-acena
Ab initio study of energy-level alignments in polymer-dye blends
Pasveer, W.F.; Bobbert, P.A.; Michels, M.A.J.; Langeveld-Voss, B.M.W.; Schoo, H.F.M.; Bastiaansen, J.J.A.M.
2003-01-01
Polymers with a small amount of dye blended in offer an attractive possibility to change the color of the emitted light by changing the dye. We present ab initio calculations within density-functional theory of the HOMO/ LUMO energies for dipyrrolomethane dyes, polyphenylenevinylene and
The Pu–U–Am system: An ab initio informed CALPHAD thermodynamic study
Energy Technology Data Exchange (ETDEWEB)
Perron, A., E-mail: perron1@llnl.gov [Lawrence Livermore National Laboratory, Livermore, CA 94550 (United States); Turchi, P.E.A.; Landa, A.; Söderlind, P. [Lawrence Livermore National Laboratory, Livermore, CA 94550 (United States); Ravat, B.; Oudot, B.; Delaunay, F. [CEA-Centre de Valduc, 21120 Is sur Tille (France)
2015-03-15
Highlights: • The ab initio informed CALPHAD assessment of the Am–U system has been realized. • A strong tendency toward phase separation across the whole composition range is predicted. • The ab initio informed Pu–U–Am thermodynamic database has been developed. • The solubility of Am and U in the liquid phase is improved by adding Pu. • The δ-Pu (fcc) phase is strongly stabilized by Am, on the contrary to the bcc phase. - Abstract: Phase diagram and thermodynamic properties of the Am–U system, that are experimentally unknown, are calculated using the CALPHAD method with input from ab initio electronic-structure calculations for the fcc and bcc phases. A strong tendency toward phase separation across the whole composition range is predicted. In addition, ab initio informed Pu–U and Am–Pu thermodynamic assessments are combined to build a Pu–U–Am thermodynamic database. Regarding the Pu-rich corner of the ternary system, predictions indicate that Am acts as a powerful δ-Pu (fcc) stabilizer. In the U-rich corner, similar predictions are made but to a lesser extent. In both cases, the bcc phase is destabilized and the fcc phase is enhanced. Finally, results and methodology are discussed and compared with previous assessments and guidelines are provided for further experimental studies.
Ab initio calculations on the inclusion complexation of cyclobis(paraquat- p-phenylene)
Zhang, Ke-Chun; Liu, Lei; Mu, Ting-Wei; Guo, Qing-Xiang
2001-01-01
Semiempirical PM3, ab initio HF/3-21g ∗, and DFT B3LYP/6-31g ∗ calculations in vacuum and in solution were performed on the inclusion complexation of cyclobis(paraquat- p-phenylene) with nine symmetric aromatic substrates. A good correlation was found between the theoretical stabilization energies and experimental free energy changes upon complexation.
Ab initio study of long-period superstructures in close-packed A3B compounds
DEFF Research Database (Denmark)
Rosengaard, N. M.; Skriver, Hans Lomholt
1994-01-01
We have performed ab initio calculations of the stability of one-dimensional long-period superstructures in Cu3Pd, Cu3Al, and Ag3Mg by means of an interface Green's function technique based on the linear-muffin-tin-orbitals method within the tight-binding and atomic-sphere approximations. The ene...
Precise Ab-initio prediction of terahertz vibrational modes in crystalline systems
DEFF Research Database (Denmark)
Jepsen, Peter Uhd; Clark, Stewart J.
2007-01-01
We use a combination of experimental THz time-domain spectroscopy and ab-initio density functional perturbative theory to accurately predict the terahertz vibrational spectrum of molecules in the crystalline phase. Our calculations show that distinct vibrational modes found in solid-state materials...
Relativistic ab initio spectroscopy study of forbidden lines of singly ionized zinc
Dixit, Gopal; Sahoo, Bijaya K.; Chaudhuri, Rajat K.; Majumder, Sonjoy
2009-01-01
The ab initio calculation has been carried out to study the astrophysically important forbidden electromagnetic transition rates of singly ionized zinc (Zn II). Electron correlations are considered to all orders using coupled-cluster theory in the relativistic framework. Calculated excitation energi
Relativistic ab initio spectroscopy study of forbidden lines of singly ionized zinc
Dixit, Gopal; Sahoo, Bijaya K.; Chaudhuri, Rajat K.; Majumder, Sonjoy
2009-01-01
The ab initio calculation has been carried out to study the astrophysically important forbidden electromagnetic transition rates of singly ionized zinc (Zn II). Electron correlations are considered to all orders using coupled-cluster theory in the relativistic framework. Calculated excitation
Setten, van M.J.; Wijs, de G.A.; Popa, V.A.; Brocks, G.
2005-01-01
Magnesium alanate Mg(AlH4)2 has recently raised interest as a potential material for hydrogen storage. We apply ab initio calculations to characterize structural, electronic and energetic properties of Mg(AlH4)2. Density functional theory calculations within the generalized gradient approximation (G
Mechanical properties of carbynes investigated by ab initio total-energy calculations
DEFF Research Database (Denmark)
Castelli, Ivano E.; Salvestrini, Paolo; Manini, Nicola
2012-01-01
As sp carbon chains (carbynes) are relatively rigid molecular objects, can we exploit them as construction elements in nanomechanics? To answer this question, we investigate their remarkable mechanical properties by ab initio total-energy simulations. In particular, we evaluate their linear...
Ab initio calculations on the structure of pyridine in its lowest triplet state
Buma, W.J.; Groenen, E.J.J.; Schmidt, J.
1990-01-01
Recently we have experimentally shown that pyridine-d5, as a guest in a single crystal of benzene-d6, adopts a boatlike structure upon excitation into the lowest triplet state T0. Here MRDCI ab initio calculations are presented that reveal that the observed nonplanarity of the molecule is not caused
Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R.
2016-07-01
Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.
Ab initio charge-carrier mobility model for amorphous molecular semiconductors
Massé, Andrea; Friederich, Pascal; Symalla, Franz; Liu, Feilong; Nitsche, Robert; Coehoorn, Reinder; Wenzel, Wolfgang; Bobbert, Peter A.
2016-05-01
Accurate charge-carrier mobility models of amorphous organic molecular semiconductors are essential to describe the electrical properties of devices based on these materials. The disordered nature of these semiconductors leads to percolative charge transport with a large characteristic length scale, posing a challenge to the development of such models from ab initio simulations. Here, we develop an ab initio mobility model using a four-step procedure. First, the amorphous morphology together with its energy disorder and intermolecular charge-transfer integrals are obtained from ab initio simulations in a small box. Next, the ab initio information is used to set up a stochastic model for the morphology and transfer integrals. This stochastic model is then employed to generate a large simulation box with modeled morphology and transfer integrals, which can fully capture the percolative charge transport. Finally, the charge-carrier mobility in this simulation box is calculated by solving a master equation, yielding a mobility function depending on temperature, carrier concentration, and electric field. We demonstrate the procedure for hole transport in two important molecular semiconductors, α -NPD and TCTA. In contrast to a previous study, we conclude that spatial correlations in the energy disorder are unimportant for α -NPD. We apply our mobility model to two types of hole-only α -NPD devices and find that the experimental temperature-dependent current density-voltage characteristics of all devices can be well described by only slightly decreasing the simulated energy disorder strength.
Computer simulation of acetonitrile and methanol with ab initio-based pair potentials
Hloucha, M.; Sum, A. K.; Sandler, S. I.
2000-10-01
This study address the adequacy of ab initio pair interaction energy potentials for the prediction of macroscopic properties. Recently, Bukowski et al. [J. Phys. Chem. A 103, 7322 (1999)] performed a comprehensive study of the potential energy surfaces for several pairs of molecules using symmetry-adapted perturbation theory. These ab initio energies were then fit to an appropriate site-site potential form. In an attempt to bridge the gap between ab initio interaction energy information and macroscopic properties prediction, we performed Gibbs ensemble Monte Carlo (GEMC) simulations using their developed pair potentials for acetonitrile and methanol. The simulations results show that the phase behavior of acetonitrile is well described by just the pair interaction potential. For methanol, on the other hand, pair interactions are insufficient to properly predict its vapor-liquid phase behavior, and its saturated liquid density. We also explored simplified forms for representing the ab initio interaction energies by refitting a selected range of the data to a site-site Lennard-Jones and to a modified Buckingham (exponential-6) potentials plus Coulombic interactions. These were also used in GEMC simulations in order to evaluate the quality and computational efficiency of these different potential forms. It was found that the phase behavior prediction for acetonitrile and methanol are highly dependent on the details of the interaction potentials developed.
Chan, Garnet Kin-Lic; Keselman, Anna; Nakatani, Naoki; Li, Zhendong; White, Steven R
2016-07-01
Current descriptions of the ab initio density matrix renormalization group (DMRG) algorithm use two superficially different languages: an older language of the renormalization group and renormalized operators, and a more recent language of matrix product states and matrix product operators. The same algorithm can appear dramatically different when written in the two different vocabularies. In this work, we carefully describe the translation between the two languages in several contexts. First, we describe how to efficiently implement the ab initio DMRG sweep using a matrix product operator based code, and the equivalence to the original renormalized operator implementation. Next we describe how to implement the general matrix product operator/matrix product state algebra within a pure renormalized operator-based DMRG code. Finally, we discuss two improvements of the ab initio DMRG sweep algorithm motivated by matrix product operator language: Hamiltonian compression, and a sum over operators representation that allows for perfect computational parallelism. The connections and correspondences described here serve to link the future developments with the past and are important in the efficient implementation of continuing advances in ab initio DMRG and related algorithms.
New ab initio based pair potential for accurate simulation of phase transitions in ZnO
Wang, Shuaiwei; Fan, Zhaochuan; Koster, Rik S.; Fang, Changming; Van Huis, Marijn A.; Yalcin, Anil O.; Tichelaar, Frans D.; Zandbergen, Henny W.; Vlugt, Thijs J H
2014-01-01
A set of interatomic pair potentials is developed for ZnO based on the partially charged rigid ion model (PCRIM). The derivation of the potentials combines lattice inversion, empirical fitting, and ab initio energy surface fitting. We show that, despite the low number of parameters in this model (8)
Ab Initio Calculations and Raman and SERS Spectral Analyses of Amphetamine Species
DEFF Research Database (Denmark)
Berg, Rolf W.; Nørbygaard, Thomas; White, Peter C.
2011-01-01
. The spectra of amphetamine and amphetamine-H+ sampleswere obtained and assigned according to a comparison of the experimental spectra and the ab initio MO calculations, performed using the Gaussian 03W program (Gaussian, Inc., Pittsburgh, PA). The analyses were based on complete geometry minimization...
Ab initio and work function and surface energy anisotropy of LaB6
Uijttewaal, M. A.; de Wijs, G. A.; de Groot, R. A.
2006-01-01
Lanthanum hexaboride is one of the cathode materials most used in high-power electronics technology, but the many experimental results do not provide a consistent picture of the surface properties. Therefore, we report the first ab initio calculations of the work functions and surface energies of th
Ab initio studies of methane and carbon dioxide affinity to carbon compounds and minerals
Wlazlo, Mateusz; Siklitskaya, Alexandra; Majewski, Jacek
2017-04-01
Understanding of physico-chemistry of capture and storage of carbon dioxide and methane might be crucial for development of the novel technologies meant: (i) to deal with the global warming process through the reduction of the CO2 atmospheric concentration by sequestration, and (ii) to enhance oil recovery, on the other hand. The accurate description of CO2 and CH4 adsorption to minerals and carbonaceous systems (which constitute the main component of sedimentary rocks) is essential to reach this goal. We have employed the ab initio molecular dynamics AIMD) based on the density functional theory (DFT) to study the affinity of CO2 and CH4 from gaseous phase, also at elevated temperatures and hydrostatic pressure, to pristine and defected graphene, spiral carbon nanoparticles (spiroids), calcite rocks (represented by the most stable (10-14) surface of CaCoO3), CaO, MgO, illite, and kaolonite. In the case of kaolonite that exhibits layered crystallographic structure, we have also studied the intercalation of CO2. These studies provide valuable quantitative predictions and shed light on physical mechanisms governing the processes of chemisorption and physisorption of the CO2 and CH4 molecules, revealing also the essential role of Van der Waals interaction. In particular, we find out that CO2 molecules in supercritical gaseous phase (i.e. at temperature of order 60oC and moderate hydrostatic pressure of 20-30 MPa) change their shape from linear one to the water like bended V-shape with angle between C-O chemical bonds smaller than 180 degrees. This shape change of CO2 molecules facilitates the CO2 adsorption. Therefore, in the temperature-pressure conditions of shale deposits, the adsorption probability of CO2 can be enhanced in comparison to the ambient conditions. It turns out that the carbon atoms in the surrounding of characteristic Stone-Wales (or 5-7) defects in graphene are more reactive towards adsorption of CO2 and CH4 molecules. In the case of CO2 adsorption
Relaxation of Small Molecules：an ab initio Study
Institute of Scientific and Technical Information of China (English)
CAOYi－Gang; A.Antons; 等
2002-01-01
Using an ab inito total energy and force method,we have relaxed several group IV and group V elemental clusters,in detail the arsenic and antimony dimers,silicon,phosphorus,arsenic and antimony tetraners,The obtained bond lengths and cohesive energies are more accurate than other calculating methods,and in excellent agreement with the experimental results.
Refinement of homology-based protein structures by molecular dynamics simulation techniques
Fan, H; Mark, AE
2004-01-01
The use of classical molecular dynamics simulations, performed in explicit water, for the refinement of structural models of proteins generated ab initio or based on homology has been investigated. The study involved a test set of 15 proteins that were previously used by Baker and coworkers to asses
Ab initio studies on [bmim][PF6]–CO2 mixture and CO2 clusters
Indian Academy of Sciences (India)
B L Bhargava; M Saharay; S Balasubramanian
2008-06-01
Ab initio molecular dynamics studies have been carried out on the room temperature ionic liquid, 1,n-butyl,3-methylimidazolium hexafluorophosphate ([bmim][PF6]) and supercritical carbon dioxide mixture at room temperature and experimental density. Partial radial distribution functions (RDF) for different sites have been computed to see the organization of CO2 molecules around the ionic liquid. Several partial RDFs around the carbon atom of CO2 molecule are compared to find out that the CO2 has specific interaction with a carbon atom present in the imidazolium ring. The CO2 is also found to be very well organized around the terminal carbon atom of the butyl chain. The partial RDFs for the oxygen atoms around oxygen and carbon atoms of the CO2 suggests that there is very good organization of CO2 molecules around themselves even in the [bmim][PF6] – CO2 mixture. The instantaneous quadrupole moment tensor has been calculated for the anion and the cation. The ensemble average of diagonal components of quadrupole moment tensor of the cation have finite values, whereas the off-diagonal components of the cation and both the diagonal and off-diagonal components of the anion have the value of zero with a large standard deviation. The CPMD studies performed on CO2 clusters reveals the greater tendency of the clusters with more CO2 units, to deviate from the linear geometry.
Kirchhoff, F; Gillan, M J
1996-01-01
Ab initio molecular-dynamics simulations have been used to investigate the structure, dynamics and electronic properties of the liquid alloy Ag(1-x)Se(x) at 1350 K and at the three compositions x=0.33, 0.42 and 0.65. The calculations are based on density-functional theory in the local density approximation and on the pseudopotential plane-wave method. The reliability of the simulations is confirmed by detailed comparisons with very recent neutron diffraction results for the partial structure factors and radial distribution functions (RDF) of the stoichiometric liquid Ag2Se. The simulations show a dramatic change of the Se-Se RDF with increasing Se content. This change is due to the formation of Se clusters bound by covalent bonds, the Se-Se bond length being almost the same as in pure c-Se and l-Se. The clusters are predominantly chain-like, but for higher x a large fraction of 3-fold coordinated Se atoms is also found. It is shown that the equilibrium fractions of Se present as isolated atoms and in clusters...
Energy Technology Data Exchange (ETDEWEB)
Olsson, Paer
2004-04-01
The efficiency of fast neutron reactors, such as for fusion, breeding and transmutation, depend strongly on the neutron radiation resistance of the materials used in the reactors. The binary Fe-Cr alloy, which has many attractive properties in this regard, is the base for the best steels of today which are, however, still not up to the required standards. Therefore, substantial effort has been devoted to finding new materials that can cope with the demands better. Experimental studies must be complemented with extensive theoretical modelling in order to understand the effects that different alloying elements has on the resistance properties of materials. To this end, the first steps of multi-scale modelling has been taken, starting out with ab initio calculations of the electronic structure of the complete concentration range range of the disordered binary Fe-C alloy. The mixing enthalpy of Fe-Cr has been quantitatively predicted and has, together with data from literature, been used in order to fit two sets of interatomic potentials for the purpose of simulating defect evolution with molecular dynamics and kinetic Monte-Carlo codes. These dedicated Fe-Cr alloy potentials are new and represent important additions to the pure element potentials that can be found in literature.
Energy Technology Data Exchange (ETDEWEB)
Cherukara, Mathew J. [Argonne National Lab. (ANL), Argonne, IL (United States). X-ray Sciences Division; Narayanan, Badri [Argonne National Lab. (ANL), Argonne, IL (United States). Center for Nanoscale Materials; Kinaci, Alper [Argonne National Lab. (ANL), Argonne, IL (United States). Center for Nanoscale Materials; Sasikumar, Kiran [Argonne National Lab. (ANL), Argonne, IL (United States). Center for Nanoscale Materials; Gray, Stephen K. [Argonne National Lab. (ANL), Argonne, IL (United States). Center for Nanoscale Materials; Univ. of Chicago, IL (United States). Computation Inst.; Chan, Maria K. Y. [Argonne National Lab. (ANL), Argonne, IL (United States). Center for Nanoscale Materials; Univ. of Chicago, IL (United States). Computation Inst.; Sankaranarayanan, Subramanian K. R. S. [Argonne National Lab. (ANL), Argonne, IL (United States). Center for Nanoscale Materials; Univ. of Chicago, IL (United States). Computation Inst.
2016-08-28
We introduce a bond order potential (BOP) for stanene based on an ab initio derived training data set. The potential is optimized to accurately describe the energetics, as well as thermal and mechanical properties of a free-standing sheet, and used to study diverse nanostructures of stanene, including tubes and ribbons. As a representative case study, using the potential, we perform molecular dynamics simulations to study stanene’s structure and temperature-dependent thermal conductivity. We find that the structure of stanene is highly rippled, far in excess of other 2-D materials (e.g., graphene), owing to its low in-plane stiffness (stanene: ~ 25 N/m; graphene: ~ 480 N/ m). The extent of stanene’s rippling also shows stronger temperature dependence compared to that in graphene. Furthermore, we find that stanene based nanostructures have significantly lower thermal conductivity compared to graphene based structures owing to their softness (i.e., low phonon group velocities) and high anharmonic response. Our newly developed BOP will facilitate the exploration of stanene based low dimensional heterostructures for thermoelectric and thermal management applications.
Ehlers, F. J. H.; Seydou, M.; Tingaud, D.; Maurel, F.; Charles, Y.; Queyreau, S.
2016-12-01
We have performed a uniaxial tensile test on the Σ5 [1 0 0] 36.87° twist grain boundary (GB) in face-centred cubic Al within the framework of density functional theory in order to derive an atomistic cohesive traction-separation law. Addressing the importance of kinetics to GB breakage, we accompanied our energy-separation curve calculations by two additional studies. Firstly, using the nudged elastic band method, we determined for a series of GB separations the heights of the zero temperature barriers separating intact and broken GB configurations. Secondly, a representative subset of these transition paths was examined at finite temperature with ab initio molecular dynamics. Contrasting prevalent conclusions on GB breakage behaviour, our results suggest that the GB likely stays intact at room temperature well into the range of separations where a broken GB represents the thermodynamically favourable configuration. Given the non-negligible resulting influence on critical tensile stress and work of separation, our findings may be viewed as stressing the need for a kinetic analysis in a general first principles based uniaxial tensile test.
Energy Technology Data Exchange (ETDEWEB)
CalderIn, L [Research Computing and Cyberinfrastructure, The Pennsylvania State University, University Park, PA 16802 (United States); Gonzalez, L E; Gonzalez, D J, E-mail: david@liq1.fam.cie.uva.es [Departamento de Fisica Teorica, Facultad de Ciencias, Universidad de Valladolid, 47011 Valladolid (Spain)
2011-09-21
Fluid Hg undergoes a metal-nonmetal (M-NM) transition when expanded toward a density of around 9 g cm{sup -3}. We have performed ab initio molecular dynamics simulations for several thermodynamic states around the M-NM transition range and the associated static, dynamic and electronic properties have been analyzed. The calculated static structure shows a good agreement with the available experimental data. It is found that the volume expansion decreases the number of nearest neighbors from 10 (near the triple point) to around 8 at the M-NM transition region. Moreover, these neighbors are arranged into two subshells and the decrease in the number of neighbors occurs in the inner subshell. The calculated dynamic structure factors agree fairly well with their experimental counterparts obtained by inelastic x-ray scattering experiments, which display inelastic side peaks. The derived dispersion relation exhibits some positive dispersion for all the states, although its value around the M-NM transition region is not as marked as suggested by the experiment. We have also calculated the electronic density of states, which shows the appearance of a gap at a density of around 8.3 g cm{sup -3}. (paper)
An ab-initio study of pyrrole and imidazole arylamides
Directory of Open Access Journals (Sweden)
Abramyan Ara M.
2013-01-01
Full Text Available Arylamide foldamers have been shown to have a number of biological and medicinal applications. For example, a class of pyrrole-imidazole polyamide foldamers is capable of binding specific DNA sequences and preventing development of various gene disorders, most importantly cancer. Molecular dynamics (MD simulations can provide crucial details in understanding the atomic level events related to foldamer/DNA binding. An important first step in the accurate simulation of these foldamer/DNA systems is the reparametrization of force field parameters for torsion around the aryl-amide bonds. Here we highlight our Density Functional Theory (DFT potential energy profiles and derived force field parameters for four aryl-amide bond types for the pyrrole and imidazole building blocks extensively used in foldamer design for the DNA-binding polyamides. These results contribute to developing of computational tools for an appropriate molecular modeling of pyrrole-imidazole polyamide/DNA binding, and provide an insight into the chemical factors that influence the flexibility of the pyrrole-imidazole polyamides, and their binding to DNA.
Allen, B. Danette; Alexandrov, Natalia
2016-01-01
Incremental approaches to air transportation system development inherit current architectural constraints, which, in turn, place hard bounds on system capacity, efficiency of performance, and complexity. To enable airspace operations of the future, a clean-slate (ab initio) airspace design(s) must be considered. This ab initio National Airspace System (NAS) must be capable of accommodating increased traffic density, a broader diversity of aircraft, and on-demand mobility. System and subsystem designs should scale to accommodate the inevitable demand for airspace services that include large numbers of autonomous Unmanned Aerial Vehicles and a paradigm shift in general aviation (e.g., personal air vehicles) in addition to more traditional aerial vehicles such as commercial jetliners and weather balloons. The complex and adaptive nature of ab initio designs for the future NAS requires new approaches to validation, adding a significant physical experimentation component to analytical and simulation tools. In addition to software modeling and simulation, the ability to exercise system solutions in a flight environment will be an essential aspect of validation. The NASA Langley Research Center (LaRC) Autonomy Incubator seeks to develop a flight simulation infrastructure for ab initio modeling and simulation that assumes no specific NAS architecture and models vehicle-to-vehicle behavior to examine interactions and emergent behaviors among hundreds of intelligent aerial agents exhibiting collaborative, cooperative, coordinative, selfish, and malicious behaviors. The air transportation system of the future will be a complex adaptive system (CAS) characterized by complex and sometimes unpredictable (or unpredicted) behaviors that result from temporal and spatial interactions among large numbers of participants. A CAS not only evolves with a changing environment and adapts to it, it is closely coupled to all systems that constitute the environment. Thus, the ecosystem that
Tummanapelli, Anil Kumar; Vasudevan, Sukumaran
2015-12-10
The tripeptide glutathione (GSH) is one of the most abundant peptides and the major repository for nonprotein sulfur in both animal and plant cells. It plays a critical role in intracellular oxidative stress management by the reversible formation of glutathione disulfide with the thiol-disulfide pair acting as a redox buffer. The state of charge of the ionizable groups of GSH can influence the redox couple, and hence the pKa value of the cysteine residue of GSH is critical to its functioning. Here we report ab initio Car-Parrinello molecular dynamics simulations of glutathione solvated by 200 water molecules, all of which are considered in the simulation. We show that the free-energy landscape for the protonation-deprotonation reaction of the cysteine residue of GSH computed using metadynamics sampling provides accurate estimates of the pKa and correctly predicts the shift in the dissociation constant values as compared with the isolated cysteine amino acid.
Energy Technology Data Exchange (ETDEWEB)
Li, Hongfei; Guo, Yuzheng; Robertson, John [Engineering Department, Cambridge University, Cambridge CB2 1PZ (United Kingdom); Okuno, Y. [Taiwan Semiconductor Manufacturing Company (TSMC), Hsinchu Science Park, Hsinchu, Taiwan (China)
2016-02-07
Models of three representative higher Miller index interfaces, Si(310):SiO{sub 2}, Si(410):SiO{sub 2}, and Si(331):SiO{sub 2}, have been built by an ab-initio molecular dynamics method. We show that each interface can be made as a fully bonded network without any defects and has a reasonable electronic structure for use in fin field effect transistors or gate-all-around nanowire devices. The differences in numbers of oxygen bridges are attributed to the intermediate sub-oxide components and the atomic step structure. The interface bonding schemes to passivate different densities of dangling bonds on different facets are also analyzed.
Farahani, Pooria; Lundberg, Marcus; Karlsson, Hans O.
2013-11-01
The SN2 substitution reactions at phosphorus play a key role in organic and biological processes. Quantum molecular dynamics simulations have been performed to study the prototype reaction Cl-+PH2Cl→ClPH2+Cl-, using one and two-dimensional models. A potential energy surface, showing an energy well for a transition complex, was generated using ab initio electronic structure calculations. The one-dimensional model is essentially reflection free, whereas the more realistic two-dimensional model displays involved resonance structures in the reaction probability. The reaction rate is almost two orders of magnitude smaller for the two-dimensional compared to the one-dimensional model. Energetic errors in the potential energy surface is estimated to affect the rate by only a factor of two. This shows that for these types of reactions it is more important to increase the dimensionality of the modeling than to increase the accuracy of the electronic structure calculation.
{\\it Ab initio} nuclear structure - the large sparse matrix eigenvalue problem
Vary, James P; Ng, Esmond; Yang, Chao; Sosonkina, Masha
2009-01-01
The structure and reactions of light nuclei represent fundamental and formidable challenges for microscopic theory based on realistic strong interaction potentials. Several {\\it ab initio} methods have now emerged that provide nearly exact solutions for some nuclear properties. The {\\it ab initio} no core shell model (NCSM) and the no core full configuration (NCFC) method, frame this quantum many-particle problem as a large sparse matrix eigenvalue problem where one evaluates the Hamiltonian matrix in a basis space consisting of many-fermion Slater determinants and then solves for a set of the lowest eigenvalues and their associated eigenvectors. The resulting eigenvectors are employed to evaluate a set of experimental quantities to test the underlying potential. For fundamental problems of interest, the matrix dimension often exceeds $10^{10}$ and the number of nonzero matrix elements may saturate available storage on present-day leadership class facilities. We survey recent results and advances in solving t...
[Photoelectron Spectra of CCl2-: Ab Initio Calculation and Franck-Condon Analysis].
Wu, Jun
2015-12-01
Geometry optimization and harmonic vibrational frequency calculations were performed on the X¹A₁ state of CCl₂ and X²B₁ state of CCl₂⁻ at the B3LYP, MP2, CCSD levels. Franck-Condon analysis and spectral simulations were carried out on the photoelectron band of CCl₂⁻ including Duschinsky effects. The simulated spectra obtained are in excellent agreement with the experiment. Note that Duschinsky effect between bending vibration and the symmetric stretch modes should be considered in the CCl₂ (X¹A₁)-CCl₂⁻ (X²B₁) photodetachment process. By combining ab initio calculations with Franck-Condon analyses, the assignment of spectrum observed is firmly established to the X¹A₁-X²B₁ photodetachment process of the CCl₂⁻ radical, and the recommended geometric parameters of which in the literature are confirmed again base on ab initio theory and IFCA process.
A highly accurate {\\it ab initio} potential energy surface for methane
Owens, Alec; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter
2016-01-01
A new nine-dimensional potential energy surface (PES) for methane has been generated using state-of-the-art \\textit{ab initio} theory. The PES is based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set limit and incorporates a range of higher-level additive energy corrections. These include: core-valence electron correlation, higher-order coupled cluster terms beyond perturbative triples, scalar relativistic effects and the diagonal Born-Oppenheimer correction. Sub-wavenumber accuracy is achieved for the majority of experimentally known vibrational energy levels with the four fundamentals of $^{12}$CH$_4$ reproduced with a root-mean-square error of $0.70{\\,}$cm$^{-1}$. The computed \\textit{ab initio} equilibrium C{--}H bond length is in excellent agreement with previous values despite pure rotational energies displaying minor systematic errors as $J$ (rotational excitation) increases. It is shown that these errors can be significantly reduced by adjusting the e...
Ab Initio No-Core Shell Model Calculations Using Realistic Two- and Three-Body Interactions
Energy Technology Data Exchange (ETDEWEB)
Navratil, P; Ormand, W E; Forssen, C; Caurier, E
2004-11-30
There has been significant progress in the ab initio approaches to the structure of light nuclei. One such method is the ab initio no-core shell model (NCSM). Starting from realistic two- and three-nucleon interactions this method can predict low-lying levels in p-shell nuclei. In this contribution, we present a brief overview of the NCSM with examples of recent applications. We highlight our study of the parity inversion in {sup 11}Be, for which calculations were performed in basis spaces up to 9{Dirac_h}{Omega} (dimensions reaching 7 x 10{sup 8}). We also present our latest results for the p-shell nuclei using the Tucson-Melbourne TM three-nucleon interaction with several proposed parameter sets.
Ab initio calculations on twisted graphene/hBN: Electronic structure and STM image simulation
Correa, J. D.; Cisternas, E.
2016-09-01
By performing ab initio calculations we obtained theoretical scanning tunneling microscopy (STM) images and studied the electronic properties of graphene on a hexagonal boron-nitrite (hBN) layer. Three different stack configurations and four twisted angles were considered. All calculations were performed using density functional theory, including van der Waals interactions as implemented in the SIESTA ab initio package. Our results show that the electronic structure of graphene is preserved, although some small changes are induced by the interaction with the hBN layer, particularly in the total density of states at 1.5 eV under the Fermi level. When layers present a twisted angle, the density of states shows several van Hove singularities under the Fermi level, which are associated to moiré patterns observed in theoretical STM images.
Ab initio calculations on the magnetic properties of transition metal complexes
Energy Technology Data Exchange (ETDEWEB)
Bodenstein, Tilmann; Fink, Karin [Karlsruhe Institute of Technology, Institute of Nanotechnology, POB 3640, 76021 Karlsruhe (Germany)
2015-12-31
We present a protocol for the ab initio determination of the magnetic properties of mono- and polynuclear transition metal compounds. First, we obtain the low lying electronic states by multireference methods. Then, we include spin-orbit coupling and an external magnetic field for the determination of zero-field splitting and g-tensors. For the polynuclear complexes the magnetic exchange coupling constants are determined by a modified complete active space self consistent field method. Based on the results of the ab initio calculations, magnetic data such as magnetic susceptibility or magnetization are simulated and compared to experimental data. The results obtained for the polynuclear complexes are further analysed by calculations on model complexes where part of the magnetic centers are substituted by diamagnetic ions. The methods are applied to different Co and Ni containing transition metal complexes.
Bridging a gap between continuum-QCD and ab initio predictions of hadron observables
Directory of Open Access Journals (Sweden)
Daniele Binosi
2015-03-01
Full Text Available Within contemporary hadron physics there are two common methods for determining the momentum-dependence of the interaction between quarks: the top-down approach, which works toward an ab initio computation of the interaction via direct analysis of the gauge-sector gap equations; and the bottom-up scheme, which aims to infer the interaction by fitting data within a well-defined truncation of those equations in the matter sector that are relevant to bound-state properties. We unite these two approaches by demonstrating that the renormalisation-group-invariant running-interaction predicted by contemporary analyses of QCD's gauge sector coincides with that required in order to describe ground-state hadron observables using a nonperturbative truncation of QCD's Dyson–Schwinger equations in the matter sector. This bridges a gap that had lain between nonperturbative continuum-QCD and the ab initio prediction of bound-state properties.
Ab Initio Calculations for the BaTiO3 (001) Surface Structure
Institute of Scientific and Technical Information of China (English)
XUE Xu-Yan; WANG Chun-Lei; ZHONG Wei-Lie
2004-01-01
@@ The ab initio method within the local density approximation is applied to calculate cubic BaTiO3 (001) surface relaxation and rumpling for two different terminations (BaO and TiO2). Our calculations demonstrate that cubic perovskite BaTiO3 crystals possess surface polarization, accompanied by the presence of the relevant electric field.We analyse their electronic structures (band structure, density of states and the electronic density redistribution with emphasis on the covalency effects). The results are also compared with that of the previous ab initio calculations. Considerable increases of Ti-O chemical bond covalency nearby the surface have been observed.The band gap reduces especially for the TiO2 termination.
Ab initio simulations and neutron scattering studies of structure and dynamics in PdH
Totolici, I E
2001-01-01
The work presented in this PhD thesis is concerned with the interpretation of the neutron scattering measurements from the palladium hydrogen system by means of ab initio electronic structure calculations. The motivation of performing such calculations was due to recent neutron scattering studies on this system that showed a strong directional dependence to the dynamical structure factor together with a complex dependence on energy. Here we attempt to describe the origin of these features by ab initio simulations of the dynamical structure factor. The method assumes an adiabatic separation of the motion of the proton and palladium atoms. The proton wave functions are calculated by a direct solution of the associated single-particle Schroedinger equation using a plane wave basis set method and a mapping of the adiabatic surface. The Fourier components of the adiabatic potential are obtained from LDA pseudopotential calculations. Using Fermi's golden rule within the Born approximation we were then able to calcu...
An ab initio potential function for the ν13 vibrational mode of 1,3-butadiene
Senent, M. L.
1995-06-01
The restricted potential of the ν13 torsional mode of 1,3-butadiene has been determined from ab initio calculations. The relative energy and geometry of the second rotamer were calculated with the optimized couple cluster method with double substitutions. This ab initio level provides that the second stable structure attaches to a gauche form situated at 140.8°. The potential energy function was obtained by fitting to a symmetry-adapted Fourier series the total electronic energies of several selected conformations. These energies were calculated by the Möller-Plesset perturbation theory up to the second order (MP2) with full and partial optimization of the geometry. Torsional Raman band positions and fundamental frequencies were determined from the periodic potentials with a good agreement with experimental data. The convenience of performing fully optimized calculations to determine the restricted function is also refuted.
Raman spectroscopy, ab-initio model calculations, and conformational, equilibria in ionic liquids
DEFF Research Database (Denmark)
Berg, Rolf W.
2009-01-01
spectroscopy and ab-initio molecular orbital calculations. A discussion is given, based mainly on some recent FT- Raman spectroscopic results on the model ionic liquid system of 1-butyl-3-methyl-imidazolium ([C4C1Im]+X-) salts. The rotational isomerism of the [C4C1Im]+ cation is described: the presence of anti...... systems in the future. A few examples will be discussed. Contents 12.1 Introduction...........307 12.2 Brief introduction to Raman spectroscopy ..............309 12.2.1 Basics .....................309 12.2.2 Experimental, fluorescence and fouriertransform- Raman spectroscopy instrumentation ...... 311 12.......3 Brief introduction to ab-initio model calculations .... 312 12.4 Case study on Raman spectroscopy and structure of imidazolium-based ionic liquids ..... 312 12.5 Raman spectra and structure of [C4C1Im]+ liquids ..... 315 12.6 Normal mode analysis and rotational isomerism of the [C4C1Im]+ cation...
Interatomic potentials for Al and Ni from experimental data and ab initio calculations
Energy Technology Data Exchange (ETDEWEB)
Mishin, Y.; Farkas, D.; Miehl, M.J.; Papaconstantopoulos, D.A.
1999-07-01
New embedded-atom potentials for Al and Ni have been developed by fitting to both experimental data and the results of ab initio calculations. The ab initio data were obtained in the form of energies of different alternative computer-generated crystalline structures of these metals. The potentials accurately reproduce basic equilibrium properties of Al and Ni such as the elastic constants, phonon dispersion curves, vacancy formation and migration energies, stacking fault energies, and surface energies. The equilibrium energies of various alternative structures not included in the fitting database are calculated with these potentials. The results are compared with predictions of total-energy tight-binding calculations for the same structures. The embedded-atom potentials correctly reproduce the structural stability trends, which suggests that they are transferable to different local environments encountered in atomistic simulations of lattice defects.
Ab initio calculation of valley splitting in monolayer δ-doped phosphorus in silicon
Drumm, Daniel W.; Budi, Akin; Per, Manolo C.; Russo, Salvy P.; L Hollenberg, Lloyd C.
2013-02-01
The differences in energy between electronic bands due to valley splitting are of paramount importance in interpreting transport spectroscopy experiments on state-of-the-art quantum devices defined by scanning tunnelling microscope lithography. Using vasp, we develop a plane-wave density functional theory description of systems which is size limited due to computational tractability. Nonetheless, we provide valuable data for the benchmarking of empirical modelling techniques more capable of extending this discussion to confined disordered systems or actual devices. We then develop a less resource-intensive alternative via localised basis functions in siesta, retaining the physics of the plane-wave description, and extend this model beyond the capability of plane-wave methods to determine the ab initio valley splitting of well-isolated δ-layers. In obtaining an agreement between plane-wave and localised methods, we show that valley splitting has been overestimated in previous ab initio calculations by more than 50%.
McKemmish, Laura K; Tennyson, Jonathan
2016-01-01
Accurate knowledge of the rovibronic near-infrared and visible spectra of vanadium monoxide (VO) is very important for studies of cool stellar and hot planetary atmospheres. Here, the required ab initio dipole moment and spin-orbit coupling curves for VO are produced. This data forms the basis of a new VO line list considering 13 different electronic states and containing over 277 million transitions. Open shell transition, metal diatomics are challenging species to model through ab initio quantum mechanics due to the large number of low-lying electronic states, significant spin-orbit coupling and strong static and dynamic electron correlation. Multi-reference configuration interaction methodologies using orbitals from a complete active space self-consistent-field (CASSCF) calculation are the standard technique for these systems. We use different state-specific or minimal-state CASSCF orbitals for each electronic state to maximise the calculation accuracy. The off-diagonal dipole moment controls the intensity...
Emergent properties of nuclei from ab initio coupled-cluster calculations
Hagen, G; Hjorth-Jensen, M; Papenbrock, T
2016-01-01
Emergent properties such as nuclear saturation and deformation, and the effects on shell structure due to the proximity of the scattering continuum and particle decay channels are fascinating phenomena in atomic nuclei. In recent years, ab initio approaches to nuclei have taken the first steps towards tackling the computational challenge of describing these phenomena from Hamiltonians with microscopic degrees of freedom. This endeavor is now possible due to ideas from effective field theories, novel optimization strategies for nuclear interactions, ab initio methods exhibiting a soft scaling with mass number, and ever-increasing computational power. This paper reviews some of the recent accomplishments. We also present new results. The recently optimized chiral interaction NNLO$_{\\rm sat}$ is shown to provide an accurate description of both charge radii and binding energies in selected light- and medium-mass nuclei up to $^{56}$Ni. We derive an efficient scheme for including continuum effects in coupled-clust...
Electrical Resistivity of Na-K Binary Liquid Alloy Using Ab-Initio Pseudopotentials
Institute of Scientific and Technical Information of China (English)
Anil Thakur; P. K. Ahluwalia
2005-01-01
@@ The study of electrical resistivity of simple binary liquid alloy Na-K is presented as a function of concentration.Hard sphere diameters of sodium (Na) and potassium (K) are obtained through the inter ionic pair potentials evaluated using Troullier and Martins ab-initio pseudopotentials, which have been used to calculate partial structure factors S(q). The Ziman formula for calculating resistivity of binary liquid alloys has been used. Form factors are calculated using ab-initio pseudopotentials. The results suggest that the first principle approach for calculating pseudopotentials with in the frame work of Ziman formalism is quite successful in explaining the electrical resistivity data of compound forming binary liquid alloys.
Properties of metals during the heating by intense laser irradiation using ab initio simulations
Holst, Bastian; Recoules, Vanina; Torrent, Marc; Mazevet, Stephane
2011-10-01
Ultrashort laser pulses irradiating a target heat the electrons to very high temperatures. In contrast, the ionic lattice is unaffected on the time scale of the laser pulse since the heat capacity of electrons is much smaller than that of the lattice. This non-equilibrium system can be described as a composition of two subsystems: one consisting of hot electrons and the other of an ionic lattice at low temperature. We studied the effect of this intense electronic excitations on the optical properties of gold using ab initio simulations. We additionally use ab initio linear response to compute the phonon spectrum and the electron-phonon coupling constant within Density Functional Theory for several electronic temperatures of few eV. LULI, Ecole Polytechnique, CNRS, CEA, UPMC, 91128 Palaiseau, France.
Ab initio calculation of valley splitting in monolayer δ-doped phosphorus in silicon.
Drumm, Daniel W; Budi, Akin; Per, Manolo C; Russo, Salvy P; L Hollenberg, Lloyd C
2013-02-27
: The differences in energy between electronic bands due to valley splitting are of paramount importance in interpreting transport spectroscopy experiments on state-of-the-art quantum devices defined by scanning tunnelling microscope lithography. Using vasp, we develop a plane-wave density functional theory description of systems which is size limited due to computational tractability. Nonetheless, we provide valuable data for the benchmarking of empirical modelling techniques more capable of extending this discussion to confined disordered systems or actual devices. We then develop a less resource-intensive alternative via localised basis functions in siesta, retaining the physics of the plane-wave description, and extend this model beyond the capability of plane-wave methods to determine the ab initio valley splitting of well-isolated δ-layers. In obtaining an agreement between plane-wave and localised methods, we show that valley splitting has been overestimated in previous ab initio calculations by more than 50%.
Energy Technology Data Exchange (ETDEWEB)
Halasyamani, Shiv [Univ. of Houston, TX (United States); Fennie, Craig [Cornell Univ., Ithaca, NY (United States)
2016-11-03
We have focused on the synthesis, characterization, and ab initio theory on multi-functional mixed-metal fluorides. With funding from the DOE, we have successfully synthesized and characterized a variety of mixed metal fluoride materials.
First fully ab initio potential energy surface of methane with a spectroscopic accuracy
Nikitin, A. V.; Rey, M.; Tyuterev, Vl. G.
2016-09-01
Full 9-dimensional ab initio potential energy surfaces for the methane molecule are constructed using extended electronic structure coupled-cluster calculations with various series of basis sets following increasing X cardinal numbers: cc-pVXZ (X = 3, 4, 5, 6), aug-cc-ACVXZ (X = 3, 4, 5), and cc-pCVXZ-F12 (X = 3, 4). High-order dynamic electron correlations including triple and quadrupole excitations as well as relativistic and diagonal Born-Oppenheimer breakdown corrections were accounted for. Analytical potential functions are parametrized as non-polynomial expansions in internal coordinates in irreducible tensor representation. Vibrational energy levels are reported using global variational nuclear motion calculations with exact kinetic energy operator and a full account of the tetrahedral symmetry of CH4. Our best ab initio surface including above-mentioned contributions provides the rms (obs.-calc.) errors of less than 0.11 cm-1 for vibrational band centers below 4700 cm-1, and ˜0.3 cm-1 for all 229 assigned experimentally determined vibrational levels up to the Icosad range <7900 cm-1 without empirically adjusted parameters. These results improve the accuracy of ab initio methane vibrational predictions by more than an order of magnitude with respect to previous works. This is an unprecedented accuracy of first-principles calculations of a five-atomic molecule for such a large data set. New ab initio potential results in significantly better band center predictions even in comparison with best available empirically corrected potential energy surfaces. The issues related to the basis set extrapolation and an additivity of various corrections at this level of accuracy are discussed.
Optical and other material properties of SiO2 from ab initio studies
Warmbier, Robert; Mohammed, Faris; Quandt, Alexander
2014-07-01
The optical properties of photonic devices largely depend on the dielectric properties of the underlying materials. We apply modern ab initio methods to study crystalline SiO2 phases, which serve as toy models for amorphous glass. We discuss the dielectric response from the infrared to the VIS/UV, which is crucial for glass based photonic applications. Low density silica, like cristobalite, may provide a good basis for high transmission optical devices.
Raman and ab initio studies of simple and binary 1-alkyl-3-methylimidazolium ionic liquids
DEFF Research Database (Denmark)
Berg, R.W.; Deetlefs, M.; Seddon, K.R.
2005-01-01
Raman spectra of the ionic liquids, 1-butyl-3-methylimidazolium hexafluorophosphate ([C(4)mim][PF6]), 1-hexyl-3-methylimidazolium chloride ([C(6)mim]Cl), and 1-hexyl-3-methylimidazolium hexafluorophosphate ([C(6)mim][PF6]), and binary mixtures thereof, have been assigned using ab initio MP2...... bonding between the imidazolium headgroup and the anions, and the invariance of the essentially 50:50 mixture of the predominant conformers informs on the nature of glass formation in these systems....
Raman Spectroscopy and Ab-Initio Model Calculations on Ionic Liquids
DEFF Research Database (Denmark)
Berg, Rolf W.
2007-01-01
spectroscopy and ab-initio molecular orbital calculations. A discussion is given, based mainly on some recent FT-Raman spectroscopic results on the model ionic liquid system of 1-butyl-3-methylimidazolium ([C4mim][X]) salts. The rotational isomerism of the [C4mim]þ cation is described: the presence of anti...... will be applied to many more systems in the future. A few examples will be discussed....
Ab Initio Study on the Anti-HIV Activities of Hydroxyflavones
Institute of Scientific and Technical Information of China (English)
ZHANG Yu
2005-01-01
Flavone and 95 hydroxyflavones have been studied with ab initio method, and their total energies, atomic charges, dipole moments, multipole moments, molecular orbital compositions, orbital energies etc. were obtained. Among them the relationship between total atomic charges and activities against HIV is basically in accordance with the experimental results. The beneficial references are provided for the extraction and synthesis of strong active anti-HIV medicines.
Ab initio study of antiphase boundaries and stacking faults in L12 and DO22 compounds
DEFF Research Database (Denmark)
Rosengaard, N. M.; Skriver, Hans Lomholt
1994-01-01
We have performed ab initio calculations of the energies of antiphase boundaries as well as complex and superlattice intrinsic stacking faults in nine intermetallic compounds observed in the face-centered-cubic L1(2) and DO22 structures. The calculations were performed by means of a Green's funct......'s function technique based on the linear-muffin-tin-orbitals method within the tight-binding and atomic-sphere approximations....
Energy Technology Data Exchange (ETDEWEB)
Herbig, Alexander
2016-02-12
An ab-initio electronic structure method for substitutionally disordered real materials is developed within a pseudopotential density functional theory approach. The method is validated against exact diagonalization and for simple disordered CuZn alloys. The developed method is applied to iron-based superconductors. In particular, band renormalization effects due to various chemical substitutions in BaFe{sub 2}As{sub 2} are investigated and their Cooper pair breaking effects are compared.
Influence of the ab-initio nd cross sections in the critical heavy-water benchmarks
Morillon, B; Carbonell, J
2013-01-01
The n-d elastic and breakup cross sections are computed by solving the three-body Faddeev equations for realistic and semi-realistic Nucleon-Nucleon potentials. These cross sections are inserted in the Monte Carlo simulation of the nuclear processes considered in the International Handbook of Evaluated Criticality Safety Benchmark Experiments (ICSBEP). The results obtained using thes ab initio n-d cross sections are compared with those provided by the most renown international libraries.
Ab initio verification of the analytical R-matrix theory for strong field ionization
Torlina, Lisa; Morales, Felipe; Muller, H. G.; Smirnova, Olga
2014-10-01
We summarize the key aspects of the recently developed analytical R-matrix (ARM) theory for strong field ionization (Torlina and Smirnova 2012 Phys. Rev. A 86 043408; Kaushal and Smirnova 2013 Phys. Rev. A 88 013421), and present tests of this theory using ab initio numerical simulations for hydrogen and helium atoms in long circularly polarized laser pulses. We find excellent agreement between the predictions of ARM and the numerical calculations.
Lattice dynamics of wurtzite CdS: Neutron scattering and ab-initio calculations
Debernardi, A.; Pyka, N. M.; Göbel, A.; Ruf, T.; Lauck, R.; Kramp, S.; Cardona, M.
1997-08-01
We have measured the phonon dispersion of wurtzite CdS by inelastic neutron scattering in a single crystal made from the nonabsorbing isotope 114Cd. One of the two silent B 1-modes occurs at 3.96 THz ( k = 0 ). It is significantly lower and less dispersive than so far assumed. Previous semiempirical lattice dynamical models need to be reanalyzed. However, the observed dispersion branches compare favorably with an ab-initio calculation.
Steady state Ab-initio Theory of Lasers with Injected Signals
Cerjan, Alexander
2013-01-01
We present an ab-initio treatment of steady-state lasing with injected signals that treats both multimode lasing and spatial hole burning, and describes the transition to injection locking or partial locking in the multimode case. The theory shows that spatial hole burning causes a shift in the frequency of free-running laser modes away from the injection frequency, in contrast to standard approaches.
Energy Technology Data Exchange (ETDEWEB)
Yamaji, Youhei [Quantum-Phase Electronics Center, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-8656 (Japan)
2015-12-31
Recently, condensed-matter ab initio approaches to strongly correlated electrons confined in crystalline solids have been developed and applied to transition-metal oxides and molecular conductors. In this paper, an ab initio scheme based on constrained random phase approximations and localized Wannier orbitals is applied to a spin liquid candidate Na{sub 2}IrO{sub 3} and is shown to reproduce experimentally observed specific heat.
Density-matrix based determination of low-energy model Hamiltonians from ab initio wavefunctions
Energy Technology Data Exchange (ETDEWEB)
Changlani, Hitesh J.; Zheng, Huihuo; Wagner, Lucas K. [Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green St., Urbana, Illinois 61801 (United States)
2015-09-14
We propose a way of obtaining effective low energy Hubbard-like model Hamiltonians from ab initio quantum Monte Carlo calculations for molecular and extended systems. The Hamiltonian parameters are fit to best match the ab initio two-body density matrices and energies of the ground and excited states, and thus we refer to the method as ab initio density matrix based downfolding. For benzene (a finite system), we find good agreement with experimentally available energy gaps without using any experimental inputs. For graphene, a two dimensional solid (extended system) with periodic boundary conditions, we find the effective on-site Hubbard U{sup ∗}/t to be 1.3 ± 0.2, comparable to a recent estimate based on the constrained random phase approximation. For molecules, such parameterizations enable calculation of excited states that are usually not accessible within ground state approaches. For solids, the effective Hamiltonian enables large-scale calculations using techniques designed for lattice models.
Thermal transport in nanocrystalline Si and SiGe by ab initio based Monte Carlo simulation.
Yang, Lina; Minnich, Austin J
2017-03-14
Nanocrystalline thermoelectric materials based on Si have long been of interest because Si is earth-abundant, inexpensive, and non-toxic. However, a poor understanding of phonon grain boundary scattering and its effect on thermal conductivity has impeded efforts to improve the thermoelectric figure of merit. Here, we report an ab-initio based computational study of thermal transport in nanocrystalline Si-based materials using a variance-reduced Monte Carlo method with the full phonon dispersion and intrinsic lifetimes from first-principles as input. By fitting the transmission profile of grain boundaries, we obtain excellent agreement with experimental thermal conductivity of nanocrystalline Si [Wang et al. Nano Letters 11, 2206 (2011)]. Based on these calculations, we examine phonon transport in nanocrystalline SiGe alloys with ab-initio electron-phonon scattering rates. Our calculations show that low energy phonons still transport substantial amounts of heat in these materials, despite scattering by electron-phonon interactions, due to the high transmission of phonons at grain boundaries, and thus improvements in ZT are still possible by disrupting these modes. This work demonstrates the important insights into phonon transport that can be obtained using ab-initio based Monte Carlo simulations in complex nanostructured materials.
Ab initio nuclear structure and reactions with chiral three-body forces
Energy Technology Data Exchange (ETDEWEB)
Langhammer, Joachim; Roth, Robert; Calci, Angelo [Institut fuer Kernphysik - Theoriezentrum, TU Darmstadt (Germany); Navratil, Petr [TRIUMF, Vancouver (Canada)
2014-07-01
One major ambition of ab initio nuclear theory is the description of nuclear-structure and reaction observables on equal footing. This is accomplished by combining the no-core shell model (NCSM) with the resonating-group method (RGM) to a unified ab initio approach to bound and continuum states, which is developed further to the no-core shell model with continuum (NCSMC). We present the formal developments to include three-nucleon interactions in both the NCSM/RGM and NCSMC formalism. This provides the possibility to assess the predictive power of chiral two- and three-nucleon forces in the variety of scattering observables. We study three-nucleon force effects on phase-shifts, cross sections and analyzing powers in first ab-initio studies of nucleon-{sup 4}He scattering with chiral two- and three-nucleon forces. Finally, we focus on heavier target nuclei using the NCSMC, e.g., in neutron-{sup 8}Be scattering and study the impact of the continuum on the spectrum of {sup 9}Be.
Energy Technology Data Exchange (ETDEWEB)
Ladd, A.J.C.
1988-08-01
The basic methodology of equilibrium molecular dynamics is described. Examples from the literature are used to illustrate how molecular dynamics has been used to resolve theoretical controversies, provide data to test theories, and occasionally to discover new phenomena. The emphasis is on the application of molecular dynamics to an understanding of the microscopic physics underlying the transport properties of simple fluids. 98 refs., 4 figs.
Ab initio and DFT Studies of Be(BH42
Directory of Open Access Journals (Sweden)
J. S. Al-Otaibi
2016-03-01
Full Text Available In this study, the Ab inito and DFT calculations of optimized geometries, energy and vibrational spectra for the Beryllium borohydride Be(BH42 at different levels are achieved by Hartre – Fock (HF, perturbation theory (MP2 and density functional theory (B3LYP methods. They utilize the 6-31G(d, 6-311G(d,p, 6-311+G(d,p and 6-311++G(d,p basis sets. The theoretical results showed that Beryllium borohydride with the D2d structure which contains two identical groups of double bridging hydrogen has the lowest energy at all levels. Consequently, this compound is considered as the most stable one and the results of IR and Raman Spectra at all levels support that. We found that both structures Cs, C3v have the structure of D2d kind at all levels. The values of bond lengths for these two structures are identical for the bond lengths to the structure D2d kind which confirms this theory.
Bergstra, J.A.; Bethke, I.
2002-01-01
Molecular dynamics is a model for the structure and meaning of object based programming systems. In molecular dynamics the memory state of a system is modeled as a fluid consisting of a collection of molecules. Each molecule is a collection of atoms with bindings between them. A computation is model
Xu, Dong; Zhang, Jian; Roy, Ambrish; Zhang, Yang
2011-01-01
I-TASSER is an automated pipeline for protein tertiary structure prediction using multiple threading alignments and iterative structure assembly simulations. In CASP9 experiments, two new algorithms, QUARK and fragment-guided molecular dynamics (FG-MD), were added to the I-TASSER pipeline for improving the structural modeling accuracy. QUARK is a de novo structure prediction algorithm used for structure modeling of proteins that lack detectable template structures. For distantly homologous targets, QUARK models are found useful as a reference structure for selecting good threading alignments and guiding the I-TASSER structure assembly simulations. FG-MD is an atomic-level structural refinement program that uses structural fragments collected from the PDB structures to guide molecular dynamics simulation and improve the local structure of predicted model, including hydrogen-bonding networks, torsion angles, and steric clashes. Despite considerable progress in both the template-based and template-free structure modeling, significant improvements on protein target classification, domain parsing, model selection, and ab initio folding of β-proteins are still needed to further improve the I-TASSER pipeline. Copyright © 2011 Wiley-Liss, Inc.
Chen, Shuang; Xiong, Wei; Zhou, Yun Shen; Lu, Yong Feng; Zeng, Xiao Cheng
2016-05-01
Ab initio molecular dynamics (AIMD) simulations are employed to investigate the chemical mechanism underlying the Ni-catalyzed transformation of amorphous carbon (a-C) into graphene in the rapid thermal processing (RTP) experiment to directly grow graphene on various dielectric surfaces via the evaporation of surplus Ni and C at 1100 °C (below the melting point of bulk Ni). It is found that the a-C-to-graphene transformation entails the metal-induced crystallization and layer exchange mechanism, rather than the conventional dissolution/precipitation mechanism typically involved in Ni-catalyzed chemical vapor deposition (CVD) growth of graphene. The multi-layer graphene can be tuned by changing the relative thicknesses of deposited a-C and Ni thin films. Our AIMD simulations suggest that the easy evaporation of surplus Ni with excess C is likely attributed to the formation of a viscous-liquid-like Ni-C solution within the temperature range of 900-1800 K and to the faster diffusion of C atoms than that of Ni atoms above 600 K. Even at room temperature, sp3-C atoms in a-C are quickly converted to sp2-C atoms in the course of the simulation, and the graphitic C formation can occur at low temperature. When the temperature is as high as 1200 K, the grown graphitic structures reversely dissolve into Ni. Because the rate of temperature increase is considerably faster in the AIMD simulations than in realistic experiments, defects in the grown graphitic structures are kinetically trapped. In this kinetic growth stage, the carbon structures grown from sp3-carbon or from sp2-carbon exhibit marked differences.Ab initio molecular dynamics (AIMD) simulations are employed to investigate the chemical mechanism underlying the Ni-catalyzed transformation of amorphous carbon (a-C) into graphene in the rapid thermal processing (RTP) experiment to directly grow graphene on various dielectric surfaces via the evaporation of surplus Ni and C at 1100 °C (below the melting point of bulk
2014-12-01
Poly(aryl-ether-ether-ketone) as a Possible Metalized Film Capacitor Dielectric: Accurate Description of the Band Gap Through Ab Initio...Possible Metalized Film Capacitor Dielectric: Accurate Description of the Band Gap Through Ab Initio Calculation Janet Ho and Marco Olguin Sensors...a Possible Metalized Film Capacitor Dielectric: Accurate Description of the Band Gap Through Ab Initio Calculation 5a. CONTRACT NUMBER 5b. GRANT
Ab initio study of the thermopower of biphenyl-based single-molecule junctions
Bürkle, M.; Zotti, L. A.; Viljas, J. K.; Vonlanthen, D.; Mishchenko, A.; Wandlowski, T.; Mayor, M.; Schön, G.; Pauly, F.
2012-09-01
By employing ab initio electronic-structure calculations combined with the nonequilibrium Green's function technique, we study the dependence of the thermopower Q on the conformation in biphenyl-based single-molecule junctions. For the series of experimentally available biphenyl molecules, alkyl side chains allow us to gradually adjust the torsion angle ϕ between the two phenyl rings from 0∘ to 90∘ and to control in this way the degree of π-electron conjugation. Studying different anchoring groups and binding positions, our theory predicts that the absolute values of the thermopower decrease slightly towards larger torsion angles, following an a+bcos2ϕ dependence. The anchoring group determines the sign of Q and a,b simultaneously. Sulfur and amine groups give rise to Q,a,b>0, while for cyano, Q,a,bbinding positions can lead to substantial variations of the thermopower mostly due to changes in the alignment of the frontier molecular orbital levels and the Fermi energy. We explain our ab initio results in terms of a π-orbital tight-binding model and a minimal two-level model, which describes the pair of hybridizing frontier orbital states on the two phenyl rings. The variations of the thermopower with ϕ seem to be within experimental resolution.
Chen, Shuang; Xiong, Wei; Zhou, Yun Shen; Lu, Yong Feng; Zeng, Xiao Cheng
2016-05-14
Ab initio molecular dynamics (AIMD) simulations are employed to investigate the chemical mechanism underlying the Ni-catalyzed transformation of amorphous carbon (a-C) into graphene in the rapid thermal processing (RTP) experiment to directly grow graphene on various dielectric surfaces via the evaporation of surplus Ni and C at 1100 °C (below the melting point of bulk Ni). It is found that the a-C-to-graphene transformation entails the metal-induced crystallization and layer exchange mechanism, rather than the conventional dissolution/precipitation mechanism typically involved in Ni-catalyzed chemical vapor deposition (CVD) growth of graphene. The multi-layer graphene can be tuned by changing the relative thicknesses of deposited a-C and Ni thin films. Our AIMD simulations suggest that the easy evaporation of surplus Ni with excess C is likely attributed to the formation of a viscous-liquid-like Ni-C solution within the temperature range of 900-1800 K and to the faster diffusion of C atoms than that of Ni atoms above 600 K. Even at room temperature, sp(3)-C atoms in a-C are quickly converted to sp(2)-C atoms in the course of the simulation, and the graphitic C formation can occur at low temperature. When the temperature is as high as 1200 K, the grown graphitic structures reversely dissolve into Ni. Because the rate of temperature increase is considerably faster in the AIMD simulations than in realistic experiments, defects in the grown graphitic structures are kinetically trapped. In this kinetic growth stage, the carbon structures grown from sp(3)-carbon or from sp(2)-carbon exhibit marked differences.
Nam, Kwangho
2014-10-14
Development of multiscale ab initio quantum mechanical and molecular mechanical (AI-QM/MM) method for periodic boundary molecular dynamics (MD) simulations and their acceleration by multiple time step approach are described. The developed method achieves accuracy and efficiency by integrating the AI-QM/MM level of theory and the previously developed semiempirical (SE) QM/MM-Ewald sum method [J. Chem. Theory Comput. 2005, 1, 2] extended to the smooth particle-mesh Ewald (PME) summation method. In the developed methods, the total energy of the simulated system is evaluated at the SE-QM/MM-PME level of theory to include long-range QM/MM electrostatic interactions, which is then corrected on the fly using the AI-QM/MM level of theory within the real space cutoff. The resulting energy expression enables decomposition of total forces applied to each atom into forces determined at the low-level SE-QM/MM method and correction forces at the AI-QM/MM level, to integrate the system using the reversible reference system propagator algorithm. The resulting method achieves a substantial speed-up of the entire calculation by minimizing the number of time-consuming energy and gradient evaluations at the AI-QM/MM level. Test calculations show that the developed multiple time step AI-QM/MM method yields MD trajectories and potential of mean force profiles comparable to single time step QM/MM results. The developed method, together with message passing interface (MPI) parallelization, accelerates the present AI-QM/MM MD simulations about 30-fold relative to the speed of single-core AI-QM/MM simulations for the molecular systems tested in the present work, making the method less than one order slower than the SE-QM/MM methods under periodic boundary conditions.
Ab initio study of the binding of collagen amino acids to graphene and A-doped (A = H, Ca) graphene
Energy Technology Data Exchange (ETDEWEB)
Cazorla, Claudio, E-mail: c.silva@ucl.ac.u
2010-09-30
We present a theoretical study of the binding of collagen amino acids (AA, namely glycine, Gly; proline, Pro; and hydroxyproline, Hyp) to graphene (Gr), Ca-doped graphene and graphane (Gra) using density functional theory calculations and ab initio molecular dynamics (AIMD) simulations. It is found that binding of Gly, Pro and Hyp to Gr and Gra is thermodynamically favorable yet dependent on the amino acid orientation and always very weak (adsorption energies E{sub ads} range from -90 to -20 meV). AIMD simulations reveal that room-temperature thermal excitations are enough to induce detachment of Gly and Pro from Gr and of all three amino acids from Gra. Interestingly, we show that collagen AA binding to Gr is enhanced dramatically by doping the carbon surface with calcium atoms (corresponding E{sub ads} values decrease by practically two orders of magnitude with respect to the non-doped case). This effect is result of electronic charge transfers from the Ca impurity (donor) to Gr (acceptor) and the carboxyl group (COOH) of the amino acid (acceptor). The possibility of using Gr and Gra as nanoframes for sensing of collagen amino acids has also been investigated by performing electronic density of states analysis. It is found that, whether Gr is hardly sensitive, the electronic band gap of Gra can be modulated by attaching different number and species of AAs onto it. The results presented in this work provide fundamental insights on the quantum interactions of collagen protein components with carbon-based nanostructures and can be useful for developments in bio and nanotechnology fields.
DiStasio, Robert A.; Santra, Biswajit; Li, Zhaofeng; Wu, Xifan; Car, Roberto
2014-08-01
In this work, we report the results of a series of density functional theory (DFT) based ab initio molecular dynamics (AIMD) simulations of ambient liquid water using a hierarchy of exchange-correlation (XC) functionals to investigate the individual and collective effects of exact exchange (Exx), via the PBE0 hybrid functional, non-local van der Waals/dispersion (vdW) interactions, via a fully self-consistent density-dependent dispersion correction, and an approximate treatment of nuclear quantum effects, via a 30 K increase in the simulation temperature, on the microscopic structure of liquid water. Based on these AIMD simulations, we found that the collective inclusion of Exx and vdW as resulting from a large-scale AIMD simulation of (H2O)128 significantly softens the structure of ambient liquid water and yields an oxygen-oxygen structure factor, SOO(Q), and corresponding oxygen-oxygen radial distribution function, gOO(r), that are now in quantitative agreement with the best available experimental data. This level of agreement between simulation and experiment demonstrated herein originates from an increase in the relative population of water molecules in the interstitial region between the first and second coordination shells, a collective reorganization in the liquid phase which is facilitated by a weakening of the hydrogen bond strength by the use of a hybrid XC functional, coupled with a relative stabilization of the resultant disordered liquid water configurations by the inclusion of non-local vdW/dispersion interactions. This increasingly more accurate description of the underlying hydrogen bond network in liquid water also yields higher-order correlation functions, such as the oxygen-oxygen-oxygen triplet angular distribution, POOO(θ), and therefore the degree of local tetrahedrality, as well as electrostatic properties, such as the effective molecular dipole moment, that are in much better agreement with experiment.
Energy Technology Data Exchange (ETDEWEB)
DiStasio, Robert A.; Santra, Biswajit [Department of Chemistry, Princeton University, Princeton, New Jersey 08544 (United States); Li, Zhaofeng [Department of Physics, Princeton University, Princeton, New Jersey 08544 (United States); Wu, Xifan [Department of Physics, Temple University, Philadelphia, Pennsylvania 19122 (United States); Car, Roberto [Department of Chemistry, Princeton University, Princeton, New Jersey 08544 (United States); Department of Physics, Princeton University, Princeton, New Jersey 08544 (United States); Princeton Institute for the Science and Technology of Materials, Princeton University, Princeton, New Jersey 08544 (United States); Program in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08544 (United States)
2014-08-28
In this work, we report the results of a series of density functional theory (DFT) based ab initio molecular dynamics (AIMD) simulations of ambient liquid water using a hierarchy of exchange-correlation (XC) functionals to investigate the individual and collective effects of exact exchange (Exx), via the PBE0 hybrid functional, non-local van der Waals/dispersion (vdW) interactions, via a fully self-consistent density-dependent dispersion correction, and an approximate treatment of nuclear quantum effects, via a 30 K increase in the simulation temperature, on the microscopic structure of liquid water. Based on these AIMD simulations, we found that the collective inclusion of Exx and vdW as resulting from a large-scale AIMD simulation of (H{sub 2}O){sub 128} significantly softens the structure of ambient liquid water and yields an oxygen-oxygen structure factor, S{sub OO}(Q), and corresponding oxygen-oxygen radial distribution function, g{sub OO}(r), that are now in quantitative agreement with the best available experimental data. This level of agreement between simulation and experiment demonstrated herein originates from an increase in the relative population of water molecules in the interstitial region between the first and second coordination shells, a collective reorganization in the liquid phase which is facilitated by a weakening of the hydrogen bond strength by the use of a hybrid XC functional, coupled with a relative stabilization of the resultant disordered liquid water configurations by the inclusion of non-local vdW/dispersion interactions. This increasingly more accurate description of the underlying hydrogen bond network in liquid water also yields higher-order correlation functions, such as the oxygen-oxygen-oxygen triplet angular distribution, P{sub OOO}(θ), and therefore the degree of local tetrahedrality, as well as electrostatic properties, such as the effective molecular dipole moment, that are in much better agreement with experiment.
Ashcraft, Robert W; Raman, Sumathy; Green, William H
2007-10-18
Ab initio molecular orbital calculations were performed and thermochemical parameters estimated for 46 species involved in the oxidation of hydroxylamine in aqueous nitric acid solution. Solution-phase properties were estimated using the several levels of theory in Gaussian03 and using COSMOtherm. The use of computational chemistry calculations for the estimation of physical properties and constants in solution is addressed. The connection between the pseudochemical potential of Ben-Naim and the traditional standard state-based thermochemistry is shown, and the connection of these ideas to computational chemistry results is established. This theoretical framework provides a basis for the practical use of the solution-phase computational chemistry estimates for real systems, without the implicit assumptions that often hide the nuances of solution-phase thermochemistry. The effect of nonidealities and a method to account for them is also discussed. A method is presented for estimating the solvation enthalpy and entropy for dilute aqueous solutions based on the solvation free energy from the ab initio calculations. The accuracy of the estimated thermochemical parameters was determined through comparison with (i) enthalpies of formation in the gas phase and in solution, (ii) Henry's law data for aqueous solutions, and (iii) various reaction equilibria in aqueous solution. Typical mean absolute deviations (MAD) for the solvation free energy in room-temperature water appear to be ~1.5 kcal/mol for most methods investigated. The MAD for computed enthalpies of formation in solution was 1.5-3 kcal/mol, depending on the methodology employed and the type of species (ion, radical, closed-shell) being computed. This work provides a relatively simple and unambiguous approach that can be used to estimate the thermochemical parameters needed to build detailed ab initio kinetic models of systems in aqueous solution. Technical challenges that limit the accuracy of the estimates are
Messina, Luca; Castin, Nicolas; Domain, Christophe; Olsson, Pär
2017-02-01
The quality of kinetic Monte Carlo (KMC) simulations of microstructure evolution in alloys relies on the parametrization of point-defect migration rates, which are complex functions of the local chemical composition and can be calculated accurately with ab initio methods. However, constructing reliable models that ensure the best possible transfer of physical information from ab initio to KMC is a challenging task. This work presents an innovative approach, where the transition rates are predicted by artificial neural networks trained on a database of 2000 migration barriers, obtained with density functional theory (DFT) in place of interatomic potentials. The method is tested on copper precipitation in thermally aged iron alloys, by means of a hybrid atomistic-object KMC model. For the object part of the model, the stability and mobility properties of copper-vacancy clusters are analyzed by means of independent atomistic KMC simulations, driven by the same neural networks. The cluster diffusion coefficients and mean free paths are found to increase with size, confirming the dominant role of coarsening of medium- and large-sized clusters in the precipitation kinetics. The evolution under thermal aging is in better agreement with experiments with respect to a previous interatomic-potential model, especially concerning the experiment time scales. However, the model underestimates the solubility of copper in iron due to the excessively high solution energy predicted by the chosen DFT method. Nevertheless, this work proves the capability of neural networks to transfer complex ab initio physical properties to higher-scale models, and facilitates the extension to systems with increasing chemical complexity, setting the ground for reliable microstructure evolution simulations in a wide range of alloys and applications.
Majumder, Moumita; Dawes, Richard; Wang, Xiao-Gang; Carrington, Tucker; Li, Jun; Guo, Hua; Manzhos, Sergei
2014-06-01
New potential energy surfaces for methane were constructed, represented as analytic fits to about 100,000 individual high-level ab initio data. Explicitly-correlated multireference data (MRCI-F12(AE)/CVQZ-F12) were computed using Molpro [1] and fit using multiple strategies. Fits with small to negligible errors were obtained using adaptations of the permutation-invariant-polynomials (PIP) approach [2,3] based on neural-networks (PIP-NN) [4,5] and the interpolative moving least squares (IMLS) fitting method [6] (PIP-IMLS). The PESs were used in full-dimensional vibrational calculations with an exact kinetic energy operator by representing the Hamiltonian in a basis of products of contracted bend and stretch functions and using a symmetry adapted Lanczos method to obtain eigenvalues and eigenvectors. Very close agreement with experiment was produced from the purely ab initio PESs. References 1- H.-J. Werner, P. J. Knowles, G. Knizia, 2012.1 ed. 2012, MOLPRO, a package of ab initio programs. see http://www.molpro.net. 2- Z. Xie and J. M. Bowman, J. Chem. Theory Comput 6, 26, 2010. 3- B. J. Braams and J. M. Bowman, Int. Rev. Phys. Chem. 28, 577, 2009. 4- J. Li, B. Jiang and Hua Guo, J. Chem. Phys. 139, 204103 (2013). 5- S Manzhos, X Wang, R Dawes and T Carrington, JPC A 110, 5295 (2006). 6- R. Dawes, X-G Wang, A.W. Jasper and T. Carrington Jr., J. Chem. Phys. 133, 134304 (2010).
Minary, Peter; Martyna, Glenn J.; Tuckerman, Mark E.
2003-02-01
In this paper (Paper I) and a companion paper (Paper II), novel new algorithms and applications of the isokinetic ensemble as generated by Gauss' principle of least constraint, pioneered for use with molecular dynamics 20 years ago, are presented for biophysical, path integral, and Car-Parrinello based ab initio molecular dynamics. In Paper I, a new "extended system" version of the isokinetic equations of motion that overcomes the ergodicity problems inherent in the standard approach, is developed using a new theory of non-Hamiltonian phase space analysis [M. E. Tuckerman et al., Europhys. Lett. 45, 149 (1999); J. Chem. Phys. 115, 1678 (2001)]. Reversible multiple time step integrations schemes for the isokinetic methods, first presented by Zhang [J. Chem. Phys. 106, 6102 (1997)] are reviewed. Next, holonomic constraints are incorporated into the isokinetic methodology for use in fast efficient biomolecular simulation studies. Model and realistic examples are presented in order to evaluate, critically, the performance of the new isokinetic molecular dynamic schemes. Comparisons are made to the, now standard, canonical dynamics method, Nosé-Hoover chain dynamics [G. J. Martyna et al., J. Chem. Phys. 97, 2635 (1992)]. The new isokinetic techniques are found to yield more efficient sampling than the Nosé-Hoover chain method in both path integral molecular dynamics and biophysical molecular dynamics calculations. In Paper II, the use of isokinetic methods in Car-Parrinello based ab initio molecular dynamics calculations is presented.
Energy Technology Data Exchange (ETDEWEB)
Razee, S.S.A.; Staunton, J.B. [Department of Physics, University of Warwick, Coventry (United Kingdom); Ginatempo, B.; Bruno, E. [Dipartimento di Fisica and Unita INFM, Universita di Messina, Messina (Italy); Pinski, F.J. [Department of Physics, University of Cincinnati, OH (United States)
2001-09-24
A theory is presented for describing the effects of annealing magnetic alloys in magnetic fields. It has an ab initio spin-polarized relativistic Korringa-Kohn-Rostoker coherent potential approximation (KKR-CPA) electronic structure basis and uses the framework of concentration waves. Alloys which would otherwise be soft magnets are found experimentally to develop directional chemical order and significant uniaxial anisotropy when annealed in magnetic fields. Our approach is able to provide a quantitative description of these effects together with the underlying electronic mechanisms. We describe applications to the soft magnetic alloys permalloy and FeCo. (author)