Kühne, Thomas D
2012-01-01
Computer simulations and molecular dynamics in particular, is a very powerful method to provide detailed and essentially exact informations of classical many-body problems. With the advent of \\textit{ab-initio} molecular dynamics, where the forces are computed on-the-fly by accurate electronic structure calculations, the scope of either method has been greatly extended. This new approach, which unifies Newton's and Schr\\"odinger's equations, allows for complex simulations without relying on any adjustable parameter. This review is intended to outline the basic principles as well as a survey of the field. Beginning with the derivation of Born-Oppenheimer molecular dynamics, the Car-Parrinello method as well as novel hybrid scheme that unifies best of either approach are discussed. The predictive power is demonstrated by a series of applications ranging from insulators to semiconductors and even metals in condensed phases.
Ab initio mass tensor molecular dynamics
Tsuchida, Eiji
2010-01-01
Mass tensor molecular dynamics was first introduced by Bennett [J. Comput. Phys. 19, 267 (1975)] for efficient sampling of phase space through the use of generalized atomic masses. Here, we show how to apply this method to ab initio molecular dynamics simulations with minimal computational overhead. Test calculations on liquid water show a threefold reduction in computational effort without making the fixed geometry approximation. We also present a simple recipe for estimating the optimal ato...
Ab Initio Molecular Dynamics: A Virtual Laboratory
Hobbi Mobarhan, Milad
2014-01-01
In this thesis, we perform ab initio molecular dynamics (MD) simulations at the Hartree-Fock level, where the forces are computed on-the-fly using the Born-Oppenheimer approximation. The theory behind the Hartree-Fock method is discussed in detail and an implementation of this method based on Gaussian basis functions is explained. We also demonstrate how to calculate the analytic energy derivatives needed for obtaining the forces acting on the nuclei. Hartree-Fock calculations on the ground s...
Young Modulus of Crystalline Polyethylene from ab Initio Molecular Dynamics
Hageman, J.C.L.; Meier, Robert J.; M. Heinemann; de Groot, R. A.
1997-01-01
The Young modulus for crystalline polyethylene is calculated using ab initio molecular dynamics based on density functional theory in the local density approximation (DFT-LDA). This modulus, which can be seen as the ultimate value for the Young modulus of polyethylene fibers, is found to be 334 GPa. For the first time the modulus is evaluated ab initio (no bias from experimental data) with demonstrated basis set convergence.
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
Young Modulus of Crystalline Polyethylene from ab Initio Molecular Dynamics
Hageman, J.C.L.; Meier, Robert J.; Heinemann, M.; Groot, R.A. de
1997-01-01
The Young modulus for crystalline polyethylene is calculated using ab initio molecular dynamics based on density functional theory in the local density approximation (DFT-LDA). This modulus, which can be seen as the ultimate value for the Young modulus of polyethylene fibers, is found to be 334 GPa.
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.
GAUSSIAN 76: an ab initio molecular orbital program
Energy Technology Data Exchange (ETDEWEB)
Binkley, J. S.; Whiteside, R.; Hariharan, P. C.; Seeger, R.; Hehre, W. J.; Lathan, W. A.; Newton, M. D.; Ditchfield, R.; Pople, J. A.
1978-06-01
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.
Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics
Makhov, Dmitry V.; Glover, William J.; Martinez, Todd J.; Shalashilin, Dmitrii V.
2014-08-01
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.
Accelerating ab initio molecular dynamics simulations by linear prediction methods
Herr, Jonathan D.; Steele, Ryan P.
2016-09-01
Acceleration of ab initio molecular dynamics (AIMD) simulations can be reliably achieved by extrapolation of electronic data from previous timesteps. Existing techniques utilize polynomial least-squares regression to fit previous steps' Fock or density matrix elements. In this work, the recursive Burg 'linear prediction' technique is shown to be a viable alternative to polynomial regression, and the extrapolation-predicted Fock matrix elements were three orders of magnitude closer to converged elements. Accelerations of 1.8-3.4× were observed in test systems, and in all cases, linear prediction outperformed polynomial extrapolation. Importantly, these accelerations were achieved without reducing the MD integration timestep.
Molecular ion LiHe+: ab initio study
International Nuclear Information System (INIS)
Highlights: ► Excited electronic states of LiHe+ are studied. ► Potential energy curves of thirteen states are calculated. ► Dipole moment and transition dipole moment functions are determined. ► Basic spectroscopic properties of the electronic states are derived. - Abstract: High level ab initio calculations are performed on the molecular ion LiHe+. Potential energy curves for the low-lying singlet and triplet electronic states are calculated using the multi-reference configuration interaction and single-reference coupled cluster methods with large basis sets. The corresponding dipole moments and transition dipole moments functions are also determined. The basic spectroscopic properties and excitation energies of the electronic states are derived from rovibrational bound state calculations.
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
2016-04-28
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. PMID:27131525
An Efficient Time-Stepping Scheme for Ab Initio Molecular Dynamics Simulations
Tsuchida, Eiji
2016-08-01
In ab initio molecular dynamics simulations of real-world problems, the simple Verlet method is still widely used for integrating the equations of motion, while more efficient algorithms are routinely used in classical molecular dynamics. We show that if the Verlet method is used in conjunction with pre- and postprocessing, the accuracy of the time integration is significantly improved with only a small computational overhead. We also propose several extensions of the algorithm required for use in ab initio molecular dynamics. The validity of the processed Verlet method is demonstrated in several examples including ab initio molecular dynamics simulations of liquid water. The structural properties obtained from the processed Verlet method are found to be sufficiently accurate even for large time steps close to the stability limit. This approach results in a 2× performance gain over the standard Verlet method for a given accuracy. We also show how to generate a canonical ensemble within this approach.
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.
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.
New approaches for molecular conformer force field analysis in combination with ab initio results
Kuramshina, G. M.; Pentin, Yu. A.; Yagola, A. G.
1999-10-01
Ab initio and DFT results on harmonic force constants for trans- and gauche-conformers of CH 3CH 2CH 2Cl, CF 3CH 2CH 2Cl and CCl 3CH 2CH 2Cl are used for formulating constraints in molecular force field models described compounds with hindered internal rotation around the C-C bond.
Stabilization of Ab Initio Molecular Dynamics Simulations at Large Time Steps
Tsuchida, Eiji
2014-01-01
The Verlet method is still widely used to integrate the equations of motion in ab initio molecular dynamics simulations. We show that the stability limit of the Verlet method may be significantly increased by setting an upper limit on the kinetic energy of each atom with only a small loss in accuracy. The validity of this approach is demonstrated for molten lithium fluoride.
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.
Timko, Jeff; Kuyucak, Serdar
2012-11-01
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.
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.
Pierce, Levi C. T.; Markwick, Phineus R. L.; McCammon, J. Andrew; Doltsinis, Nikos L.
2011-01-01
A biased potential molecular dynamics simulation approach, accelerated molecular dynamics (AMD), has been implemented in the framework of ab initio molecular dynamics for the study of chemical reactions. Using two examples, the double proton transfer reaction in formic acid dimer and the hypothetical adiabatic ring opening and subsequent rearrangement reactions in methylenecyclopropane, it is demonstrated that ab initio AMD can be readily employed to efficiently explore the reactive potential energy surface, allowing the prediction of chemical reactions and the identification of metastable states. An adaptive variant of the AMD method is developed, which additionally affords an accurate representation of both the free-energy surface and the mechanism associated with the chemical reaction of interest and can also provide an estimate of the reaction rate. PMID:21548673
An efficient time-stepping scheme for ab initio molecular dynamics simulations
Tsuchida, Eiji
2015-01-01
In ab initio molecular dynamics simulations of real-world problems, the simple Verlet method is still widely used for integrating the equations of motion, while more efficient algorithms are routinely used in classical molecular dynamics. We show that if the Verlet method is used in conjunction with pre- and postprocessing, the accuracy of the time integration is significantly improved with only a small computational overhead. The validity of the processed Verlet method is demonstrated in several examples including ab initio molecular dynamics simulations of liquid water. The structural properties obtained from the processed Verlet method are found to be sufficiently accurate even for large time steps close to the stability limit. This approach results in a 2x performance gain over the standard Verlet method for a given accuracy.
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.
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 simulations on specific interactions between amyloid beta and monosaccharides
Nomura, Kazuya; Okamoto, Akisumi; Yano, Atsushi; Higai, Shin'ichi; Kondo, Takashi; Kamba, Seiji; Kurita, Noriyuki
2012-09-01
Aggregation of amyloid β (Aβ) peptides, which is a key pathogenetic event in Alzheimer's disease, can be caused by cell-surface saccharides. We here investigated stable structures of the solvated complexes of Aβ with some types of monosaccharides using molecular simulations based on protein-ligand docking and classical molecular mechanics methods. Moreover, the specific interactions between Aβ and the monosaccharides were elucidated at an electronic level by ab initio fragment molecular orbital calculations. Based on the results, we proposed which type of monosaccharide prefers to have large binding affinity to Aβ and inhibit the Aβ aggregation.
Electronic properties of liquid Hg-In alloys : Ab-initio molecular dynamics study
Sharma, Nalini; Thakur, Anil; Ahluwalia, P. K.
2016-05-01
Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Three liquid Hg-In alloys (Hg10In90, Hg30In70,. Hg50In50, Hg70In30, and Hg90Pb10) at 299 K are considered. The calculated results for liquid Hg (l-Hg) and lead (l-In) are also drawn. Along with the calculated results of considered five liquid alloys of Hg-In alloy. The results obtained from electronic properties namely total density of state and partial density of states help to find the local arrangement of Hg and In atoms and the presence of liquid state in the considered five alloys.
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.
Study of atomic structure of liquid Hg-In alloys using ab-initio molecular dynamics
International Nuclear Information System (INIS)
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 (Hg10In90, Hg30In70, Hg50In50, Hg70In30 and Hg90In10) 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
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.
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 simulations of reactions occurring in molecular crystals
Kochman, Michal
2014-01-01
Although the solid state may not usually be thought of as an environment suitable for chemical reactions under mild conditions, a growing number of organic compounds are known to undergo interesting and, in many cases, practically useful chemistry in the molecular crystal phase. Of particular interest are photochemical reactions occurring in molecular crystals, which possess a number of characteristic features that make them attractive to study using the methods of theoretical chemistry. Firs...
Molecular Dipole Moment Computed with Ab Initio MKS Charges
Institute of Scientific and Technical Information of China (English)
无
2002-01-01
Molecular dipole moments computed at the levels of HF/STO-3G, HF/6-31G(d, p), HF/6-311+G(2d, 2p), MP2/6-31G(d, p) and MP2/6-311+G(2d, 2p) have been investigated. HF/6-311+G(2d, 2p) was found to be the relatively good choice to compute MKS charges for reproducing the experimental values of molecular dipole moments. Root mean square deviation of computed dipole moments for 21 small polar molecules is about 0.1969 D.
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.
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)
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...
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...
DEFF Research Database (Denmark)
Bork, Nicolai Christian; Du, Lin; Reiman, Heidi;
2014-01-01
Gibbs free binding energies in molecular complexes and clusters based on gas phase FTIR spectroscopy. The acetonitrile-HCl molecular complex is identified via its redshifted H-Cl stretching vibrational mode. We determine the Gibbs free binding energy, ΔG°295 K, to between 4.8 and 7.9 kJ mol(-1) and......Models of formation and growth of atmospheric aerosols are highly dependent on accurate cluster binding energies. These are most often calculated by ab initio electronic structure methods but remain associated with significant uncertainties. We present a computational benchmarking study of the...
Ab initio molecular orbital calculations on ion pair-water complexes of metal halides and oxides
Mohandas, P; Singh, S.; Chandrasekhar, J
1994-01-01
Ab initio MO calculations are performed on a series of ion-molecular and ion pair-molecular complexes of H2O + MX (MX = LiF, LiCl, NaCl, BeO and MgO) systems. BSSE-corrected stabilization energies, optimized geometrical parameters, internal force constants and harmonic vibrational frequencies have been evaluated for all the structures of interest. The trends observed in the geometrical parameters and other properties calculated for the mono-hydrated contact ion pair complexes parallel those c...
An ab initio molecular dynamics study of the roaming mechanism of the H2+HOC+ reaction
Yu, Hua-Gen
2011-08-01
We report here a direct ab initio molecular dynamics study of the p-/o-H2+HOC+ reaction on the basis of the accurate SAC-MP2 potential energy surface. The quasi-classical trajectory method was employed. This work largely focuses on the study of reaction mechanisms. A roaming mechanism was identified for this molecular ion-molecule reaction. The driving forces behind the roaming mechanism were thoroughly investigated by using a trajectory dynamics approach. In addition, the thermal rate coefficients of the H2+HOC+ reaction were calculated in the temperature range [25, 300] K and are in good agreement with experiments.
Ab initio based force field and molecular dynamics simulations of crystalline TATB.
Gee, Richard H; Roszak, Szczepan; Balasubramanian, Krishnan; Fried, Laurence E
2004-04-15
An all-atom force field for 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) is presented. The classical intermolecular interaction potential for TATB is based on single-point energies determined from high-level ab initio calculations of TATB dimers. The newly developed potential function is used to examine bulk crystalline TATB via molecular dynamics simulations. The isobaric thermal expansion and isothermal compression under hydrostatic pressures obtained from the molecular dynamics simulations are in good agreement with experiment. The calculated volume-temperature expansion is almost one dimensional along the c crystallographic axis, whereas under compression, all three unit cell axes participate, albeit unequally. PMID:15267608
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.
Quantum chemistry the development of ab initio methods in molecular electronic structure theory
Schaefer III, Henry F
2004-01-01
This guide is guaranteed to prove of keen interest to the broad spectrum of experimental chemists who use electronic structure theory to assist in the interpretation of their laboratory findings. A list of 150 landmark papers in ab initio molecular electronic structure methods, it features the first page of each paper (which usually encompasses the abstract and introduction). Its primary focus is methodology, rather than the examination of particular chemical problems, and the selected papers either present new and important methods or illustrate the effectiveness of existing methods in predi
Ishimura, Hiromi; Kadoya, Ryushi; Suzuki, Tomoya; Murakawa, Takeru; Shulga, Sergiy; Kurita, Noriyuki
2015-07-01
Alzheimer's disease is caused by accumulation of amyloid-β (Aβ) peptides in a brain. To suppress the production of Aβ peptides, it is effective to inhibit the cleavage of amyloid precursor protein (APP) by secretases. However, because the secretases also play important roles to produce vital proteins for human body, inhibitors for the secretases may have side effects. To propose new agents for protecting the cleavage site of APP from the attacking of the γ-secretase, we have investigated here the specific interactions between a short APP peptide and curcumin derivatives, using protein-ligand docking as well as ab initio molecular simulations.
Energy Technology Data Exchange (ETDEWEB)
Kimberg, Victor, E-mail: victor.kimberg@pks.mpi.de [Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Straße 38, 01187 Dresden (Germany); Miron, Catalin, E-mail: miron@synchrotron-soleil.fr [Synchrotron SOLEIL, l’Orme des Merisiers, Saint-Aubin, BP 48, FR-91192 Gif-sur-Yvette Cedex (France)
2014-08-15
Highlights: • Some studies related to the vibrational wave functions mapping phenomenon are reviewed. • The core-excited vibrational wave functions were mapped using dissociative and bound final states. • High-resolution experimental data is accompanied by ab initio calculations. • The mapping phenomenon allows one to extract constants of the molecular potentials. • The mapping techniques are general and can be applied for the study of many systems. - Abstract: The recent development of high brightness 3{sup rd} generation soft X-ray sources and high energy resolution electron spectrometers made it possible to accurately trace quantum phenomena associated to the vibrational dynamics in core-excited molecules. The present paper reviews the recent results on mapping of vibrational wave functions and molecular potentials based on electron spectroscopy. We discuss and compare the mapping phenomena in various systems, stressing the advantages of the resonant X-ray scattering for studying of the nuclear dynamics and spectroscopic constants of small molecules. The experimental results discussed in the paper are most often accompanied by state-of-the-art ab initio calculations allowing for a deeper understanding of the quantum effects. Besides its fundamental interest, the vibrational wave function mapping is shown to be useful for the analysis of core- and valence-excited molecular states based on the reflection principle.
Tunneling of electrons via rotor-stator molecular interfaces: combined ab initio and model study
Petreska, Irina; Pejov, Ljupco; Kocarev, Ljupco
2015-01-01
Tunneling of electrons through rotor-stator anthracene aldehyde molecular interfaces is studied with a combined ab initio and model approach. Molecular electronic structure calculated from first principles is utilized to model different shapes of tunneling barriers. Together with a rectangular barrier, we also consider a sinusoidal shape that captures the effects of the molecular internal structure more realistically. Quasiclassical approach with the Simmons' formula for current density is implemented. Special attention is paid on conformational dependence of the tunneling current. Our results confirm that the presence of the side aldehyde group enhances the interesting electronic properties of the pure anthracene molecule, making it a bistable system with geometry dependent transport properties. We also investigate the transition voltage and we show that confirmation dependent field emission could be observed in these molecular interfaces at realistically low voltages. The present study accompanies our previ...
Embedding parameters in ab initio theory to develop approximations based on molecular similarity
Tanha, Matteus; Kaul, Shiva; Cappiello, Alexander; Gordon, Geoffrey J; Yaron, David J
2015-01-01
A means to take advantage of molecular similarity to lower the computational cost of electronic structure theory is explored, in which parameters are embedded into a low-cost, low-level (LL) ab initio model and adjusted to obtain agreement with results from a higher-level (HL) ab initio model. A parametrized LL (pLL) model is created by multiplying selected matrix elements of the Hamiltonian operators by scaling factors that depend on element types. Various schemes for applying the scaling factors are compared, along with the impact of making the scaling factors linear functions of variables related to bond lengths, atomic charges, and bond orders. The models are trained on ethane and ethylene, substituted with -NH2, -OH and -F, and tested on substituted propane, propylene and t-butane. Training and test datasets are created by distorting the molecular geometries and applying uniform electric fields. The fitted properties include changes in total energy arising from geometric distortions or applied fields, an...
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.
A set of molecular models based on quantum mechanical ab initio calculations and thermodynamic data
Eckl, Bernhard; Hasse, Hans
2009-01-01
A parameterization strategy for molecular models on the basis of force fields is proposed, which allows a rapid development of models for small molecules by using results from quantum mechanical (QM) ab initio calculations and thermodynamic data. The geometry of the molecular models is specified according to the atom positions determined by QM energy minimization. The electrostatic interactions are modeled by reducing the electron density distribution to point dipoles and point quadrupoles located in the center of mass of the molecules. Dispersive and repulsive interactions are described by Lennard-Jones sites, for which the parameters are iteratively optimized to experimental vapor-liquid equilibrium (VLE) data, i.e. vapor pressure, saturated liquid density, and enthalpy of vaporization of the considered substance. The proposed modeling strategy was applied to a sample set of ten molecules from different substance classes. New molecular models are presented for iso-butane, cyclohexane, formaldehyde, dimethyl...
Design of two-photon molecular tandem architectures for solar cells by ab initio theory
DEFF Research Database (Denmark)
Ørnsø, Kristian Baruël; García Lastra, Juan Maria; De La Torre, Gema;
2015-01-01
An extensive database of spectroscopic properties of molecules from ab initio calculations is used to design molecular complexes for use in tandem solar cells that convert two photons into a single electron–hole pair, thereby increasing the output voltage while covering a wider spectral range...... of the structural and energetic properties of several thousand porphyrin dyes. The third design is a molecular analogy of the intermediate band solar cell, and involves a single dye molecule with strong intersystem crossing to ensure a long lifetime of the intermediate state. Based on the calculated energy levels...... and molecular orbitals, energy diagrams are presented for the individual steps in the operation of such tandem solar cells. We find that theoretical open circuit voltages of up to 1.8 V can be achieved using these tandem designs. Questions about the practical implementation of prototypical devices...
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.
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
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.
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...
Lattice thermal conductivity of UO2 using ab-initio and classical molecular dynamics
International Nuclear Information System (INIS)
We applied the non-equilibrium ab-initio molecular dynamics and predict the lattice thermal conductivity of the pristine uranium dioxide for up to 2000 K. We also use the equilibrium classical molecular dynamics and heat-current autocorrelation decay theory to decompose the lattice thermal conductivity into acoustic and optical components. The predicted optical phonon transport is temperature independent and small, while the acoustic component follows the Slack relation and is in good agreement with the limited single-crystal experimental results. Considering the phonon grain-boundary and pore scatterings, the effective lattice thermal conductivity is reduced, and we show it is in general agreement with the sintered-powder experimental results. The charge and photon thermal conductivities are also addressed, and we find small roles for electron, surface polaron, and photon in the defect-free structures and for temperatures below 1500 K
Casolo, S; Tantardini, G F; Martinazzo, R
2016-07-14
We studied Eley-Rideal molecular hydrogen formation on graphite using ab initio molecular dynamics, in the energy range relevant for the chemistry of the interstellar medium and for terrestrial experiments employing cold plasma (0.02-1 eV). We found substantial projectile steering effects that prevent dimer formation at low energies, thereby ruling out any catalytic synthetic pathways that form hydrogen molecules. Ortho and para dimers do form efficiently thanks to preferential sticking, but only at energies that are too high to be relevant for the chemistry of the interstellar medium. Computed reaction cross sections and ro-vibrational product populations are in good agreement with available experimental data and capable of generating adsorbate configurations similar to those observed with scanning tunneling microscopy techniques. PMID:26905385
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.
Steinmann, Casper; Jensen, Jan H
2012-01-01
We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path of chorismate mutase in less than four days using 80 cores on 20 nodes, where the whole system containing 2398 atoms is treated in the ab initio fashion without using any force fields. The reaction path is constructed automatically with the only assumption of defining the reaction coordinate a priori. We determine the reaction barrier of chorismate mutase to be $18.3\\pm 3.6$ kcal mol$^{-1}$ using ONIOM with MP2/cc-pVDZ and EFMO/6-31G(d) for the high and low layers, respectively.
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.
International Nuclear Information System (INIS)
The atomistic mechanism of dissociative adsorption of ethylene molecules on a Ni cluster is investigated by ab initio molecular-dynamics simulations. The activation free energy to dehydrogenate an ethylene molecule on the Ni cluster and the corresponding reaction rate is estimated. A remarkable finding is that the adsorption energy of ethylene molecules on the Ni cluster is considerably larger than the activation free energy, which explains why the actual reaction rate is faster than the value estimated based on only the activation free energy. It is also found from the dynamic simulations that hydrogen molecules and an ethane molecule are formed from the dissociated hydrogen atoms, whereas some exist as single atoms on the surface or in the interior of the Ni cluster. On the other hand, the dissociation of the C-C bonds of ethylene molecules is not observed. On the basis of these simulation results, the nature of the initial stage of carbon nanotube growth is discussed. (paper)
Chaban, Vitaly V; Prezhdo, Oleg V
2016-07-01
The Haber-Bosch process is the main industrial method for producing ammonia from diatomic nitrogen and hydrogen. We use a combination of ab initio thermochemical analysis and reactive molecular dynamics to demonstrate that a significant increase in the ammonia production yield can be achieved using hydroxylated graphene and related species. Exploiting the polarity difference between N2/H2 and NH3, as well as the universal proton acceptor behavior of NH3, we demonstrate a strong shift of the equilibrium of the Haber-Bosch process toward ammonia (ca. 50 kJ mol(-1) enthalpy gain and ca. 60-70 kJ mol(-1) free energy gain). The modified process is of significant importance to the chemical industry.
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.
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.
Molecular orbital ab initio and density functional theoretical study on reaction between PH2 and NO
Institute of Scientific and Technical Information of China (English)
胡正发; 王振亚; 李海洋; 周士康
2002-01-01
The theoretical study of reaction between PH2 and NO on the ground state potential energy surface is reported by using molecular orbital ab initio calculation and density function theory (DFT). Equilibrium structural parameters, harmonic vibrational frequencies, total energies and zero point energies of all species during reaction are computed by HF, MP2 (full) and B3LYP theory levels with the medium basis set 6-31G*. Theoretical results indicate that intermediate IM1(H2PNO) is firstly formed by overcoming a small energy barrier TS1, and then two four-membered ring transient states TS2 and TS5, with energy barriers 103.3 and 102.6 kJ/mol respectively,then H-migration and isomerization are completed and the products PN and H2O are formed. The reaction is exothermic one with -189.6 k J/mol released.
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.
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.
Ab initio theory for current-induced molecular switching: Melamine on Cu(001)
Ohto, Tatsuhiko
2013-05-28
Melamine on Cu(001) is mechanically unstable under the current of a scanning tunneling microscope tip and can switch among configurations. However, these are not equally accessible, and the switching critical current depends on the bias polarity. In order to explain such rich phenomenology, we have developed a scheme to evaluate the evolution of the reaction paths and activation barriers as a function of bias, which is rooted in the nonequilibrium Green\\'s function method implemented within density functional theory. This, combined with the calculation of the inelastic electron tunneling spectroscopy signal, allows us to identify the vibrational modes promoting the observed molecular conformational changes. Finally, once our ab initio results are used within a resonance model, we are able to explain the details of the switching behavior, such as its dependence on the bias polarity, and the noninteger power relation between the reaction rate constants and both the bias voltage and the electric current. © 2013 American Physical Society.
Sorella, Sandro
2016-01-01
We propose an ab-initio molecular dynamics method, capable to reduce dramatically the autocorrelation time required for the simulation of classical and quantum particles at finite temperature. The method is based on an efficient implementation of a first order Langevin dynamics modified by means of a suitable, position dependent acceleration matrix $S$. Here we apply this technique, within a Quantum Monte Carlo (QMC) based wavefuntion approach and within the Born-Oppheneimer approximation, for determining the phase diagram of high-pressure Hydrogen with simulations much longer than the autocorrelation time. With the proposed method, we are able to equilibrate in few hundreds steps even close to the liquid-liquid phase transition (LLT). Within our approach we find that the LLT transition is consistent with recent density functionals predicting a much larger transition pressures when the long range dispersive forces are taken into account.
Hu, Hao; Yang, Weitao
2008-05-01
Combined quantum mechanics/molecular mechanics (QM/MM) methods provide an accurate and efficient energetic description of complex chemical and biological systems, leading to significant advances in the understanding of chemical reactions in solution and in enzymes. Here we review progress in QM/MM methodology and applications, focusing on ab initio QM-based approaches. Ab initio QM/MM methods capitalize on the accuracy and reliability of the associated quantum-mechanical approaches, however, at a much higher computational cost compared with semiempirical quantum-mechanical approaches. Thus reaction-path and activation free-energy calculations based on ab initio QM/MM methods encounter unique challenges in simulation timescales and phase-space sampling. This review features recent developments overcoming these challenges and enabling accurate free-energy determination for reaction processes in solution and in enzymes, along with applications.
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
Giovannetti, Gianluca; Brocks, Geert; Brink, van den Jeroen
2008-01-01
We investigate the effect that potassium intercalation has on the electronic structure of copper phthalocyanine (CuPc) molecular crystals by means of ab initio density functional calculations. Pristine CuPc (in its alpha and beta structures) is found to be an insulator containing local magnetic mome
Tunneling of electrons via rotor-stator molecular interfaces: Combined ab initio and model study
Petreska, Irina; Ohanesjan, Vladimir; Pejov, Ljupčo; Kocarev, Ljupčo
2016-07-01
Tunneling of electrons through rotor-stator anthracene aldehyde molecular interfaces is studied with a combined ab initio and model approach. Molecular electronic structure calculated from first principles is utilized to model different shapes of tunneling barriers. Together with a rectangular barrier, we also consider a sinusoidal shape that captures the effects of the molecular internal structure more realistically. Quasiclassical approach with the Simmons' formula for current density is implemented. Special attention is paid on conformational dependence of the tunneling current. Our results confirm that the presence of the side aldehyde group enhances the interesting electronic properties of the pure anthracene molecule, making it a bistable system with geometry dependent transport properties. We also investigate the transition voltage and we show that conformation-dependent field emission could be observed in these molecular interfaces at realistically low voltages. The present study accompanies our previous work where we investigated the coherent transport via strongly coupled delocalized orbital by application of Non-equilibrium Green's Function Formalism.
Marsalek, Ondrej; Markland, Thomas E
2016-02-01
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 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. PMID:26851913
International Nuclear Information System (INIS)
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
Energy Technology Data Exchange (ETDEWEB)
Marsalek, Ondrej; Markland, Thomas E., E-mail: tmarkland@stanford.edu [Department of Chemistry, Stanford University, Stanford, California 94305 (United States)
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
ab initio Studies on Molecular Conductor (BEDSe-TTF)2[Fe(CN)5NO
Institute of Scientific and Technical Information of China (English)
YAO Kai-Lun; TU Hai-Bo; WANG Wei-Zhong
2001-01-01
In this paper the ab initio study using pseudopotential plane wave method with the local spin density functional approximation is presented for the molecular conductor (BEDSe-TTF)2[Fe(CN)5NO]. The mean electronic density distributions are obtained, and we find that the extended π orbital of the selenium does not affect the properties of material as assumed in other papers and the "side-by-side" type S...S interaction is the primary interaction between donors. From band structure calculations we analyze the influence of the NO groups on the electronic structure and magnetic properties of molecule. It is shown that the itinerant electrons important to electronic properties in these types of hybrids are delocalized electrons contributed by NO groups, instead of by the 3d electrons of Fe. Additionally, we have found that the localized magnetic moment is also contributed by the NO groups in this molecular conductor. From total energy calculations the molecular structure with the lowest energy is found due to the interaction between split spins, and the particular positions of the NO groups are obtained.
An ab initio molecular dynamics analysis of lignin as a potential antioxidant for hydrocarbons.
Pan, Tongyan; Cheng, Cheng
2015-11-01
Lignins are complex phenolic polymers with limited industrial uses. To identify new applications of lignins, this study aims to evaluate the conifer alcohol lignin as a potential antioxidant for hydrocarbons, using the petroleum asphalt as an example. Using the ab initio molecular dynamics (AIMD) method, the evaluation is accomplished by tracking the generation of critical species in a lignin-asphalt mixture under a simulated oxidative condition. The generation of new species was detected using nuclear magnetic resonance and four analytical methods including density of states analysis, highest occupied molecular orbital and lowest unoccupied molecular orbital analyses, bonding and energy level analysis, and electrostatic potential energy analysis. Results of the analyses show that the chemical radicals of carbon, nitrogen and sulfur generated in the oxidation process could enhance the agglomeration and/or decomposition tendency of asphalt. The effectiveness of lignins as an antioxidant depends on their chemical compositions. Lignins with a HOMO-LUMO gap larger than the HOMO-LUMO gap of the hydrocarbon system to be protected, such as the conifer alcohol lignin to protect petroleum asphalt as was studied in this work, do not demonstrate beneficial anti-oxidation capacity. Lignins, however, may be effective oxidants for hydrocarbon systems with a larger HOMO-LUMO gap. In addition, lignins may contain more polar sites than the hydrocarbons to be protected; thus the lignins' hydrophobicity and compatibility with the host hydrocarbons need to be well evaluated. The developed AIMD model provides a useful tool for developing antioxidants for generic hydrocarbons. PMID:26562413
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
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.
Born-Oppenheimer Ab Initio QM/MM Molecular Dynamics Simulations of Enzyme Reactions.
Zhou, Y; Wang, S; Li, Y; Zhang, Y
2016-01-01
There are two key requirements for reliably simulating enzyme reactions: one is a reasonably accurate potential energy surface to describe the bond-forming/breaking process as well as to adequately model the heterogeneous enzyme environment; the other is to perform extensive sampling since an enzyme system consists of at least thousands of atoms and its energy landscape is very complex. One attractive approach to meet both daunting tasks is Born-Oppenheimer ab initio QM/MM molecular dynamics (aiQM/MM-MD) simulation with umbrella sampling. In this chapter, we describe our recently developed pseudobond Q-Chem-Amber interface, which employs a combined electrostatic-mechanical embedding scheme with periodic boundary condition and the particle mesh Ewald method for long-range electrostatics interactions. In our implementation, Q-Chem and the sander module of Amber are combined at the source code level without using system calls, and all necessary data communications between QM and MM calculations are achieved via computer memory. We demonstrate the applicability of this pseudobond Q-Chem-Amber interface by presenting two examples, one reaction in aqueous solution and one enzyme reaction. Finally, we describe our established aiQM/MM-MD enzyme simulation protocol, which has been successfully applied to study more than a dozen enzymes. PMID:27498636
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).
Direct molecular simulation of nitrogen dissociation based on an ab initio potential energy surface
Energy Technology Data Exchange (ETDEWEB)
Valentini, Paolo, E-mail: vale0142@umn.edu; Schwartzentruber, Thomas E., E-mail: schwart@aem.umn.edu; Bender, Jason D., E-mail: jbender73@gmail.com; Nompelis, Ioannis, E-mail: nompelis@umn.edu; Candler, Graham V., E-mail: candler@umn.edu [Department of Aerospace Engineering and Mechanics, College of Science and Engineering, University of Minnesota, Minneapolis, Minnesota 55455 (United States)
2015-08-15
The direct molecular simulation (DMS) approach is used to predict the internal energy relaxation and dissociation dynamics of high-temperature nitrogen. An ab initio potential energy surface (PES) is used to calculate the dynamics of two interacting nitrogen molecules by providing forces between the four atoms. In the near-equilibrium limit, it is shown that DMS reproduces the results obtained from well-established quasiclassical trajectory (QCT) analysis, verifying the validity of the approach. DMS is used to predict the vibrational relaxation time constant for N{sub 2}–N{sub 2} collisions and its temperature dependence, which are in close agreement with existing experiments and theory. Using both QCT and DMS with the same PES, we find that dissociation significantly depletes the upper vibrational energy levels. As a result, across a wide temperature range, the dissociation rate is found to be approximately 4–5 times lower compared to the rates computed using QCT with Boltzmann energy distributions. DMS calculations predict a quasi-steady-state distribution of rotational and vibrational energies in which the rate of depletion of high-energy states due to dissociation is balanced by their rate of repopulation due to collisional processes. The DMS approach simulates the evolution of internal energy distributions and their coupling to dissociation without the need to precompute rates or cross sections for all possible energy transitions. These benchmark results could be used to develop new computational fluid dynamics models for high-enthalpy flow applications.
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.
Ab initio computational studies on molecular conformation of N-methyl-glyphosate
Kaliannan, P.; Naseer Ali, M. Mohamed; Venuvanalingam, P.
Conformational analysis of N-methyl-glyphosate has been carried out using an ab initio molecular orbital (MO) method at the HF/3-21G* levels of theory and the results are compared with the results of a previously studied compound, namely glyphosate. The potential energy surface of the molecule obtained by varying the central torsion angles (Φ, Ψ) was investigated in detail. Fourteen conformers with 5 kcal mol-1 energy cut-off have been selected from the potential energy surface for geometry optimization to locate the true minimum on the conformational space. The minimum has been found to be at (-62°, 110°) for the central torsion angles. This conformation is stabilized by hydrogen bond interactions (O-H···O and C-H···O) and the interactions due to protons nearer to each other. This cationic field leads to the formation of a hydrophobic patch in this structure, as well as in the structures closer to the global minimum. This patch may destabilize the favourable interaction of N-methyl-glyphosate with the surrounding amino acid residues in the binding cavity as they form the cationic field throughout the glyphosate binding region.
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.
Surface electron density models for accurate ab initio molecular dynamics with electronic friction
Novko, D.; Blanco-Rey, M.; Alducin, M.; Juaristi, J. I.
2016-06-01
Ab initio molecular dynamics with electronic friction (AIMDEF) is a valuable methodology to study the interaction of atomic particles with metal surfaces. This method, in which the effect of low-energy electron-hole (e-h) pair excitations is treated within the local density friction approximation (LDFA) [Juaristi et al., Phys. Rev. Lett. 100, 116102 (2008), 10.1103/PhysRevLett.100.116102], can provide an accurate description of both e-h pair and phonon excitations. In practice, its applicability becomes a complicated task in those situations of substantial surface atoms displacements because the LDFA requires the knowledge at each integration step of the bare surface electron density. In this work, we propose three different methods of calculating on-the-fly the electron density of the distorted surface and we discuss their suitability under typical surface distortions. The investigated methods are used in AIMDEF simulations for three illustrative adsorption cases, namely, dissociated H2 on Pd(100), N on Ag(111), and N2 on Fe(110). Our AIMDEF calculations performed with the three approaches highlight the importance of going beyond the frozen surface density to accurately describe the energy released into e-h pair excitations in case of large surface atom displacements.
Ab-initio molecular modeling of interfaces in tantalum-carbon system
International Nuclear Information System (INIS)
Processing of ultrahigh temperature TaC ceramic material with sintering additives of B4C and reinforcement of carbon nanotubes (CNTs) gives rise to possible formation of several interfaces (Ta2C-TaC, TaC-CNT, Ta2C-CNT, TaB2-TaC, and TaB2-CNT) that could influence the resultant properties. Current work focuses on interfaces developed during spark plasma sintering of TaC-system and performing ab initio molecular modeling of the interfaces generated during processing of TaC-B4C and TaC-CNT composites. The energy of the various interfaces has been evaluated and compared with TaC-Ta2C interface. The iso-surface electronic contours are extracted from the calculations eliciting the enhanced stability of TaC-CNT interface by 72.2%. CNTs form stable interfaces with Ta2C and TaB2 phases with a reduction in the energy by 35.8% and 40.4%, respectively. The computed Ta-C-B interfaces are also compared with experimentally observed interfaces in high resolution TEM images.
International Nuclear Information System (INIS)
We have studied the correlation between chemical composition, structure, chemical bonding and elastic properties of amorphous B6O based solids using ab initio molecular dynamics. These solids are of different chemical compositions, but the elasticity data appear to be a function of density. This is in agreement with previous experimental observations. As the density increases from 1.64 to 2.38 g cm-3, the elastic modulus increases from 74 to 253 GPa. This may be understood by analyzing the cohesive energy and the chemical bonding of these compounds. The cohesive energy decreases from -7.051 to -7.584 eV/atom in the elastic modulus range studied. On the basis of the electron density distributions, Mulliken analysis and radial distribution functions, icosahedral bonding is the dominating bonding type. C and N promote cross-linking of icosahedra and thus increase the density, while H hinders the cross-linking by forming OH groups. The presence of icosahedral bonding is independent of the density
Ab-initio molecular modeling of interfaces in tantalum-carbon system
Energy Technology Data Exchange (ETDEWEB)
Balani, Kantesh; Mungole, Tarang [Materials Science and Engineering, Indian Institute of Technology, Kanpur-208016 (India); Bakshi, Srinivasa Rao [Mechanical and Materials Engineering, Florida International University, Miami, Florida 33174 (United States); Metallurgical and Materials Engineering, Indian Institute of Technology Madras, Chennai 600036 (India); Agarwal, Arvind [Mechanical and Materials Engineering, Florida International University, Miami, Florida 33174 (United States)
2012-03-15
Processing of ultrahigh temperature TaC ceramic material with sintering additives of B{sub 4}C and reinforcement of carbon nanotubes (CNTs) gives rise to possible formation of several interfaces (Ta{sub 2}C-TaC, TaC-CNT, Ta{sub 2}C-CNT, TaB{sub 2}-TaC, and TaB{sub 2}-CNT) that could influence the resultant properties. Current work focuses on interfaces developed during spark plasma sintering of TaC-system and performing ab initio molecular modeling of the interfaces generated during processing of TaC-B{sub 4}C and TaC-CNT composites. The energy of the various interfaces has been evaluated and compared with TaC-Ta{sub 2}C interface. The iso-surface electronic contours are extracted from the calculations eliciting the enhanced stability of TaC-CNT interface by 72.2%. CNTs form stable interfaces with Ta{sub 2}C and TaB{sub 2} phases with a reduction in the energy by 35.8% and 40.4%, respectively. The computed Ta-C-B interfaces are also compared with experimentally observed interfaces in high resolution TEM images.
He, Rongxing; Li, Lei; Zhong, Jie; Zhu, Chongqin; Francisco, Joseph S; Zeng, Xiao Cheng
2016-04-26
Solar emission produces copious nitrosonium ions (NO(+)) in the D layer of the ionosphere, 60 to 90 km above the Earth's surface. NO(+) is believed to transfer its charge to water clusters in that region, leading to the formation of gaseous nitrous acid (HONO) and protonated water cluster. The dynamics of this reaction at the ionospheric temperature (200-220 K) and the associated mechanistic details are largely unknown. Using ab initio molecular dynamics (AIMD) simulations and transition-state search, key structures of the water hydrates-tetrahydrate NO(+)(H2O)4 and pentahydrate NO(+)(H2O)5-are identified and shown to be responsible for HONO formation in the ionosphere. The critical tetrahydrate NO(+)(H2O)4 exhibits a chain-like structure through which all of the lowest-energy isomers must go. However, most lowest-energy isomers of pentahydrate NO(+)(H2O)5 can be converted to the HONO-containing product, encountering very low barriers, via a chain-like or a three-armed, star-like structure. Although these structures are not the global minima, at 220 K, most lowest-energy NO(+)(H2O)4 and NO(+)(H2O)5 isomers tend to channel through these highly populated isomers toward HONO formation. PMID:27071120
The ab initio calculation of molecular electric, magnetic and geometric properties.
Bast, Radovan; Ekström, Ulf; Gao, Bin; Helgaker, Trygve; Ruud, Kenneth; Thorvaldsen, Andreas J
2011-02-21
We give an account of some recent advances in the development of ab initio methods for the calculation of molecular response properties, involving electric, magnetic, and geometric perturbations. Particular attention is given to properties in which the basis functions depend explicitly both on time and on the applied perturbations such as perturbations involving nuclear displacements or external magnetic fields when London atomic orbitals are used. We summarize a general framework based on the quasienergy for the calculation of arbitrary-order molecular properties using the elements of the density matrix in the atomic-orbital basis as the basic variables. We demonstrate that the necessary perturbed density matrices of arbitrary order can be determined from a set of linear equations that have the same formal structure as the set of linear equations encountered when determining the linear response equations (or time-dependent self-consistent-field equations). Additional components needed to calculate properties involving perturbation-dependent basis sets are flexible one- and two-electron integral techniques for geometric or magnetic-field differentiated integrals; in Kohn-Sham density-functional theory (KS-DFT), we also need to calculate derivatives of the exchange-correlation functional. We describe a recent proposal for evaluating these contributions based on automatic differentiation. Within this framework, it is now possible to calculate any molecular property for an arbitrary self-consistent-field reference state, including two- and four-component relativistic self-consistent-field wave functions. Examples of calculations that can be performed with this formulation are presented. PMID:21180690
AB INITIO HF AND DFT STUDIES ON MOLECULAR STRUCTURE AND VIBRATIONAL ANALYSIS OF 2,5-DIBROMOPYRIDINE
ÇIRAK, Çağrı; KOÇ, Nurettin
2014-01-01
Theoretical study on molecular structure and vibrational spectra of 2,5-dibromopyridine (2,5-DBP) have been investigated. The optimized geometry, theoretical vibration frequencies and intensities were calculated by using ab initio Hartree-Fock and density functional B3LYP method with 6-31G(d,p) basis sets. The vibrational analysis of title molecule was done and its optimized geometry parameters (bond lengths and bond angles) were given. Scaled theoretical frequencies have been compared with e...
Leszek Bober; Tomasz Baczek; Piotr Kawczak
2012-01-01
Pharmacological and physicochemical classification of the furan and thiophene amide derivatives by multiple regression analysis and partial least square (PLS) based on semi-empirical ab initio molecular modeling studies and high-performance liquid chromatography (HPLC) retention data is proposed. Structural parameters obtained from the PCM (Polarizable Continuum Model) method and the literature values of biological activity (antiproliferative for the A431 cells) expressed...
Mal-Soon Lee; B. Peter McGrail; Roger Rousseau; Vassiliki-Alexandra Glezakou
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 ent...
Ab initio molecular dynamics study of liquid sodium and cesium up to critical point
Energy Technology Data Exchange (ETDEWEB)
Yuryev, Anatoly A. [Institute of Metallurgy of Ural Branch of the Russian Academy of Sciences, Amundsen st. 101,620016, Yekaterinburg (Russian Federation); Ural Federal University, Vira st. 19, 620002, Yekaterinburg (Russian Federation); Gelchinski, Boris R. [Institute of Metallurgy of Ural Branch of the Russian Academy of Sciences, Amundsen st. 101,620016, Yekaterinburg (Russian Federation)
2015-08-17
Ab initio modeling of liquid metals Na and K is carried out using the program SIESTA. We have determined the parameters of the model (the optimal step, the number of particles, the initial state etc) and calculated a wide range of properties: the total energy, pair correlation function, coefficient of self-diffusion, heat capacity, statistics of Voronoi polyhedra, the density of electronic states up to the critical temperature.
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.
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.
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.
Diffusion within α-CuI studied using ab initio molecular dynamics simulations
International Nuclear Information System (INIS)
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 A and 60 deg. 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 (111) 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 (100) 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 x 10-5 cm2 s-1, is in excellent agreement with that found experimentally.
Energy Technology Data Exchange (ETDEWEB)
Kim, B.
1990-10-01
This report discusses the following topics: molecular structure of NO{sub 3} radical studied by laser induced fluorescence; photodissociation and fluorescence spectroscopy of NO{sub 3} in molecular beam; vertical electronic spectrum of NO{sub 3}:{sup 2}A{prime}{sub 2}, {sup 2}E{double prime}({sup 2}A{sub 2}{sup 2}B{sub 1}), and {sup 2}E{prime} states; and Ab initio study of the vibrational spectra of NO{sub 3}.
An ab initio molecular dynamics study of the roaming mechanism of the H{sub 2}+HOC{sup +} reaction
Energy Technology Data Exchange (ETDEWEB)
Yu Huagen, E-mail: hgy@bnl.gov [Department of Chemistry, Brookhaven National Laboratory, Upton, NY 11973 (United States)
2011-08-01
We report here a direct ab initio molecular dynamics study of the p-/o-H{sub 2}+HOC{sup +} reaction on the basis of the accurate SAC-MP2 potential energy surface. The quasi-classical trajectory method was employed. This work largely focuses on the study of reaction mechanisms. A roaming mechanism was identified for this molecular ion-molecule reaction. The driving forces behind the roaming mechanism were thoroughly investigated by using a trajectory dynamics approach. In addition, the thermal rate coefficients of the H{sub 2}+HOC{sup +} reaction were calculated in the temperature range [25, 300] K and are in good agreement with experiments.
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
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.
Energy Technology Data Exchange (ETDEWEB)
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.
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.
International Nuclear Information System (INIS)
Ab initio molecular dynamics simulations have been used to inspect the adsorption of O2 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 O2 and consequently widens the reaction channel for the adsorption process. Conversely, a pure Au cluster on the same graphene support is inactive for the O2 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
Ab initio molecular dynamics study of hydrogen removal by ion-surface interactions
Energy Technology Data Exchange (ETDEWEB)
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)
Guo, Xun; Zhang, Xitong; Zhao, Shijun; Huang, Qing; Xue, Jianming
2016-01-01
Density functional theory (DFT) calculation is employed to study the adsorption properties of Pb and Cu on recently synthesized two-dimensional materials MXenes, including Ti3C2, V2C1 and Ti2C1. The influence of surface decoration with functional groups such as H, OH and F have also been investigated. Most of these studied MXenes exhibit excellent capability to adsorb Pb and Cu, especially the adsorption capacity of Pb on Ti2C1 is as high as 2560 mg g(-1). Both the binding energies and the adsorption capacities are sensitive to the functional groups attached to the MXenes' surface. Ab initio molecular dynamics (ab-init MD) simulation confirms that Ti2C1 remains stable at room temperature after adsorbing Pb atoms. Our calculations imply that these newly emerging two-dimensional MXenes are promising candidates for wastewater treatment and ion separation. PMID:26602974
International Nuclear Information System (INIS)
Aggregation of amyloid-β (Aβ) peptides is believed to play a key role in the mechanism of molecular pathogenesis of Alzheimer's disease (AD). To inhibit the aggregation and prevent AD, numerous compounds have been synthesized. A previous experimental study elucidated that a triazine derivative AA3E2 has anti-amyloidogenic ability, while a triazine derivative AA3D2 having a different substituent has no inhibitory effect. However, the reason for this remarkable difference in the ability cannot be explained by the chemical structures of these derivatives. In the present study, we present stable structures of the solvated complexes with Aβ and AA3E2/AA3D2 obtained by classical molecular mechanics method. The specific interactions between Aβ and AA3E2/AA3D2 in the complexes are investigated by ab initio fragment molecular orbital calculations. Based on the results obtained, we attempt to propose new potent inhibitors for the Aβ aggregation.
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.
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.
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. PMID:27176426
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...
Yousaf, Masood; Shin, Dongbin; Ruoff, Rodney; Park, Noejung
2015-12-17
We used ab initio molecular dynamics (AIMD) to investigate the effect of a monochromatic oscillating electric field in resonance with a particular molecular vibration on surfaces. As a case study, AIMD simulations were carried out for hydroxyl functional groups on graphene. When the frequency of the applied field matches with the C-OH vibration frequency, the amplitude is monotonically amplified, leading to a complete desorption from the surface, overcoming the substantial barrier. This suggests the possibility of activating a particular bond without damaging the remaining surface. We extended this work to the case of the amination of sp(2)-bonded carbon surfaces and discussed the general perspective that, in general, an unfavorable chemical process can be activated by applying an external electric field with an appropriate resonance frequency.
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
Kafka, Graeme R; Masters, Sarah L; Rankin, David W H
2007-07-01
A new method of incorporating ab initio theoretical data dynamically into the gas-phase electron diffraction (GED) refinement process has been developed to aid the structure determination of large, sterically crowded molecules. This process involves calculating a set of differences between parameters that define the positions of peripheral atoms (usually hydrogen), as determined using molecular mechanics (MM), and those which use ab initio methods. The peripheral-atom positions are then updated continually during the GED refinement process, using MM, and the returned positions are modified using this set of differences to account for the differences between ab initio and MM methods, before being scaled back to the average parameters used to define them, as refined from experimental data. This allows the molecule to adopt a completely asymmetric structure if required, without being constrained by the MM parametrization, whereas the calculations can be performed on a practical time scale. The molecular structures of tri-tert-butylphosphine oxide and tri-tert-butylphosphine imide have been re-examined using this new technique, which we call SEMTEX (Structure Enhancement Methodology using Theory and EXperiment).
Energy Technology Data Exchange (ETDEWEB)
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.
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.
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.
Energy Technology Data Exchange (ETDEWEB)
Orlando, Roberto, E-mail: roberto.orlando@unito.it; Erba, Alessandro; Dovesi, Roberto [Dipartimento di Chimica, Università di Torino and NIS, Nanostructured Interfaces and Surfaces, Centre of Excellence, Via P. Giuria 7, 10125 Torino (Italy); De La Pierre, Marco [Dipartimento di Chimica, Università di Torino and NIS, Nanostructured Interfaces and Surfaces, Centre of Excellence, Via P. Giuria 7, 10125 Torino (Italy); Nanochemistry Research Institute, Department of Chemistry, Curtin University, GPO Box U1987, Perth, WA 6845 (Australia); Zicovich-Wilson, Claudio M. [Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Av. Universidad, 1001, Col. Chamilpa, 62209 Cuernavaca (Morelos) (Mexico)
2014-09-14
Use of symmetry can dramatically reduce the computational cost (running time and memory allocation) of self-consistent-field ab initio calculations for molecular and crystalline systems. Crucial for running time is symmetry exploitation in the evaluation of one- and two-electron integrals, diagonalization of the Fock matrix at selected points in reciprocal space, reconstruction of the density matrix. As regards memory allocation, full square matrices (overlap, Fock, and density) in the Atomic Orbital (AO) basis are avoided and a direct transformation from the packed AO to the symmetry adapted crystalline orbital basis is performed, so that the largest matrix to be handled has the size of the largest sub-block in the latter basis. Quantitative examples, referring to the implementation in the CRYSTAL code, are given for high symmetry families of compounds such as carbon fullerenes and nanotubes.
Energy Technology Data Exchange (ETDEWEB)
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.
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.
Energy Technology Data Exchange (ETDEWEB)
Song, Chi [Key Laboratory of Materials Physics, Institute of Solid State Physics, Chinese Academy of Sciences, P. O. Box 1129, Hefei 230031 (China); Li, Dongdong [National Laboratory for Physical Sciences at Microscale and Department of Physics, University of Science and Technology of China, Hefei 230026 (China); Xu, Yichun [Key Laboratory of Materials Physics, Institute of Solid State Physics, Chinese Academy of Sciences, P. O. Box 1129, Hefei 230031 (China); Pan, B.C. [National Laboratory for Physical Sciences at Microscale and Department of Physics, University of Science and Technology of China, Hefei 230026 (China); Liu, C.S., E-mail: csliu@issp.ac.cn [Key Laboratory of Materials Physics, Institute of Solid State Physics, Chinese Academy of Sciences, P. O. Box 1129, Hefei 230031 (China); Wang, Zhiguang [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China)
2013-11-15
Considerable attention has been devoted to liquid lead-bismuth eutectic (LBE) alloy due to its potential application as spallation target and coolant in future sub-critical reactors. Whether there exists an abnormal structural change at high temperatures in this liquid alloy is still under debate. In this paper, we perform ab initio molecular dynamics simulation on the structure and dynamics of liquid LBE at different temperatures from 573 to 1173 K. Through the analysis of the pair correlation function, static structure factor, coordination number, atomic bonded pair, excess entropy, and diffusion constant with increasing temperature, we find that these structure-sensitive quantities change gradually with temperature and exhibit linear temperature dependence. No abnormal structural transformations with temperature variation are observed.
Calderín, L; González, L E; González, D J
2009-05-21
We report a study on several static, dynamic, and electronic properties of liquid Hg at room temperature. We have performed ab initio molecular dynamics simulations using Kohn-Sham density functional theory combined with a nonlocal ultrasoft pseudopotential. The calculated static structure shows good agreement with the available experimental data. We present results for the single-particle dynamics, and recent experimental data are analyzed. The calculated dynamic structure factors S(q,omega) fairly agree with their experimental counterparts as measured by inelastic x-ray (and neutron) scattering experiments. The dispersion relation exhibits a positive dispersion, which however is not so marked as suggested by the experiment; moreover, its slope at the long-wavelength limit provides a good estimate of the experimental sound velocity. We have also analyzed the dynamical processes behind the S(q,omega) in terms of a model including a relaxation mechanism with both fast and slow characteristic time scales. PMID:19466841
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.
International Nuclear Information System (INIS)
Based on the ab initio molecular orbital theory at the HF/6-31G(d) level, the effect of hydration on the reduced partition function ratio (RPFR) of the boric acid molecule (B(OH)3) was evaluated in order to better understand boron isotope fractionation observed in aqueous systems. The B(OH)3(H2O)n species with n up to 12 were considered and their geometry optimization and RPFR calculations were carried out. It was induced that hydration decreased the RPFR of B(OH)3 and the degree of decrease in ln(RPFR) was ca. 1.5%, which was nearly equivalent to that of B(OH)4-. (author)
Grenier, Romain; To, Quy-Dong; de Lara-Castells, María Pilar; Léonard, Céline
2015-07-01
Global potentials for the interaction between the Ar atom and gold surfaces are investigated and Ar-Au pair potentials suitable for molecular dynamics simulations are derived. Using a periodic plane-wave representation of the electronic wave function, the nonlocal van-der-Waals vdW-DF2 and vdW-OptB86 approaches have been proved to describe better the interaction. These global interaction potentials have been decomposed to produce pair potentials. Then, the pair potentials have been compared with those derived by combining the dispersionless density functional dlDF for the repulsive part with an effective pairwise dispersion interaction. These repulsive potentials have been obtained from the decomposition of the repulsive interaction between the Ar atom and the Au2 and Au4 clusters and the dispersion coefficients have been evaluated by means of ab initio calculations on the Ar+Au2 complex using symmetry adapted perturbation theory. The pair potentials agree very well with those evaluated through periodic vdW-DF2 calculations. For benchmarking purposes, CCSD(T) calculations have also been performed for the ArAu and Ar+Au2 systems using large basis sets and extrapolations to the complete basis set limit. This work highlights that ab initio calculations using very small surface clusters can be used either as an independent cross-check to compare the performance of state-of-the-art vdW-corrected periodic DFT approaches or, directly, to calculate the pair potentials necessary in further molecular dynamics calculations. PMID:26046588
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.
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
Lumbroso, H.; Liégeois, C.; Pappalardo, G. C.; Grassi, A.
From the ab initio molecular energies of the possible conformers and from a classical dipole moment analysis of 2-oxopyrrolidin-l-ylacetamide (μ = 4.02 D in dioxan at 30.0°C), the preferred conformation in solution of this novel nootropic agent has been determined. The exocyclic N-CH 2 bond is rotated in one sense by 90° and the exocyclic CH 2-C bond rotated in the same sense by 120° from the "planar" ( OO)- cis conformation. The structures of the two enantiomers in solution differ from that of the crystalline molecule.
International Nuclear Information System (INIS)
The dissociative chemisorption of methane on metal surfaces is of great practical and fundamental importance. Not only is it the rate-limiting step in the steam reforming of natural gas, the reaction exhibits interesting mode-selective behavior and a strong dependence on the temperature of the metal. We present a quantum model for this reaction on Ni(100) and Ni(111) surfaces based on the reaction path Hamiltonian. The dissociative sticking probabilities computed using this model agree well with available experimental data with regard to variation with incident energy, substrate temperature, and the vibrational state of the incident molecule. We significantly expand the vibrational basis set relative to earlier studies, which allows reaction probabilities to be calculated for doubly excited initial vibrational states, though it does not lead to appreciable changes in the reaction probabilities for singly excited initial states. Sudden models used to treat the center of mass motion parallel to the surface are compared with results from ab initio molecular dynamics and found to be reasonable. Similar comparisons for molecular rotation suggest that our rotationally adiabatic model is incorrect, and that sudden behavior is closer to reality. Such a model is proposed and tested. A model for predicting mode-selective behavior is tested, with mixed results, though we find it is consistent with experimental studies of normal vs. total (kinetic) energy scaling. Models for energy transfer into lattice vibrations are also examined
Collective rotation from ab initio theory
Caprio, M A; Vary, J P; Smith, R
2015-01-01
Through ab initio approaches in nuclear theory, we may now seek to quantitatively understand the wealth of nuclear collective phenomena starting from the underlying internucleon interactions. No-core configuration interaction (NCCI) calculations for p-shell nuclei give rise to rotational bands, as evidenced by rotational patterns for excitation energies, electromagnetic moments, and electromagnetic transitions. In this review, NCCI calculations of 7-9Be are used to illustrate and explore ab initio rotational structure, and the resulting predictions for rotational band properties are compared with experiment. We highlight the robustness of ab initio rotational predictions across different choices for the internucleon interaction.
International Nuclear Information System (INIS)
Spin Orbit Coupling (SOC) is introduced to molecular ab initio density matrix renormalization group (DMRG) calculations. In the presented scheme, one first approximates the electronic ground state and a number of excited states of the Born-Oppenheimer (BO) Hamiltonian with the aid of the DMRG algorithm. Owing to the spin-adaptation of the algorithm, the total spin S is a good quantum number for these states. After the non-relativistic DMRG calculation is finished, all magnetic sublevels of the calculated states are constructed explicitly, and the SOC operator is expanded in the resulting basis. To this end, spin orbit coupled energies and wavefunctions are obtained as eigenvalues and eigenfunctions of the full Hamiltonian matrix which is composed of the SOC operator matrix and the BO Hamiltonian matrix. This treatment corresponds to a quasi-degenerate perturbation theory approach and can be regarded as the molecular equivalent to atomic Russell-Saunders coupling. For the evaluation of SOC matrix elements, the full Breit-Pauli SOC Hamiltonian is approximated by the widely used spin-orbit mean field operator. This operator allows for an efficient use of the second quantized triplet replacement operators that are readily generated during the non-relativistic DMRG algorithm, together with the Wigner-Eckart theorem. With a set of spin-orbit coupled wavefunctions at hand, the molecular g-tensors are calculated following the scheme proposed by Gerloch and McMeeking. It interprets the effective molecular g-values as the slope of the energy difference between the lowest Kramers pair with respect to the strength of the applied magnetic field. Test calculations on a chemically relevant Mo complex demonstrate the capabilities of the presented method
Roemelt, Michael
2015-07-01
Spin Orbit Coupling (SOC) is introduced to molecular ab initio density matrix renormalization group (DMRG) calculations. In the presented scheme, one first approximates the electronic ground state and a number of excited states of the Born-Oppenheimer (BO) Hamiltonian with the aid of the DMRG algorithm. Owing to the spin-adaptation of the algorithm, the total spin S is a good quantum number for these states. After the non-relativistic DMRG calculation is finished, all magnetic sublevels of the calculated states are constructed explicitly, and the SOC operator is expanded in the resulting basis. To this end, spin orbit coupled energies and wavefunctions are obtained as eigenvalues and eigenfunctions of the full Hamiltonian matrix which is composed of the SOC operator matrix and the BO Hamiltonian matrix. This treatment corresponds to a quasi-degenerate perturbation theory approach and can be regarded as the molecular equivalent to atomic Russell-Saunders coupling. For the evaluation of SOC matrix elements, the full Breit-Pauli SOC Hamiltonian is approximated by the widely used spin-orbit mean field operator. This operator allows for an efficient use of the second quantized triplet replacement operators that are readily generated during the non-relativistic DMRG algorithm, together with the Wigner-Eckart theorem. With a set of spin-orbit coupled wavefunctions at hand, the molecular g-tensors are calculated following the scheme proposed by Gerloch and McMeeking. It interprets the effective molecular g-values as the slope of the energy difference between the lowest Kramers pair with respect to the strength of the applied magnetic field. Test calculations on a chemically relevant Mo complex demonstrate the capabilities of the presented method.
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
International Nuclear Information System (INIS)
Use of a beam of biradicaloid such as dialkyl group-III nitrene produced by the method of photodissociation of energetic compound beams (PDECB) is expected to be advantageous to the low-temperature thin-film growth of stoichiometric group-III nitride. Through the clarification of fundamental processes involved in pyrolysis as well as photolysis of dimethylgallium azide [(CH3)2GaN3], dimethylaluminum azide [(CH3)2AlN3], and dimethylboron azide [(CH3)2BN3] based on post-self-consistent field ab initio molecular orbital methods, we discuss the suitability of these possible source compounds for the production of beams of dimethylgalliumnitrene [(CH3)2GaN], dimethylaluminumnitrene [(CH3)2AlN], and dimethylboronnitrene [(CH3)2BN] by the PDECB method. The theoretical results suggested that (CH3)2GaN3 is a promising PDECB source material in that this molecule possesses the nature of unimolecular metastable dye
International Nuclear Information System (INIS)
The structural organization of water at a model of amorphous silica–liquid water interface is investigated by ab initio molecular dynamics (AIMD) simulations at room temperature. The amorphous surface is constructed with isolated, H-bonded vicinal and geminal silanols. In the absence of water, the silanols have orientations that depend on the local surface topology (i.e. presence of concave and convex zones). However, in the presence of liquid water, only the strong inter-silanol H-bonds are maintained, whereas the weaker ones are replaced by H-bonds formed with interfacial water molecules. All silanols are found to act as H-bond donors to water. The vicinal silanols are simultaneously found to be H-bond acceptors from water. The geminal pairs are also characterized by the formation of water H-bonded rings, which could provide special pathways for proton transfer(s) at the interface. The first water layer above the surface is overall rather disordered, with three main domains of orientations of the water molecules. We discuss the similarities and differences in the structural organization of the interfacial water layer at the surface of the amorphous silica and at the surface of the crystalline (0 0 0 1) quartz surface. (paper)
Song, Bingyi; Jiang, Wenlong; Yang, Bin; Chen, Xiumin; Xu, Baoqiang; Kong, Lingxin; Liu, Dachun; Dai, Yongnian
2016-07-01
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.
Free energy of liquid water on the basis of quasi-chemical theory and ab initio molecular dynamics
Asthagiri, D; Kress, J D; Pratt, Lawrence R.
2003-01-01
We use ab initio molecular dynamics as a basis for quasi-chemical theory evaluation of the free energy of water near conventional liquid thermodynamic states. The PW91, PBE, and revised PBE (rPBE) functionals are employed. The oxygen radial density distribution, gOO(r), using the rPBE functional is in reasonable agreement with current experiments, whereas the PW91 and PBE functionals predict a more structured gOO(r). The diffusion coefficient with the rPBE functional is in reasonable accord with experiments. Using a maximum entropy procedure, we obtain x_0 from the coordination number distribution x_n for oxygen atoms having n neighbors. Likewise, we obtain p_0 from p_n, the probability of observing cavities of specified radius containing n water molecules. The probability x_0 is a measure of the local chemical interactions and is central to the quasi-chemical theory of solutions. The probability p_0, central to the theory of liquids, is a measure of the free energy required to open cavities of defined sizes ...
Rajesh, C.; Majumder, C.; Rajan, M. G. R.; Kulshreshtha, S. K.
2005-12-01
The geometric and electronic structure of the Pbn clusters (n=2-15) has been calculated to elucidate its structural evolution and compared with other group-IV elemental clusters. The search for several low-lying isomers was carried out using the ab initio molecular dynamics simulations under the framework of the density functional theory formalism. The results suggest that unlike Si, Ge, and Sn clusters, which favor less compact prolate shape in the small size range, Pb clusters favor compact spherical structures consisting of fivefold or sixfold symmetries. The difference in the growth motif can be attributed to their bulk crystal structure, which is diamond-like for Si, Ge, and Sn but fcc for Pb. The relative stability of Pbn clusters is analyzed based on the calculated binding energies and second difference in energy. The results suggest that n=4 , 7, 10, and 13 clusters are more stable than their respective neighbors, reflecting good agreement with experimental observation. Based on the fragmentation pattern it is seen that small clusters up to n=12 favor monomer evaporation, larger ones fragment into two stable daughter products. The experimental observation of large abundance for n=7 and lowest abundance of n=14 have been demonstrated from their fragmentation pattern. Finally a good agreement of our theoretical results with that of the experimental findings reported earlier implies accurate predictions of the ground state geometries of these clusters.
Postupna, Olena; Long, Run; Prezhdo, Oleg
2012-02-01
Outstanding physical properties of carbon nanotubes (CNTs), such as well-defined optical resonance and ultrafast nonlinear response, result in CNTs gaining popularity in academic and industrial endeavors as potential effective energy generating devices. Following recent experiments on ultrafast excitation energy transfer in small semiconducting carbon nanotube aggregates [1], we report results of ab initio nonadiabatic molecular dynamics simulation of the energy transfer taking place in two carbon nanotube systems. We investigate the energy transfer between (8,4) and (10,0) CNTs, as well as (8,4) and (13,0) CNTs. In both cases, the CNTs are orthogonal to each other. Luer et al. in [1] elucidate the second excitonic transitions followed by fast intratube relaxation and energy transfer from the (8,4) CNT toward other acceptor tubes. Our project aims to provide a better understanding of the energy transfer mechanism in the given systems, which should foster development of a theory for the electronic structure and dynamics of CNT networks, hence enhancing their tailoring and application in the future. References 1.Larry Luer, Jared Crochet, Tobias Hertel, Giulio Cerullo, Gugliermo Lanzani. ACSNano. Vol.4, No. 7, 4265-4273
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.
Ab initio molecular dynamics investigations of low-energy recoil events in Ni and NiCo
International Nuclear Information System (INIS)
Low-energy recoil events in pure Ni and the equiatomic NiCo alloy are studied using ab initio molecular dynamics simulations. We found that the threshold displacement energies are strongly dependent on orientation and weakly dependent on composition. The minimum threshold displacement energies are along the [1 1 0] direction in both pure Ni and the NiCo alloy. Compared to pure Ni, the threshold displacement energies increase slightly in the NiCo alloy due to the stronger bonds in the alloy, irrespective of the element type of the PKA. A single Ni interstitial occupying the center of a tetrahedron formed by four Ni atoms and a <1 0 0> split interstitial is produced in pure Ni by the recoils, while only the <1 0 0> split interstitial is formed in the NiCo alloy. Compared to the replacement sequences in pure Ni, anti-site defect sequences are observed in the alloy, which have high efficiency for both producing defects and transporting energy outside of the cascade core. These results provide insights into energy transfer processes occurring in equiatomic alloys under irradiation. (paper)
Energy Technology Data Exchange (ETDEWEB)
Bankura, Arindam; Klein, Michael L.; Carnevale, Vincenzo, E-mail: vincenzo.carnevale@temple.edu
2013-08-30
Highlights: • The estimated pK{sub a} is in agreement with the experimental one. • The affinity for protons is similar to that of a histidine residue in aqueous solution. • The electrostatic environment is responsible for the stabilization of the charged imidazolium moiety. - Abstract: Ab initio molecular dynamics calculations have been used to compare and contrast the deprotonation reaction of a histidine residue in aqueous solution with the situation arising in a histidine-tryptophan cluster. The latter is used as a model of the proton storage unit present in the pore of the M2 proton conducting ion channel. We compute potentials of mean force for the dissociation of a proton from the Nδ and N∊ positions of the imidazole group to estimate the pK{sub a}s. Anticipating our results, we will see that the estimated pK{sub a} for the first protonation event of the M2 channel is in good agreement with experimental estimates. Surprisingly, despite the fact that the histidine is partially desolvated in the M2 channel, the affinity for protons is similar to that of a histidine in aqueous solution. Importantly, the electrostatic environment provided by the indoles is responsible for the stabilization of the charged imidazolium.
Kent, P. R. C.; Ganesh, P.; Jiang, De-En; Borodin, O.
2012-02-01
Optimizing the choice of electrolyte in lithium ion batteries and an understanding of the solid-electrolyte interphase (SEI) is required to optimize the balance between high-energy storage, high rate capability, and lifetime. We perform accurate ab initio molecular-dynamics simulations of common cyclic carbonates and LiPF6 to build solvation models which explain available Neutron and NMR spectroscopies. Our results corroborate why ethylene carbonate is a preferred choice for battery applications over propylene carbonate and how mixtures with dimethyl carbonate improve Li-ion diffusion. We study the role of functionalization of graphite-anode edges on the reducibility of the electrolyte and the ease of Li-ion intercalation at the initial stages of SEI formation. We find that oxygen terminated edges readily act as strong reductive sites, while hydrogen terminated edges are less reactive and allow faster Li diffusion. Orientational ordering of the solvent molecules precedes reduction at the interphase. Inorganic reductive components are seen to readily migrate to the anode edges, leading to increased surface passivation of the anode. We are currently quantifying Li-intercalation barriers across realistic SEI models, and progress along these lines will be presented.
Energy Technology Data Exchange (ETDEWEB)
Scholes, G.D.; Fleming, G.R. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry]|[Lawrence Berkeley National Lab., CA (United States). Physical Biosciences Div.; Gould, I.R. [Imperial Coll. of Science, Technology and Medicine, London (United Kingdom). Dept. of Chemistry; Cogdell, R.J. [Univ. of Glasgow (United Kingdom). Div. of Biochemistry and Molecular Biology
1999-04-01
The results of ab initio molecular orbital calculations of excited states and electronic couplings (for energy transfer) between the B800 and B850 bacteriochlorophyll a (Bchl) chromophores in the peripheral light-harvesting complex (LH2) of the purple photosynthetic bacterium Rhodopseudomonas acidophila are reported. Electronic couplings are estimated from supermolecule calculations of Bchl dimers using the Ci-singles methodology and 3-21G{sup *} or 6-31G{sup *} basis sets. A scheme for dissecting the coupling into contributions from the Coulombic coupling and the short-range coupling (i.e., dependent on interchromophore orbital overlap) is reported. B850 couplings are calculated to be [total (Coulombic + short)]: intrapolypeptide dimer 320 (265 + 55) cm{sup {minus}1} and interpolypeptide dimer 255 (195 + 60) cm{sup {minus}1} at the CIS/6-31G{sup *} level. These results differ significantly from those estimated using the point dipole approximation. The effect of including Mg ligands (His residues) and H-bonding residues (Trp and Tyr) is also investigated. The consequences for superradiance and energy transfer dynamics and mechanism are discussed.
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.
Ab initio molecular dynamics simulation of the atom packing and density of Al-Ni amorphous alloys
Institute of Scientific and Technical Information of China (English)
无
2010-01-01
Al-Ni alloys have better glass forming ability (GFA) than other Al-based alloys. However, the relationship among the atomic arrangement, glass transition, packing density and composition hasn’t been systematically studied. In this paper the ab initio molecular dynamics simulation (AIMD) was performed on the atom packing and density of AlxNi100-x (x=80, 83, 85, 86, 87 and 90) alloys. The pair correlation function and Voronoi tessellation indicated that there are obvious topological and chemical short-range orders in these alloys. The topological structure consists of Al-centered icosahedra like and Ni-centered tri-capped trigonal prism (TTP) like polyhedra. There is strong chemical short-range ordering between Al and Ni atoms indicated by the bond-length of Al-Ni pair shorter than the sum of the radii of Al and Ni atoms, which increases with the increasing of Ni content. It is shown that the densities of amorphous alloys don’t agree with the linear law with a peak at x=85. Based on the features of the structure and density, it is concluded that Al-Ni alloys at x=84–86 have high GFA, which can be extended to multi-component Al-based alloys.
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.
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.
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.
High Throughput Ab initio Modeling of Charge Transport for Bio-Molecular-Electronics
Bruque, Nicolas A.
2009-01-01
Self-assembled nanostructures, composed of inorganic and organic materials, have multiple applications in the fields of engineering and nanotechnology. Experimental research using nanoscaled materials, such as semiconductor/metallic nanocrystals, nanowires (NW), and carbon nanotube (CNT)-molecular systems have potential applications in next generation nano electronic devices. Many of these molecular systems exhibit electronic device functionality. However, experimental analytical techniques t...
An adaptive mass algorithm for Car-Parrinello and Ehrenfest ab initio molecular dynamics
Kadir, Ashraful; Szepessy, Anders
2014-01-01
Ehrenfest and Car-Parrinello molecular dynamics are computational alternatives to approximate Born-Oppenheimer molecular dynamics without solving the electron eigenvalue problem at each time-step. A non-trivial issue is to choose the artificial electron mass parameter appearing in the Car-Parrinello method to achieve both good accuracy and high computational efficiency. In this paper, we propose an algorithm, motivated by the Landau-Zener probability, to systematically choose an artificial mass dynamically, which makes the Car-Parrinello and Ehrenfest molecular dynamics methods dependent only on the problem data. Numerical experiments for simple model problems show that the time-dependent adaptive artificial mass parameter improves the efficiency of the Car-Parrinello and Ehrenfest molecular dynamics.
Electronic Transport Properties of a Naphthopyran-Based Optical Molecular Switch:an ab initio Study
Institute of Scientific and Technical Information of China (English)
XIA Cai-Juan; LIU De-Sheng; ZHANG Ying-Tang
2011-01-01
The electronic transport properties of a. Naphthopyran-based molecular optical switch are investigated by using the nonequilibrium Green's Function formalism combined with first-principles density functional theory. The molecule that comprises the switch can convert between its open and closed forms upon photoexcitation. Theoretical results show that the current through the open form is significantly larger than that through the closed form, which is different from other optical switches based on ring-opening reactions of the molecular bridge. The maximum on-off ratio (about 90) can be obtained at 1.4 V. The physical origin of the switching behavior is interpreted based on the spatial distributions of molecular orbitals and the HOMO-LUMO gap. Our result shows that the naphthopyran-based molecule is a good candidate for optical molecular switches and will be useful in the near future.%@@ ronic transport properties of a naphthopyran-based molecular optical switch are investigated by using the nonequilibrium Green's function formalism combined with first-principles density functional theory.The molecule that comprises the switch can convert between its open and closed forms upon photoexcitation.Theoretical results show that the current through the open form is significantly larger than that through the closed form,which is different from other optical switches based on ring-opening reactions of the molecular bridge.The maximum on-off ratio(about 90)can be obtained at 1.4 V.The physical origin of the switching behavior is interpreted based on the spatial distributions of molecular orbitals and the HOMO-LUMO gap.Our result shows that the naphthopyran-based molecule is a good candidate for optical molecular switches and will be useful in the near future.
DEFF Research Database (Denmark)
Svendsen, Casper Steinmann; Jensen, Jan; Fedorov, Dmitri
2013-01-01
We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path of ...
Storing of molecular hydrogen in graphite cell. An ab initio study
International Nuclear Information System (INIS)
Full text: Weakly-bounded hydrogen bonds are of fundamental importance in structural chemistry and biology, supramolecular chemistry and crystal engineering. Molecular hydrogen (H2) holds a promise of the ideal energy source for production of electricity in transportable devices. Carbon-based materials, such as nano-structured graphite platelets (graphene) or cells are among the most attractive physisorption substrates. A computationally tractable model of graphene is provided by polycyclic aromatic hydrocarbons (PAH's) such as benzene. The importance of benzene and molecular hydrogen complex as a model system for molecular hydrogen storage in graphite cells as well as the importance of noncovalent interactions in a variety of different systems prompted us to study the H2-π interaction. Adequate quantum-chemical description of H2-PAH interactions require post-Hartree-Fock treatment of electron correlation and of basis set superposition error (BSSE) effects. In a previous study we analyzed the weakly-bounded hydrogen bonds between acetylene and different proton donors as a model of C-H-π interaction. Important BSSE effects have been found due to the long range interaction of electron correlation, especially for the dispersion energy component. Similar effects can be found in case of benzene and molecular hydrogen complex. To treat this effect, we use the well-known a posteriori counterpoise (CP) BSSE correction scheme introduced by Boys and Bernardi. The theoretical values of interaction energies between the benzene ring and the molecular hydrogen as well as the intermolecular distances between them show an important BSSE and basis size effects. (author)
Marqués, M.; González, D. J.; González, L. E.
2016-07-01
The melting curve of sodium for a pressure range up to 100 GPa has been evaluated by the orbital free ab initio molecular dynamics method. This method uses the electronic density as the basic variable combined with an approximate electronic kinetic energy functional and a local ionic pseudopotential and makes it possible to perform simulations with a large number of particles and for long simulation times. The calculated melting curve shows a maximum melting temperature at a pressure around 30 GPa followed by a steep decrease up to 100 GPa. For various pressures and temperatures we have evaluated several static properties, including average and local structure, electronic properties, like the electron localization function (ELF), and dynamic properties, both single-particle and collective ones, from which some transport coefficients are deduced. Despite the accurate reproduction of the available experimental data, we do not observe any indication of an early transition from a bcc-like to an fcc-like liquid, as suggested previously by other authors, but rather pressure-induced change in the variation of icosahedral-like order and bcc-like order, with no sign of fcc-like structures in the whole liquid range studied. We also consider the evolution of the ELF within this type of local arrangement upon pressurization. In the dynamic realm, we find an enlarged wave-vector region where atomic collisions play an important role in the dynamic properties of the system as pressure is increased and temperature decreased along the melting line, leading to a peculiar behavior of the dynamic properties.
Isayev, Olexandr; Gorb, Leonid; Qasim, Mo; Leszczynski, Jerzy
2008-09-01
CL-20 (2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane or HNIW) is a high-energy nitramine explosive. To improve atomistic understanding of the thermal decomposition of CL-20 gas and solid phases, we performed a series of ab initio molecular dynamics simulations. We found that during unimolecular decomposition, unlike other nitramines (e.g., RDX, HMX), CL-20 has only one distinct initial reaction channelhomolysis of the N-NO2 bond. We did not observe any HONO elimination reaction during unimolecular decomposition, whereas the ring-breaking reaction was followed by NO 2 fission. Therefore, in spite of limited sampling, that provides a mostly qualitative picture, we proposed here a scheme of unimolecular decomposition of CL-20. The averaged product population over all trajectories was estimated at four HCN, two to four NO2, two to four NO, one CO, and one OH molecule per one CL-20 molecule. Our simulations provide a detailed description of the chemical processes in the initial stages of thermal decomposition of condensed CL-20, allowing elucidation of key features of such processes as composition of primary reaction products, reaction timing, and Arrhenius behavior of the system. The primary reactions leading to NO2, NO, N 2O, and N2 occur at very early stages. We also estimated potential activation barriers for the formation of NO2, which essentially determines overall decomposition kinetics and effective rate constants for NO2 and N2. The calculated solid-phase decomposition pathways correlate with available condensed-phase experimental data. PMID:18686996
Energy Technology Data Exchange (ETDEWEB)
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.
Derivatization and diffusive motion of molecular fullerenes: Ab initio and atomistic simulations
Energy Technology Data Exchange (ETDEWEB)
Berdiyorov, G., E-mail: gberdiyorov@qf.org.qa; Tabet, N. [Qatar Environment and Energy Research Institute (QEERI), Hamad Ben Khalifa University (HBKU), Qatar Foundation, P.O. Box 5825, Doha (Qatar); Harrabi, K. [Department of Physics, King Fahd University of Petroleum and Minerals, 31261 Dhahran (Saudi Arabia); Mehmood, U.; Hussein, I. A. [Department of Chemical Engineering, King Fahd University of Petroleum and Minerals, 31261 Dharan (Saudi Arabia); Peeters, F. M. [Departement Fysica, Universiteit Antwerpen, Groenenborgerlaan 171, B-2020 Antwerpen (Belgium); Zhang, J. [Department of Materials and London Centre for Nanotechnology, Imperial College London, SW7 2AZ London (United Kingdom); McLachlan, M. A. [Department of Materials and Centre for Plastic Electronics, Imperial College London, SW7 2AZ London (United Kingdom)
2015-07-14
Using first principles density functional theory in combination with the nonequilibrium Green's function formalism, we study the effect of derivatization on the electronic and transport properties of C{sub 60} fullerene. As a typical example, we consider [6,6]-phenyl-C{sub 61}-butyric acid methyl ester (PCBM), which forms one of the most efficient organic photovoltaic materials in combination with electron donating polymers. Extra peaks are observed in the density of states (DOS) due to the formation of new electronic states localized at/near the attached molecule. Despite such peculiar behavior in the DOS of an isolated molecule, derivatization does not have a pronounced effect on the electronic transport properties of the fullerene molecular junctions. Both C{sub 60} and PCBM show the same response to finite voltage biasing with new features in the transmission spectrum due to voltage induced delocalization of some electronic states. We also study the diffusive motion of molecular fullerenes in ethanol solvent and inside poly(3-hexylthiophene) lamella using reactive molecular dynamics simulations. We found that the mobility of the fullerene reduces considerably due to derivatization; the diffusion coefficient of C{sub 60} is an order of magnitude larger than the one for PCBM.
Sagdinc, Seda; Kandemirli, Fatma; Bayari, Sevgi Haman
2007-02-01
Sertraline hydrochloride is a highly potent and selective inhibitor of serotonin (5HT). It is a basic compound of pharmaceutical application for antidepressant treatment (brand name: Zoloft). Ab initio and density functional computations of the vibrational (IR) spectrum, the molecular geometry, the atomic charges and polarizabilities were carried out. The infrared spectrum of sertraline is recorded in the solid state. The observed IR wave numbers were analysed in light of the computed vibrational spectrum. On the basis of the comparison between calculated and experimental results and the comparison with related molecules, assignments of fundamental vibrational modes are examined. The X-ray geometry and experimental frequencies are compared with the results of our theoretical calculations.
Infrared Spectroscopy of N-Methylacetamide Revisited by ab Initio Molecular Dynamics Simulations.
Gaigeot, M P; Vuilleumier, R; Sprik, M; Borgis, D
2005-09-01
The density functional theory based molecular dynamics simulation method ("Car-Parrinello") was applied in a numerical study of the electronic properties, hydrogen bonding, and infrared spectroscopy of the trans and cis isomer of N-methylacetamide in aqueous solution. A detailed analysis of the electronic structure of the solvated molecules, in terms of localized Wannier functions and Born atomic charges, is presented. Two schemes for the computation of the solute infrared absorption spectrum are investigated: In the first method the spectrum is determined by Fourier transforming the time correlation function of the solute dipole as determined from the Wannier function analysis. The second method uses instead the molecular current-current correlation function computed from the Born charges and atomic velocities. The resulting spectral properties of trans- and cis-NMA are carefully compared to each other and to experimental results. We find that the two solvated isomers can be clearly distinguished by their infrared spectral profile in the 1000-2000 cm(-)(1) range. PMID:26641894
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.
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.
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.
Schiffmann, Florian; VandeVondele, Joost
2015-06-01
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.
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.
Sound velocity in shock compressed molybdenum obtained by ab initio molecular dynamics
Lukinov, Tymofiy; Belonoshko, Anatoly; Simak, Sergey
The sound velocity of Mo along the Hugoniot adiabat is calculated from first principles using density-functional theory based molecular dynamics. These data are compared to the sound velocity as measured in recent experiments. The theoretical and experimental Hugoniot and sound velocities are in very good agreement up to pressures of 210 GPa and temperatures of 3700 K on the Hugoniot. However, above that point the experiment and theory diverge. This implies that Mo undergoes a phase transition at about the same point. Considering that the melting point of Mo is likely much higher at that pressure, the related change in the sound velocity in experiment can be ascribed to a solid-solid transition.
Simkovic, Felix; Thomas, Jens M H; Keegan, Ronan M; Winn, Martyn D; Mayans, Olga; Rigden, Daniel J
2016-07-01
For many protein families, the deluge of new sequence information together with new statistical protocols now allow the accurate prediction of contacting residues from sequence information alone. This offers the possibility of more accurate ab initio (non-homology-based) structure prediction. Such models can be used in structure solution by molecular replacement (MR) where the target fold is novel or is only distantly related to known structures. Here, AMPLE, an MR pipeline that assembles search-model ensembles from ab initio structure predictions ('decoys'), is employed to assess the value of contact-assisted ab initio models to the crystallographer. It is demonstrated that evolutionary covariance-derived residue-residue contact predictions improve the quality of ab initio models and, consequently, the success rate of MR using search models derived from them. For targets containing β-structure, decoy quality and MR performance were further improved by the use of a β-strand contact-filtering protocol. Such contact-guided decoys achieved 14 structure solutions from 21 attempted protein targets, compared with nine for simple Rosetta decoys. Previously encountered limitations were superseded in two key respects. Firstly, much larger targets of up to 221 residues in length were solved, which is far larger than the previously benchmarked threshold of 120 residues. Secondly, contact-guided decoys significantly improved success with β-sheet-rich proteins. Overall, the improved performance of contact-guided decoys suggests that MR is now applicable to a significantly wider range of protein targets than were previously tractable, and points to a direct benefit to structural biology from the recent remarkable advances in sequencing. PMID:27437113
Directory of Open Access Journals (Sweden)
Felix Simkovic
2016-07-01
Full Text Available For many protein families, the deluge of new sequence information together with new statistical protocols now allow the accurate prediction of contacting residues from sequence information alone. This offers the possibility of more accurate ab initio (non-homology-based structure prediction. Such models can be used in structure solution by molecular replacement (MR where the target fold is novel or is only distantly related to known structures. Here, AMPLE, an MR pipeline that assembles search-model ensembles from ab initio structure predictions (`decoys', is employed to assess the value of contact-assisted ab initio models to the crystallographer. It is demonstrated that evolutionary covariance-derived residue–residue contact predictions improve the quality of ab initio models and, consequently, the success rate of MR using search models derived from them. For targets containing β-structure, decoy quality and MR performance were further improved by the use of a β-strand contact-filtering protocol. Such contact-guided decoys achieved 14 structure solutions from 21 attempted protein targets, compared with nine for simple Rosetta decoys. Previously encountered limitations were superseded in two key respects. Firstly, much larger targets of up to 221 residues in length were solved, which is far larger than the previously benchmarked threshold of 120 residues. Secondly, contact-guided decoys significantly improved success with β-sheet-rich proteins. Overall, the improved performance of contact-guided decoys suggests that MR is now applicable to a significantly wider range of protein targets than were previously tractable, and points to a direct benefit to structural biology from the recent remarkable advances in sequencing.
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.
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)
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...
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.
Altun, Ahmet; Yokoyama, Shozo; Morokuma, Keiji
2008-01-01
We have investigated photoabsorption spectra of bovine rhodopsin and its mutants (E122Q and E113Q) by hybrid quantum mechanical/molecular mechanical (QM/MM) calculations as well as retinal in vacuo by pure QM calculations, employing multireference (MR) ab initio and TD-B3LYP methods. The sophisticated MR-SORCI+Q and MRCISD+Q methods extrapolated with respect to adopted approximations can reproduce the experimental absorption maxima of retinal very well. The relatively inexpensive MR-DDCI2+Q m...
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.
Halpern, Arthur M.; Glendening, Eric D.
2013-01-01
A project for students in an upper-level course in quantum or computational chemistry is described in which they are introduced to the concepts and applications of a high quality, ab initio treatment of the ground-state potential energy curve (PEC) for H[subscript 2] and D[subscript 2]. Using a commercial computational chemistry application and a…
Fakhraee, Mostafa; Zandkarimi, Borna; Salari, Hadi; Gholami, Mohammad Reza
2014-12-11
The influences of hydroxyl functional group (-OH) on the thermodynamic and structural properties of ionic liquids (ILs) composed of 1-(2-Hydroxyethyl)-3-methyl imidazolium ([C2OHmim](+)) cation and the six different conventional anions, including [Cl](-), [NO3](-), [BF4](-), [PF6](-), [TfO](-), and [Tf2N](-) have been extensively investigated using classical molecular dynamics (MD) simulations combined with ab initio calculations over a wide range of temperature (298-550 K). The volumetric thermodynamic properties, enthalpy of vaporization, cohesive energy density, Hildebrand solubility parameter, and heat capacity at constant pressure were estimated at desired temperature. The simulated densities were in good agreement with the experimental data with a slight overestimation. The interionic interaction of selected ILs was also computed using both the MD simulations and ab initio calculations. It was found that the highest association of cation and anion is attributed to [C2OHmim][Cl] followed by [C2OHmim][NO3], and [C2OHmim][Tf2N] with the bulkiest anion has the weakest interionic interaction among chosen ILs. The similar trend of interactions energies was nearly observed from cohesive energy density results. Additional structural details were comprehensively yielded by calculating radial distribution functions (RDFs) and spatial distribution function (SDFs) at 358 K. The most stable configurations of isolated and dimer ion pairs of these ILs were in excellent consistency with RDFs and SDFs results. Significant changes in arrangement of anions around the [C2OHmim](+) cation in comparison with conventional imidazolium-based ILs can be inferred from the MD simulations and ab initio results. Also, microscopic structural properties disclosed that the most strong cation-cation interaction is ascribed to the hydroxyl-functionalized ILs composed of bulkier anions, whereas ILs incorporating [Cl](-) and [NO3](-) anions are mainly involved in cation-anion interactions. The
International Nuclear Information System (INIS)
Highlights: ► A theoretical study of hydroxide ion-water clusters is carried for varying cluster size and temperature. ► The structures of OH−(H2O)n are found out through quantum chemical calculations for n = 4, 8, 16 and 20. ► The finite temperature behavior of the clusters is studied through ab initio dynamical simulations. ► The spectral features of OH modes (deuterated) and their dependence on hydrogen bonding states of water are discussed. ► The mechanism and kinetics of proton transfer processes in these anionic clusters are also investigated. - Abstract: We have investigated the hydration structure and dynamics of OH−(H2O)n clusters (n = 4, 8, 16 and 20) by means of quantum chemical and ab initio molecular dynamics calculations. Quantum chemical calculations reveal that the solvation structure of the hydroxide ion transforms from three and four-coordinated surface states to five-coordinated interior state with increase in cluster size. Several other isomeric structures with energies not very different from the most stable isomer are also found. Ab initio simulations show that the most probable configurations at higher temperatures need not be the lowest energy isomeric structure. The rates of proton transfer in these clusters are found to be slower than that in bulk water. The vibrational spectral calculations reveal distinct features for free OH (deuterated) stretch modes of water in different hydrogen bonding states. Effects of temperature on the structural and dynamical properties are also investigated for the largest cluster considered here.
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.
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
Directory of Open Access Journals (Sweden)
Leszek Bober
2012-05-01
Full Text Available Pharmacological and physicochemical classification of the furan and thiophene amide derivatives by multiple regression analysis and partial least square (PLS based on semi-empirical ab initio molecular modeling studies and high-performance liquid chromatography (HPLC retention data is proposed. Structural parameters obtained from the PCM (Polarizable Continuum Model method and the literature values of biological activity (antiproliferative for the A431 cells expressed as LD_{50} of the examined furan and thiophene derivatives was used to search for relationships. It was tested how variable molecular modeling conditions considered together, with or without HPLC retention data, allow evaluation of the structural recognition of furan and thiophene derivatives with respect to their pharmacological properties.
Emission spectra of p-Si and p-Si:H models generated by ab initio molecular dynamics methods
Loustau, E R L
2011-01-01
We created 4 p-Si models and 4 p-Si:H models all with 50% porosity. The models contain 32, 108, 256 and 500 silicon atoms with a pore parallel to one of the simulational cell axes and a regular cross-section. We obtained the densities of states of our models by means of ab initio computational methods. We wrote a code to simulate the emission spectra of our structures considering particular excitations an decay conditions. After comparing the simulated spectra with the experimental results, we observe that the position of the maximum of the emission spectra might be related with the size of the silicon backbone for the p-Si models as the quantum confinement models say and with the hydrogen concentration for the p-Si:H structures. We conclude that the quantum confinement model can be used to explain the emission of the p-Si structures but, in the case of the p-Si:H models it is necessary to consider others theories.
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.
Highly scalable Ab initio genomic motif identification
Marchand, Benoît
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.
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
Molexpl: a tool for ab initio data exploration and visualization
Wang, Xueying; Onofrio, Nicolas,; Strachan, Alejandro
2015-01-01
Density functional theory (DFT) based on ab initio theory, is a powerful method to resolve the electronic structure of atoms, molecules and solids. However, in practical, DFT is limited to few hundreds of atoms. To overcome this limitation, researchers have developed empirical interatomic potentials implemented in molecular dynamics (MD) simulations. MD ignores the movements of electrons and describes bonding and non-bonding interaction as a function of the distance between atoms called force...
International Nuclear Information System (INIS)
We performed the simulation of near edge X-ray absorption fine structure (NEXAFS) spectra of a photo-reactive copolymer with considerably large monomer units by ab initio molecular orbital calculation, in order to explain the spectral change induced by irradiation of the linearly polarized near ultra-violet (LPNUV) light. The 'building block approach' is applied for the theoretical calculation to calculate the core-excited states of the polymer with such large monomer units; the monomer unit is divided into subunits, whose core-excited states are calculated individually, and the results are summed up to simulate the spectra of the polymer. With the result of the simulation, the peaks in the observed spectra were assigned. The spectral change after the LPNUV-irradiation is attributed to the change in the electronic structure caused by the breakdown of the π-conjugation system of chalconyl group after photo-dimerization
International Nuclear Information System (INIS)
In the work reported in this paper, ab initio molecular dynamics simulation was performed on Fe85Si2B9P4 amorphous alloy. Preferred atomic environment of the elements was analyzed with Voronoi polyhedrons. It showed that B and P atoms prefer less neighbors compared with Fe and Si, making them structurally incompatible with Fe rich structure and repulsive to the formation of α-Fe. However, due to the low bonding energy of B and P caused by low coordination number, the diffusion rates of them were considerably large, resulting in the requirement of fast annealing for achieving optimum nano-crystallization for its soft magnetic property. The simulation work also indicates that diffusion rate in amorphous alloy is largely determined by bonding energy rather than atomic size
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.
Understanding phonon transport in thermoelectric materials using ab initio approaches
Broido, David
Good thermoelectric materials have low phonon thermal conductivity, kph. Accurate theories to describe kph are important components in developing predictive models of thermoelectric efficiency that can help guide synthesis and measurement efforts. We have developed ab initio approaches to calculate kph, in which phonon modes and phonon scattering rates are computed using interatomic force constants determined from density functional theory, and a full solution of the Boltzmann transport equation for phonons is implemented. A recent approach to calculate interatomic force constants using ab initio molecular dynamics has yielded a good description of the thermal properties of Bi2Te3. But, the complexity of new promising candidate thermoelectric materials introduces computational challenges in assessing their thermal properties. An example is germanane, a germanium based hydrogen-terminated layered semiconductor, which we will discuss in this talk.
Ab-initio calculations on melting of thorium
Mukherjee, D.; Sahoo, B. D.; Joshi, K. D.; Kaushik, T. C.; Gupta, Satish C.
2016-05-01
Ab-initio molecular dynamics study has been performed on face centered cubic structured thorium to determine its melting temperature at room pressure. The ion-electron interaction potential energy calculated as a function of temperature for three volumes (a0)3 and (1.02a0)3 and (1.04a0)3 increases gradually with temperature and undergoes a sharp jump at ~2200 K, ~2100 K and ~1800 K, respectively. Here, a0 = 5.043 Å is the equilibrium lattice parameter at 0 K obtained from ab-initio calculations. These jumps in interaction energy are treated as due to the onset of melting and corresponding temperatures as melting point. The melting point of 2100 K is close to the experimental value of 2023K. Further, the same has been verified by plotting the atomic arrangement evolved at various temperatures and corresponding pair correlation functions.
Ab Initio Study on Hypothetical Silver Nitride
Institute of Scientific and Technical Information of China (English)
DELIGOZ Engin; COLAKOGLU Kemal; CIFTCI Yasemin Oztekin
2008-01-01
We perform the ab initio calculations based on norm-conserving pseudopotentials and density functional theory to investigate the structural, elastic, and thermodynamical properties for silver nitride (AgN) compound that is a member of the 4d transition metal group and has not been synthesized yet. The obtained results are compared with the other available theoretical data, and the agreement is, generally, quite good. We also present the pressure-dependent behaviour of some mechanical and thermodynamical properties for the same compounds.
Wood, Geoffrey P F; Sreedhara, Alavattam; Moore, Jamie M; Wang, John; Trout, Bernhardt L
2016-05-12
An assessment of the mechanisms of (•)OH and (•)OOH radical-mediated oxidation of tryptophan was performed using density functional theory calculations and ab initio plane-wave Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics simulations. For the (•)OH reactions, addition to the pyrrole ring at position 2 is the most favored site with a barrierless reaction in the gas phase. The subsequent degradation of this adduct through a H atom transfer to water was intermittently observed in aqueous-phase molecular dynamics simulations. For the (•)OOH reactions, addition to the pyrrole ring at position 2 is the most favored pathway, in contrast to the situation in the model system ethylene, where concerted addition to the double bond is preferred. From the (•)OOH position 2 adduct QM/MM simulations show that formation of oxy-3-indolanaline occurs readily in an aqueous environment. The observed transformation starts from an initial rupture of the O-O bond followed by a H atom transfer with the accompanying loss of an (•)OH radical to solution. Finally, classical molecular dynamics simulations were performed to equate observed differential oxidation rates of various tryptophan residues in monoclonal antibody fragments. It was found that simple parameters derived from simulation correlate well with the experimental data. PMID:27082439
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.
Energy Technology Data Exchange (ETDEWEB)
Rousseau, Roger J.; Schenter, Gregory K.; Fulton, John L.; Linehan, John C.; Engelhard, Mark H.; Autrey, Thomas
2009-08-05
We present the results of a detailed operando XAFS and density functional theory (DFT) based ab initio molecular dynamics (AIMD) investigation of the proposed mechanism of dehydrogenation of dimethylaminoborane (DMAB) by a homogeneous Rh4 cluster catalyst. Our AIMD simulations reveal that the previously proposed Rh structures are highly fluxional exhibiting both metal cluster and ligand isomerizations and dissociaton which can only be accounted for by a examining finite temperature ensemble as generated by AIMD. It is found that a highly fluxional species Rh4((H2BNMe2)82+ is fully compatible with operando XAFS measurements which suggest that this species may be the catalyst resting state. Based on this assignment we propose a catalytic mechanism for DMAB dehydrogenation which exhibits a maximum energy barrier of 24 kcal/mol, which is half that observed for the uncatalyzed thermal reaction. This work was supported by the U.S. Department of Energy's (DOE) Office of Basic Energy Sciences, Chemical Sciences program, and was performed in part using the Molecular Science Computing Facility (MSCF) in the William R. Wiley Environmental Molecular Sciences Laboratory, a DOE national scientific user facility located at the Pacific Northwest National Laboratory (PNNL). PNNL is operated by Battelle for the U.S. Department of Energy.
Energy Technology Data Exchange (ETDEWEB)
Zheng Xiaohong; Dai Zhenxiang; Zeng Zhi [Key Laboratory of Materials Physics, Institute of Solid State Physics, Chinese Academy of Sciences, Hefei 230031 (China)
2009-04-08
The role of electrodes in the transport properties of molecular devices is investigated by taking C{sub 60} as an example and using gold nanowire and a gold atomic chain as the electrodes. The calculations are done by an ab initio method combined with the non-equilibrium Green function technique. We find that devices in which a single C{sub 60} molecule is connected with different electrodes show completely different transport behavior. In the case of nanowire/C{sub 60}/nanowire the device shows a metallic behavior with a big equilibrium conductance (about 2.18G{sub 0}) and the current increases rapidly and almost linearly starting from zero. The transmission function shows wide peaks and platforms around the Fermi level. While in the atomic-chain/C{sub 60}/atomic-chain case, the device shows resonant tunneling behavior and the Fermi level lies between the HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital) transmission peaks. This results in a current that is one order of magnitude smaller than that in the nanowire/C{sub 60}/nanowire system and the current increases very slowly until the bias is big enough to include the LUMO peak in the bias window. The big difference in the conductance and the current arises from the different coupling between the electrodes and the C{sub 60} and the different number of channels in the electrodes.
Knyazev, D. V.; Levashov, P. R.
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. ...
Kopplung von Dichtefunktional- und ab-initio-Methoden
Goll, Erich
2008-01-01
Im Rahmen der Doktorarbeit wurde untersucht, inwieweit die Kopplung von Dichtefunktionalmethoden und ab-initio-Korrelationsmethoden der Quantenchemie eine Verbesserung bezüglich beider Grenzmethoden erbringt. Die Kopplung erfolgt durch eine Aufspaltung des interelektronischen Hamiltonoperators (abstoßende Coulombwechselwirkung). Die kurzreichweitige Wechselwirkung wird mit Dichtefunktionaltheorie behandelt, die langreichweitige mit Hilfe von ab-initio-Methoden. Diese Aufteilung soll dazu dien...
Gwaltney, Steven R; Rosokha, Sergiy V; Head-Gordon, Martin; Kochi, Jay K
2003-03-19
The highly disparate rates of aromatic nitrosation and nitration, despite the very similar (electrophilic) properties of the active species: NO(+) and NO(2)(+) in Chart 1, are quantitatively reconciled. First, the thorough mappings of the potential-energy surfaces by high level (ab initio) molecular-orbital methodologies involving extensive coupled-cluster CCSD(T)/6-31G optimizations establish the intervention of two reactive intermediates in nitration (Figure 8) but only one in nitrosation (Figure 7). Second, the same distinctive topologies involving double and single potential-energy minima (Figures 6 and 5) also emerge from the semiquantitative application of the Marcus-Hush theory to the transient spectral data. Such a striking convergence from quite different theoretical approaches indicates that the molecular-orbital and Marcus-Hush (potential-energy) surfaces are conceptually interchangeable. In the resultant charge-transfer mechanism, the bimolecular interactions of arene donors with both NO(+) and NO(2)(+) spontaneously lead (barrierless) to pi-complexes in which electron transfer is concurrent with complexation. Such a pi-complex in nitration is rapidly converted to the sigma-complex, whereas this Wheland adduct in nitrosation merely represents a high energy (transition-state) structure. Marcus-Hush analysis thus demonstrates how the strongly differentiated (arene) reactivities toward NO(+) and NO(2)(+) can actually be exploited in the quantitative development of a single coherent (electron-transfer) mechanism for both aromatic nitrosation and nitration.
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.
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.
Ab initio molar volumes and Gaussian radii.
Parsons, Drew F; Ninham, Barry W
2009-02-12
Ab initio molar volumes are calculated and used to derive radii for ions and neutral molecules using a spatially diffuse model of the electron distribution with Gaussian spread. The Gaussian radii obtained can be used for computation of nonelectrostatic ion-ion dispersion forces that underlie Hofmeister specific ion effects. Equivalent hard-sphere radii are also derived, and these are in reasonable agreement with crystalline ionic radii. The Born electrostatic self-energy is derived for a Gaussian model of the electronic charge distribution. It is shown that the ionic volumes used in electrostatic calculations of strongly hydrated cosmotropic ions ought best to include the first hydration shell. Ionic volumes for weakly hydrated chaotropic metal cations should exclude electron overlap (in electrostatic calculations). Spherical radii are calculated as well as nonisotropic ellipsoidal radii for nonspherical ions, via their nonisotropic static polarizability tensors. PMID:19140766
Ab Initio Path to Heavy Nuclei
Binder, Sven; Calci, Angelo; Roth, Robert
2014-01-01
We present the first ab initio calculations of nuclear ground states up into the domain of heavy nuclei, spanning the range from 16-O to 132-Sn based on two- plus three-nucleon interactions derived within chiral effective field theory. We employ the similarity renormalization group for preparing the Hamiltonian and use coupled-cluster theory to solve the many-body problem for nuclei with closed sub-shells. Through an analysis of theoretical uncertainties resulting from various truncations in this framework, we identify and eliminate the technical hurdles that previously inhibited the step beyond medium-mass nuclei, allowing for reliable validations of nuclear Hamiltonians in the heavy regime. Following this path we show that chiral Hamiltonians qualitatively reproduce the systematics of nuclear ground-state energies up to the neutron-rich Sn isotopes.
Ab initio alpha-alpha scattering
Elhatisari, Serdar; Lee, Dean; Rupak, Gautam; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A.; Luu, Thomas; Meißner, Ulf-G.
2015-12-01
Processes such as the scattering of alpha particles (4He), the triple-alpha reaction, and alpha capture play a major role in stellar nucleosynthesis. In particular, alpha capture on carbon determines the ratio of carbon to oxygen during helium burning, and affects subsequent carbon, neon, oxygen, and silicon burning stages. It also substantially affects models of thermonuclear type Ia supernovae, owing to carbon detonation in accreting carbon-oxygen white-dwarf stars. In these reactions, the accurate calculation of the elastic scattering of alpha particles and alpha-like nuclei—nuclei with even and equal numbers of protons and neutrons—is important for understanding background and resonant scattering contributions. First-principles calculations of processes involving alpha particles and alpha-like nuclei have so far been impractical, owing to the exponential growth of the number of computational operations with the number of particles. Here we describe an ab initio calculation of alpha-alpha scattering that uses lattice Monte Carlo simulations. We use lattice effective field theory to describe the low-energy interactions of protons and neutrons, and apply a technique called the ‘adiabatic projection method’ to reduce the eight-body system to a two-cluster system. We take advantage of the computational efficiency and the more favourable scaling with system size of auxiliary-field Monte Carlo simulations to compute an ab initio effective Hamiltonian for the two clusters. We find promising agreement between lattice results and experimental phase shifts for s-wave and d-wave scattering. The approximately quadratic scaling of computational operations with particle number suggests that it should be possible to compute alpha scattering and capture on carbon and oxygen in the near future. The methods described here can be applied to ultracold atomic few-body systems as well as to hadronic systems using lattice quantum chromodynamics to describe the interactions of
Ab initio alpha-alpha scattering.
Elhatisari, Serdar; Lee, Dean; Rupak, Gautam; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A; Luu, Thomas; Meißner, Ulf-G
2015-12-01
Processes such as the scattering of alpha particles ((4)He), the triple-alpha reaction, and alpha capture play a major role in stellar nucleosynthesis. In particular, alpha capture on carbon determines the ratio of carbon to oxygen during helium burning, and affects subsequent carbon, neon, oxygen, and silicon burning stages. It also substantially affects models of thermonuclear type Ia supernovae, owing to carbon detonation in accreting carbon-oxygen white-dwarf stars. In these reactions, the accurate calculation of the elastic scattering of alpha particles and alpha-like nuclei--nuclei with even and equal numbers of protons and neutrons--is important for understanding background and resonant scattering contributions. First-principles calculations of processes involving alpha particles and alpha-like nuclei have so far been impractical, owing to the exponential growth of the number of computational operations with the number of particles. Here we describe an ab initio calculation of alpha-alpha scattering that uses lattice Monte Carlo simulations. We use lattice effective field theory to describe the low-energy interactions of protons and neutrons, and apply a technique called the 'adiabatic projection method' to reduce the eight-body system to a two-cluster system. We take advantage of the computational efficiency and the more favourable scaling with system size of auxiliary-field Monte Carlo simulations to compute an ab initio effective Hamiltonian for the two clusters. We find promising agreement between lattice results and experimental phase shifts for s-wave and d-wave scattering. The approximately quadratic scaling of computational operations with particle number suggests that it should be possible to compute alpha scattering and capture on carbon and oxygen in the near future. The methods described here can be applied to ultracold atomic few-body systems as well as to hadronic systems using lattice quantum chromodynamics to describe the interactions of
Tsuzuki, Seiji; Hayamizu, Kikuko; Seki, Shiro; Ohno, Yasutaka; Kobayashi, Yo; Miyashiro, Hajime
2008-08-14
Interactions of the lithium bis(trifluoromethylsulfonyl)amide (LiTFSA) complex with N, N-diethyl-N-methyl-N-(2-methoxyethyl) ammonium (DEME), 1-ethyl-3-methylimidazolium (EMIM) cations, neutral diethylether (DEE), and the DEMETFSA complex were studied by ab initio molecular orbital calculations. An interaction energy potential calculated for the DEME cation with the LiTFSA complex has a minimum when the Li atom has contact with the oxygen atom of DEME cation, while potentials for the EMIM cation with the LiTFSA complex are always repulsive. The MP2/6-311G**//HF/6-311G** level interaction energy calculated for the DEME cation with the LiTFSA complex was -18.4 kcal/mol. The interaction energy for the neutral DEE with the LiTFSA complex was larger (-21.1 kcal/mol). The interaction energy for the DEMETFSA complex with LiTFSA complex is greater (-23.2 kcal/mol). The electrostatic and induction interactions are the major source of the attraction in the two systems. The substantial attraction between the DEME cation and the LiTFSA complex suggests that the interaction between the Li cation and the oxygen atom of DEME cation plays important roles in determining the mobility of the Li cation in DEME-based room temperature ionic liquids.
Rempe, S B; Pratt, L R; Rempe, Susan B.; Pratt, Lawrence R.
2003-01-01
K+(aq) ion is an integral component of many cellular processes, amongst which the most important, perhaps, is its role in transmitting electrical impulses along the nerve. Understanding its hydration structure and thermodynamics is crucial in dissecting its role in such processes. Her we address these questions using both the statistical mechanical quasi-chemical theory of solutions and ab initio molecular dynamics simulations. Simulations predict an interesting hydration structure for K+(aq): the population of about six (6) water molecules within the initial minimum of the observed g_{KO}(r) at infinite dilution involves four (4) inner-most molecules that the quasi-chemical theory suggests should be taken as the theoretical inner shell. The contribution of the 5th and 6th closest water molecules is observable as a distinct shoulder on the principal maximum of the g_{KO}(r). The quasi-chemical estimate of solvation free energy for the neutral pair KOH is also in good agreement with experiments.
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)
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.
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.
Nattino, Francesco; Galparsoro, Oihana; Costanzo, Francesca; Díez Muiño, Ricardo; Alducin, Maite; Kroes, Geert-Jan
2016-06-28
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.
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.
Lee, T. H.; Simdyankin, S. I.; Hegedus, J.; Heo, J.; Elliott, S. R.
2010-03-01
The spatial distribution of Nd3+ ions and GaS4 tetrahedral units in Nd-doped Ge-As-Ga-S glasses has been studied by laser spectroscopy and ab initio molecular dynamics (MD) simulations. A sharp increase in Nd3+ fluorescence intensities and lifetimes was observed with increasing Ga content, and attributed to the formation of tightly bound Nd3+ clusters in Ga-free glasses and the subsequent dissolution of such clusters upon Ga doping. A large modification in Nd3+ sites was also identified from low-temperature site-selective excitation spectra, suggesting preferential spatial correlations between Nd3+ and GaS4 tetrahedra even at low Ga-doping levels. MD simulations of these materials in the liquid state showed a tendency for Ga cluster formation as well as spatial correlations between Nd and Ga atoms consistent with the experimental results. On the basis of this result, a comprehensive structural model for Nd- and Ga-doped sulfide glasses is proposed.
Ab initio derivation of model energy density functionals
Dobaczewski, Jacek
2016-08-01
I propose a simple and manageable method that allows for deriving coupling constants of model energy density functionals (EDFs) directly from ab initio calculations performed for finite fermion systems. A proof-of-principle application allows for linking properties of finite nuclei, determined by using the nuclear nonlocal Gogny functional, to the coupling constants of the quasilocal Skyrme functional. The method does not rely on properties of infinite fermion systems but on the ab initio calculations in finite systems. It also allows for quantifying merits of different model EDFs in describing the ab initio results.
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 study of transport properties of an all-carbon molecular switch based on C20 molecule
Institute of Scientific and Technical Information of China (English)
OUYANG Fang-ping; XU Hui
2007-01-01
Choosing closed-ended armchair (5, 5) singlewall carbon nanotubes (CCNTs) as electrodes, we have investigated the electron transport properties across a carbon molecular junction consisting of a C20 molecule sandwiched between two semi-infinite carbon nanotubes. It is shown that the Landauer conductance of this carbon hybrid system can be tuned within several orders of magnitude not only by varying the tube-C20 distance, but more importantly by changing the orientation of the C20 molecule and rotating the C20 molecule or one of the tubes around the symmetry axis of the system at fixed distances. This fact could make this all-carbon molecular system a possible candidate for a nanoelectronic switching device. Moreover, our study also reveals that molecular configuration selection and structural relaxation would play an important role in the design of such devices.
Tachikawa, Hiroto
2014-06-01
The mechanism of dissolution of the Li(+) ion in an electrolytic solvent is investigated by the direct ab initio molecular dynamics (AIMD) method. Lithium fluoroborate (Li(+)BF4(-)) and ethylene carbonate (EC) are examined as the origin of the Li(+) ion and the solvent molecule, respectively. This salt is widely utilized as the electrolyte in the lithium ion secondary battery. The binding of EC to the Li(+) moiety of the Li(+)BF4(-) salt is exothermic, and the binding energies at the CAM-B3LYP/6-311++G(d,p) level for n=1, 2, 3, and 4, where n is the number of EC molecules binding to the Li(+) ion, (EC)n(Li(+)BF4(-)), are calculated to be 91.5, 89.8, 87.2, and 84.0 kcal mol(-1) (per EC molecule), respectively. The intermolecular distances between Li(+) and the F atom of BF4(-) are elongated: 1.773 Å (n=0), 1.820 Å (n=1), 1.974 Å (n=2), 1.942 Å (n=3), and 4.156 Å (n=4). The atomic bond populations between Li(+) and the F atom for n=0, 1, 2, 3, and 4 are 0.202, 0.186, 0.150, 0.038, and 0.0, respectively. These results indicate that the interaction of Li(+) with BF4(-) becomes weaker as the number of EC molecules is increased. The direct AIMD calculation for n=4 shows that EC reacts spontaneously with (EC)3(Li(+)BF4(-)) and the Li(+) ion is stripped from the salt. The following substitution reaction takes place: EC+(EC)3(Li(+)BF4(-))→(EC)4Li(+)-(BF4(-)). The reaction mechanism is discussed on the basis of the theoretical results. PMID:24616076
International Nuclear Information System (INIS)
The MIRS software for the modeling of ro-vibrational spectra of polyatomic molecules was considerably extended and improved. The original version [Nikitin AV, Champion JP, Tyuterev VlG. The MIRS computer package for modeling the rovibrational spectra of polyatomic molecules. J Quant Spectrosc Radiat Transf 2003;82:239-49.] was especially designed for separate or simultaneous treatments of complex band systems of polyatomic molecules. It was set up in the frame of effective polyad models by using algorithms based on advanced group theory algebra to take full account of symmetry properties. It has been successfully used for predictions and data fitting (positions and intensities) of numerous spectra of symmetric and spherical top molecules within the vibration extrapolation scheme. The new version offers more advanced possibilities for spectra calculations and modeling by getting rid of several previous limitations particularly for the size of polyads and the number of tensors involved. It allows dealing with overlapping polyads and includes more efficient and faster algorithms for the calculation of coefficients related to molecular symmetry properties (6C, 9C and 12C symbols for C3v, Td, and Oh point groups) and for better convergence of least-square-fit iterations as well. The new version is not limited to polyad effective models. It also allows direct predictions using full ab initio ro-vibrational normal mode Hamiltonians converted into the irreducible tensor form. Illustrative examples on CH3D, CH4, CH3Cl, CH3F and PH3 are reported reflecting the present status of data available. It is written in C++ for standard PC computer operating under Windows. The full package including on-line documentation and recent data are freely available at (http://www.iao.ru/mirs/mirs.htm) or (http://xeon.univ-reims.fr/Mirs/) or (http://icb.u-bourgogne.fr/OMR/SMA/SHTDS/MIRS.html) and as supplementary data from the online version of the article.
Energy Technology Data Exchange (ETDEWEB)
Oda, Y.; Koyama, T.; Funasaka, H. [Japan Nuclear Cycle Development Institute, Tokai Works (Japan)
2000-07-01
Ab initio molecular orbital calculations on the structure and stability of the complex of uranyl nitrate with water or tri-methyl phosphate (TMP) was performed using the Density Functional Theory with the basis set including the relativistic effects. When the aqua uranyl nitrate complex structure was calculated with two water molecules at the first coordination sphere, the optimized complex structure was not in agreement with the experimental data of [UO{sub 2}(NO{sub 3}){sub 2}(H{sub 2}O){sub 6}]. The optimization of the complex structure was improved by taking into account the influence of outer four water molecules at the second coordination sphere, which should bond with inner water molecules through the water hydrogen. It means the solution effect is not negligible for the coordination of the ligands such as water. For the H{sub 3}PO{sub 4} coordination, eight models were preferred, one group had the coordination angle of U-O-P in H{sub 3}PO{sub 4} is bent, and other group had straight and the four combinations of the direction of three O-H groups. [UO{sub 2}(NO{sub 3})2(H{sub 3}PO{sub 4}){sub 2}] had greater stability, when U-O-P angle was bent, and there were on the equatorial plane. Finally, the structure of [UO{sub 2}(NO{sub 3}){sub 2}TMP{sub 2}] is optimized, and the optimized geometry has agreement with experimental values. From the comparison of H{sub 3}PO{sub 4} and TMP coordination, the alkyl group in the organophosphorus ligand strongly influences the bond angle of U-O-P. (authors)
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.
Ab Initio Study of KCl and NaCl Clusters
Brownrigg, Clifton; Hira, Ajit; Pacheco, Jose; Salazar, Justin
2013-03-01
We continue our interest in the theoretical study of molecular clusters to examine the chemical properties of small KnCln and NanCln clusters (n = 2 - 15). The potentially important role of these molecular species in biochemical and medicinal processes is well known. This work applies the hybrid ab initio methods of quantum chemistry to derive the different alkali-halide (MnHn) geometries. Of particular interest is the competition between hexagonal ring geometries and rock salt structures. Electronic energies, rotational constants, dipole moments, and vibrational frequencies for these geometries are calculated. Magic numbers for cluster stability are identified and are related to the property of cluster compactness. Mapping of the singlet, triplet, and quintet, potential energy surfaces is performed. Calculations have been performed to examine the interactions of these clusters with some atoms and molecules of biological interest, including O, O2, and Fe. The potential for design of new medicinal drugs is explored.
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.
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.
Abe, Akihiro; Furuya, Hidemine; Ichimura, Noriko; Kawauchi, Susumu
1997-02-01
The gas-phase NMR analysis of 5-methoxy-1,3-dioxanes was carried out. The conformational energies estimated from the observed coupling constant data were compared with the results of ab initio MO calculations using d95 + (2df,p) basis set at the MP2 level. While the energy difference between the axial-out and equatorial-out forms was in a reasonable agreement, the 1,5 interaction energy between the methoxy methyl and the ring oxygens was not in accord.
Analytic ab initio-based molecular interaction potential for the BrOṡH2O complex
Hoehn, Ross D.; Yeole, Sachin D.; Kais, Sabre; Francisco, Joseph S.
2016-05-01
Radical halogen oxide species play important roles within atmospheric processes, specifically those responsible for the removal of O3. To facilitate future investigations on this family of compounds, RCCSD(T)/aug-cc-pVQZ-level electronic structure calculations were employed to generate individual-molecule optimized geometries, as well as to determine the global minimum energy structure for the BrOṡH2O complex. This information facilitated the generation of several one-dimensional potential energy surface (PES) scans for the BrOṡH2O complex. Scans were performed for both the ground state and the first excited state; this inclusion is due to a low-lying first electronic excited-state energy. These rigid-geometry PES scans were used both to generate a novel analytic interaction potential by modifying the existing Thole-type model used for water and to the fitted potential function. This interaction potential features anisotropic atomic polarizabilities facilitating appropriate modeling of the physics regarding the unpaired electron residing within the p-orbitals of the oxygen atom of the bromine oxide radical. The intention of this work is to facilitate future molecular dynamics simulations involving the interaction between the BrO radical and water clusters as a first step in devising possible novel chemistries taking place at the water interface of clouds within the atmosphere.
Ab Initio Calculations of Deuterium Isotope Effects on Chemical Shifts of Salt-Bridged Lysines
DEFF Research Database (Denmark)
Ullah, Saif; Ishimoto, Takayoshi; Williamson, Mike P.;
2011-01-01
Deuterium isotope effects measure the change in chemical shift on substitution of a proton by deuterium. They have been calculated by direct treatment of the H/D nuclear quantum effect using a multicomponent ab initio molecular orbital method based on a non-Born−Oppenheimer approximation. This me......Deuterium isotope effects measure the change in chemical shift on substitution of a proton by deuterium. They have been calculated by direct treatment of the H/D nuclear quantum effect using a multicomponent ab initio molecular orbital method based on a non-Born−Oppenheimer approximation...
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.
Energy Technology Data Exchange (ETDEWEB)
Barrett, B R; Navratil, P; Vary, J P
2011-04-11
A long-standing goal of nuclear theory is to determine the properties of atomic nuclei based on the fundamental interactions among the protons and neutrons (i.e., nucleons). By adopting nucleon-nucleon (NN), three-nucleon (NNN) and higher-nucleon interactions determined from either meson-exchange theory or QCD, with couplings fixed by few-body systems, we preserve the predictive power of nuclear theory. This foundation enables tests of nature's fundamental symmetries and offers new vistas for the full range of complex nuclear phenomena. Basic questions that drive our quest for a microscopic predictive theory of nuclear phenomena include: (1) What controls nuclear saturation; (2) How the nuclear shell model emerges from the underlying theory; (3) What are the properties of nuclei with extreme neutron/proton ratios; (4) Can we predict useful cross sections that cannot be measured; (5) Can nuclei provide precision tests of the fundamental laws of nature; and (6) Under what conditions do we need QCD to describe nuclear structure, among others. Along with other ab initio nuclear theory groups, we have pursued these questions with meson-theoretical NN interactions, such as CD-Bonn and Argonne V18, that were tuned to provide high-quality descriptions of the NN scattering phase shifts and deuteron properties. We then add meson-theoretic NNN interactions such as the Tucson-Melbourne or Urbana IX interactions. More recently, we have adopted realistic NN and NNN interactions with ties to QCD. Chiral perturbation theory within effective field theory ({chi}EFT) provides us with a promising bridge between QCD and hadronic systems. In this approach one works consistently with systems of increasing nucleon number and makes use of the explicit and spontaneous breaking of chiral symmetry to expand the strong interaction in terms of a dimensionless constant, the ratio of a generic small momentum divided by the chiral symmetry breaking scale taken to be about 1 GeV/c. The
International Nuclear Information System (INIS)
A long-standing goal of nuclear theory is to determine the properties of atomic nuclei based on the fundamental interactions among the protons and neutrons (i.e., nucleons). By adopting nucleon-nucleon (NN), three-nucleon (NNN) and higher-nucleon interactions determined from either meson-exchange theory or QCD, with couplings fixed by few-body systems, we preserve the predictive power of nuclear theory. This foundation enables tests of nature's fundamental symmetries and offers new vistas for the full range of complex nuclear phenomena. Basic questions that drive our quest for a microscopic predictive theory of nuclear phenomena include: (1) What controls nuclear saturation; (2) How the nuclear shell model emerges from the underlying theory; (3) What are the properties of nuclei with extreme neutron/proton ratios; (4) Can we predict useful cross sections that cannot be measured; (5) Can nuclei provide precision tests of the fundamental laws of nature; and (6) Under what conditions do we need QCD to describe nuclear structure, among others. Along with other ab initio nuclear theory groups, we have pursued these questions with meson-theoretical NN interactions, such as CD-Bonn and Argonne V18, that were tuned to provide high-quality descriptions of the NN scattering phase shifts and deuteron properties. We then add meson-theoretic NNN interactions such as the Tucson-Melbourne or Urbana IX interactions. More recently, we have adopted realistic NN and NNN interactions with ties to QCD. Chiral perturbation theory within effective field theory (χEFT) provides us with a promising bridge between QCD and hadronic systems. In this approach one works consistently with systems of increasing nucleon number and makes use of the explicit and spontaneous breaking of chiral symmetry to expand the strong interaction in terms of a dimensionless constant, the ratio of a generic small momentum divided by the chiral symmetry breaking scale taken to be about 1 GeV/c. The resulting NN
Sun, Geng; Jiang, Hong
2015-12-21
A comprehensive understanding of surface thermodynamics and kinetics based on first-principles approaches is crucial for rational design of novel heterogeneous catalysts, and requires combining accurate electronic structure theory and statistical mechanics modeling. In this work, ab initio molecular dynamics (AIMD) combined with the integrated tempering sampling (ITS) method has been explored to study thermodynamic and kinetic properties of elementary processes on surfaces, using a simple reaction CH2⇌CH+H on the Ni(111) surface as an example. By a careful comparison between the results from ITS-AIMD simulation and those evaluated in terms of the harmonic oscillator (HO) approximation, it is found that the reaction free energy and entropy from the HO approximation are qualitatively consistent with the results from ITS-AIMD simulation, but there are also quantitatively significant discrepancies. In particular, the HO model misses the entropy effects related to the existence of multiple adsorption configurations arising from the frustrated translation and rotation motion of adsorbed species, which are different in the reactant and product states. The rate constants are evaluated from two ITS-enhanced approaches, one using the transition state theory (TST) formulated in terms of the potential of mean force (PMF) and the other one combining ITS with the transition path sampling (TPS) technique, and are further compared to those based on harmonic TST. It is found that the rate constants from the PMF-based TST are significantly smaller than those from the harmonic TST, and that the results from PMF-TST and ITS-TPS are in a surprisingly good agreement. These findings indicate that the basic assumptions of transition state theory are valid in such elementary surface reactions, but the consideration of statistical averaging of all important adsorption configurations and reaction pathways, which are missing in the harmonic TST, are critical for accurate description of
Sun, Geng; Jiang, Hong
2015-12-01
A comprehensive understanding of surface thermodynamics and kinetics based on first-principles approaches is crucial for rational design of novel heterogeneous catalysts, and requires combining accurate electronic structure theory and statistical mechanics modeling. In this work, ab initio molecular dynamics (AIMD) combined with the integrated tempering sampling (ITS) method has been explored to study thermodynamic and kinetic properties of elementary processes on surfaces, using a simple reaction CH 2 ⇌ CH + H on the Ni(111) surface as an example. By a careful comparison between the results from ITS-AIMD simulation and those evaluated in terms of the harmonic oscillator (HO) approximation, it is found that the reaction free energy and entropy from the HO approximation are qualitatively consistent with the results from ITS-AIMD simulation, but there are also quantitatively significant discrepancies. In particular, the HO model misses the entropy effects related to the existence of multiple adsorption configurations arising from the frustrated translation and rotation motion of adsorbed species, which are different in the reactant and product states. The rate constants are evaluated from two ITS-enhanced approaches, one using the transition state theory (TST) formulated in terms of the potential of mean force (PMF) and the other one combining ITS with the transition path sampling (TPS) technique, and are further compared to those based on harmonic TST. It is found that the rate constants from the PMF-based TST are significantly smaller than those from the harmonic TST, and that the results from PMF-TST and ITS-TPS are in a surprisingly good agreement. These findings indicate that the basic assumptions of transition state theory are valid in such elementary surface reactions, but the consideration of statistical averaging of all important adsorption configurations and reaction pathways, which are missing in the harmonic TST, are critical for accurate description of
Ab initio simulation of transport phenomena in rarefied gases.
Sharipov, Felix; Strapasson, José L
2012-09-01
Ab initio potentials are implemented into the direct simulation Monte Carlo (DSMC) method. Such an implementation allows us to model transport phenomena in rarefied gases without any fitting parameter of intermolecular collisions usually extracted from experimental data. Applying the method proposed by Sharipov and Strapasson [Phys. Fluids 24, 011703 (2012)], the use of ab initio potentials in the DSMC requires the same computational efforts as the widely used potentials such as hard spheres, variable hard sphere, variable soft spheres, etc. At the same time, the ab initio potentials provide more reliable results than any other one. As an example, the transport coefficients of a binary mixture He-Ar, viz., viscosity, thermal conductivity, and thermal diffusion factor, have been calculated for several values of the mole fraction. PMID:23030889
Ab initio calculations versus polarized neutron diffraction for the spin density of free radicals
International Nuclear Information System (INIS)
The determination of the magnetization distribution using polarized neutron diffraction has played a key role during the last twenty years in the field of molecular magnetism. This distribution can also be obtained by first principle ab initio calculations. Such calculations always rely on approximations and the question that arises is to know whether the obtained results are reliable enough to represent accurately the properties of these molecules. The comparison between polarized neutron experimental results and ab initio calculations has turned to provide stringent tests for these methods. In the resent article a comparison between experimental and theoretical results is made and is illustrated by examples based on magnetic free radicals. (author)
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.
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.
Towards new horizons in ab initio nuclear structure theory
International Nuclear Information System (INIS)
We review recent advances in ab initio nuclear structure theory, which have changed the horizons of this field. Starting from chiral effective field theory to construct the nuclear Hamiltonian and the similarity renormalization group to further soften it, we address several many-body approaches that have seen major developments over the past few years. We show that the domain of ab initio nuclear structure theory has been pushed well beyond the p-shell and that quantitative QCD-based predictions are becoming possible all the way from the proton to the neutron drip line up into the medium-mass regime. (authors)
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.
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.
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 respo...
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...
DEFF Research Database (Denmark)
Wolf, T. J. A.; Kuhlman, Thomas Scheby; Schalk, O.;
2014-01-01
comparing time-resolved photoelectron spectroscopy (TRPES) with ab initio multiple spawning (AIMS) simulations on the MS-MR-CASPT2 level of theory. We disentangle the relationship between two phenomena that dominate the immediate molecular response upon light absorption: a spectrally dependent delay of the...
Cyanogen Azide. Ionization Potentials and Ab Initio SCF MO Calculation
DEFF Research Database (Denmark)
Bak, Börge; Jansen, Peter; Stafast, Herbert
1975-01-01
The Ne(I) and He(I) photoelectron(PE) spectra of cyanogen azide, NCN3, have been recorded at high resolution. Their interpretation is achieved by comparison with the PE spectrum of HN3 and an ab initio LCGO SCF MO calculation. Deviations from Koopmans' theorem of quite different magnitudes are fo...
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.
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 ...
Surface Tension of Ab Initio Liquid Water at the Water-Air Interface
Nagata, Yuki; Ohto, Tatsuhiko; 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 sim...
Ab initio studies of O2−(H2On and O3−(H2On anionic molecular clusters, n≤12
Directory of Open Access Journals (Sweden)
H. Svensmark
2011-05-01
Full Text Available An ab initio study of gaseous clusters of O2− and O2− with water is presented. Based on thorough scans of configurational space, we determine the thermodynamics of cluster growth. The results are in good agreement with benchmark computational methods and existing experimental data. We find that anionic O2−(H2On and O3−(H2On clusters are thermally stabilized at typical atmospheric conditions for at least n = 5. The first 4 water molecules are strongly bound to the anion due to delocalization of the excess charge while stabilization of more than 4 H2O is due to normal hydrogen bonding. Although clustering up to 12 H2O, we find that the O2 and O3 anions retain at least ca. 80 % of the charge and are located at the surface of the cluster. The O2− and O3− speicies are thus accessible for further reactions. Finally, the thermodynamics of a few relevant cluster reactions are considered.
Ab initio studies of phoshorene island single electron transistor.
Ray, S J; Venkata Kamalakar, M; Chowdhury, R
2016-05-18
Phosphorene is a newly unveiled two-dimensional crystal with immense potential for nanoelectronic and optoelectronic applications. Its unique electronic structure and two dimensionality also present opportunities for single electron devices. Here we report the behaviour of a single electron transistor (SET) made of a phosphorene island, explored for the first time using ab initio calculations. We find that the band gap and the charging energy decrease monotonically with increasing layer numbers due to weak quantum confinement. When compared to two other novel 2D crystals such as graphene and MoS2, our investigation reveals larger adsorption energies of gas molecules on phosphorene, which indicates better a sensing ability. The calculated charge stability diagrams show distinct changes in the presence of an individual molecule which can be applied to detect the presence of different molecules with sensitivity at a single molecular level. The higher charging energies of the molecules within the SET display operational viability at room temperature, which is promising for possible ultra sensitive detection applications. PMID:27093536
Ab initio studies of phosphorene island single electron transistor
Ray, S. J.; Venkata Kamalakar, M.; Chowdhury, R.
2016-05-01
Phosphorene is a newly unveiled two-dimensional crystal with immense potential for nanoelectronic and optoelectronic applications. Its unique electronic structure and two dimensionality also present opportunities for single electron devices. Here we report the behaviour of a single electron transistor (SET) made of a phosphorene island, explored for the first time using ab initio calculations. We find that the band gap and the charging energy decrease monotonically with increasing layer numbers due to weak quantum confinement. When compared to two other novel 2D crystals such as graphene and MoS2, our investigation reveals larger adsorption energies of gas molecules on phosphorene, which indicates better a sensing ability. The calculated charge stability diagrams show distinct changes in the presence of an individual molecule which can be applied to detect the presence of different molecules with sensitivity at a single molecular level. The higher charging energies of the molecules within the SET display operational viability at room temperature, which is promising for possible ultra sensitive detection applications.
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)
Augmented wave ab initio EFG calculations: some methodological warnings
Energy Technology Data Exchange (ETDEWEB)
Errico, Leonardo A. [Departamento de Fisica-IFLP (CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CC67 (1900) La Plata (Argentina); Renteria, Mario [Departamento de Fisica-IFLP (CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, CC67 (1900) La Plata (Argentina); Petrilli, Helena M. [Instituto de Fisica-DFMT, Universidade de Sao Paulo, C.P. 66318, 05315-970 Sao Paulo, SP (Brazil)]. E-mail: hmpetril@macbeth.if.usp.br
2007-02-01
We discuss some accuracy aspects inherent to ab initio electronic structure calculations in the understanding of nuclear quadrupole interactions. We use the projector augmented wave method to study the electric-field gradient (EFG) at both Sn and O sites in the prototype cases SnO and SnO{sub 2}. The term ab initio is used in the standard context of the also called first principles methods in the framework of the Density Functional Theory. As the main contributions of EFG calculations to problems in condensed matter physics are related to structural characterizations on the atomic scale, we discuss the 'state of the art' on theoretical EFG calculations and make a brief critical review on the subject, calling attention to some fundamental theoretical aspects.
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...
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.
The density matrix renormalization group for ab initio quantum chemistry
Wouters, Sebastian
2015-01-01
During the past 15 years, the density matrix renormalization group (DMRG) has become increasingly important for ab initio quantum chemistry. It is used as a numerically exact solver for highly correlated regions in molecules. While the method works extremely well for one-dimensional systems, the correlated regions of interest are often far from one-dimensional. In this introductory talk, I will discuss the DMRG algorithm from a quantum information perspective, how quantum information theory h...
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.
P-V Relation for Mercuric Calcogenides: Ab Initio Method
G. Misra; S. Tenguria; Gautam, M.
2011-01-01
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 a...
Ab-initio calculations for dilute magnetic semiconductors
Belhadji, Brahim
2008-01-01
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 approximatio...
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.
Rudolph, Wolfram W; Fischer, Dieter; Irmer, Gert; Pye, Cory C
2009-09-01
Raman spectra of aqueous beryllium perchlorate, chloride, nitrate, and sulfate solutions have been measured over a broad concentration (0.098-4.950 mol L(-1)) range. The Raman spectroscopic data suggest that the tetra-aqua beryllium(II) ion is thermodynamically stable in perchlorate, chloride, and nitrate solutions over the concentration range measured. No inner-sphere complexes in these solutions could be detected spectroscopically except in very concentrated beryllium nitrate solutions. Beryllium sulfate solutions however, show a different picture, namely the existence of a thermodynamically stable beryllium sulfato complex most likely monodentate even at very low concentrations. At very high beryllium sulfate concentrations, a small quantity of a bidentate sulfato complex was found. With a temperature increase, the sulfato complex formation increases and this demonstrates the entropically driven sulfato complex formation. Furthermore, with increased temperature the hydrolysis increases, measured by the formation of hydrogen sulfate. Ab initio geometry optimizations and frequency calculations are reported for beryllium-water clusters with only inner sphere waters, clusters with an inner sphere and an incomplete second hydration, and clusters with a higher number of waters in the second hydration sphere. The cluster, [Be(OH2)(12)(2+)] (Be[4 + 8]) with 4 water molecules in the first sphere and 8 water molecules in the second sphere gave sufficiently realistic frequencies for BeO4 skeleton in comparison to the experimental ones. However, the cluster, [Be(OH2)(18)(2+)] (Be[6 + 12]) with 6 water molecules in the inner sphere and 12 water molecules in the outer sphere on an energy minimum gave unrealistically low BeO4 frequencies. This fact demonstrates that a six-fold coordination of Be2+ can be ruled out.
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).
A highly accurate ab initio potential energy surface for methane
Owens, Alec; Yurchenko, Sergei N.; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter
2016-09-01
A new nine-dimensional potential energy surface (PES) for methane has been generated using state-of-the-art 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 12CH4 reproduced with a root-mean-square error of 0.70 cm-1. The computed 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 equilibrium geometry. The PES represents the most accurate ab initio surface to date and will serve as a good starting point for empirical refinement.
Acceleration of the Convergence in ab initio Atomic Relaxations
Zhao, Zhengji; Wang, Lin-Wang; Meza, Juan
2006-03-01
Atomic relaxations is often required to accurately describe the properties of nanosystems. In ab initio calculations, a common practice is to use a standard search algorithm, such as BFGS (Broyden-Fletcher-Goldfarb-Shanno) or CG (conjugate gradient) method, which starts the atomic relaxations without any knowledge of the Hessian matrix of the system. For example, the initial Hessian in BFGS method is often set to identity, and there is no preconditioning to CG method. One way to accelerate the convergence of the atomic relaxations is to estimate an approximate Hessian matrix of the system and then use it as the initial Hessian in BFGS method or a preconditioner in CG method. Previous attempts to obtain the approximated Hessian were focused on the use of classical force field models which rely on the existence of good parameters. Here, we present an alternative method to estimate the Hessian matrix of a nanosystem. First, we decompose the system into motifs which consist of a few atoms, then calculate the Hessian matrix elements on different motif types from ab initio calculations for small prototype systems. Then we generate the Hessian Matrix of the whole system by putting together these motif Hessians. We have applied our motif-based Hessian matrix in ab initio atomic relaxations in several bulk (with/without impurity) and quantum dot systems, and have found a speed up factor of 2 to 4 depending on the system size.
A Complete and Accurate Ab Initio Repeat Finding Algorithm.
Lian, Shuaibin; Chen, Xinwu; Wang, Peng; Zhang, Xiaoli; Dai, Xianhua
2016-03-01
It has become clear that repetitive sequences have played multiple roles in eukaryotic genome evolution including increasing genetic diversity through mutation, changes in gene expression and facilitating generation of novel genes. However, identification of repetitive elements can be difficult in the ab initio manner. Currently, some classical ab initio tools of finding repeats have already presented and compared. The completeness and accuracy of detecting repeats of them are little pool. To this end, we proposed a new ab initio repeat finding tool, named HashRepeatFinder, which is based on hash index and word counting. Furthermore, we assessed the performances of HashRepeatFinder with other two famous tools, such as RepeatScout and Repeatfinder, in human genome data hg19. The results indicated the following three conclusions: (1) The completeness of HashRepeatFinder is the best one among these three compared tools in almost all chromosomes, especially in chr9 (8 times of RepeatScout, 10 times of Repeatfinder); (2) in terms of detecting large repeats, HashRepeatFinder also performed best in all chromosomes, especially in chr3 (24 times of RepeatScout and 250 times of Repeatfinder) and chr19 (12 times of RepeatScout and 60 times of Repeatfinder); (3) in terms of accuracy, HashRepeatFinder can merge the abundant repeats with high accuracy. PMID:26272474
Ab initio nuclear structure - the large sparse matrix eigenvalue problem
International Nuclear Information System (INIS)
The structure and reactions of light nuclei represent fundamental and formidable challenges for microscopic theory based on realistic strong interaction potentials. Several ab initio methods have now emerged that provide nearly exact solutions for some nuclear properties. The 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 1010 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 this large sparse matrix eigenvalue problem. We also outline the challenges that lie ahead for achieving further breakthroughs in fundamental nuclear theory using these ab initio approaches.
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)
2015-05-07
In the work reported in this paper, ab initio molecular dynamics simulation was performed on Fe{sub 85}Si{sub 2}B{sub 9}P{sub 4} amorphous alloy. Preferred atomic environment of the elements was analyzed with Voronoi polyhedrons. It showed that B and P atoms prefer less neighbors compared with Fe and Si, making them structurally incompatible with Fe rich structure and repulsive to the formation of α-Fe. However, due to the low bonding energy of B and P caused by low coordination number, the diffusion rates of them were considerably large, resulting in the requirement of fast annealing for achieving optimum nano-crystallization for its soft magnetic property. The simulation work also indicates that diffusion rate in amorphous alloy is largely determined by bonding energy rather than atomic size.
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.
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.
Knyazev, D. V.; Levashov, P. R.
2013-01-01
This work is devoted to the \\textit{ab initio} calculation of transport and optical properties of aluminum. The calculation is based on the quantum molecular dynamics simulation, density functional theory and the Kubo-Greenwood formula. Mainly the calculations are performed for liquid aluminum at near-normal densities for the temperatures from melting up to 20000 K. The results on dynamic electrical conductivity, static electrical conductivity and thermal conductivity are obtained and compare...
Ab initio simulations of liquid NaSn alloys: Zintl anions and network formation
Schoene, M.; Kaschner, R.; Seifert, G
1994-01-01
Using the Car-Parrinello technique, ab initio molecular dynamics simulations are performed for liquid NaSn alloys in five different compositions (20, 40, 50, 57 and 80 % sodium). The obtained structure factors agree well with the data from neutron scattering experiments. The measured prepeak in the structure factor is reproduced qualitatively for most compositions. The calculated and measured positions of all peaks show the same trend as function of the composition.\\\\ The dynamic simulations ...
B28: the smallest all-boron cage from an ab initio global search
Zhao, Jijun; Huang, Xiaoming; Shi, Ruili; Liu, Hongsheng; Su, Yan; King, R. Bruce
2015-09-01
Our ab initio global searches reveal the lowest-energy cage for B28, which is built from two B12 units and prevails over the competing structural isomers such as planar, bowl, and tube. This smallest boron cage extends the scope of all-boron fullerene and provides a new structural motif of boron clusters and nanostructures.Our ab initio global searches reveal the lowest-energy cage for B28, which is built from two B12 units and prevails over the competing structural isomers such as planar, bowl, and tube. This smallest boron cage extends the scope of all-boron fullerene and provides a new structural motif of boron clusters and nanostructures. Electronic supplementary information (ESI) available: Planar isomer structures of B28 and spatial distributions of front molecular orbitals. See DOI: 10.1039/c5nr04034e
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.
Electrostriction coefficient of ferroelectric materials from ab initio computation
Directory of Open Access Journals (Sweden)
Z. Jiang
2016-06-01
Full Text Available Electrostriction is an important material property that characterizes how strain changes with the development of polarization inside a material. We show that ab initio techniques developed in recent years can be exploited to compute and understand electrostriction of ferroelectric materials. Here, electrostriction coefficients of ferroelectric BaTiO3, PbTiO3, as well as dielectric BaZrO3, are obtained and analyzed. Possible causes of the difference between experimental and numerical results are discussed. We also identified that relative displacements between certain ions at a given polarization could be a good indicator of a material’s electrostriction property.
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 study of neutron drops with chiral Hamiltonians
Directory of Open Access Journals (Sweden)
H.D. Potter
2014-12-01
Full Text Available We report ab initio calculations for neutron drops in a 10 MeV external harmonic-oscillator trap using chiral nucleon–nucleon plus three-nucleon interactions. We present total binding energies, internal energies, radii and odd–even energy differences for neutron numbers N=2–18 using the no-core shell model with and without importance truncation. Furthermore, we present total binding energies for N=8,16,20,28,40,50 obtained in a coupled-cluster approach. Comparisons with quantum Monte Carlo results, where available, using Argonne v8′ with three-nucleon interactions reveal important dependences on the chosen Hamiltonian.
Equations of state of heavy metals: ab initio approaches
International Nuclear Information System (INIS)
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)
Ab initio calculations and modelling of atomic cluster structure
DEFF Research Database (Denmark)
Solov'yov, Ilia; Lyalin, Andrey G.; Solov'yov, Andrey V.;
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...... framework for modelling the fusion process of noble gas clusters is presented. We report the striking correspondence of the peaks in the experimentally measured abundance mass spectra with the peaks in the size-dependence of the second derivative of the binding energy per atom calculated for the chain...... of the noble gas clusters up to 150 atoms....
Ab initio Study of He Stability in hcp-Ti
Institute of Scientific and Technical Information of China (English)
DAI Yun-Ya; YANG Li; PENG Shu-Ming; LONG Xing-Gui; GAO Fei; ZU Xiao-Tao
2010-01-01
@@ The stability of He in hcp-Ti is studied using the ab initio method based on the density functional theory.The results indicate that a single He atom prefers to occupy the tetrahedral site rather than the octahedral site.The interaction of He defects with Ti atoms is employed to explain the relative stabilities of He point defects in hcp-Ti.The relative stability of He defects in hcp-Ti is useful for He clustering and bubble nucleation in metal tritides,which provides the basis for development of improved atomistic models.
Polymeric nitrogen in a graphene matrix: An ab initio study
Timoshevskii, V.; Ji, Wei; Abou-Rachid, Hakima; Lussier, Louis-Simon; Guo, H.
2009-09-01
A hybrid material where polymeric nitrogen chains are sandwiched between graphene sheets in the form of a three-dimensional crystal, is predicted by means of ab initio simulations. It is demonstrated that chainlike polymeric nitrogen phase becomes stable at ambient pressure when intercalated in a multilayer graphene matrix. The physical origin of this stabilization is identified by studying the electronic properties of the system. This approach of stabilizing polymeric nitrogen by means of external three-dimensional matrix constitutes a path toward synthesizing different types of nitrogen-based high-energy materials.
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.
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 Protein Structure Prediction Using Pathway Models
Directory of Open Access Journals (Sweden)
Christopher Bystroff
2006-04-01
Full Text Available Ab initio prediction is the challenging attempt to predict protein structures based only on sequence information and without using templates. It is often divided into two distinct sub-problems: (a the scoring function that can distinguish native, or native-like structures, from non-native ones; and (b the method of searching the conformational space. Currently, there is no reliable scoring function that can always drive a search to the native fold, and there is no general search method that can guarantee a significant sampling of near-natives. Pathway models combine the scoring function and the search. In this short review, we explore some of the ways pathway models are used in folding, in published works since 2001, and present a new pathway model, HMMSTR-CM, that uses a fragment library and a set of nucleation/propagation-based rules. The new method was used for ab initio predictions as part of CASP5. This work was presented at the Winter School in Bioinformatics, Bologna, Italy, 10Ã¢Â€Â“14 February 2003.
Unified ab initio approaches to nuclear structure and reactions
Navrátil, Petr; Quaglioni, Sofia; Hupin, Guillaume; Romero-Redondo, Carolina; Calci, Angelo
2016-05-01
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 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 6He halo nucleus, of five- and six-nucleon scattering, and an investigation of the role of chiral three-nucleon interactions in the structure of 9Be. Further, we discuss applications to the 7Be {({{p}},γ )}8{{B}} radiative capture. Finally, we highlight our efforts to describe transfer reactions including the 3H{({{d}},{{n}})}4He fusion.
Three-cluster dynamics within an ab initio framework
Quaglioni, S; Navrátil, P
2013-01-01
We introduce a fully antisymmetrized treatment of three-cluster dynamics within the ab initio framework of the no-core shell model/resonating-group method (NCSM/RGM). Energy-independent non-local interactions among the three nuclear fragments are obtained from realistic nucleon-nucleon interactions and consistent ab initio many-body wave functions of the clusters. The three-cluster Schr\\"odinger equation is solved with bound-state boundary conditions by means of the hyperspherical-harmonic method on a Lagrange mesh. We discuss the formalism in detail and give algebraic expressions for systems of two single nucleons plus a nucleus. Using a soft similarity-renormalization-group evolved chiral nucleon-nucleon potential, we apply the method to an $^4$He+$n+n$ description of $^6$He and compare the results to experiment and to a six-body diagonalization of the Hamiltonian performed within the harmonic-oscillator expansions of the NCSM. Differences between the two calculations provide a measure of core ($^4$He) pola...
AB INITIO SIMULATIONS FOR MATERIAL PROPERTIES ALONG THE JUPITER ADIABAT
International Nuclear Information System (INIS)
We determine basic thermodynamic and transport properties of hydrogen-helium-water mixtures for the extreme conditions along Jupiter's adiabat via ab initio simulations, which are compiled in an accurate and consistent data set. In particular, we calculate the electrical and thermal conductivity, the shear and longitudinal viscosity, and diffusion coefficients of the nuclei. We present results for associated quantities like the magnetic and thermal diffusivity and the kinematic shear viscosity along an adiabat that is taken from a state-of-the-art interior structure model. Furthermore, the heat capacities, the thermal expansion coefficient, the isothermal compressibility, the Grüneisen parameter, and the speed of sound are calculated. We find that the onset of dissociation and ionization of hydrogen at about 0.9 Jupiter radii marks a region where the material properties change drastically. In the deep interior, where the electrons are degenerate, many of the material properties remain relatively constant. Our ab initio data will serve as a robust foundation for applications that require accurate knowledge of the material properties in Jupiter's interior, e.g., models for the dynamo generation.
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.......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...... 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...
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...
In pursuit of the ab initio limit for conformational energy prototypes
Császár, Attila G.; Allen, Wesley D.; Schaefer, Henry F.
1998-06-01
The convergence of ab initio predictions to the one- and n-particle limits has been systematically explored for several conformational energy prototypes: the inversion barriers of ammonia, water, and isocyanic acid, the torsional barrier of ethane, the E/Z rotamer separation of formic acid, and the barrier to linearity of silicon dicarbide. Explicit ab initio results were obtained with atomic-orbital basis sets as large as [7s6p5d4f3g2h1i/6s5p4d3f2g1h] and electron correlation treatments as extensive as fifth-order Møller-Plesset perturbation theory (MP5), the full coupled-cluster method through triple excitations (CCSDT), and Brueckner doubles theory including perturbational corrections for both triple and quadruple excitations [BD(TQ)]. Subsequently, basis set and electron correlation extrapolation schemes were invoked to gauge any further variations in arriving at the ab initio limit. Physical effects which are tacitly neglected in most theoretical work have also been quantified by computations of non-Born-Oppenheimer (BODC), relativistic, and core correlation shifts of relative energies. Instructive conclusions are drawn for the pursuit of spectroscopic accuracy in theoretical conformational analyses, and precise predictions for the key energetic quantities of the molecular prototypes are advanced.
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. PMID:26374007
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.
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.
An ab initio study of the structural and physical properties of a novel rigid-rod polymer : PIPD
Hageman, J.C.L.; Horst, J.W. van der; Groot, R.A. de
1999-01-01
In this article, we present the first ab initio calculations on the novel rigid-rod polymer PIPD using density functional techniques. The behaviour of the molecular chain under strain is studied and the chain modulus agrees excellently with experiment. Two crystal structures are considered and hydro
Ab initio studies of equations of state and chemical reactions of reactive structural materials
Zaharieva, Roussislava
subject of studies of the shock or thermally induced chemical reactions of the two solids comprising these reactive materials, from first principles, is a relatively new field of study. The published literature on ab initio techniques or quantum mechanics based approaches consists of the ab initio or ab initio-molecular dynamics studies in related fields that contain a solid and a gas. One such study in the literature involves a gas and a solid. This is an investigation of the adsorption of gasses such as carbon monoxide (CO) on Tungsten. The motivation for these studies is to synthesize alternate or synthetic fuel technology by Fischer-Tropsch process. In this thesis these studies are first to establish the procedure for solid-solid reaction and then to extend that to consider the effects of mechanical strain and temperature on the binding energy and chemisorptions of CO on tungsten. Then in this thesis, similar studies are also conducted on the effect of mechanical strain and temperature on the binding energies of Titanium and hydrogen. The motivations are again to understand the method and extend the method to such solid-solid reactions. A second motivation is to seek strained conditions that favor hydrogen storage and strain conditions that release hydrogen easily when needed. Following the establishment of ab initio and ab initio studies of chemical reactions between a solid and a gas, the next step of research is to study thermally induced chemical reaction between two solids (Ni+Al). Thus, specific new studies of the thesis are as follows: (1) Ab initio Studies of Binding energies associated with chemisorption of (a) CO on W surfaces (111, and 100) at elevated temperatures and strains and (b) adsorption of hydrogen in titanium base. (2) Equations of state of mixtures of reactive material structures from ab initio methods. (3) Ab initio studies of the reaction initiation, transition states and reaction products of intermetallic mixtures of (Ni+Al) at elevated
Byrne, Aaron
2015-12-24
Ab initio, density functional theory (DFT)-based molecular dynamics (MD) has been carried out to investigate the effect of explicit solvation on the dynamical and structural properties of a [bmim][NTf2] room-temperature ionic liquid (RTIL), solvating a N719 sensitizing dye adsorbed onto an anatase titania (101) surface. The effect of explicit dispersion on the properties of this dye-sensitized solar cell (DSC) interface has also been studied. Upon inclusion of dispersion interactions in simulations of the solvated system, the average separation between the cations and anions decreases by 0.6 Å; the mean distance between the cations and the surface decreases by about 0.5 Å; and the layering of the RTIL is significantly altered in the first layer surrounding the dye, with the cation being on average 1.5 Å further from the center of the dye. Inclusion of dispersion effects when a solvent is not explicitly included (to dampen longer-range interactions) can result in unphysical "kinking" of the adsorbed dye\\'s configuration. The inclusion of solvent shifts the HOMO and LUMO levels of the titania surface by +3 eV. At this interface, the interplay between the effects of dispersion and solvation combines in ways that are often subtle, such as enhancement or inhibition of specific vibrational modes. © 2015 American Chemical Society.
Choudhuri, Jyoti Roy; Chandra, Amalendu
2014-11-21
We have presented a first principles simulation study of the structural and dynamical properties of a liquid-vapor interfacial system of a concentrated (5.3 M) aqueous NaCl solution. We have used ab initio molecular dynamics to examine the structural and dynamical properties of the bulk and interfacial regions. The structural aspects of the system that have been considered here include the inhomogeneous density profiles of ions and water molecules, hydrogen bond distributions, orientational profiles, and also vibrational frequency distributions in the bulk and interfacial regions. It is found that the sodium ions are mostly located in the interior, while the chloride anions occupy a significant portion of the interface of the slab. The water dipoles at the interface prefer to orient parallel to the surface. The dynamical aspects of the interfaces are investigated in terms of diffusion, orientational relaxation, hydrogen bond dynamics, and vibrational spectral diffusion. The results of the interfacial dynamics are compared with those of the corresponding bulk region. It is observed that the interfacial molecules exhibit faster diffusion and orientational relaxation with respect to the bulk. However, the interfacial molecules are found to have longer hydrogen bond lifetimes than those of the bulk. We have also investigated the correlations of hydrogen bond relaxation with the vibrational frequency fluctuations of interfacial water molecules. PMID:25416903
The ab-initio density matrix renormalization group in practice
Energy Technology Data Exchange (ETDEWEB)
Olivares-Amaya, Roberto; Hu, Weifeng; Sharma, Sandeep; Yang, Jun; Chan, Garnet Kin-Lic [Department of Chemistry, Princeton University, Princeton, New Jersey 08544 (United States); Nakatani, Naoki [Department of Chemistry, Princeton University, Princeton, New Jersey 08544 (United States); Catalysis Research Center, Hokkaido University, Kita 21 Nishi 10, Sapporo, Hokkaido 001-0021 (Japan)
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.
High-throughput ab-initio dilute solute diffusion database.
Wu, Henry; Mayeshiba, Tam; Morgan, Dane
2016-01-01
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. PMID:27434308
Transport coefficients in diamond from ab-initio calculations
Löfâs, Henrik; Grigoriev, Anton; Isberg, Jan; Ahuja, Rajeev
2013-03-01
By combining the Boltzmann transport equation with ab-initio electronic structure calculations, we obtain transport coefficients for boron-doped diamond. We find the temperature dependence of the resistivity and the hall coefficients in good agreement with experimental measurements. Doping in the samples is treated via the rigid band approximation and scattering is treated in the relaxation time approximation. In contrast to previous results, the acoustic phonon scattering is the dominating scattering mechanism for the considered doping range. At room temperature, we find the thermopower, S, in the range 1-1.6 mV/K and the power factor, S2σ, in the range 0.004-0.16 μW /cm K2.
Efficient Ab initio Modeling of Random Multicomponent Alloys.
Jiang, Chao; Uberuaga, Blas P
2016-03-11
We present in this Letter a novel small set of ordered structures (SSOS) method that allows extremely efficient ab initio modeling of random multicomponent alloys. Using inverse II-III spinel oxides and equiatomic quinary bcc (so-called high entropy) alloys as examples, we demonstrate that a SSOS can achieve the same accuracy as a large supercell or a well-converged cluster expansion, but with significantly reduced computational cost. In particular, because of this efficiency, a large number of quinary alloy compositions can be quickly screened, leading to the identification of several new possible high-entropy alloy chemistries. The SSOS method developed here can be broadly useful for the rapid computational design of multicomponent materials, especially those with a large number of alloying elements, a challenging problem for other approaches. PMID:27015491
Efficient Ab initio Modeling of Random Multicomponent Alloys
Jiang, Chao; Uberuaga, Blas P.
2016-03-01
We present in this Letter a novel small set of ordered structures (SSOS) method that allows extremely efficient ab initio modeling of random multicomponent alloys. Using inverse II-III spinel oxides and equiatomic quinary bcc (so-called high entropy) alloys as examples, we demonstrate that a SSOS can achieve the same accuracy as a large supercell or a well-converged cluster expansion, but with significantly reduced computational cost. In particular, because of this efficiency, a large number of quinary alloy compositions can be quickly screened, leading to the identification of several new possible high-entropy alloy chemistries. The SSOS method developed here can be broadly useful for the rapid computational design of multicomponent materials, especially those with a large number of alloying elements, a challenging problem for other approaches.
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.
Ab initio H2O in realistic hydrophilic confinement.
Allolio, Christoph; Klameth, Felix; Vogel, Michael; Sebastiani, Daniel
2014-12-15
A protocol for the ab initio construction of a realistic cylindrical pore in amorphous silica, serving as a geometric nanoscale confinement for liquids and solutions, is presented. Upon filling the pore with liquid water at different densities, the structure and dynamics of the liquid inside the confinement can be characterized. At high density, the pore introduces long-range oscillations into the water density profile, which makes the water structure unlike that of the bulk across the entire pore. The tetrahedral structure of water is also affected up to the second solvation shell of the pore wall. Furthermore, the effects of the confinement on hydrogen bonding and diffusion, resulting in a weakening and distortion of the water structure at the pore walls and a slowdown in diffusion, are characterized. PMID:25208765
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.
Highly anisotropic thermal conductivity of arsenene: An ab initio study
Zeraati, Majid; Vaez Allaei, S. Mehdi; Abdolhosseini Sarsari, I.; Pourfath, Mahdi; Donadio, Davide
2016-02-01
Elemental two-dimensional (2D) materials exhibit intriguing heat transport and phononic properties. Here we have investigated the lattice thermal conductivity of newly proposed arsenene, the 2D honeycomb structure of arsenic, using ab initio calculations. Solving the Boltzmann transport equation for phonons, we predict a highly anisotropic thermal conductivity of 30.4 and 7.8 W/mK along the zigzag and armchair directions, respectively, at room temperature. Our calculations reveal that phonons with mean free paths between 20 nm and 1 μ m provide the main contribution to the large thermal conductivity in the zigzag direction; mean free paths of phonons contributing to heat transport in the armchair directions range between 20 and 100 nm. The obtained anisotropic thermal conductivity and feasibility of synthesis, in addition to high electron mobility reported elsewhere, make arsenene a promising material for nanoelectronic applications and thermal management.
Ab initio methods for electron-molecule collisions
International Nuclear Information System (INIS)
This review concentrates on the recent advances in treating the electronic aspect of the electron-molecule interaction and leaves to other articles the description of the rotational and vibrational motions. Those methods which give the most complete treatment of the direct, exchange, and correlation effects are focused on. Such full treatments are generally necessary at energies below a few Rydbergs (≅ 60 eV). This choice unfortunately necessitates omission of those active and vital areas devoted to the development of model potentials and approximate scattering formulations. The ab initio and model approaches complement each other and are both extremely important to the full explication of the electron-scattering process. Due to the rapid developments of recent years, the approaches that provide the fullest treatment are concentrated on. 81 refs
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...
Ab-initio melting curve and principal Hugoniot of tantalum
International Nuclear Information System (INIS)
We report first principles calculations of the melting curve and principal Hugoniot (P - V curve) of body centered cubic (bcc) tantalum in the pressure range 0-300 GPa. A description of lattice dynamics and thermal properties of bcc Ta using finite temperature density functional theory (DFT) is presented. The approach works within the projector augmented wave (PAW) implementation of DFT and explicitly treats in valence the 5p, 6s and 5d electrons. The principal Hugoniot (P - V curve), obtained using the Rankine-Hugoniot equation, is investigated using the generalized gradient approximations (GGA). Very good agreement with the shock experiments is obtained with GGA in all the range of pressure. We also report the temperature-pressure relation on the shock Hugoniot and the full ab-initio melting curve of Ta
Ab initio electronic stopping power of protons in bulk materials
Shukri, Abdullah Atef; Bruneval, Fabien; Reining, Lucia
2016-01-01
The electronic stopping power is a crucial quantity for ion irradiation: it governs the deposited heat, the damage profile, and the implantation depth. Whereas experimental data are readily available for elemental solids, the data are much more scarce for compounds. Here we develop a fully ab initio computational scheme based on linear response time-dependent density-functional theory to predict the random electronic stopping power (RESP) of materials without any empirical fitting. We show that the calculated RESP compares well with experimental data, when at full convergence, with the inclusion of the core states and of the exchange correlation. We evaluate the unexpectedly limited magnitude of the nonlinear terms in the RESP by comparing with other approaches based on the time propagation of time-dependent density-functional theory. Finally, we check the validity of a few empirical rules of thumbs that are commonly used to estimate the electronic stopping power.
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 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 Potential Energy Surface for H-H2
Partridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene
1993-01-01
Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- (mu)E(sub h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(sub 0) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.
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 Prediction of 29Si-NMR Chemical Shifts
Institute of Scientific and Technical Information of China (English)
CHU Shidong; LI Yingxia; SONG Ni; GUAN Huashi
2002-01-01
The ability of several ab initio models to predict experimental 29Si-NMR chemical shift is examined. The shielding values of trimethylsilyl chloride (A), t-butyldimethylsilyl chloride (B) and allyltrimethylsilane (C) are calculated by GIAO, CSGT and IGAIM methods, using HF/6-31G*, B3LYP/6-31G*, HF/6-311+G**, B3LYP/6-311+G** and MPWlPW91/6-311+G** models respectively. The 29Si chemical shifts calculated by GIAO method using HF/6-311+G**model are highly in agreement with those obtained experimentally. All of the models above reproduce the trends of chemical shifts in all cases studied, suggesting that the models are of practical value.
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...
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. PMID:22612082
Ab initio engineering of materials with stacked hexagonal tin frameworks
Shao, Junping; Beaufils, Clément; Kolmogorov, Aleksey N.
2016-01-01
The group-IV tin has been hypothesized to possess intriguing electronic properties in an atom-thick hexagonal form. An attractive pathway of producing sizable 2D crystallites of tin is based on deintercalation of bulk compounds with suitable tin frameworks. Here, we have identified a new synthesizable metal distannide, NaSn2, with a 3D stacking of flat hexagonal layers and examined a known compound, BaSn2, with buckled hexagonal layers. Our ab initio results illustrate that despite being an exception to the 8-electron rule, NaSn2 should form under pressures easily achievable in multi-anvil cells and remain (meta)stable under ambient conditions. Based on calculated Z2 invariants, the predicted NaSn2 may display topologically non-trivial behavior and the known BaSn2 could be a strong topological insulator. PMID:27387140
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.
Monte Carlo methods in AB initio quantum chemistry quantum Monte Carlo for molecules
Lester, William A; Reynolds, PJ
1994-01-01
This book presents the basic theory and application of the Monte Carlo method to the electronic structure of atoms and molecules. It assumes no previous knowledge of the subject, only a knowledge of molecular quantum mechanics at the first-year graduate level. A working knowledge of traditional ab initio quantum chemistry is helpful, but not essential.Some distinguishing features of this book are: Clear exposition of the basic theory at a level to facilitate independent study. Discussion of the various versions of the theory: diffusion Monte Carlo, Green's function Monte Carlo, and release n
Curchod, Basile F. E.; Rauer, Clemens; Marquetand, Philipp; González, Leticia; Martínez, Todd J.
2016-03-01
Full multiple spawning is a formally exact method to describe the excited-state dynamics of molecular systems beyond the Born-Oppenheimer approximation. However, it has been limited until now to the description of radiationless transitions taking place between electronic states with the same spin multiplicity. This Communication presents a generalization of the full and ab initio multiple spawning methods to both internal conversion (mediated by nonadiabatic coupling terms) and intersystem crossing events (triggered by spin-orbit coupling matrix elements) based on a spin-diabatic representation. The results of two numerical applications, a model system and the deactivation of thioformaldehyde, validate the presented formalism and its implementation.
Renison, C Alicia; Fernandes, Kyle D; Naidoo, Kevin J
2015-07-01
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. PMID:25975864
Accelerating Ab Initio Path Integral Simulations via Imaginary Multiple-Timestepping.
Cheng, Xiaolu; Herr, Jonathan D; Steele, Ryan P
2016-04-12
This work investigates the use of multiple-timestep schemes in imaginary time for computationally efficient ab initio equilibrium path integral simulations of quantum molecular motion. In the simplest formulation, only every n(th) path integral replica is computed at the target level of electronic structure theory, whereas the remaining low-level replicas still account for nuclear motion quantum effects with a more computationally economical theory. Motivated by recent developments for multiple-timestep techniques in real-time classical molecular dynamics, both 1-electron (atomic-orbital basis set) and 2-electron (electron correlation) truncations are shown to be effective. Structural distributions and thermodynamic averages are tested for representative analytic potentials and ab initio molecular examples. Target quantum chemistry methods include density functional theory and second-order Møller-Plesset perturbation theory, although any level of theory is formally amenable to this framework. For a standard two-level splitting, computational speedups of 1.6-4.0x are observed when using a 4-fold reduction in time slices; an 8-fold reduction is feasible in some cases. Multitiered options further reduce computational requirements and suggest that quantum mechanical motion could potentially be obtained at a cost not significantly different from the cost of classical simulations. PMID:26966920
Ab Initio Potential Curve for ArH＋%ArH＋势能曲线的从头计算
Institute of Scientific and Technical Information of China (English)
王胜龙; 屈军艳; 郭锐; 赵新生
2001-01-01
The molecular parameters of ArH＋ have been calculated with different quantum chemistry methods and basis sets.Based on the data from QCISD/Aug cc pVTZ ab initio calculation for different configurations of ArH＋ and the experimental data,an accurate potential curve for ArH＋ has been constructed.The molecular properties,such as dissociation energy,equilibrium bond length,and vibrational energy levels,can be accurately reproduced.
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.
Tscherbul, T.V.; Grinev, T. A.; Yu, H.-G.; Dalgarno, A.; Klos, Jacek; Ma, Lifang; Alexander, Millard H.
2012-01-01
We develop a rigorous quantum mechanical theory for collisions of polyatomic molecular radicals with S-state atoms in the presence of an external magnetic field. The theory is based on a fully uncoupled space-fixed basis set representation of the multichannel scattering wavefunction. Explicit expressions are presented for the matrix elements of the scattering Hamiltonian for spin-1/2 and spin-1 polyatomic molecular radicals interacting with structureless targets. The theory is applied to calc...
International Nuclear Information System (INIS)
The first coordination sphere of trivalent lanthanum in a highly concentrated (14 M) lithium chloride solution is studied with a combination of classical molecular dynamics and density functional theory based first principle molecular dynamics. This method enables us to obtain a solvation shell of La3+ containing 2 chloride ions and 6 water molecules. After refinement using first principle molecular dynamics, the resulting cation-water and cation-anion distances are in very good agreement with experiment. The 2 Cl- and the 6 water molecules arrange in a square anti-prism around La3+. Exchange of water molecules was also observed in the first-principle simulation, with an intermediate structure comprising 7 water molecules stable for 2.5 ps. Finally, evaluation of dipole moments using maximally localized Wannier functions shows a substantial polarization of the chloride anions and the water molecules in the first solvation shell of trivalent lanthanum. (authors)
International Nuclear Information System (INIS)
Full text : The molecular geometry and vibrational frequencies of anhydrous zinc acetate and anhydrous magesium acetate in the ground state have been calculated using the Hartree-Fock and density functional method with 6-31G basic set. The optimized geometric band tengths and bond angles obtained by using HF and DFT show the best agreement with the experimental data. Comparison of the observed fundamental vibrational frequencies of melamine diborate with calculated results by density functional B3LYP and Hatree-Fock methods indicate that B3LYP is superior to the scaled Hatree-Fock approach for molecular vibrational problems
Gaigeot, Marie-Pierre
2009-03-01
We present finite temperature DFT-based Car-Parrinello molecular dynamics (MD) simulations for the calculation of infrared spectra of complex molecular systems, either in the gas phase or in the condensed phase. We will review the fundamentals of the method, as well as the applicability and originality of finite temperature MD simulations for the purpose of modeling infrared spectra. Illustrations are taken from the infrared spectroscopy of alanine peptides of increasing size and complexity (from dipeptides to an octo-peptide) in the gas phase, in relation with IR-MPD (Infrared Multi Photon Dissociation) experiments : 300-400 K gas-phase action spectroscopy as devised on the CLIO platform at the University of Orsay-France or on the platform developed in the group of L. Snoek at Oxford-UK. A special emphasis on vibrational anharmonicities and how they can be extracted from molecular dynamics simulations will be put forward. Furthermore, band assignments in terms of atomic movements from MD is challenging and we have introduced a general method for obtaining effective normal modes of molecular systems from MD simulations.
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}.
Experimental and ab initio investigations on textured Li–Mn–O spinel thin film cathodes
International Nuclear Information System (INIS)
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 LiMn2O4-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 LiMn2O4-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 LiMn2O4
Solomonik, Victor G; Stanton, John F; Boggs, James E
2008-06-28
The electronic excitation energies, molecular geometry, quadratic force fields, and vibrational frequencies in the ground (5)Delta(g) and low-lying excited (5)Sigma(g) (+) and (5)Pi(g) electronic states of iron difluoride are studied at sophisticated levels of theory. Two families of basis sets, nonrelativistic and Douglas-Kroll-Hess relativistic, are used that range in quality from triple-zeta to quintuple-zeta. These are augmented by additional diffuse functions (on fluorine atoms) and tight functions (on all atoms) for the description of core-valence correlation and utilized to determine complete basis set molecular properties. The quality of electron correlation treatment using conventional single reference coupled cluster methods CCSD and CCSD(T) is compared to that attained at the multiconfigurational quasidegenerate second-order perturbation theory (CASSCF+MCQDPT2) and the electron attachment equation-of-motion coupled cluster (EOMEA-CCSD) levels. Spin-orbit coupling effects are studied by the SO-MCQDPT2 method using the full Breit-Pauli spin-orbit operator. Effects of spin contamination in the coupled cluster molecular calculations are carefully analyzed. Results of the single reference CCSD(T) and multireference calculations are found to be in a remarkable agreement. The calculations indicate that the EOMEA-CC approach provides a suitable tool for an accurate treatment of FeF(2) and other systems where delicate electron correlation effects have to be carefully dealt with. The inclusion of relativistic effects is shown to be necessary for an accurate description of the molecular geometry and excitation energies of FeF(2). The results of calculations are in good agreement with the experimental data available. The predicted FeF(2) molecular properties are compared to those of the related FeF(3). PMID:18601314
Maity, Surajit; Dangi, Beni B; Parker, Dorian S N; Kaiser, Ralf I; An, Yi; Sun, Bing-Jian; Chang, A H H
2014-10-16
The reaction dynamics of boron monoxide ((11)BO; X(2)Σ(+)) with propylene (CH(3)CHCH(2); X(1)A') were investigated under single collision conditions at a collision energy of 22.5 ± 1.3 kJ mol(-1). The crossed molecular beam investigation combined with ab initio electronic structure and statistical (RRKM) calculations reveals that the reaction follows indirect scattering dynamics and proceeds via the barrierless addition of boron monoxide radical with its radical center located at the boron atom. This addition takes place to either the terminal carbon atom (C1) and/or the central carbon atom (C2) of propylene reactant forming (11)BOC(3)H(6) intermediate(s). The long-lived (11)BOC(3)H(6) doublet intermediate(s) underwent unimolecular decomposition involving at least three competing reaction mechanisms via an atomic hydrogen loss from the vinyl group, an atomic hydrogen loss from the methyl group, and a methyl group elimination to form cis-/trans-1-propenyl-oxo-borane (CH(3)CHCH(11)BO), 3-propenyl-oxo-borane (CH(2)CHCH(2)(11)BO), and ethenyl-oxo-borane (CH(2)CH(11)BO), respectively. Utilizing partially deuterated propylene (CD(3)CHCH(2) and CH(3)CDCD(2)), we reveal that the loss of a vinyl hydrogen atom is the dominant hydrogen elimination pathway (85 ± 10%) forming cis-/trans-1-propenyl-oxo-borane, compared to the loss of a methyl hydrogen atom (15 ± 10%) leading to 3-propenyl-oxo-borane. The branching ratios for an atomic hydrogen loss from the vinyl group, an atomic hydrogen loss from the methyl group, and a methyl group loss are experimentally derived to be 26 ± 8%:5 ± 3%:69 ± 15%, respectively; these data correlate nicely with the branching ratios calculated via RRKM theory of 19%:5%:75%, respectively.
Rocha, Mariana; Di Santo, Alejandro; Arias, Juan Marcelo; Gil, Diego M.; Altabef, Aída Ben
2015-02-01
The experimental and theoretical study on the molecular structure and a new vibrational analysis of 4-(Dimethylamino) Benzaldehyde (DMABA) is presented. The IR and Raman spectra were recorded in solid state. Optimized geometry, vibrational frequencies and various thermodynamic parameters of the title compound were calculated using DFT methods and are in agreement with the experimental values. A detailed interpretation of the IR and Raman spectra of the title compound were reported. The stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using NBO analysis and AIM approach. The HOMO and LUMO analysis were used to determine the charge transfer within the molecule and some molecular properties such as ionization potential, electron affinity, electronegativity, chemical potential, hardness, softness and global electrophilicity index. The TD-DFT approach was applied to assign the electronic transitions observed in the UV-visible spectrum measured experimentally. Molecular electrostatic potential map was performed by the DFT method. According to DSC measurements, the substance presents a melting point of 72.34 °C and decomposes at temperatures higher than 193 °C.
Rocha, Mariana; Di Santo, Alejandro; Arias, Juan Marcelo; Gil, Diego M; Ben Altabef, Aída
2015-02-01
The experimental and theoretical study on the molecular structure and a new vibrational analysis of 4-(Dimethylamino) Benzaldehyde (DMABA) is presented. The IR and Raman spectra were recorded in solid state. Optimized geometry, vibrational frequencies and various thermodynamic parameters of the title compound were calculated using DFT methods and are in agreement with the experimental values. A detailed interpretation of the IR and Raman spectra of the title compound were reported. The stability of the molecule arising from hyper-conjugative interactions and charge delocalization has been analyzed using NBO analysis and AIM approach. The HOMO and LUMO analysis were used to determine the charge transfer within the molecule and some molecular properties such as ionization potential, electron affinity, electronegativity, chemical potential, hardness, softness and global electrophilicity index. The TD-DFT approach was applied to assign the electronic transitions observed in the UV-visible spectrum measured experimentally. Molecular electrostatic potential map was performed by the DFT method. According to DSC measurements, the substance presents a melting point of 72.34°C and decomposes at temperatures higher than 193°C.
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.
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....
Tscherbul, T V; Yu, H -G; Dalgarno, A; Klos, Jacek; Ma, Lifang; Alexander, Millard H; 10.1063/1.4748258
2012-01-01
We develop a rigorous quantum mechanical theory for collisions of polyatomic molecular radicals with S-state atoms in the presence of an external magnetic field. The theory is based on a fully uncoupled space-fixed basis set representation of the multichannel scattering wavefunction. Explicit expressions are presented for the matrix elements of the scattering Hamiltonian for spin-1/2 and spin-1 polyatomic molecular radicals interacting with structureless targets. The theory is applied to calculate the cross sections and thermal rate constants for spin relaxation in low-temperature collisions of the prototypical organic molecule methylene [CH2(X)] with He atoms. To this end, two highly accurate three-dimensional potential energy surfaces (PESs) of the He-CH2(X) complex are developed using the state-of-the-art CCSD(T) method and large basis sets. Both PESs exhibit shallow minima and are weakly anisotropic. Our calculations show that spin relaxation in collisions of CH2, CHD, and CD2 molecules with He atoms occu...
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.
Ab initio no-core solutions for $^6$Li
Shin, Ik Jae; Maris, Pieter; Vary, James P; Forssén, Christian; Rotureau, Jimmy; Michel, Nicolas
2016-01-01
We solve for properties of $^6$Li in the ab initio No-Core Full Configuration approach and we separately solve for its ground state and $J^{\\pi}=2_{2}^{+}$ resonance with the Gamow Shell Model in the Berggren basis. We employ both the JISP16 and chiral NNLO$_{opt}$ realistic nucleon-nucleon interactions and investigate the ground state energy, excitation energies, point proton root-mean-square radius and a suite of electroweak observables. We also extend and test methods to extrapolate the ground state energy, point proton root-mean-square radius, and electric quadrupole moment. We attain improved estimates of these observables in the No-Core Full Configuration approach by using basis spaces up through N$_{max}$=18 that enable more definitive comparisons with experiment. Using the Density Matrix Renormalization Group approach with the JISP16 interaction, we find that we can significantly improve the convergence of the Gamow Shell Model treatment of the $^6$Li ground state and $J^{\\pi}=2_{2}^{+}$ resonance by ...
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 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 calculation of double ionization of atoms
Energy Technology Data Exchange (ETDEWEB)
Serov, V. V., E-mail: vladislav.serov@mail.ru [Saratov State University, Department of Theoretical Physics (Russian Federation)
2013-02-15
The Solov'ev-Vinitsky method was used to perform an ab initio calculation of the triple-differential cross section for the double single-photon photoionization of helium for the case of equal emitted-electron energies. A Gaussian width {gamma} describing angular electron-electron correlations at the total electron energy E taking values in range between 0.1 and 100 eV was obtained for this cross section. The results agree with available experimental data, but they raise a doubt as to whether the well-known Wannier law {gamma} {proportional_to} E{sup 1/4} is applicable at experimentally accessible energies. The Gaussian width {gamma} was investigated as a function of the total emitted-electron energy for targets that have a strongly asymmetric configuration of the initial state-specifically, a negative atomic-hydrogen ion H{sup -} and heliumin the 1s2s{sup 1}S and 1s3s{sup 1}S excited states. It was found that this function, {gamma}(E), had a maximum at low energies. It was also shown that, at low energies, the dependence of the double-differential cross section on the angle between the emitted-electron momenta for the targets indicated above differed substantially from the Gaussian dependence, featuring maxima whose number was equal to the number of radial nodes in the initial state. This opens new possibilities for a qualitative analysis of the electron structure of targets.
Accurate ab initio vibrational energies of methyl chloride
Energy Technology Data Exchange (ETDEWEB)
Owens, Alec, E-mail: owens@mpi-muelheim.mpg.de [Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany); Department of Physics and Astronomy, University College London, Gower Street, WC1E 6BT London (United Kingdom); Yurchenko, Sergei N.; Yachmenev, Andrey; Tennyson, Jonathan [Department of Physics and Astronomy, University College London, Gower Street, WC1E 6BT London (United Kingdom); Thiel, Walter [Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr (Germany)
2015-06-28
Two new nine-dimensional potential energy surfaces (PESs) have been generated using high-level ab initio theory for the two main isotopologues of methyl chloride, CH{sub 3}{sup 35}Cl and CH{sub 3}{sup 37}Cl. The respective PESs, CBS-35{sup HL}, and CBS-37{sup HL}, are based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set (CBS) limit, and incorporate a range of higher-level (HL) additive energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms, scalar relativistic effects, and diagonal Born-Oppenheimer corrections. Variational calculations of the vibrational energy levels were performed using the computer program TROVE, whose functionality has been extended to handle molecules of the form XY {sub 3}Z. Fully converged energies were obtained by means of a complete vibrational basis set extrapolation. The CBS-35{sup HL} and CBS-37{sup HL} PESs reproduce the fundamental term values with root-mean-square errors of 0.75 and 1.00 cm{sup −1}, respectively. An analysis of the combined effect of the HL corrections and CBS extrapolation on the vibrational wavenumbers indicates that both are needed to compute accurate theoretical results for methyl chloride. We believe that it would be extremely challenging to go beyond the accuracy currently achieved for CH{sub 3}Cl without empirical refinement of the respective PESs.
Volumic omit maps in ab initio dual-space phasing.
Oszlányi, Gábor; Sütő, András
2016-07-01
Alternating-projection-type dual-space algorithms have a clear construction, but are susceptible to stagnation and, thus, inefficient for solving the phase problem ab initio. To improve this behaviour new omit maps are introduced, which are real-space perturbations applied periodically during the iteration process. The omit maps are called volumic, because they delete some predetermined subvolume of the unit cell without searching for atomic regions or analysing the electron density in any other way. The basic algorithms of positivity, histogram matching and low-density elimination are tested by their solution statistics. It is concluded that, while all these algorithms based on weak constraints are practically useless in their pure forms, appropriate volumic omit maps can transform them to practically useful methods. In addition, the efficiency of the already useful reflector-type charge-flipping algorithm can be further improved. It is important that these results are obtained by using non-sharpened structure factors and without any weighting scheme or reciprocal-space perturbation. The mathematical background of volumic omit maps and their expected applications are also discussed. PMID:27357850
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 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.
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.
Nikitin, Andrei; Champion, Jean Paul; Tyuterev, Vladimir
2012-01-01
The MIRS software for the modeling of ro-vibrational spectra of polyatomic molecules was considerably extended and improved. The original version (Nikitin, et al. JQSRT, 2003, pp. 239--249) was especially designed for separate or simultaneous treatments of complex band systems of polyatomic molecules. It was set up in the frame of effective polyad models by using algorithms based on advanced group theory algebra to take full account of symmetry properties. It has been successfully used for predictions and data fitting (positions and intensities) of numerous spectra of symmetric and spherical top molecules within the vibration extrapolation scheme. The new version offers more advanced possibilities for spectra calculations and modeling by getting rid of several previous limitations particularly for the size of polyads and the number of tensors involved. It allows dealing with overlapping polyads and includes more efficient and faster algorithms for the calculation of coefficients related to molecular symmetry ...
Tscherbul, T. V.; Grinev, T. A.; Yu, H.-G.; Dalgarno, A.; Kłos, Jacek; Ma, Lifang; Alexander, Millard H.
2012-09-01
We develop a rigorous quantum mechanical theory for collisions of polyatomic molecular radicals with S-state atoms in the presence of an external magnetic field. The theory is based on a fully uncoupled space-fixed basis set representation of the multichannel scattering wave function. Explicit expressions are presented for the matrix elements of the scattering Hamiltonian for spin-1/2 and spin-1 polyatomic molecular radicals interacting with structureless targets. The theory is applied to calculate the cross sections and thermal rate constants for spin relaxation in low-temperature collisions of the prototypical organic molecule methylene [CH_2(tilde{X}^3B_1)] with He atoms. To this end, two accurate three-dimensional potential energy surfaces (PESs) of the He-CH_2(tilde{X}^3B_1) complex are developed using the state-of-the-art coupled-cluster method including single and double excitations along with a perturbative correction for triple excitations and large basis sets. Both PESs exhibit shallow minima and are weakly anisotropic. Our calculations show that spin relaxation in collisions of CH2, CHD, and CD2 molecules with He atoms occurs at a much slower rate than elastic scattering over a large range of temperatures (1 μK-1 K) and magnetic fields (0.01-1 T), suggesting excellent prospects for cryogenic helium buffer-gas cooling of ground-state ortho-CH_2(tilde{X}^3B_1) molecules in a magnetic trap. Furthermore, we find that ortho-CH2 undergoes collision-induced spin relaxation much more slowly than para-CH2, which indicates that magnetic trapping can be used to separate nuclear spin isomers of open-shell polyatomic molecules.
Tscherbul, T V; Grinev, T A; Yu, H-G; Dalgarno, A; Kłos, Jacek; Ma, Lifang; Alexander, Millard H
2012-09-14
We develop a rigorous quantum mechanical theory for collisions of polyatomic molecular radicals with S-state atoms in the presence of an external magnetic field. The theory is based on a fully uncoupled space-fixed basis set representation of the multichannel scattering wave function. Explicit expressions are presented for the matrix elements of the scattering Hamiltonian for spin-1/2 and spin-1 polyatomic molecular radicals interacting with structureless targets. The theory is applied to calculate the cross sections and thermal rate constants for spin relaxation in low-temperature collisions of the prototypical organic molecule methylene [CH(2)(X(3)B(1))] with He atoms. To this end, two accurate three-dimensional potential energy surfaces (PESs) of the He-CH(2)(X(3)B(1)) complex are developed using the state-of-the-art coupled-cluster method including single and double excitations along with a perturbative correction for triple excitations and large basis sets. Both PESs exhibit shallow minima and are weakly anisotropic. Our calculations show that spin relaxation in collisions of CH(2), CHD, and CD(2) molecules with He atoms occurs at a much slower rate than elastic scattering over a large range of temperatures (1 μK-1 K) and magnetic fields (0.01-1 T), suggesting excellent prospects for cryogenic helium buffer-gas cooling of ground-state ortho-CH(2)(X(3)B(1)) molecules in a magnetic trap. Furthermore, we find that ortho-CH(2) undergoes collision-induced spin relaxation much more slowly than para-CH(2), which indicates that magnetic trapping can be used to separate nuclear spin isomers of open-shell polyatomic molecules. PMID:22979854
Ford, Thomas A
2005-05-01
The molecular structures, interaction energies, charge transfer properties and vibrational spectra of the van der Waals complexes formed between boron trifluoride and the noble gases neon, argon, krypton and xenon have been computed using second and fourth order Møller-Plesset perturbation theory and the Los Alamos National Laboratory LANL2DZ basis set. The complexes are all symmetric tops, with the noble gas atom acting as a sigma electron donor along the C3 axis of the BF3 molecule. The interaction energies are all vanishingly small, and the amount of charge transferred in each case is of the order of 0.01e. The directions of the wavenumber shifts of the symmetric bending (nu2) and antisymmetric stretching (nu3) modes of the BF3 fragment confirm those determined experimentally, and the shifts are shown to correlate well with the polarizability of the noble gas atom and the inverse sixth power of the intermonomer separation. The nu2 mode is substantially more sensitive to complexation than the nu3 vibration.
McDonnell, Marshall T; Xu, Haixuan; Keffer, David J
2016-06-16
We investigate the solvation shell structures, the distribution of protonic defects, mechanistic details, kinetics, and dynamics of proton transfer for an excess proton in bulk water and for an excess proton in an aqueous solution of triethylene glycol (TEG) via Car-Parrinello molecular dynamics simulations. The PW91, PBE, and PBE with the Tkatchenko-Scheffler (TS) density-dependent dispersion functionals were used and compared for bulk water and the TEG-water mixtures. The excess proton is found to reside predominantly on water molecules but also resides on hydroxyl groups of TEG. The lifetimes associated with structural diffusion time scales of the protonated water were found to be on the order of ∼1 ps. All three functionals studied support the presolvation requirement for structural diffusion. The highest level of theory shows a reduction in the free energy barrier for water-water proton transfer in TEG-water mixtures compared to bulk water. The effect of TEG shows no strong change in the kinetics for TEG-water mixtures compared to bulk water for this same level of theory. The excess proton displays burst-rest behavior in the presence of TEG, similar to that found in bulk water. We find that the TEG chain disrupts the hydrogen-bond network, causing the solvation shell around water to be populated by TEG chain groups instead of other waters, reducing the rigidity of the hydrogen-bond network. Methylene is a dominant hydrogen bond donor for the protonated water in hydrogen-bond networks associated with proton transfer and structural diffusion. This is consistent with previous studies that have found the hydronium ion to be amphiphilic in nature and to have higher proton mobility at oil-water interfaces. PMID:27218455
Harvey, Jean-Philippe; Gheribi, Aïmen E.; Asimow, Paul D.
2015-07-01
We propose a new approach to parameterizing the Gibbs energy of a multicomponent solution as a function of temperature, pressure and composition. It uses the quasichemical model in the second nearest neighbor approximation and considers both a polynomial representation (for low pressure) and an exponential decay representation (for moderate-to-high pressure) of the excess molar volume νxs to extend thermodynamic behavior to elevated pressure. This approach differs from previous configuration-independent regular or associated solution-type models of multicomponent silicate liquids at elevated pressure and can account for any structural or short-range order data that may be available. A simultaneous least squares fit of the molar volume and the molar enthalpy of mixing data obtained from First Principles Molecular Dynamics (FPMD) simulations at various pressures enables complete parameterization of the excess thermodynamic properties of the solution. Together with consistently optimized properties of coexisting solids, this enables prediction of pressure-temperature-composition phase diagrams associated with melting. Although the method is extensible to natural multicomponent systems, we apply the procedure as a first test case to the important planetary model system MgO-SiO2 using FPMD data found in the literature. One key result of this optimization, which depends only on the derived excess properties of the liquid phase, is that the consolute temperature of the SiO2-rich miscibility gap is predicted to decrease with increasing pressure. This appears to be in disagreement with available experimental constraints and suggests possible thermodynamic inconsistency between FPMD data and experimental phase equilibrium data in the 0-5 GPa pressure range. We propose a new thermodynamic consistency criterion relating the signs of νxs and other excess properties and discuss the need for precise calculations of derivatives of excess properties. Finally, the potential
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.
International Nuclear Information System (INIS)
We have calculated the intermolecular interaction energies of the chloroform dimer in 12 orientations using the second-order Møller-Plesset perturbation theory. Single point energies of important geometries were calibrated by the coupled cluster with single and double and perturbative triple excitation method. Dunning's correlation consistent basis sets up to aug-cc-pVQZ have been employed in extrapolating the interaction energies to the complete basis set limit values. With the ab initio potential data we constructed a 5-site force field model for molecular dynamics simulations. We compared the simulation results with recent experiments and obtained quantitative agreements for the detailed atomwise radial distribution functions. Our results were also consistent with previous results using empirical force fields with polarization effects. Moreover, the calculated diffusion coefficients reproduced the experimental data over a wide range of thermodynamic conditions. To the best of our knowledge, this is the first ab initio force field which is capable of competing with existing empirical force fields for liquid chloroform
Ji, Pengfei; Zhang, Yuwen
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 ...
ESTUDIO TEÓRICO DE LA MOLÉCULA DE HIDROGENO CALCULO AB-INITIO
Quitián, N.
2010-01-01
Utilizando la técnica LCGO-SCF-MO (Combinación Lineal de los Orbitales Moleculares en Orbitales Gausianos, en el método del Campo Auto-Coherente), se determinaron las energías de orbital, la energía electrónica total, la energía de repulsión nuclear y la energía de Hartree-Fock de la molécula de hidrógeno en su estado fundamental, mediante un cálculo ab initio y utilizando una base de funciones gausianas. Los orbitales moleculares fueron desarrollados en términos de una función Is contraída p...
Hydrogen-Water Mixtures in Giant Planet Interiors Studied with Ab Initio Simulations
Soubiran, Francois
2015-01-01
We study water-hydrogen mixtures under planetary interior conditions using ab initio molecular dynamics simulations. We determine the thermodynamic properties of various water-hydrogen mixing ratios at temperatures of 2000 and 6000 K for pressures of a few tens of GPa. These conditions are relevant for ice giant planets and for the outer envelope of the gas giants. We find that at 2000 K the mixture is in a molecular regime, while at 6000 K the dissociation of hydrogen and water is important and affects the thermodynamic properties. We study the structure of the liquid and analyze the radial distribution function. We provide estimates for the transport properties, diffusion and viscosity, based on autocorrelation functions. We obtained viscosity estimates of the order of a few tenths of mPa.s for the conditions under consideration. These results are relevant for dynamo simulations of ice giant planets.
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 study of the low-lying electronic states of the CaO molecule
International Nuclear Information System (INIS)
Graphical abstract: Highly correlated ab initio calculations have been performed for an accurate determination of the electronic structure of the low-lying electronic states of the CaO molecule. The computations are done using the aug-cc-pV5Z basis set for O and the cc-pCV5Z for Ca. The potential energy curves for the molecular states correlating to the lowest three asymptotes are calculated at the CASSCF level. The potential curves of the lowest five molecular states, X1Σ+, a3Π, A'1Π, b3Σ+ and A1Σ+, and the corresponding dipole moment functions have been determined using internally contracted multi-reference configuration interaction approaches. The spectroscopic constants associated with these electronic states are compared to experimental values. The corresponding electronic wavefunctions have also been analyzed using the dipole moment functions. Display Omitted Highlights: → The five lowest electronic states of Cao have been determined ab initio at a high level of accuracy. → Large active space, core-valence correlation and configuration interaction are required. → The multi-configurational nature of the electronic ground state is confirmed as well as its monovalent and divalent ionic nature using dipole moment analysis. → These interacting potentials will serve for future obtention of spin-rovibronic levels. - Abstract: Highly correlated ab initio calculations have been performed for an accurate determination of the electronic structure of the low-lying electronic states of the CaO molecule. The computations are done using the aug-cc-pV5Z basis set for O and the cc-pCV5Z for Ca. The potential energy curves for the molecular states correlating to the lowest three asymptotes are calculated at the CASSCF level. The potential curves of the lowest five molecular states, X1Σ+, a3Π, A'1Π, b3Σ+ and A1Σ+, and the corresponding dipole moment functions have been determined using internally contracted multi-reference configuration interaction approaches
Ab initio study of the low-lying electronic states of the CaO molecule
Energy Technology Data Exchange (ETDEWEB)
Khalil, Hossain; Brites, Vincent; Quere, Frederic Le [Universite Paris-Est, Laboratoire de Modelisation et Simulation Multi Echelle, UMR 8208 CNRS, Batiment Lavoisier, 5 boulevard Descartes, Champs sur Marne, 77454 Marne-la-Vallee, Cedex 2 (France); Leonard, Celine, E-mail: celine.leonard@univ-paris-est.fr [Universite Paris-Est, Laboratoire de Modelisation et Simulation Multi Echelle, UMR 8208 CNRS, Batiment Lavoisier, 5 boulevard Descartes, Champs sur Marne, 77454 Marne-la-Vallee, Cedex 2 (France)
2011-07-28
Graphical abstract: Highly correlated ab initio calculations have been performed for an accurate determination of the electronic structure of the low-lying electronic states of the CaO molecule. The computations are done using the aug-cc-pV5Z basis set for O and the cc-pCV5Z for Ca. The potential energy curves for the molecular states correlating to the lowest three asymptotes are calculated at the CASSCF level. The potential curves of the lowest five molecular states, X{sup 1}{Sigma}{sup +}, a{sup 3}{Pi}, A'{sup 1{Pi}}, b{sup 3}{Sigma}{sup +} and A{sup 1}{Sigma}{sup +}, and the corresponding dipole moment functions have been determined using internally contracted multi-reference configuration interaction approaches. The spectroscopic constants associated with these electronic states are compared to experimental values. The corresponding electronic wavefunctions have also been analyzed using the dipole moment functions. Display Omitted Highlights: {yields} The five lowest electronic states of Cao have been determined ab initio at a high level of accuracy. {yields} Large active space, core-valence correlation and configuration interaction are required. {yields} The multi-configurational nature of the electronic ground state is confirmed as well as its monovalent and divalent ionic nature using dipole moment analysis. {yields} These interacting potentials will serve for future obtention of spin-rovibronic levels. - Abstract: Highly correlated ab initio calculations have been performed for an accurate determination of the electronic structure of the low-lying electronic states of the CaO molecule. The computations are done using the aug-cc-pV5Z basis set for O and the cc-pCV5Z for Ca. The potential energy curves for the molecular states correlating to the lowest three asymptotes are calculated at the CASSCF level. The potential curves of the lowest five molecular states, X{sup 1}{Sigma}{sup +}, a{sup 3}{Pi}, A'{sup 1}{Pi}, b{sup 3}{Sigma}{sup +} and A{sup 1
Ab initio no-core shell model with continuum
Navratil, Petr
2008-04-01
The ab initio no-core shell model (NCSM) is a many-body approach to nuclear structure of light nuclei. The NCSM adopts an effective interaction theory to transform fundamental inter-nucleon interactions into effective interactions for a specified nucleus in a selected harmonic oscillator basis space [1]. The method is capable of predicting nuclear structure from inter-nucleon forces derived from quantum chromodynamics by means of chiral effective field theory [2]. NCSM extensions to the microscopic description of nuclear reactions are now under development. In my talk, I will first discuss our recent calculations of the ^4He total photo-absorption cross section using two- and three-nucleon interactions from chiral effective field theory [3]. I will then outline our effort to augment the NCSM by the resonating group method (RGM) technique to develop a new method capable of describing simultaneously both bound states and nuclear reactions on light nuclei [4]. This approach, which preserves translational symmetry and the Pauli principle, will allow us to calculate cross sections of reactions important for astrophysics and describe weakly-bound systems from first principles. I will present our first phase shift results for neutron scattering off ^3H, ^4He and ^7Li and proton scattering off ^3He, ^4He and ^7Be using realistic nucleon-nucleon potentials. 3mm [1] P. Navr'atil, J. P. Vary and B. R. Barrett, Phys. Rev. C 62, 054311 (2000). [2] P. Navr'atil and V. G. Gueorguiev and J. P. Vary, W. E. Ormand and A. Nogga, Phys. Rev. Lett. 99, 042501 (2007). [3] S. Quaglioni and P. Navr'atil, Phys. Lett. B 652, 370 (2007). [4] S. Quaglioni and P. Navr'atil, arXiv:0712.0855.
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.
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.
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。
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)
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.
International Nuclear Information System (INIS)
We report an investigation of the structure and vibrational modes of (AgI)x (AsSe)100-x, bulk glasses using Raman spectroscopy and first principles calculations. The short- and medium-range structural order of the glasses was elucidated by analyzing the reduced Raman spectra, recorded at off-resonance conditions. Three distinct local environments were revealed for the AsSe glass including stoichiometric-like and As-rich network sub-structures, and cage-like molecules (As4Sen, n=3, 4) decoupled from the network. To facilitate the interpretation of the Raman spectra ab initio calculations are employed to study the geometric and vibrational properties of As4Sen molecular units that are parts of the glass structure. The incorporation of AgI causes appreciable structural changes into the glass structure. AgI is responsible for the population reduction of molecular units and for the degradation of the As-rich network-like sub-structure via the introduction of As-I terminal bonds. Ab initio calculations of mixed chalcohalide pyramids AsSemI3-m provided useful information augmenting the interpretation of the Raman spectra. -- Graphical abstract: Raman scattering and ab initio calculations are employed to study the structure of AgI-AsSe superionic glasses. The role of mixed chalcohalide pyramidal units as illustrated in the figure is elucidated. Display Omitted Research highlights: → Doping binary As-Se glasses with AgI cause dramatic changes in glass structure. → Raman scattering and ab initio calculations determine changes in short- and medium-range order. → Three local environments exist in AsSe glass including a network sub-structure and cage-like molecules. → Mixed chalcohalide pyramids AsSemI3-m dominate the AgI-doped glass structure.
AB INITIO STUDY ON VALENCE INDICES AND REACTIVITIES OF SOME BORAENS
Institute of Scientific and Technical Information of China (English)
曹阳; 王友良
1991-01-01
In the pressnt paper, 3-21G ab initio molecular orbital calculations arc performed on diborane B2H6 and the substituted bridged-atom species H4B2X2(X=F, C1, OH, NH2, CH3),and these geometries are optimized with the energy gradient technique. According to the quantum chemical definition of atomic valence, the valences of the bridged-atoms are calculated to studtd the characteristion of the bridging bond B-X-B. Some larger boranes B4H10, B5H9, and B5H11 are also calculated to discuss the valence indices and analyze the reactiveities of the bridged-atoms.
Iftimie, R; Schofield, J P; Iftimie, Radu; Salahub, Dennis; Schofield, Jeremy
2003-01-01
In this article, we propose an efficient method for sampling the relevant state space in condensed phase reactions. In the present method, the reaction is described by solving the electronic Schr\\"{o}dinger equation for the solute atoms in the presence of explicit solvent molecules. The sampling algorithm uses a molecular mechanics guiding potential in combination with simulated tempering ideas and allows thorough exploration of the solvent state space in the context of an ab initio calculation even when the dielectric relaxation time of the solvent is long. The method is applied to the study of the double proton transfer reaction that takes place between a molecule of acetic acid and a molecule of methanol in tetrahydrofuran. It is demonstrated that calculations of rates of chemical transformations occurring in solvents of medium polarity can be performed with an increase in the cpu time of factors ranging from 4 to 15 with respect to gas-phase calculations.
Ab initio/DFT calculations of butyl ammonium salt of O,O‧-dibornyl dithiophosphate
Kart, H. H.; Özdemir Kart, S.; Karakuş, M.; Kurt, M.
2014-08-01
O,O‧-dibornyl dithiophosphete has been synthesized by the reaction of P2S5 and borneol in toluene. Fourier Transform Infrared spectra (FT-IR) of the title compound are measured. The molecular geometry, vibrational frequencies, infrared intensities and NMR spectrum of the title compound in the ground state have been calculated by using the density functional theory (DFT) and ab initio Hartree-Fock (HF) methods with the basis set of 6-31G(d). The computed bond lengths and bond angles show the good agreement with the experimental data. Moreover, the vibrational frequencies are calculated and the scaled values have been compared with experimental FT-IR spectra. Assignments of the vibrational modes are made on the basis of total energy distribution (TED) calculated with scaled quantum mechanical (SQM) method. The observed and calculated FT-IR and NMR spectra are in good agreement with each other.
Ab initio/DFT calculations of butyl ammonium salt of O,O'-dibornyl dithiophosphate.
Kart, H H; Ozdemir Kart, S; Karakuş, M; Kurt, M
2014-08-14
O,O'-dibornyl dithiophosphete has been synthesized by the reaction of P2S5 and borneol in toluene. Fourier Transform Infrared spectra (FT-IR) of the title compound are measured. The molecular geometry, vibrational frequencies, infrared intensities and NMR spectrum of the title compound in the ground state have been calculated by using the density functional theory (DFT) and ab initio Hartree-Fock (HF) methods with the basis set of 6-31G(d). The computed bond lengths and bond angles show the good agreement with the experimental data. Moreover, the vibrational frequencies are calculated and the scaled values have been compared with experimental FT-IR spectra. Assignments of the vibrational modes are made on the basis of total energy distribution (TED) calculated with scaled quantum mechanical (SQM) method. The observed and calculated FT-IR and NMR spectra are in good agreement with each other. PMID:24747929
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.
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.
Knyazev, D V
2013-01-01
This work is devoted to the \\textit{ab initio} calculation of transport and optical properties of aluminum. The calculation is based on the quantum molecular dynamics simulation, density functional theory and the Kubo-Greenwood formula. Mainly the calculations are performed for liquid aluminum at near-normal densities for the temperatures from melting up to 20000 K. The results on dynamic electrical conductivity, static electrical conductivity and thermal conductivity are obtained and compared with available reference and experimental data and the calculations of other authors. The influence of the technical parameters on the results is investigated in detail. The error of static electrical conductivity calculation is estimated to be about 20%; more accurate results require bigger number of atoms.
Wood, Brandon; Choi, Woon Ih; Schwegler, Eric; Ogitsu, Tadashi
2013-03-01
Photoelectrodes made of III-V semiconductors are known to exhibit very high solar-to-hydrogen conversion efficiency (from solar energy to chemical energy as H2 bond); however, photocorrosion of the electrode in electrolyte solution remains an issue. Based on ab-initio molecular dynamics simulations, we study the structure, stability, and chemical activity of GaP/InP(001) semiconductor electrodes in contact with water. We will show how surface oxygen and hydroxyl change the electronic and chemical properties of water at the interface, leading to the formation of a strong hydrogen-bond network where fast surface hydrogen transport seems to be realized. Implications from our findings will be discussed in detail at the presentation. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52- 07NA27344.
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.
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.
Raman Spectroscopy and Ab-Initio Model Calculations on Ionic Liquids
DEFF Research Database (Denmark)
Berg, Rolf W.
2007-01-01
A review of the recent developments in the study and understanding of room temperature ionic liquids are given. An intimate picture of how and why these liquids are not crystals at ambient conditions is attempted, based on evidence from crystallographical results combined with vibrational...... 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...... and gauche conformers that has been elucidated in remarkable papers by Hamaguchi et al. Such presence of a conformational equilibrium seems to be a general feature of the room temperature liquids. Then the ‘‘localized structure features’’ that apparently exist in ionic liquids are described. It is hoped...
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
An Ab-Initio Calculation of Raman Spectra of Binary Sodium Silicates
Institute of Scientific and Technical Information of China (English)
尤静林; 蒋国昌; 侯怀宇; 陈辉; 吴永全; 徐匡迪
2004-01-01
Raman spectra of binary sodium silicates are calculated by self-consistent field (SCF) molecular orbital ab initio calculation of the quantum chemical method with several poly silicon-oxygen tetrahedral model clusters when both the basis sets of 6-31 G and 6-31 G(d) are applied. The symmetric stretching vibrational frequency of non-bridging oxygen in a high frequency range and its Raman optical activity and scattering cross section are deduced and analysed. The correlation between this vibrational Raman shift and its microscopic environment of the silicon-oxygen tetrahedron is found based on interior stress of configuration, which depends on the connecting topology of adjacent silicon-oxygen tetrahedra (SiOT). A newly established empirical stress index of tetrahedron is introduced to elucidate the above relationship.
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.
Ionization dynamics of the water trimer: A direct ab initio MD study
Energy Technology Data Exchange (ETDEWEB)
Tachikawa, Hiroto, E-mail: hiroto@eng.hokudai.ac.jp [Division of Materials Chemistry, Graduate School of Engineering, Hokkaido University, Kita-ku, Sapporo 060-8628 (Japan); Takada, Tomoya [Department of Material Chemistry, Asahikawa National College of Technology, Syunkodai, Asahikawa 071-8142 (Japan)
2013-03-29
Highlights: ► We calculated ionization dynamics of water trimer. ► Direct ab initio molecular dynamics (MD) method is applied. ► Proton transfer dynamics were discussed. ► The proton transfer process calculated are well reproduced in recent experiments. - Abstract: Ionization dynamics of the cyclic water trimer (H{sub 2}O){sub 3} have been investigated by means of direct ab initio molecular dynamics (AIMD) method. Two reaction channels, complex formation and OH dissociation, were found following the ionization of (H{sub 2}O){sub 3}. In both channels, first, a proton was rapidly transferred from H{sub 2}O{sup +} to H{sub 2}O (time scale is ∼15 fs after the ionization). In complex channel, an ion–radical contact pair (H{sub 3}O{sup +}–OH) solvated by the third water molecule was formed as a long-lived H{sub 3}O{sup +}(OH)H{sub 2}O complex. In OH dissociation channel, the second proton transfer further takes place from H{sub 3}O{sup +}(OH) to H{sub 2}O (time scale is 50–100 fs) and the OH radical is separated from the H{sub 3}O{sup +}. At the same time, the OH dissociation takes place when the excess energy is efficiently transferred into the kinetic energy of OH radical. The OH dissociation channel is significantly minor, and almost all product channels were the complex formation. The reaction mechanism was discussed on the basis of theoretical results.
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)
Comparative studies of the spectroscopy of CuCl2: DFT versus standard ab initio approaches.
Ramírez-Solís, A; Poteau, R; Vela, A; Daudey, J P
2005-04-22
values. These findings show that not only large variational ab initio calculations can produce reliable spectroscopic results for extremely complex systems where delicate electronic correlation effects have to be carefully dealt with. However, those functionals that were recently shown to perform best for a series of molecular properties [J. Chem. Phys. 121 3405 (2004)] are not the ones that produce the best transition energies for this complex case. PMID:15945683
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
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.
Energy Technology Data Exchange (ETDEWEB)
Sahli, Beat [Integrated Systems Laboratory, ETH Zurich, Gloriastrasse 35, 8092 Zurich (Switzerland)], E-mail: sahli@iis.ee.ethz.ch; Vollenweider, Kilian [Integrated Systems Laboratory, ETH Zurich, Gloriastrasse 35, 8092 Zurich (Switzerland); Zographos, Nikolas; Zechner, Christoph [Synopsys Switzerland LLC, Affolternstrasse 52, 8050 Zurich (Switzerland)
2008-12-05
We present the results of extensive ab initio simulations for phosphorus clusters, arsenic clusters and mixed phosphorus/arsenic clusters in silicon. The specific defects and the parameters that are investigated are selected according to the needs of state-of-the-art diffusion and activation models, taking into account the availability of experimental data, the capabilities of current ab initio methods and the requirements for advanced technology development. The calculated binding energies are used to determine a good starting point for the calibration of a new clustering model implemented in an atomistic process simulator. The defect species V, I, P, PV, PI, As, AsV, AsI and clusters containing up to four dopant atoms and up to one V or I are considered in all relevant charge states. The ab initio results are discussed as well as the challenges arising in the transfer of this information into the process simulation model.
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...
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...
Sakane, Shinichi; Yezdimer, Eric M.; Liu, Wenbin; Barriocanal, Jose A.; Doren, Douglas J.; Wood, Robert H.
2000-08-01
The ab initio/classical free energy perturbation (ABC-FEP) method proposed previously by Wood et al. [J. Chem. Phys. 110, 1329 (1999)] uses classical simulations to calculate solvation free energies within an empirical potential model, then applies free energy perturbation theory to determine the effect of changing the empirical solute-solvent interactions to corresponding interactions calculated from ab initio methods. This approach allows accurate calculation of solvation free energies using an atomistic description of the solvent and solute, with interactions calculated from first principles. Results can be obtained at a feasible computational cost without making use of approximations such as a continuum solvent or an empirical cavity formation energy. As such, the method can be used far from ambient conditions, where the empirical parameters needed for approximate theories of solvation may not be available. The sources of error in the ABC-FEP method are the approximations in the ab initio method, the finite sample of configurations, and the classical solvent model. This article explores the accuracy of various approximations used in the ABC-FEP method by comparing to the experimentally well-known free energy of hydration of water at two state points (ambient conditions, and 973.15 K and 600 kg/m3). The TIP4P-FQ model [J. Chem. Phys. 101, 6141 (1994)] is found to be a reliable solvent model for use with this method, even at supercritical conditions. Results depend strongly on the ab initio method used: a gradient-corrected density functional theory is not adequate, but a localized MP2 method yields excellent agreement with experiment. Computational costs are reduced by using a cluster approximation, in which ab initio pair interaction energies are calculated between the solute and up to 60 solvent molecules, while multi-body interactions are calculated with only a small cluster (5 to 12 solvent molecules). Sampling errors for the ab initio contribution to
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.
Beyond Born-Mayer: Improved models for short-range repulsion in ab initio force fields
Van Vleet, Mary J; Stone, Anthony J; Schmidt, J R
2016-01-01
Short-range repulsion within inter-molecular force fields is conventionally described by either Lennard-Jones (${A}/{r^{12}}$) or Born-Mayer ($A\\exp(-Br)$) forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of inter-molecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, and robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Finally, we show how this methodology can be adapted to yield the standard Born-Mayer functional for...
ESTUDIO TEÓRICO DE LA MOLÉCULA DE HIDROGENO CALCULO AB-INITIO
Directory of Open Access Journals (Sweden)
N. Quitián
2010-09-01
Full Text Available Utilizando la técnica LCGO-SCF-MO (Combinación Lineal de los Orbitales Moleculares en Orbitales Gausianos, en el método del Campo Auto-Coherente, se determinaron las energías de orbital, la energía electrónica total, la energía de repulsión nuclear y la energía de Hartree-Fock de la molécula de hidrógeno en su estado fundamental, mediante un cálculo ab initio y utilizando una base de funciones gausianas. Los orbitales moleculares fueron desarrollados en términos de una función Is contraída por átomo de hidrógeno, obtenida por la minimización de los coeficientes y de los exponentes de los orbitales gausianos para el átomo aislado. Los resultados obtenidos nos permiten afirmar que la base molecular mejora sensiblemente los resultados, acercándose más al límite de Hartree-Fock.
Ab initio calculation of the electronic absorption spectrum of liquid water
International Nuclear Information System (INIS)
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
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. PMID:27394094
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 prediction of vacancy properties in concentrated alloys: The case of fcc Cu-Ni
Zhang, X.; Sluiter, M.H.F.
2015-01-01
Vacancy properties in concentrated alloys continue to be of great interest because nowadays ab initio supercell simulations reach a scale where even defect properties in disordered alloys appear to be within reach. We show that vacancy properties cannot generally be extracted from supercell total en
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
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.
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.
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)
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
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, and...
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...
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
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 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, ...
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.
All-electron ab initio investigations of the electronic states of the NiC molecule
DEFF Research Database (Denmark)
Shim, Irene; Gingerich, Karl. A.
1999-01-01
The low-lying electronic states of NiC are investigated by all-electron ab initio multi-configuration self-consistent-field (CASSCF) calculations including relativistic corrections. The electronic structure of NiC is interpreted as perturbed antiferromagnetic couplings of the localized angular...
Study on the surface hydroxyl group on solid breeding materials by ab-initio calculations
Energy Technology Data Exchange (ETDEWEB)
Tanaka, Satoru; Taniguchi, Masaki [Tokyo Univ. (Japan). Faculty of Engineering
1996-10-01
The nature of -OH on the surface of Li{sub 2}O was analyzed with the ab-initio quantum chemical calculation technique. Calculation results showed that the stretching vibration of O-H is affected by the chemical species around the -OH. (author)
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.
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.
Vonci, Michele; Giansiracusa, Marcus J; Gable, Robert W; Van den Heuvel, Willem; Latham, Kay; Moubaraki, Boujemaa; Murray, Keith S; Yu, Dehong; Mole, Richard A; Soncini, Alessandro; Boskovic, Colette
2016-02-01
Ab initio calculations carried out on the Tb analogue of the single-molecule magnet family Na9[Ln(W5O18)2] (Ln = Nd, Gd, Ho and Er) have allowed interpretation of the inelastic neutron scattering spectra. The combined experimental and theoretical approach sheds new light on the sensitivity of the electronic structure of the Tb(III) ground and excited states to small structural distortions from axial symmetry, thus revealing the subtle relationship between molecular geometry and magnetic properties of the two isostructural species that comprise the sample. PMID:26690503
Surface tension of ab initio liquid water at the water-air interface
Nagata, Yuki; Ohto, Tatsuhiko; Bonn, Mischa; Kühne, Thomas D.
2016-05-01
We report calculations on the surface tension of the water-air interface using ab initio molecular dynamics (AIMD) simulations. We investigate the influence of the cell size on surface tension of water from force field molecular dynamics simulations. We find that the calculated surface tension increases with increasing simulation cell size, thereby illustrating that a correction for finite size effects is essential for small systems that are customary in AIMD simulations. Moreover, AIMD simulations reveal that the use of a double-ζ basis set overestimates the experimentally measured surface tension due to the Pulay stress while more accurate triple and quadruple-ζ basis sets give converged results. We further demonstrate that van der Waals corrections critically affect the surface tension. AIMD simulations without the van der Waals correction substantially underestimate the surface tension while the van der Waals correction with the Grimme's D2 technique results in a value for the surface tension that is too high. The Grimme's D3 van der Waals correction provides a surface tension close to the experimental value. Whereas the specific choices for the van der Waals correction and basis sets critically affect the calculated surface tension, the surface tension is remarkably insensitive to the details of the exchange and correlation functionals, which highlights the impact of long-range interactions on the surface tension. Our simulated values provide important benchmarks, both for improving van der Waals corrections and AIMD simulations of aqueous interfaces.
PSI3: an open-source Ab Initio electronic structure package.
Crawford, T Daniel; Sherrill, C David; Valeev, Edward F; Fermann, Justin T; King, Rollin A; Leininger, Matthew L; Brown, Shawn T; Janssen, Curtis L; Seidl, Edward T; Kenny, Joseph P; Allen, Wesley D
2007-07-15
PSI3 is a program system and development platform for ab initio molecular electronic structure computations. The package includes mature programming interfaces for parsing user input, accessing commonly used data such as basis-set information or molecular orbital coefficients, and retrieving and storing binary data (with no software limitations on file sizes or file-system-sizes), especially multi-index quantities such as electron repulsion integrals. This platform is useful for the rapid implementation of both standard quantum chemical methods, as well as the development of new models. Features that have already been implemented include Hartree-Fock, multiconfigurational self-consistent-field, second-order Møller-Plesset perturbation theory, coupled cluster, and configuration interaction wave functions. Distinctive capabilities include the ability to employ Gaussian basis functions with arbitrary angular momentum levels; linear R12 second-order perturbation theory; coupled cluster frequency-dependent response properties, including dipole polarizabilities and optical rotation; and diagonal Born-Oppenheimer corrections with correlated wave functions. This article describes the programming infrastructure and main features of the package. PSI3 is available free of charge through the open-source, GNU General Public License. PMID:17420978
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.
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
Energy Technology Data Exchange (ETDEWEB)
Zhai, Huanchen; Lin, Shi Ying, E-mail: sylin@sdu.edu.cn
2015-07-09
Highlights: • A hybrid scheme to construct potential energy surfaces (PESs) is proposed. • The hybrid scheme shows enhanced stability and accuracy. • The hybrid scheme is shown to be able to construct high quality PESs. • A new analytic ab initio PES for N({sup 2}D) + H{sub 2} reactive system is constructed. - Abstract: A hybrid fitting scheme is proposed for the construction of global analytic ab initio potential energy surfaces (PESs) by means of applying reproducing kernel Hilbert space (RKHS) interpolation and cubic spline interpolation onto different dimensions of the molecular configuration space. In addition to inheriting most advantages of the pure RKHS method, this scheme offers the following extra benefits: short initiation time and enhanced stability and accuracy. We also propose a fast algorithm for the scheme allowing the PES computation time to be independent of the number of ab initio points. We have constructed an adiabatic PES of N({sup 2}D) + H{sub 2}→NH + H reactive system from more than twenty thousand ab initio points using this scheme. The accurate quantum dynamics results calculated on the constructed PES demonstrate high accuracy and efficiency of this new scheme.
Directory of Open Access Journals (Sweden)
Nguyen Thanh Duoc
2015-12-01
Full Text Available The results presented in this paper are the ab initio intermolecular potentials and the second virial coefficient, B2 (T of the dimer Cl2-Cl2. These ab initio potentials were proposed by the quantum chemical calculations at high level of theory CCSD (T with basis sets of Dunning’s valence correlation-consistent aug-cc-pVmZ (m = 2, 3; these results were extrapolated to complete basis set limit aug-cc-pV23Z. The ab initio energies of complete basis set limit aug-cc-pV23Z resulted from the exponential extrapolation were used to construct the 5-site pair potential functions. The second virial coefficients for this dimer were predicted from those with four-dimensional integration. The second virial coefficients were also corrected to first-order quantum effects. The results turn out to be in good agreement with experimental data, if available, or with those from empirical correlation. The quality of ab initio 5-site potentials proved the reliability for prediction of molecular thermodynamic properties.
Energy Technology Data Exchange (ETDEWEB)
Monteseguro, V. [Departamento de Física and MALTA Consolider Team, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Santa Cruz de Tenerife (Spain); Rodríguez-Hernández, P.; Muñoz, A., E-mail: amunoz@ull.es [Departamento de Física and MALTA Consolider Team, Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Santa Cruz de Tenerife (Spain); Instituto de Materiales y Nanotecnología. Universidad de La Laguna, 38200 San Cristóbal de La Laguna, Santa Cruz de Tenerife (Spain)
2015-12-28
The structural, elastic, and vibrational properties of yttrium aluminum garnet Y{sub 3}Al{sub 5}O{sub 12} are studied under high pressure by ab initio calculations in the framework of the density functional theory. The calculated ground state properties are in good agreement with the available experimental data. Pressure dependences of bond length and bulk moduli of the constituent polyhedra are reported. The evolution of the elastic constants and the major elastic properties, Young and shear modulus, Poisson's ratios, and Zener anisotropy ratio, are described. The mechanical stability is analyzed, on the light of “Born generalized stability criteria,” showing that the garnet is mechanically unstable above 116 GPa. Symmetries, frequencies, and pressure coefficients of the Raman-active modes are discussed on the basis of the calculated total and partial phonon density of states, which reflect the dynamical contribution of each atom. The relations between the phonon modes of Y{sub 3}Al{sub 5}O{sub 12} and the internal and external molecular modes of the different polyhedra are discussed. Infrared-active modes, as well as the silent modes, and their pressure dependence are also investigated. No dynamical instabilities were found below 116 GPa.
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.
Oreshko, A P; Ovchinnikova, E N; Beutier, G; Collins, S P; Nisbet, G; Kolchinskaya, A M; Dmitrienko, V E
2012-06-20
Thermal-motion induced (TMI) scattering is caused by the influence of atomic displacements on electronic states in crystals and strongly depends on temperature. It corresponds to dipole-dipole resonant x-ray scattering, but is usually accompanied by dipole-quadrupole scattering. The phenomenological theory supposes the dipole-quadrupole term to be temperature independent (TI). As a result, the transformation of the energy spectra with temperature observed experimentally in ZnO and GaN corresponds to the interference between the TMI and TI terms. In the present paper the direct confirmation of this theoretical prediction is given. Ab initio molecular dynamics was used to simulate the sets of atomic sites at various temperatures followed by quantum mechanical calculation of resonant Bragg reflection energy spectra. The results of simulation are in excellent coincidence with experimental energy spectra of forbidden reflections and confirm the earlier phenomenological conjecture about the interference between the TI dipole-quadrupole and TMI dipole-dipole contributions to the resonant atomic factor. PMID:22627099
Steady-state ab initio laser theory for complex gain media
Cerjan, Alexander; Stone, A Douglas
2014-01-01
We derive and test a generalization of Steady-State Ab Initio Laser Theory (SALT) to treat complex gain media. The generalized theory (C-SALT) is able to treat atomic and molecular gain media with diffusion and multiple lasing transitions, and semiconductor gain media in the free carrier approximation including fully the effect of Pauli blocking. The key assumption of the theory is stationarity of the level populations, which leads to coupled self-consistent equations for the populations and the lasing modes that fully include the effects of openness and non-linear spatial hole-burning. These equations can be solved efficiently for the steady-state lasing properties by a similar iteration procedure as in SALT, where a static gain medium with a single transition is assumed. The theory is tested by comparison to much less efficient Finite Difference Time Domain (FDTD) methods and excellent agreement is found. Using C-SALT to analyze the effects of varying gain diffusion constant we demonstrate a cross-over betw...
Structural insights and ab initio sequencing within the DING proteins family
International Nuclear Information System (INIS)
DING proteins constitute a recently discovered protein family that is ubiquitous in eukaryotes. The structural insights and the physiological involvements of these intriguing proteins are hereby deciphered. DING proteins constitute an intriguing family of phosphate-binding proteins that was identified in a wide range of organisms, from prokaryotes and archae to eukaryotes. Despite their seemingly ubiquitous occurrence in eukaryotes, their encoding genes are missing from sequenced genomes. Such a lack has considerably hampered functional studies. In humans, these proteins have been related to several diseases, like atherosclerosis, kidney stones, inflammation processes and HIV inhibition. The human phosphate binding protein is a human representative of the DING family that was serendipitously discovered from human plasma. An original approach was developed to determine ab initio the complete and exact sequence of this 38 kDa protein by utilizing mass spectrometry and X-ray data in tandem. Taking advantage of this first complete eukaryotic DING sequence, a immunohistochemistry study was undertaken to check the presence of DING proteins in various mice tissues, revealing that these proteins are widely expressed. Finally, the structure of a bacterial representative from Pseudomonas fluorescens was solved at sub-angstrom resolution, allowing the molecular mechanism of the phosphate binding in these high-affinity proteins to be elucidated
Ab initio Study on Structures and Isomerization of Magnesium Fluorosilylenoid H2SiFMgF
Institute of Scientific and Technical Information of China (English)
Yi-jian Zhang; Mei-jiang Li; Guo-qiao Lai; Da-cheng Feng; Sheng-yu Feng
2008-01-01
The structures and isomerization of magnesium fluorosilylenoid H2SiFMgF were investigated by ab initio molecular orbital theory. Four equilibrium structures and three isomeric transition states were located and fully optimized at the B3LYP/6-31G(d,p) and G3MP2B3 levels, respectively. Based on the B3LYP/6-31G(d,p) optimized geometries, harmonic frequencies of various structures were obtained and 29Si chemical shifts were calculated. The solvent effects were investigated by means of the polarizable continuum model using THF as a solvent at B3LYP/6-31G(d,p) level. Isomerization paths for isomers were confirmed by in-trinsic reaction coordinate calculations. The calculated results show that tetrahedral structure has the lowest energy and is the most stable; tetrahedral, three-membered ring, and p-complex structures are suggested to be the experimentally detectable ones; and σ-complex structure has the highest energy and will not exist.
Communication: Towards ab initio self-energy embedding theory in quantum chemistry
Energy Technology Data Exchange (ETDEWEB)
Lan, Tran Nguyen, E-mail: latran@umich.edu [Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109 (United States); Department of Physics, University of Michigan, Ann Arbor, Michigan 48109 (United States); Kananenka, Alexei A.; Zgid, Dominika [Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109 (United States)
2015-12-28
The self-energy embedding theory (SEET), in which the active space self-energy is embedded in the self-energy obtained from a perturbative method treating the non-local correlation effects, was recently developed in our group. In SEET, the double counting problem does not appear and the accuracy can be improved either by increasing the perturbation order or by enlarging the active space. This method was first calibrated for the 2D Hubbard lattice showing promising results. In this paper, we report an extension of SEET to quantum chemical ab initio Hamiltonians for applications to molecular systems. The self-consistent second-order Green’s function method is used to describe the non-local correlations, while the full configuration interaction method is carried out to capture strong correlation within the active space. Using few proof-of-concept examples, we show that SEET yields results of comparable quality to n-electron valence state second-order perturbation theory with the same active space, and furthermore, the full active space can be split into smaller active spaces without further implementation. Moreover, SEET avoids intruder states and does not require any high-order reduced density matrices. These advantages show that SEET is a promising method to describe physical and chemical properties of challenging molecules requiring large active spaces.
Towards ab initio self-energy embedding theory in quantum chemistry
Lan, Tran Nguyen; Zgid, Dominika
2015-01-01
The self-energy embedding theory (SEET), in which the active space self-energy is embedded in the self-energy obtained from a perturbative method treating the non-local correlation effects, was recently developed in our group. In SEET the double counting problem does not appear and the accuracy can be improved either by increasing the perturbation order or by enlarging the active space. This method was first calibrated for the 2D Hubbard lattice showing promising results. In this paper, we report an extension of SEET to quantum chemical ab initio Hamiltonians for applications to molecular systems. The self-consistent second-order Green's function (GF2) method is used to describe the non-local correlations, while the full configuration interaction (FCI) method is carried out to capture strong correlation within the active space. Using few proof-of-concept examples, we show that SEET yields results of comparable quality to $n-$electron valence state second-order perturbation theory (NEVPT2) with the same active...
Role of ab-initio calculations in elucidating properties of hydrated and ammoniated electrons
International Nuclear Information System (INIS)
The properties of solvated electrons are analyzed in terms of a self-consistent modified continuum model based on the techniques of ab initio molecular quantum mechanics. The model is semiclassical in spirit, employing the quantum mechanical density for the excess charge and the first solvation shell in conjunction with classical electrostatics, and is developed in a general form which can be straightforwardly applied to special cases of interest, such as the solvated mono- and dielectron complexes. The advantages and disadvantages of the technique are discussed in relation to other more empirical approaches. Computational results are presented for excess electrons (mono- and dielectrons) in water and ammonia, and the role of long-range polarization of the medium in localizing the excess charge is analyzed. The variationally determined ground states are characterized in terms of equilibrium solvation shell geometry (appreciable cavities are implied for both water and ammonia), solvation energy, photoionization energy, and charge distribution. The finding of negative spin densities at the first solvent shell protons underscores the importance of a many electron theoretical treatment. Preliminary results for excited states are also reported. The calculated results are compared with experimental and other theoretical data, and the sensitivity of the results to various features of the model is discussed. Particular attention is paid to the number of solvent molecules required to trap the excess electron
Communication: Towards ab initio self-energy embedding theory in quantum chemistry
International Nuclear Information System (INIS)
The self-energy embedding theory (SEET), in which the active space self-energy is embedded in the self-energy obtained from a perturbative method treating the non-local correlation effects, was recently developed in our group. In SEET, the double counting problem does not appear and the accuracy can be improved either by increasing the perturbation order or by enlarging the active space. This method was first calibrated for the 2D Hubbard lattice showing promising results. In this paper, we report an extension of SEET to quantum chemical ab initio Hamiltonians for applications to molecular systems. The self-consistent second-order Green’s function method is used to describe the non-local correlations, while the full configuration interaction method is carried out to capture strong correlation within the active space. Using few proof-of-concept examples, we show that SEET yields results of comparable quality to n-electron valence state second-order perturbation theory with the same active space, and furthermore, the full active space can be split into smaller active spaces without further implementation. Moreover, SEET avoids intruder states and does not require any high-order reduced density matrices. These advantages show that SEET is a promising method to describe physical and chemical properties of challenging molecules requiring large active spaces
Patil, Amol Baliram; Bhanage, Bhalchandra Mahadeo
2016-06-21
The nature of bonding interactions between the cation and the anion of an ionic liquid is at the heart of understanding ionic liquid properties. A particularly interesting case is a special class of ionic liquids known as protic ionic liquids. The extent of proton transfer in protic ionic liquids has been observed to vary according to the interacting species. Back proton transfer renders protic ionic liquids volatile and to be considered as inferior ionic liquids. We try to address this issue by employing modern ab initio valence bond theory calculations. The results indicate that the bonding in the cation and the anion of a prototypical ionic liquid, ethylammonium nitrate, is fundamentally different. It is neither characteristic of covalent/polar covalent bonding nor ionic bonding but rather charge shift bonding as a resonance hybrid of two competing ionic molecular electronic structure configurations. An investigation of other analogous protic ionic liquids reveals that this charge shift bonding seems to be a typical characteristic of protic ionic liquids while the ionic solid analogue compound ammonium nitrate has less charge shift bonding character as compared to protic ionic liquids. Further the extent of charge shift bonding character has been found to be congruent with the trends in many physicochemical properties such as melting point, conductivity, viscosity, and ionicity of the studied ionic liquids indicating that percentage charge shift character may serve as a key descriptor for large scale computational screening of ionic liquids with desired properties.
Ab initio Mechanism Study on the Reaction of Chlorine Atom with Formic Acid
Institute of Scientific and Technical Information of China (English)
于海涛; 付宏刚; 等
2003-01-01
The potential energy surface(PES) for the reaction of Cl atom with HCOOH is predicted using ab initio molecular orbital calculation methods at UQCIDS(T,full)6-311++G(3df,2p)//UMP2(full)/6-311+G(d,P) level of theory with zero-point vibrational energy (ZPVE) correction.The calculated results show that the reaction mechanism of Cl atom with formic acid is a C-site hydrogen abstraction reaction from cis-HOC(H)O molecule by Cl atom with a 3.73kJ/mol reaction barrier height,leading to the formation of cis-HOCO radical which will reacts with Cl atom or other molecules in such a reaction system.Because the reaction barrier height of O-site hydrogen abstraction reaction from cis-HOC(H)O molecule by Cl atom which leads to the formation of HCO2 radical is 67.95kJ/mol,it is a secondary reaction channel in experiment,This is in good agreement with the prediction based on the previous experiments.
Jackels, C. F.; Phillips, D. H.
1986-01-01
Ab initio quantum chemical techniques have been used to investigate covalently-bonded and hydrogen-bonded species that may be important intermediates in the reaction of hydroxyl and hydroperoxyl radicals. Stable structures of both types were identified. Basic sets of polarized double-zeta quality and large scale configuration interaction wave functions have been utilized. Based upon electronic energies, the covalently-bonded HOOOH species is found to be 26.4 kcal/mol more stable than the OH and HO2 radicals. Similarly, the hydrogen-bonded HO-HO2 species is found to have an electronic energy 4.7 kcal/mol below that of the component radicals, after correction is made for the basis set superposition error. The hydrogen-bonded form is found to be planar, to possess one relatively 'normal' hydrogen bond, and to have lowest energy 3A-prime and 1A-prime states that are essentially degenerate. The 1A-double prime and 3A-double prime excited states produced by rotation of the unpaired OH electron into the molecular plane are found to be very slightly bound.
Communication: Towards ab initio self-energy embedding theory in quantum chemistry.
Lan, Tran Nguyen; Kananenka, Alexei A; Zgid, Dominika
2015-12-28
The self-energy embedding theory (SEET), in which the active space self-energy is embedded in the self-energy obtained from a perturbative method treating the non-local correlation effects, was recently developed in our group. In SEET, the double counting problem does not appear and the accuracy can be improved either by increasing the perturbation order or by enlarging the active space. This method was first calibrated for the 2D Hubbard lattice showing promising results. In this paper, we report an extension of SEET to quantum chemical ab initio Hamiltonians for applications to molecular systems. The self-consistent second-order Green's function method is used to describe the non-local correlations, while the full configuration interaction method is carried out to capture strong correlation within the active space. Using few proof-of-concept examples, we show that SEET yields results of comparable quality to n-electron valence state second-order perturbation theory with the same active space, and furthermore, the full active space can be split into smaller active spaces without further implementation. Moreover, SEET avoids intruder states and does not require any high-order reduced density matrices. These advantages show that SEET is a promising method to describe physical and chemical properties of challenging molecules requiring large active spaces.
Structural insights and ab initio sequencing within the DING proteins family
Energy Technology Data Exchange (ETDEWEB)
Elias, Mikael, E-mail: mikael.elias@weizmann.ac.il [Weizmann Institute of Science, Rehovot (Israel); Liebschner, Dorothee [CRM2, Nancy Université (France); Gotthard, Guillaume; Chabriere, Eric [AFMB, Université Aix-Marseille II (France)
2011-01-01
DING proteins constitute a recently discovered protein family that is ubiquitous in eukaryotes. The structural insights and the physiological involvements of these intriguing proteins are hereby deciphered. DING proteins constitute an intriguing family of phosphate-binding proteins that was identified in a wide range of organisms, from prokaryotes and archae to eukaryotes. Despite their seemingly ubiquitous occurrence in eukaryotes, their encoding genes are missing from sequenced genomes. Such a lack has considerably hampered functional studies. In humans, these proteins have been related to several diseases, like atherosclerosis, kidney stones, inflammation processes and HIV inhibition. The human phosphate binding protein is a human representative of the DING family that was serendipitously discovered from human plasma. An original approach was developed to determine ab initio the complete and exact sequence of this 38 kDa protein by utilizing mass spectrometry and X-ray data in tandem. Taking advantage of this first complete eukaryotic DING sequence, a immunohistochemistry study was undertaken to check the presence of DING proteins in various mice tissues, revealing that these proteins are widely expressed. Finally, the structure of a bacterial representative from Pseudomonas fluorescens was solved at sub-angstrom resolution, allowing the molecular mechanism of the phosphate binding in these high-affinity proteins to be elucidated.
Ab initio parameterization of YFF1, a universal force field for drug-design applications.
Yakovenko, Olexandr Ya; Li, Yvonne Y; Oliferenko, Alexander A; Vashchenko, Ganna M; Bdzhola, Volodymyr G; Jones, Steven J M
2012-02-01
The YFF1 is a new universal molecular mechanic force field designed for drug discovery purposes. The electrostatic part of YFF1 has already been parameterized to reproduce ab initio calculated dipole and quadrupole moments. Now we report a parameterization of the van der Waals interactions (vdW) for the same atom types that were previously defined. The 6-12 Lennard-Jones potential terms were parameterized against homodimerization energies calculated at the MP2/6-31 G level of theory. The Boys-Bernardi counterpoise correction was employed to account for the basis-set superposition error. As a source of structural information we used about 2,400 neutral compounds from the ZINC2007 database. About 6,600 homodimeric configurations were generated from this dataset. A special "closure" procedure was designed to accelerate the parameters fitting. As a result, dimerization energies of small organic compounds are reproduced with an average unsigned error of 1.1 kcal mol(-1). Although the primary goal of this work was to parameterize nonbonded interactions, bonded parameters were also derived, by fitting to PM6 semiempirically optimized geometries of approximately 20,000 compounds. PMID:21562826
Ab initio calculations for the far infrared collision induced absorption by N2 gas.
Bussery-Honvault, Béatrice; Hartmann, Jean-Michel
2014-02-01
We present (far-infrared) Collision Induced Absorption (CIA) spectra calculations for pure gaseous N2 made for the first time, from first-principles. They were carried out using classical molecular dynamics simulations based on ab initio predictions of both the intermolecular potential and the induced-dipole moment. These calculations reproduce satisfactory well the experimental values (intensity and band profile) with agreement within 3% at 149 K. With respect to results obtained with only the long range (asymptotic) dipole moment (DM), including the short range overlap contribution improves the band intensity and profile at 149 K, but it deteriorates them at 296 K. The results show that the relative contribution of the short range DM to the band intensity is typically around 10%. We have also examined the sensitivity of the calculated CIA to the intermolecular potential anisotropy, providing a test of the so-called isotropic approximation used up to now in all N2 CIA calculations. As all these effects interfere simultaneously with quantitatively similar influences (around 10%), it is rather difficult to assert which one could explain remaining deviations with the experimental results. Furthermore, the rather large uncertainties and sometimes inconsistencies of the available measurements forbid any definitive conclusion, stressing the need for new experiments. PMID:24511942
Ab initio carbon capture in open-site metal-organic frameworks.
Dzubak, Allison L; Lin, Li-Chiang; Kim, Jihan; Swisher, Joseph A; Poloni, Roberta; Maximoff, Sergey N; Smit, Berend; Gagliardi, Laura
2012-10-01
During the formation of metal-organic frameworks (MOFs), metal centres can coordinate with the intended organic linkers, but also with solvent molecules. In this case, subsequent activation by removal of the solvent molecules creates unsaturated 'open' metal sites known to have a strong affinity for CO(2) molecules, but their interactions are still poorly understood. Common force fields typically underestimate by as much as two orders of magnitude the adsorption of CO(2) in open-site Mg-MOF-74, which has emerged as a promising MOF for CO(2) capture. Here we present a systematic procedure to generate force fields using high-level quantum chemical calculations. Monte Carlo simulations based on an ab initio force field generated for CO(2) in Mg-MOF-74 shed some light on the interpretation of thermodynamic data from flue gas in this material. The force field describes accurately the chemistry of the open metal sites, and is transferable to other structures. This approach may serve in molecular simulations in general and in the study of fluid-solid interactions.
Ab initio calculations on the magnetic properties of transition metal complexes
International Nuclear Information System (INIS)
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
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...
Knoop, S.; Żuchowski, P. S.; KÈ©dziera, D.; Mentel, Ł.; Puchalski, M.; Mishra, H. P.; Flores, A. S.; Vassen, W.
2014-08-01
We have investigated the ultracold interspecies scattering properties of metastable triplet He and Rb. We performed state-of-the-art ab initio calculations of the relevant interaction potential, and measured the interspecies elastic cross section for an ultracold mixture of metastable triplet He4 and Rb87 in a quadrupole magnetic trap at a temperature of 0.5 mK. Our combined theoretical and experimental study gives an interspecies scattering length a4+87=+17-4+1a0, which prior to this work was unknown. More general, our work shows the possibility of obtaining accurate scattering lengths using ab initio calculations for a system containing a heavy, many-electron atom, such as Rb.
Ab initio study of AlxMoNbTiV high-entropy alloys.
Cao, Peiyu; Ni, Xiaodong; Tian, Fuyang; Varga, Lajos K; Vitos, Levente
2015-02-25
The Al(x)MoNbTiV (x = 0-1.5) high-entropy alloys (HEAs) adopt a single solid-solution phase, having the body centered cubic (bcc) crystal structure. Here we employ the ab initio exact muffin-tin orbitals method in combination with the coherent potential approximation to investigate the equilibrium volume, elastic constants, and polycrystalline elastic moduli of Al(x)MoNbTiV HEAs. A comparison between the ab initio and experimental equilibrium volumes demonstrates the validity and accuracy of the present approach. Our results indicate that Al addition decreases the thermodynamic stability of the bcc structure with respect to face-centered cubic and hexagonal close packed lattices. For the elastically isotropic Al(0.4)MoNbTiV HEAs, the valence electron concentration (VEC) is about 4.82, which is slightly different from VEC ∼ 4.72 obtained for the isotropic Gum metals and refractory--HEAs. PMID:25640032
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.
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.
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.
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
For the first time, the differences between the spectra of amphetamine and amphetamine-H+ and between different conformers are thoroughly studied by ab initio model calculations, and Raman and surface-enhanced Raman spectroscopy (SERS) spectra are measured for different species of amphetamine....... 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...... of the conformational energy of the S-plus-amphetamine molecule and the S-plus-amphetamine-H+ ion. The harmonic frequency calculations provide information about the characteristic features of the Raman spectra and the nature of the bonding in the molecule. It is concluded that vibrational bands from salt anions...
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.
Large-scale ab initio configuration interaction calculations for light nuclei
Maris, Pieter; Metin Aktulga, H.; Caprio, Mark A.; Çatalyürek, Ümit V.; Ng, Esmond G.; Oryspayev, Dossay; Potter, Hugh; Saule, Erik; Sosonkina, Masha; Vary, James P.; Yang, Chao; Zhou, Zheng
2012-12-01
In ab-initio Configuration Interaction calculations, the nuclear wavefunction is expanded in Slater determinants of single-nucleon wavefunctions and the many-body Schrodinger equation becomes a large sparse matrix problem. The challenge is to reach numerical convergence to within quantified numerical uncertainties for physical observables using finite truncations of the infinite-dimensional basis space. We discuss strategies for constructing and solving the resulting large sparse matrix eigenvalue problems on current multicore computer architectures. Several of these strategies have been implemented in the code MFDn, a hybrid MPI/OpenMP Fortran code for ab-initio nuclear structure calculations that can scale to 100,000 cores and more. Finally, we will conclude with some recent results for 12C including emerging collective phenomena such as rotational band structures using SRG evolved chiral N3LO interactions.
Ab-initio Gorkov-Green's function calculations of open-shell nuclei
Soma, V; Duguet, T
2012-01-01
We present results from a new ab-initio method that uses the self-consistent Gorkov Green's function theory to address truly open-shell systems. The formalism has been recently worked out up to second order and is implemented here in nuclei for the first time on the basis of realistic nuclear forces. We find good convergence of the results with respect to the basis size in Ca44 and Ni74 and discuss quantities of experimental interest including ground-state energies, pairing gaps and particle addition/removal spectroscopy. These results demonstrate that the Gorkov method is a valid alternative to multireference approaches for tackling degenerate or near degenerate quantum systems. In particular, it increases the number of mid-mass nuclei accessible in an ab-initio fashion from a few tens to a few hundreds.
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%.
A fully ab initio potential energy surface for ClH2 reactive system
Institute of Scientific and Technical Information of China (English)
无
2000-01-01
An ab initio analytical potential energy surface called BW3 for the ClH2 reactive system is presented. The fit of this surface is based on about 1 200 ab initio energy points, computed with multi-reference configuration interaction(MRCI) and scaling external correlation (SEC) method and a very large basis set. The precision in the fit is very high. The BW3 surface could reproduce correctly the dissociation energy of H2 and HCl, and the endothermicity of the Cl + H2 abstraction reaction. For the Cl + H2 abstraction reaction, the saddle point of BW3 lies in collinear geometries, and the barrier height is 32.84 kJ/mol; for the H + ClH exchange reaction, the barrier of BW3 is also linear, with a height of 77.40 kJ/mol.
A fully ab initio potential energy surface for C1H2 reactive system
Institute of Scientific and Technical Information of China (English)
边文生; 刘成卜; H.J.Werner
2000-01-01
An ab initio analytical potential energy surface called BW3 for the CIH2 reactive system is presented. The fit of this surface is based on about 1 200 ab initio energy points, computed with multi-reference configuration interaction(MRCI) and scaling external correlation (SEC) method and a very large basis set. The precision in the fit is very high. The BW3 surface could reproduce correctly the dissociation energy of H2 and HCI, and the endothermicity of the Cl + H2 abstraction reaction. For the Cl + H2 abstraction reaction, the saddle point of BW3 lies in collinear geometries, and the barrier height is 32.84 kJ/mol; for the H + CIH exchange reaction, the barrier of BW3 is also linear, with a height of 77.40 kJ/mol.
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.
{\\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...
Ab initio modelling of the behaviour of point defects and fission products in nuclear fuel
International Nuclear Information System (INIS)
The aim of this work is to determine precisely the mechanisms of formation and migration of defects and fission products as well as the associated energies. Examples on uranium dioxide UO2 (standard nuclear fuel) and on uranium carbide UC (potential fuel for new generation reactors) are given. The obtained results are discussed and compared with the experimental results carried out. The ab initio method used is the Projector Augmented-Wave (PAW) method based on the density functional theory. The particular electronic properties of actinides are especially studied because, on account of their 5f orbitals more or less localized around the nucleus, it is difficult to model the actinide compounds by the DFT method. In particular, the modelling of the exchange-correlation interaction of the 5f electrons of UO2 requires approximations (as GGA+U) beyond those more currently used in ab initio calculations (LDA or GGA). (O.M.)
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...
Experimental studies and ab initio calculations on characteristics of the C state of SF2 radical
International Nuclear Information System (INIS)
SF2 radicals were generated by a pulsed dc discharge in the mixture gas beam of SF2 and Ar. The (2+1) resonance-enhanced multiphoton ionization (REMPI) excitation spectroscopy of SF2 radical was obtained between 325 and 365 nm. The SF+ ion signals were also observed in the same wavelength range. The analysis shows that the spectrum can be assigned as the two-photon resonant excitation of SF2 radical (B-tilde1 B1 and (C-tilde1 A1 states). And also, ab initio calculations suggest that the C-tilde state is a bonding state with Rydberg characteristic. The potential energy surfaces (PESs) of SF2 and SF2+ by ab initio calculations suggest that SF+ ions originate from dissociation processes of excited SF2+ ions. (author)
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...
A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction
Spencer, Matt; Eickholt, Jesse; Cheng, Jianlin
2014-01-01
Ab initio protein secondary structure (SS) predictions are utilized to generate tertiary structure predictions, which are increasingly demanded due to the rapid discovery of proteins. Although recent developments have slightly exceeded previous methods of SS prediction, accuracy has stagnated around 80% and many wonder if prediction cannot be advanced beyond this ceiling. Disciplines that have traditionally employed neural networks are experimenting with novel deep learning techniques in atte...
Ab-initio simulation and experimental validation of beta-titanium alloys
Raabe, D.; Sander, B.; Friák, M.; Ma, D.; Neugebauer, J.
2008-01-01
In this progress report we present a new approach to the ab-initio guided bottom up design of beta-Ti alloys for biomedical applications using a quantum mechanical simulation method in conjunction with experiments. Parameter-free density functional theory calculations are used to provide theoretical guidance in selecting and optimizing Ti-based alloys with respect to three constraints: (i) the use of non-toxic alloy elements; (ii) the stabilization of the body centered cubic beta phase at roo...
Ab Initio Studies on Hematite Surface and the Adsorption of Phosphate
Swati Chaudhury; Chandrika Varadachari; Kunal Ghosh
2014-01-01
This investigation explores the ab initio DFT method for understanding surface structure of hematite and the nature and energetics of phosphate adsorption. Using the full potential linearized plane wave method (FP-LAPW), we derived the structure and energies of various magnetic forms of hematite. The antiferromagnetic (AFM) form was observed to be the most stable. Hematite surfaces with Fe-termination, O-termination, or OH-termination were studied. The OH-terminated surface was the most stabl...
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.
Ab initio potential energy surface for the highly nonlinear dynamics of the KCN molecule
Energy Technology Data Exchange (ETDEWEB)
Párraga, H.; Arranz, F. J., E-mail: fj.arranz@upm.es; Benito, R. M., E-mail: rosamaria.benito@upm.es [Grupo de Sistemas Complejos, ETSI Agrónomos, Universidad Politécnica de Madrid, 28040 Madrid (Spain); Borondo, F., E-mail: f.borondo@uam.es [Departamento de Química and Instituto de Ciencias Matemáticas (ICMAT), Universidad Autónoma de Madrid, Cantoblanco, 28049-Madrid (Spain)
2013-11-21
An accurate ab initio quantum chemistry study at level of quadratic configuration interaction method of the electronic ground state of the KCN molecule is presented. A fitting of the results to an analytical series expansion was performed to obtain a global potential energy surface suitable for the study of the associated vibrational dynamics. Additionally, classical Poincaré surfaces of section for different energies and quantum eigenstates were calculated, showing the highly nonlinear behavior of this system.
Ab initio calculation of positron distribution, ACAR and lifetime in TTF-TCNQ
International Nuclear Information System (INIS)
We have performed ab initio calculations of positron distribution, ACAR and lifetime in the quasi-one-dimensional organic conductor TTF-TCNQ. The electronic structure is obtained within the LDA, while the positron state is calculated either with the LDA or with the GGA. Except the positron lifetime, differences between the LDA and GGA results are rather small. The obtained results are compared with our previous experiments and calculations.
Ab initio calculation of positron distribution, ACAR and lifetime in TTF-TCNQ
Ishibashi, Shoji; Kohyama, Masanori
2000-06-01
We have performed ab initio calculations of positron distribution, ACAR and lifetime in the quasi-one-dimensional organic conductor TTF-TCNQ. The electronic structure is obtained within the LDA, while the positron state is calculated either with the LDA or with the GGA. Except the positron lifetime, differences between the LDA and GGA results are rather small. The obtained results are compared with our previous experiments and calculations.
Large scale ab initio calculations based on three levels of parallelization
Bottin, François; Leroux, Stéphane; Knyazev, Andrew; Zérah, Gilles
2007-01-01
We suggest and implement a parallelization scheme based on an efficient multiband eigenvalue solver, called the locally optimal block preconditioned conjugate gradient LOBPCG method, and using an optimized three-dimensional (3D) fast Fourier transform (FFT) in the ab initio}plane-wave code ABINIT. In addition to the standard data partitioning over processors corresponding to different k-points, we introduce data partitioning with respect to blocks of bands as well as spatial partitioning in t...
Ab initio study on the magnetostructural properties of MnAs
Sanvito, Stefano; RUNGGER, IVAN
2006-01-01
The magnetic and structural properties of MnAs are studied with ab initio methods, and by mapping total energies onto a Heisenberg model. The stability of the different phases is found to depend mainly on the volume and on the amount of magnetic order, confirming previous experimental findings and phenomenological models. It is generally found that for large lattice constants the ferromagnetic state is favored, whereas for small lattice constants different antiferromagnetic states can be stab...
On limits of ab initio calculations of pairing gap in nuclei
Saperstein, E. E.; Baldo, M.; Lombardo, U.; Pankratov, S. S.; Zverev, M. V.
2010-01-01
A brief review of recent microscopic calculations of nuclear pairing gap is given. A semi-microscopic model is suggested in which the ab-initio effective pairing interaction is supplemented with a small phenomenological addendum. It involves a parameter which is universal for all medium and heavy nuclei. Calculations for several isotopic and isotonic chains of semi-magic nuclei confirm the relevance of the model.
Ab initio theory of galvanomagnetic phenomena in ferromagnetic metals and disordered alloys
Turek, Ilja; Kudrnovsky, Josef; Drchal, Vaclav
2011-01-01
We present an ab initio theory of transport quantities of metallic ferromagnets developed in the framework of the fully relativistic tight-binding linear muffin-tin orbital method. The approach is based on the Kubo-Streda formula for the conductivity tensor, on the coherent potential approximation for random alloys, and on the concept of interatomic electron transport. The developed formalism is applied to pure 3d transition metals (Fe, Co, Ni) and to random Ni-based ferromagnetic alloys (Ni-...
Belousov, Roman; Prencipe, Mauro
2014-01-01
The isothermal compression of magnesium perovskite and postperovskite is examined through the F-f plot and the diagnostic plot of Vinet universal model theoretically from the ab initio quantum-mechanical calculations at the hybrid Hartree-Fock / Density Functional Theory level. A purely numerical approach, first time applied in this paper, shows that the discrepancies largely observed between studies on the perovskite and criticized in geophysical applications are due to the inadequate choice...
Hyperfine tensors of nitrogen-vacancy center in diamond from \\emph{ab initio} calculations
Gali, Adam
2009-01-01
We determine and analyze the charge and spin density distributions of nitrogen-vacancy (N-V) center in diamond for both the ground and excited states by \\emph{ab initio} supercell calculations. We show that the hyperfine tensor of $^{15}$N nuclear spin is negative and strongly anisotropic in the excited state, in contrast to previous models used extensively to explain electron spin resonance measurements. In addition, we detect a significant redistribution of the spin density due to excitatio...
Structures of 13-atom clusters of fcc transition metals by ab initio and semiempirical calculations
Longo, R. C.; Gallego, L. J.
2006-11-01
We report the results of ab initio calculations of the structures and magnetic moments of Ni13 , Pd13 , Pt13 , Cu13 , Ag13 , and Au13 that were performed using a density-functional method that employs linear combinations of pseudoatomic orbitals as basis sets (SIESTA). Our structural results for Pt13 , Cu13 , Ag13 , and Au13 show that a buckled biplanar structure (BBP) is more stable than the icosahedral configuration, in keeping with results obtained recently by Chang and Chou [Phys. Rev. Lett. 93, 133401 (2004)] using the Vienna ab initio simulation package with a plane-wave basis. However, for Ni13 and Pd13 we found that the icosahedral structure is more stable than BBP. For all these clusters, two semiempirical methods based on spherically symmetric potentials both found the icosahedral structure to be the more stable, while the modified embedded atom model method, which uses a direction-dependent potential, found BBP to be the more stable structure. When low-energy structures found in recent ab initio studies of Pt13 , Cu13 , and Au13 other than Chang and Chou were optimized with SIESTA, those reported for Pt13 and Cu13 were found to be less stable than BBP, but the two-dimensional planar configuration reported for Au13 proved to be more stable than BBP.
Ab initio atomic thermodynamics investigation on oxygen defects in the anatase TiO{sub 2}
Energy Technology Data Exchange (ETDEWEB)
Cheng, Zhijun [College of Science, University of Shanghai for Science and Technology, Shanghai 200093 (China); Liu, Tingyu, E-mail: liutyyxj@163.com [College of Science, University of Shanghai for Science and Technology, Shanghai 200093 (China); Yang, Chenxing; Gan, Haixiu [College of Science, University of Shanghai for Science and Technology, Shanghai 200093 (China); Chen, Jianyu [Key Laboratory of Materials for High Power Laser, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai 201800 (China); Zhang, Feiwu [Nanochemistry Research Institute, Curtin University, GPO Box U1987, Perth, WA 6845 (Australia)
2013-01-05
Highlights: Black-Right-Pointing-Pointer Three typical oxygen defects under the different annealing conditions have been studied. Black-Right-Pointing-Pointer The oxygen vacancy is easier to form at the surface than in the bulk. Black-Right-Pointing-Pointer The adsorption of O{sub 2} whose orientation is parallel to the surface should be more favorable. Black-Right-Pointing-Pointer The reduction reaction may firstly undertake at the surface during the annealing treatment. Black-Right-Pointing-Pointer The interstitial oxygen has important contribution to lead to the reduction of the band gap. - Abstract: In the framework of the ab initio atomic thermodynamics, the preliminary analysis of the oxygen defects in anatase TiO{sub 2} has been done by investigating the influence of the annealing treatment under representative conditions on three typical oxygen defects, that is, oxygen vacancy, oxygen adsorption and oxygen interstitial. Our results in this study agree well with the related experimental results. The molecular species of the adsorbed O{sub 2} is subject to the ratio of the number of the O{sub 2} to that of the vacancy, as well as to the initial orientation of O{sub 2} relative to the surface (101). Whatever the annealing condition is, the oxygen vacancy is easier to form at the surface than in the bulk indicating that the reduction reaction may firstly undertake at the surface during the annealing treatment, which is consistent with the phase transformation experiments. The molecular ion, peroxide species, caused by the interstitial oxygen has important contribution to the top of the valence band and lead to the reduction of the band gap.
Iron -chromium alloys and free surfaces: from ab initio calculations to thermodynamic modeling
International Nuclear Information System (INIS)
Ferritic steels possibly strengthened by oxide dispersion are candidates as structural materials for generation IV and fusion nuclear reactors. Their use is limited by incomplete knowledge of the iron-chromium phase diagram at low temperatures and of the phenomena inducing preferential segregation of one element at grain boundaries or at surfaces. In this context, this work contributes to the multi-scale study of the model iron-chromium alloy and their free surfaces by numerical simulations. This study begins with ab initio calculations of properties related to the mixture of atoms of iron and chromium. We highlight complex dependency of the magnetic moments of the chromium atoms on their local chemical environment. Surface properties are also proving sensitive to magnetism. This is the case of impurity segregation of chromium in iron and of their interactions near the surface. In a second step, we construct a simple energy model for high numerical efficiency. It is based on pair interactions on a rigid lattice to which are given local chemical environment and temperature dependencies. With this model, we reproduce the ab initio results at zero temperature and experimental results at high temperature. We also deduce the solubility limits at all intermediate temperatures with mean field approximations that we compare to Monte Carlo simulations. The last step of our work is to introduce free surfaces in our model. We then study the effect of ab initio calculated bulk and surface properties on surface segregation.Finally, we calculate segregation isotherms. We therefore propose an evolution model of surface composition of iron-chromium alloys as a function of bulk composition. which are given local chemical environment and temperature dependencies. With this model, we reproduce the ab initio results at zero temperature and experimental results at high temperature. We also deduce the solubility limits at all intermediate temperatures with mean field approximations that
Energy Technology Data Exchange (ETDEWEB)
Alipour, Mojtaba, E-mail: malipour@shirazu.ac.ir [Department of Chemistry, College of Sciences, Shiraz University, Shiraz 71454 (Iran, Islamic Republic of); Mohajeri, Afshan, E-mail: amohajeri@shirazu.ac.ir [Department of Chemistry, College of Sciences, Shiraz University, Shiraz 71454 (Iran, Islamic Republic of)
2011-08-25
Graphical abstract: The electronic properties such as the static dipole polarizability, anisotropy of the polarizability, and dipole moment of yttrium bromide, YBr (X{sup 1}{Sigma}) have been theoretically studied. Highlights: {yields} Conventional ab initio and density functional theory methods were employed to study linear optical properties of YBr molecule. {yields} Properties derivatives and their level of theory dependence were studied. {yields} Electron correlation effects and rovibrational corrections have also been discussed. - Abstract: We have employed conventional ab initio and density functional theory methods to study the electronic properties such as the mean static dipole polarizability, {alpha}-bar, anisotropy of the polarizability, {Delta}{alpha}, and dipole moment, {mu}, of yttrium bromide. The bond length dependence of properties is determined at different levels of theory and appropriate expansions around experimental internuclear distance have been presented. Moreover, the first and second geometrical derivatives for each property are quantified and their level of theory dependence has been analyzed. To study the effect of molecular rotation and vibration on the electronic properties, the rovibrational corrections have also been carried out. It is found that these corrections are less pronounced for considered properties of YBr. In all calculations, the electron correlation effects have been considered and discussed. The obtained results show that the electron correlation is more significant in the calculation of the mean and the anisotropy of dipole polarizability.
High-resolution, near-infrared CW-CRDS, and ab initio investigations of N2O-HDO
Földes, T.; Lauzin, C.; Vanfleteren, T.; Herman, M.; Liévin, J.; Didriche, K.
2015-03-01
We have investigated the N2O-HDO molecular complex using ab initio calculations at the CCSD(T)-F12a/aug-cc-pVTZ level of theory and using cavity ring-down spectroscopy to probe an HDO/N2O/Ar supersonic jet around 1.58 μm. A single a-type vibrational band was observed, 13 cm-1 redshifted compared to the OH+OD excited band in HDO, and 173 vibration-rotation lines were assigned (Trot ≈ 20 K). A weighted fit of existing microwave and present near infrared (NIR) data was achieved using a standard Watson's Hamiltonian (σ = 1.26), producing ground and excited states rotational constants. The comparison of the former with those calculated ab initio suggests a planar geometry in which the OD rather than the OH bond in water is almost parallel to NNO. The equilibrium geometry and dissociation energy (De = -11.7 kJ/mol) of the water-nitrous oxide complex were calculated. The calculations further demonstrate and allow characterising another minimum, 404 cm-1 (ΔE0) higher in energy. Harmonic vibrational frequencies and dissociation energies, D0, were calculated for various conformers and isotopic forms of the complex, in both minima. The absence of N2O-D2O from dedicated NIR experiments is reported and discussed.
Towards Microscopic Ab Initio Calculations of Astrophysical S-Factors
Neff, Thomas; Langanke, Karlheinz
2010-01-01
Low energy capture cross sections are calculated within a microscopic many-body approach using an effective Hamiltonian derived from the Argonne V18 potential. The dynamics is treated within Fermionic Molecular Dynamics (FMD) which uses a Gaussian wave-packet basis to represent the many-body states. A phase-shift equivalent effective interaction derived within the Unitary Correlation Operator Method (UCOM) that treats explicitly short-range central and tensor correlations is employed. As a first application the 3He(alpha,gamma)7Be reaction is presented. Within the FMD approach the microscopic many-body wave functions of the 3/2- and 1/2- bound states in 7Be as well as the many-body scattering states in the 1/2+, 3/2+ and 5/2+ channels are calculated as eigenstates of the same microscopic effective Hamiltonian. Finally the S-factor is calculated from E1 transition matrix elements between the many-body scattering and bound states. For 3He(alpha,gamma)7Be the S-factor agrees very well, both in absolute normaliza...
Reaction mechanisms and kinetics of the iminovinylidene radical with NO: Ab initio study
Energy Technology Data Exchange (ETDEWEB)
Hsiao, Ming-Kai; Chung, Yi-Hua; Hung, Yu-Ming; Chen, Hui-Lung, E-mail: chl3@faculty.pccu.edu.tw [Department of Chemistry and Institute of Applied Chemistry, Chinese Culture University, Taipei 111, Taiwan (China)
2014-05-28
The nitric oxide (NO) is a notorious compound for polluting environment. Recent year, removing nitric oxide from the atmosphere becomes a focus of the investigation. In our work, we study the iminovinylidene (HNCC) radical reacted with NO molecule. The mechanism and kinetic for reaction of the HNCC radical with the NO molecule is investigated via considering the possible channels of the N and O atoms of NO attacking the N and C atoms of the HNCC based on the high level ab initio molecular orbital calculations in conjunction with variational TST and RRKM calculations. The species involved have been optimized at the B3LYP/6-311++G(3df,2p) level and their single-point energies are refined by the CCSD(T)/aug-cc-PVQZ//B3LYP/6-311++G(3df,2p) method. The calculated potential energy surfaces indicated that energetically the most favorable channel for the HNCC + NO reaction was predicted to be the formation of HNC+CNO (P8) product via the addition reaction of the C atom of HNCC radical and the N atom of NO with the head to head orientation. To rationalize the scenario of the calculated results, we also employ the Fukui functions and HSAB theory to seek for a possible explanation. In addition, the reaction rate constants were calculated using VariFlex code, and the results show that the total rate coefficient, k{sub total}, at Ar pressure 760 Torr can be represented with an equation: k{sub total} = 6.433 × 10{sup −11} T {sup 0.100} exp(0.275 kcal mol{sup −1}/RT) at T = 298–3000 K, in units of cm{sup 3} molecule{sup −1} s{sup −1}.
Rotational study of the CH4-CO complex: Millimeter-wave measurements and ab initio calculations
Surin, L. A.; Tarabukin, I. V.; Panfilov, V. A.; Schlemmer, S.; Kalugina, Y. N.; Faure, A.; Rist, C.; van der Avoird, A.
2015-10-01
The rotational spectrum of the van der Waals complex CH4-CO has been measured with the intracavity OROTRON jet spectrometer in the frequency range of 110-145 GHz. Newly observed and assigned transitions belong to the K = 2-1 subband correlating with the rotationless jCH4 = 0 ground state and the K = 2-1 and K = 0-1 subbands correlating with the jCH4 = 2 excited state of free methane. The (approximate) quantum number K is the projection of the total angular momentum J on the intermolecular axis. The new data were analyzed together with the known millimeter-wave and microwave transitions in order to determine the molecular parameters of the CH4-CO complex. Accompanying ab initio calculations of the intermolecular potential energy surface (PES) of CH4-CO have been carried out at the explicitly correlated coupled cluster level of theory with single, double, and perturbative triple excitations [CCSD(T)-F12a] and an augmented correlation-consistent triple zeta (aVTZ) basis set. The global minimum of the five-dimensional PES corresponds to an approximately T-shaped structure with the CH4 face closest to the CO subunit and binding energy De = 177.82 cm-1. The bound rovibrational levels of the CH4-CO complex were calculated for total angular momentum J = 0-6 on this intermolecular potential surface and compared with the experimental results. The calculated dissociation energies D0 are 91.32, 94.46, and 104.21 cm-1 for A (jCH4 = 0), F (jCH4 = 1), and E (jCH4 = 2) nuclear spin modifications of CH4-CO, respectively.
Red-Shifting versus Blue-Shifting Hydrogen Bonds: Perspective from Ab Initio Valence Bond Theory.
Chang, Xin; Zhang, Yang; Weng, Xinzhen; Su, Peifeng; Wu, Wei; Mo, Yirong
2016-05-01
Both proper, red-shifting and improper, blue-shifting hydrogen bonds have been well-recognized with enormous experimental and computational studies. The current consensus is that there is no difference in nature between these two kinds of hydrogen bonds, where the electrostatic interaction dominates. Since most if not all the computational studies are based on molecular orbital theory, it would be interesting to gain insight into the hydrogen bonds with modern valence bond (VB) theory. In this work, we performed ab initio VBSCF computations on a series of hydrogen-bonding systems, where the sole hydrogen bond donor CF3H interacts with ten hydrogen bond acceptors Y (═NH2CH3, NH3, NH2Cl, OH(-), H2O, CH3OH, (CH3)2O, F(-), HF, or CH3F). This series includes four red-shifting and six blue-shifting hydrogen bonds. Consistent with existing findings in literature, VB-based energy decomposition analyses show that electrostatic interaction plays the dominating role and polarization plays the secondary role in all these hydrogen-bonding systems, and the charge transfer interaction, which denotes the hyperconjugation effect, contributes only slightly to the total interaction energy. As VB theory describes any real chemical bond in terms of pure covalent and ionic structures, our fragment interaction analysis reveals that with the approaching of a hydrogen bond acceptor Y, the covalent state of the F3C-H bond tends to blue-shift, due to the strong repulsion between the hydrogen atom and Y. In contrast, the ionic state F3C(-) H(+) leads to the red-shifting of the C-H vibrational frequency, owing to the attraction between the proton and Y. Thus, the relative weights of the covalent and ionic structures essentially determine the direction of frequency change. Indeed, we find the correlation between the structural weights and vibrational frequency changes. PMID:27074500
Ab initio calculation of thermodynamic, transport, and optical properties of CH{sub 2} plastics
Energy Technology Data Exchange (ETDEWEB)
Knyazev, D. V. [Joint Institute for High Temperatures RAS, Izhorskaya 13 bldg. 2, Moscow 125412 (Russian Federation); Moscow Institute of Physics and Technology (State University), Institutskiy per. 9, Dolgoprudny, Moscow Region 141700 (Russian Federation); State Scientific Center of the Russian Federation – Institute for Theoretical and Experimental Physics of National Research Centre “Kurchatov Institute,” Bolshaya Cheremushkinskaya 25, 117218 Moscow (Russian Federation); Levashov, P. R. [Joint Institute for High Temperatures RAS, Izhorskaya 13 bldg. 2, Moscow 125412 (Russian Federation); Tomsk State University, Lenin Prospekt 36, Tomsk 634050 (Russian Federation)
2015-05-15
This work covers an ab initio calculation of thermodynamic, transport, and optical properties of plastics of the effective composition CH{sub 2} at density 0.954 g/cm{sup 3} in the temperature range from 5 kK up to 100 kK. The calculation is based on the quantum molecular dynamics, density functional theory, and the Kubo-Greenwood formula. The temperature dependence of the static electrical conductivity σ{sub 1{sub D{sub C}}}(T) has a step-like shape: σ{sub 1{sub D{sub C}}}(T) grows rapidly for 5 kK ≤ T ≤ 10 kK and is almost constant for 20 kK ≤ T ≤ 60 kK. The additional analysis based on the investigation of the electron density of states (DOS) is performed. The rapid growth of σ{sub 1{sub D{sub C}}}(T) at 5 kK ≤ T ≤ 10 kK is connected with the increase of DOS at the electron energy equal to the chemical potential ϵ = μ. The frequency dependence of the dynamic electrical conductivity σ{sub 1}(ω) at 5 kK has the distinct non-Drude shape with the peak at ω ≈ 10 eV. This behavior of σ{sub 1}(ω) was explained by the dip at the electron DOS.
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 modeling of energy dissipation during chemical reactions at transition metal surfaces
Energy Technology Data Exchange (ETDEWEB)
Meyer, Joerg
2012-02-16
In this work energy dissipation during exothermic chemical reactions in the context of heterogeneous catalysis is investigated in great detail, based on and substantially further developing ab initio methodologies. The dissociation of oxygen molecules (O{sub 2}) on the Pd(100) surface serves as a representative showcase, involving a release of about 2.6 eV of chemisorption energy. The impingement of O{sub 2} from the gas phase onto the surface occurs with randomly distributed initial molecular orientation and lateral position. In order to properly capture the breaking of the oxygen-oxygen bond, the latter is described on the level of density functional theory (DFT) with a semi-local exchange-correlation functional. Following a ''divide-and-conquer'' strategy, this description is decoupled from the dynamics to reduce the computational cost. The resulting interpolation problem is tackled with the help of neural networks using only a very limited number of data points. The initial sticking coefficient resulting from thousands of trajectories shows good agreement with available experimental data. Quite in contrast to Al(111) surfaces, the spin transition of the oxygen molecule ({sup 3}{sigma}{sup -}{sub g} spin triplet in gas phase to singlet-like state on the surface) can apparently be described adiabatically. In order to characterize this further and at the same time assess the relevance of one possible energy dissipation channel, excitations of electron-hole (e-h) pairs in the metal substrate are investigated using time-dependent perturbation theory - based on time-dependent density functional theory (TDDFT) and the Kohn-Sham band structure of the substrate. As a consequence, focus is inevitably shifted on phonons as major energy dissipation channel. A new embedding scheme called QM/Me was developed. In the present context it allows to model realistic (surface) phonons on the level of a ''modified embedded atom method'' (MEAM
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.
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.
Kowalski, Piotr M; Jahn, Sandro
2012-01-01
Over the last decade experimental studies have shown a large B isotope fractionation between materials carrying boron incorporated in trigonally and tetrahedrally coordinated sites, but the mechanisms responsible for producing the observed isotopic signatures are poorly known. In order to understand the boron isotope fractionation processes and to obtain a better interpretation of the experimental data and isotopic signatures observed in natural samples, we use first principles calculations based on density functional theory in conjunction with ab initio molecular dynamics and a new pseudofrequency analysis method to investigate the B isotope fractionation between B-bearing minerals (such as tourmaline and micas) and aqueous fluids containing H_3BO_3 and H_4BO_4- species. We confirm the experimental finding that the isotope fractionation is mainly driven by the coordination of the fractionating boron atoms and have found in addition that the strength of the produced isotopic signature is strongly correlated w...
Transport coefficients of helium-argon mixture based on ab initio potential.
Sharipov, Felix; Benites, Victor J
2015-10-21
The viscosity, thermal conductivity, diffusion coefficient, and thermal diffusion factor of helium-argon mixtures are calculated for a wide range of temperature and for various mole fractions up to the 12th order of the Sonine polynomial expansion with an ab initio intermolecular potential. The calculated values for these transport coefficients are compared with other data available in the open literature. The comparison shows that the obtained transport coefficients of helium-argon mixture have the best accuracy for the moment. PMID:26493894
Ab initio calculation of the spectrum and structure of $^{16}$O
Epelbaum, Evgeny; Lähde, Timo A; Lee, Dean; Meißner, Ulf-G; Rupak, Gautam
2013-01-01
We present ab initio lattice calculations of the low-energy even-parity states of $^{16}$O using chiral nuclear effective field theory. We find good agreement with the empirical energy spectrum, and with the electromagnetic properties and transition rates. For the ground state, we find that the nucleons are arranged in a tetrahedral configuration of alpha clusters. For the first excited spin-0 state, we find that the predominant structure is a square configuration of alpha clusters, with rotational excitations that include the first spin-2 state.
Ab initio description of second-harmonic generation from crystal surfaces
Tancogne-Dejean, Nicolas; Giorgetti, Christine; Véniard, Valérie
2016-09-01
We propose an ab initio framework to derive the dielectric and the second-order susceptibility tensors for crystal surfaces. The single-surface response is extracted from a supercell scheme. We evaluate macroscopic quantities, taking into account the local fields. The first- and second-order susceptibilities are evaluated within time-dependent density functional theory, in the long-wavelength limit. We apply our formalism to the calculation of the second-harmonic generation for clean and hydrogenated silicon surfaces. The agreement with measured second-order susceptibility components is significantly better, illustrating the importance of local-field effects.
Structure and lattice dynamics of PrFe3(BO3)4: Ab initio calculation
Chernyshev, V. A.; Nikiforov, A. E.; Petrov, V. P.
2016-06-01
The crystal structure and phonon spectrum of PrFe3(BO3)4 are ab initio calculated in the context of the density functional theory. The ion coordinates in the unit cell of a crystal and the lattice parameters are evaluated from the calculations. The types and frequencies of the fundamental vibrations, as well as the line intensities of the IR spectrum, are determined. The elastic constants of the crystal are calculated. A "seed" frequency of the vibration strongly interacting with the electron excitation on the praseodymium ion is obtained for low-frequency A 2 mode. The calculated results are in agreement with the known experimental data.
Ab-initio GMR and current-induced torques in Au/Cr multilayers
Haney, P. M.; Waldron, D; Duine, R. A.; Nunez, A. S.; Guo, H; MacDonald, A.H.
2006-01-01
We report on an {\\em ab-initio} study of giant magnetoresistance (GMR) and current-induced-torques (CITs) in Cr/Au multilayers that is based on non-equilibrium Green's functions and spin density functional theory. We find substantial GMR due primarily to a spin-dependent resonance centered at the Cr/Au interface and predict that the CITs are strong enough to switch the antiferromagnetic order parameter at current-densities $\\sim 100$ times smaller than typical ferromagnetic metal circuit swit...