Ab initio dynamical vertex approximation
NASA Astrophysics Data System (ADS)
Galler, Anna; Thunström, Patrik; Gunacker, Patrik; Tomczak, Jan M.; Held, Karsten
2017-03-01
Diagrammatic extensions of dynamical mean-field theory (DMFT) such as the dynamical vertex approximation (DΓ A) allow us to include nonlocal correlations beyond DMFT on all length scales and proved their worth for model calculations. Here, we develop and implement an Ab initio DΓ A approach (AbinitioDΓ A ) for electronic structure calculations of materials. The starting point is the two-particle irreducible vertex in the two particle-hole channels which is approximated by the bare nonlocal Coulomb interaction and all local vertex corrections. From this, we calculate the full nonlocal vertex and the nonlocal self-energy through the Bethe-Salpeter equation. The AbinitioDΓ A approach naturally generates all local DMFT correlations and all nonlocal G W contributions, but also further nonlocal correlations beyond: mixed terms of the former two and nonlocal spin fluctuations. We apply this new methodology to the prototypical correlated metal SrVO3.
Ab initio non-relativistic spin dynamics
Ding, Feizhi; Goings, Joshua J.; Li, Xiaosong; Frisch, Michael J.
2014-12-07
Many magnetic materials do not conform to the (anti-)ferromagnetic paradigm where all electronic spins are aligned to a global magnetization axis. Unfortunately, most electronic structure methods cannot describe such materials with noncollinear electron spin on account of formally requiring spin alignment. To overcome this limitation, it is necessary to generalize electronic structure methods and allow each electron spin to rotate freely. Here, we report the development of an ab initio time-dependent non-relativistic two-component spinor (TDN2C), which is a generalization of the time-dependent Hartree-Fock equations. Propagating the TDN2C equations in the time domain allows for the first-principles description of spin dynamics. A numerical tool based on the Hirshfeld partitioning scheme is developed to analyze the time-dependent spin magnetization. In this work, we also introduce the coupling between electron spin and a homogenous magnetic field into the TDN2C framework to simulate the response of the electronic spin degrees of freedom to an external magnetic field. This is illustrated for several model systems, including the spin-frustrated Li{sub 3} molecule. Exact agreement is found between numerical and analytic results for Larmor precession of hydrogen and lithium atoms. The TDN2C method paves the way for the ab initio description of molecular spin transport and spintronics in the time domain.
Ab initio two-component Ehrenfest dynamics
Ding, Feizhi; Goings, Joshua J.; Liu, Hongbin; Lingerfelt, David B.; Li, Xiaosong
2015-09-21
We present an ab initio two-component Ehrenfest-based mixed quantum/classical molecular dynamics method to describe the effect of nuclear motion on the electron spin dynamics (and vice versa) in molecular systems. The two-component time-dependent non-collinear density functional theory is used for the propagation of spin-polarized electrons while the nuclei are treated classically. We use a three-time-step algorithm for the numerical integration of the coupled equations of motion, namely, the velocity Verlet for nuclear motion, the nuclear-position-dependent midpoint Fock update, and the modified midpoint and unitary transformation method for electronic propagation. As a test case, the method is applied to the dissociation of H{sub 2} and O{sub 2}. In contrast to conventional Ehrenfest dynamics, this two-component approach provides a first principles description of the dynamics of non-collinear (e.g., spin-frustrated) magnetic materials, as well as the proper description of spin-state crossover, spin-rotation, and spin-flip dynamics by relaxing the constraint on spin configuration. This method also holds potential for applications to spin transport in molecular or even nanoscale magnetic devices.
Real-world predictions from ab initio molecular dynamics simulations.
Kirchner, Barbara; di Dio, Philipp J; Hutter, Jürg
2012-01-01
In this review we present the techniques of ab initio molecular dynamics simulation improved to its current stage where the analysis of existing processes and the prediction of further chemical features and real-world processes are feasible. For this reason we describe the relevant developments in ab initio molecular dynamics leading to this stage. Among them, parallel implementations, different basis set functions, density functionals, and van der Waals corrections are reported. The chemical features accessible through AIMD are discussed. These are IR, NMR, as well as EXAFS spectra, sampling methods like metadynamics and others, Wannier functions, dipole moments of molecules in condensed phase, and many other properties. Electrochemical reactions investigated by ab initio molecular dynamics methods in solution, on surfaces as well as complex interfaces, are also presented.
Multiple time step integrators in ab initio molecular dynamics
Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.
2014-02-28
Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.
Bicanonical ab Initio Molecular Dynamics for Open Systems.
Frenzel, Johannes; Meyer, Bernd; Marx, Dominik
2017-08-08
Performing ab initio molecular dynamics simulations of open systems, where the chemical potential rather than the number of both nuclei and electrons is fixed, still is a challenge. Here, drawing on bicanonical sampling ideas introduced two decades ago by Swope and Andersen [ J. Chem. Phys. 1995 , 102 , 2851 - 2863 ] to calculate chemical potentials of liquids and solids, an ab initio simulation technique is devised, which introduces a fictitious dynamics of two superimposed but otherwise independent periodic systems including full electronic structure, such that either the chemical potential or the average fractional particle number of a specific chemical species can be kept constant. As proof of concept, we demonstrate that solvation free energies can be computed from these bicanonical ab initio simulations upon directly superimposing pure bulk water and the respective aqueous solution being the two limiting systems. The method is useful in many circumstances, for instance for studying heterogeneous catalytic processes taking place on surfaces where the chemical potential of reactants rather than their number is controlled and opens a pathway toward ab initio simulations at constant electrochemical potential.
Ab initio molecular dynamics using hybrid density functionals.
Guidon, Manuel; Schiffmann, Florian; Hutter, Jürg; VandeVondele, Joost
2008-06-07
Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.
Ab initio molecular dynamics using hybrid density functionals
NASA Astrophysics Data System (ADS)
Guidon, Manuel; Schiffmann, Florian; Hutter, Jürg; Vandevondele, Joost
2008-06-01
Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.
Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics
NASA Astrophysics Data System (ADS)
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.
Diffusion in liquid Germanium using ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Kulkarni, R. V.; Aulbur, W. G.; Stroud, D.
1996-03-01
We describe the results of calculations of the self-diffusion constant of liquid Ge over a range of temperatures. The calculations are carried out using an ab initio molecular dynamics scheme which combines an LDA model for the electronic structure with the Bachelet-Hamann-Schlüter norm-conserving pseudopotentials^1. The energies associated with electronic degrees of freedom are minimized using the Williams-Soler algorithm, and ionic moves are carried out using the Verlet algorithm. We use an energy cutoff of 10 Ry, which is sufficient to give results for the lattice constant and bulk modulus of crystalline Ge to within 1% and 12% of experiment. The program output includes not only the self-diffusion constant but also the structure factor, electronic density of states, and low-frequency electrical conductivity. We will compare our results with other ab initio and semi-empirical calculations, and discuss extension to impurity diffusion. ^1 We use the ab initio molecular dynamics code fhi94md, developed at 1cm the Fritz-Haber Institute, Berlin. ^2 Work supported by NASA, Grant NAG3-1437.
Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics.
Makhov, Dmitry V; Glover, William J; Martinez, Todd J; Shalashilin, Dmitrii V
2014-08-07
We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as "cloning," in analogy to the "spawning" procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, "trains," as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.
Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics
Makhov, Dmitry V.; Shalashilin, Dmitrii V.; Glover, William J.; Martinez, Todd J.
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.
NASA Astrophysics Data System (ADS)
Ohta, Yasuhito; Ohta, Koji; Kinugawa, Kenichi
2004-01-01
An ab initio centroid molecular dynamics (CMD) method is developed by combining the CMD method with the ab initio molecular orbital method. The ab initio CMD method is applied to vibrational dynamics of diatomic molecules, H2 and HF. For the H2 molecule, the temperature dependence of the peak frequency of the vibrational spectral density is investigated. The results are compared with those obtained by the ab initio classical molecular dynamics method and exact quantum mechanical treatment. It is shown that the vibrational frequency obtained from the ab initio CMD approaches the exact first excitation frequency as the temperature lowers. For the HF molecule, the position autocorrelation function is also analyzed in detail. The present CMD method is shown to well reproduce the exact quantum result for the information on the vibrational properties of the system.
Accelerating ab initio molecular dynamics simulations by linear prediction methods
NASA Astrophysics Data System (ADS)
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.
Ab initio dynamics of the cytochrome P450 hydroxylation reaction
Elenewski, Justin E.; Hackett, John C
2015-01-01
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. PMID:25681906
Three-cluster dynamics within an ab initio framework
Quaglioni, Sofia; Romero-Redondo, Carolina; Navratil, Petr
2013-09-26
In this study, we introduce a fully antisymmetrized treatment of three-cluster dynamics within the ab initio framework of the no-core shell model/resonating-group method. Energy-independent nonlocal 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 Schrödinger 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 amore » 4He+n+n description of 6He and compare the results to experiment and to a six-body diagonalization of the Hamiltonian performed within the harmonic-oscillator expansions of the no-core shell model. Differences between the two calculations provide a measure of core (4He) polarization effects.« less
Ab initio dynamics of the cytochrome P450 hydroxylation reaction
NASA Astrophysics Data System (ADS)
Elenewski, Justin E.; Hackett, John C.
2015-02-01
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 dynamics of the cytochrome P450 hydroxylation reaction
Elenewski, Justin E.; Hackett, John C
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 dynamical exchange interactions in frustrated antiferromagnets
NASA Astrophysics Data System (ADS)
Simoni, Jacopo; Stamenova, Maria; Sanvito, Stefano
2017-08-01
The ultrafast response to an optical pulse excitation of the spin-spin exchange interaction in transition metal antiferromagnets is studied within the framework of the time-dependent spin-density functional theory. We propose a formulation for the full dynamical exchange interaction, which is nonlocal in space, and it is derived starting from ab initio arguments. Then, we investigate the effect of the laser pulse on the onset of the dynamical process. It is found that we can distinguish two types of excitations, both activated immediately after the action of the laser pulse. While the first one can be associated to a Stoner-like excitation and involves the transfer of spin from one site to another, the second one is related to the ultrafast modification of a Heisenberg-like exchange interaction and can trigger the formation of spin waves in the first few hundred femtoseconds of the time evolution.
Ab initio electronic and lattice dynamical properties of cerium dihydride
NASA Astrophysics Data System (ADS)
Gurel, Tanju; Eryigit, Resul
2007-03-01
The rare-earth metal hydrides are interesting systems because of the dramatic structural and electronic changes due to the hydrogen absorption and desorption. Among them, cerium dihydride (CeH2) is one of the less studied rare-earth metal-hydride. To have a better understanding, we have performed an ab initio study of electronic and lattice dynamical properties of CeH2 by using pseudopotential density functional theory within local density approximation (LDA) and a plane-wave basis. Electronic band structure of CeH2 have been obtained within LDA and as well as GW approximation. Lattice dynamical properties are calculated using density functional perturbation theory. The phonon spectrum is found to contain a set of high-frequency (˜ 850-1000 cm-1) optical bands, mostly hydrogen related, and low frequency cerium related acoustic modes climbing to 160 cm^ -1 at the zone boundary.
Ab Initio Multiple Spawning Photochemical Dynamics of DMABN Using GPUs
Curchod, Basile F. E.; Sisto, Aaron; Martinez, Todd J.
2016-12-15
The ultrafast decay dynamics of 4-(N,N-dimethylamino)benzonitrile (DMABN) following photoexcitation was studied with the ab initio multiple spawning (AIMS) method, combined with GPU-accelerated linear-response time-dependent density functional theory (LR-TDDFT). We validate the LR-TDDFT method for this case and then present a detailed analysis of the first ≈200 fs of DMABN excited-state dynamics. Almost complete nonadiabatic population transfer from S2 (the initially populated bright state) to S1 takes place in less than 50 fs, without significant torsion of the dimethylamino (DMA) group. Significant torsion of the DMA group is only observed after the nuclear wavepacket reaches S1 and acquires locally excited electronicmore » character. Here, our results show that torsion of the DMA group is not prerequisite for nonadiabatic transitions in DMABN, although such motion is indeed relevant on the lowest excited state (S1).« less
Thermal neutron scattering law calculations using ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Wormald, Jonathan; Hawari, Ayman I.
2017-09-01
In recent years, methods for the calculation of the thermal scattering law (i.e. S(α,β), where α and β are dimensionless momentum and energy transfer variables, respectively) were developed based on ab initio lattice dynamics (AILD) and/or classical molecular dynamics (CMD). While these methods are now mature and efficient, further advancement in the application of such atomistic techniques is possible using ab initio molecular dynamics (AIMD) methods. In this case, temperature effects are inherently included in the calculation, e.g. phonon density of states (DOS), while using ab initio force fields that eliminate the need for parameterized semi-empirical force fields. In this work, AIMD simulations were performed to predict the phonon spectra as a function of temperature for beryllium and graphite, which are representative nuclear reactor moderator and reflector materials. Subsequently, the calculated phonon spectra were utilized to predict S(α,β) using the LEAPR module of the NJOY code. The AIMD models of beryllium and graphite were 5 × 5 × 5 crystal unit cells (250 atoms and 500 atoms respectively). Electronic structure calculations for the prediction of Hellman-Feynman forces were performed using density functional theory with a GGA exchange correlation functional and corresponding core electron pseudopotentials. AIMD simulations of 1000-10,000 time-steps were performed with the canonical ensemble (NVT thermostat) for several temperatures between 300 K and 900 K. The phonon DOS were calculated as the power spectrum of the AIMD predicted velocity autocorrelation functions. The resulting AIMD phonon DOS and corresponding inelastic thermal neutron scattering cross sections at 300 K, where anharmonic effects are expected to be small, were found to be in reasonable agreement with the results generated using traditional AILD. This illustrated the validity of the AIMD approach. However, since the impact of the temperature on the phonon DOS (e.g. broadening of
Vibrational and ab initio molecular dynamics studies of bradykinin
NASA Astrophysics Data System (ADS)
Święch, Dominika; Kubisiak, Piotr; Andrzejak, Marcin; Borowski, Piotr; Proniewicz, Edyta
2016-07-01
In this study, the comprehensive theoretical and experimental investigations of Raman (RS) and infrared absorption (IR) spectra of bradykinin (BK) are presented. The ab initio Born-Oppenheimer molecular dynamics (BOMD) calculations, in the presence of water molecules that form the first coordination sphere, were used for conformational analysis of the BK structure. Based on the Density Functional Theory (DFT) calculations at the B3LYP/6-311G(d) level the vibrational spectra were interpreted. The calculated frequencies were scaled by means of the effective scaling frequency factor (ESFF) method. The theoretical data, which confirm the compact structure of BK in the presence of the water molecules revealed the remarkable effect of the intermolecular hydrogen bonding on the BK structural properties.
Protons in polar media: An ab initio molecular dynamics study
NASA Astrophysics Data System (ADS)
von Rosenvinge, Tycho
1998-10-01
The hydrates of hydrogen chloride are ionic crystals that contain hydronium (H3O+). The hydronium in the monohydrate has been reported to be statistically disordered between two possible sites related by inversion symmetry. Ab initio molecular dynamics calculations are presented for the monohydrate, as well as the di-, and tri-hydrates, of hydrogen chloride using the density functional based Car-Parrinello technique. The simulations were carried out with the goal of investigating proton disorder in these crystals. The possible role of nuclear quantum effects has been explored via path integral molecular dynamic simulations. The present results suggest that the proposed disordered sites in the monohydrate are dynamically unstable and therefore unlikely to be responsible for the reported disorder. No useful information was obtained for the dihydrate because the large unit cell leads to difficulties in carrying out the simulations. Nuclear quantum effects are shown to be important for characterizing the proton distributions in the trihydrate. The structure and dynamical behavior of liquid HF with dissolved KF have been investigated using the Car- Parrinello ab initio molecular dynamics scheme. Specifically, a system with stoichiometry KFċ2HF was studied at temperatures of 400K and 1000K. This system, which was started from a phase separated mixture, rapidly formed into solvated potassium ions and HnFn+1/sp- polyfluoride anions with n = 1, 2, 3, and 4. The resulting polyfluoride anions were classified, and their structures and dynamical behavior were compared with the known structures and spectra of crystalline compounds KF/cdot xHF and with theoretical predictions of isolated gas phase species. The present study reveals dramatic frequency shifts in the H atom vibrational modes with variation in the HF coordination number of the polyfluoride anion. In particular the FH wagging motion red shifts while the FH stretch blue shifts as n increases. The present calculations
Ab-Initio Molecular Dynamics Simulation of Graphene Sheet
NASA Astrophysics Data System (ADS)
Kolev, S.; Balchev, I.; Cvetkov, K.; Tinchev, S.; Milenov, T.
2017-01-01
The study of graphene is important because it is a promising material for a variety of applications in the electronic industry. In the present work, the properties of а 2D periodic graphene sheet are studied with the use of ab initio molecular dynamics. DFT in the generalized gradient approximation is used in order to carry out the dynamical simulations. The PBE functional and DZVP-MOLOPT basis set are implemented in the CP2K/Quickstep package. A periodic box, consisting of 288 carbon atoms is chosen for the simulations. After geometry optimization it has dimensions 2964 x 2964 x 1500 pm and form angles of 90, 90, 60 degrees. The dynamical simulation is run for 1 ps in the NPT ensemble, at temperature T = 298.15 K. The radial distribution function shows a first peak at 142 pm, marking the bond length between carbon atoms. The density of states for the periodic systems is simulated as occupied orbitals represent the valence band and unoccupied ones the conduction band. The calculated bandgap, as expected is close to 0 eV.
Ab initio calculations of correlated electron dynamics in ultrashort pulses
NASA Astrophysics Data System (ADS)
Feist, Johannes
2010-03-01
The availability of ultrashort and intense light pulses on the femtosecond and attosecond timescale promises to allow to directly probe and control electron dynamics on their natural timescale. A crucial ingredient to understanding the dynamics in many-electron systems is the influence of electron correlation, induced by the interelectronic repulsion. In order to study electron correlation in ultrafast processes, we have implemented an ab initio simulation of the two-electron dynamics in helium atoms. We solve the time-dependent Schr"odinger equation in its full dimensionality, with one temporal and five spatial degrees of freedom in linearly polarized laser fields. In our computational approach, the wave function is represented through a combination of time-dependent close coupling with the finite element discrete variable representation, while time propagation is performed using an Arnoldi-Lanczos approximation with adaptive step size. This approach is optimized to allow for efficient parallelization of the program and has been shown to scale linearly using up to 1800 processor cores for typical problem sizes. This has allowed us to perform highly accurate and well- converged computations for the interaction of ultrashort laser pulses with He. I will present some recent results on using attosecond and femtosecond pulses to probe and control the temporal structure of the ionization process. This work was performed in collaboration with Stefan Nagele, Renate Pazourek, Andreas Kaltenb"ack, Emil Persson, Barry I. Schneider, Lee A. Collins, and Joachim Burgd"orfer.
Ab initio path integral ring polymer molecular dynamics: Vibrational spectra of molecules
NASA Astrophysics Data System (ADS)
Shiga, Motoyuki; Nakayama, Akira
2008-01-01
The path integral ring polymer molecular dynamics method is combined with 'on-the-fly' ab initio electronic structure calculations and applied to vibrational spectra of small molecules, LiH and H 2O, at the room temperature. The results are compared with those of the numerically exact solution and ab initio path integral centroid molecular dynamics calculation. The peak positions in the calculated spectra are found to be reasonable, showing the red-shift due to potential anharmonicity. This unification enables the investigation of real-time quantum dynamics of chemically complex molecular systems on the ab initio Born-Oppenheimer potential energy surface.
Ab Initio Multiple Spawning Photochemical Dynamics of DMABN Using GPUs
Curchod, Basile F. E.; Sisto, Aaron; Martinez, Todd J.
2016-12-15
The ultrafast decay dynamics of 4-(N,N-dimethylamino)benzonitrile (DMABN) following photoexcitation was studied with the ab initio multiple spawning (AIMS) method, combined with GPU-accelerated linear-response time-dependent density functional theory (LR-TDDFT). We validate the LR-TDDFT method for this case and then present a detailed analysis of the first ≈200 fs of DMABN excited-state dynamics. Almost complete nonadiabatic population transfer from S_{2} (the initially populated bright state) to S_{1} takes place in less than 50 fs, without significant torsion of the dimethylamino (DMA) group. Significant torsion of the DMA group is only observed after the nuclear wavepacket reaches S_{1} and acquires locally excited electronic character. Here, our results show that torsion of the DMA group is not prerequisite for nonadiabatic transitions in DMABN, although such motion is indeed relevant on the lowest excited state (S_{1}).
Exploring the free energy surface using ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Samanta, Amit; Morales, Miguel A.; Schwegler, Eric
2016-04-01
Efficient exploration of configuration space and identification of metastable structures in condensed phase systems are challenging from both computational and algorithmic perspectives. In this regard, schemes that utilize a set of pre-defined order parameters to sample the relevant parts of the configuration space [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006); J. B. Abrams and M. E. Tuckerman, J. Phys. Chem. B 112, 15742 (2008)] have proved useful. Here, we demonstrate how these order-parameter aided temperature accelerated sampling schemes can be used within the Born-Oppenheimer and the Car-Parrinello frameworks of ab initio molecular dynamics to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways. We have used these methods to identify the metastable structures and reaction pathways in SiO2 and Ti. In addition, we have used the string method [W. E, W. Ren, and E. Vanden-Eijnden, Phys. Rev. B 66, 052301 (2002); L. Maragliano et al., J. Chem. Phys. 125, 024106 (2006)] within the density functional theory to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hexagonal closed packed to face centered cubic phase transition in Ti.
Ab initio molecular dynamics calculations of ion hydration free energies.
Leung, Kevin; Rempe, Susan B; von Lilienfeld, O Anatole
2009-05-28
We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or "lambda-path" technique to compute the intrinsic hydration free energies of Li(+), Cl(-), and Ag(+) ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential (phi) contributions, we obtain absolute AIMD hydration free energies (DeltaG(hyd)) within a few kcal/mol, or better than 4%, of Tissandier et al.'s [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model phi predictions. The sums of Li(+)/Cl(-) and Ag(+)/Cl(-) AIMD DeltaG(hyd), which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag(+)+Ni(+)-->Ag+Ni(2+) in water. The predictions for this reaction suggest that existing estimates of DeltaG(hyd) for unstable radiolysis intermediates such as Ni(+) may need to be extensively revised.
Ab initio molecular dynamics of liquid hydrogen chloride
NASA Astrophysics Data System (ADS)
Dubois, Vincent; Pasquarello, Alfredo
2005-03-01
We carried out an ab initio molecular dynamics simulation of liquid hydrogen chloride (ℓ-HCl) at a temperature of 313 K. Comparison with inelastic neutron scattering data shows that the simulation achieves an overall good description of the structural correlations, improving significantly upon a description based on classical interaction potentials. Despite some minor differences between theory and experiment in the H-H partial structure factor, the simulation gives a description of the hydrogen bonding in impressive agreement with experiment, for both the amount and the bond-length distribution of the bonds. In the simulation, 40% of the molecules are nonbonded, while the hydrogen-bonded chains are short, principally consisting of dimers (25%) and trimers (15%). Neighboring molecules in the simulation are found to form L-shaped arrangements, like in the isolated (HCl)2 dimer and in crystalline phases of HCl. The time correlation of the molecular-axis orientation is found to be characterized by a very short decay time (0.13 ps), consistent with the short length of the hydrogen-bonded chains. Other dynamical properties investigated in this work include the diffusion coefficient and the vibrational density of states. We evaluated the molecular dipole of the HCl molecule in the liquid using a definition based on the coupling of rotational modes to an external electric field. The average dipole moment (1.53 D) derived in this way is found to be considerably larger than for the isolated molecule (1.11 D). Our results show that the dipole moment in ℓ-HCl undergoes large fluctuations, both in orientation and in modulus. Upon the onset of an external field, such dipole fluctuations concur to reduce the fluctuations of the dielectric response.
Ab initio molecular dynamics of heme in cytochrome c.
Furlan, Sara; Penna, Giovanni La; Banci, Lucia; Mealli, Carlo
2007-02-08
Ab initio molecular dynamics (AIMD) calculations, based on the Car-Parrinello method, have been carried out for three models of heme c that is present in cytochrome c. Both the reduced (Fe(II)) and oxidized (Fe(III)) forms have been analyzed. The simplest models (1R and 1O, respectively) consist of a unsubstituted porphyrin (with no side chains) and two axially coordinated imidazole and ethylmethylthioether ligands. Density functional theory optimizations of these models confirm the basic electronic features and are the starting point for building more complex derivatives. AIMD simulations were performed after reaching the thermal stability at T = 300 K. The evolution of the Fe-L(ax) bond strengths is examined together with the relative rotations of the imidazole and methionine about the axial vector, which appear rather independent from each other. The next models (2R and 2O) contain side chains at the heme to better simulate the actual active site. It is observed that two adjacent propionate groups induce some important effects. The axial Fe-Sdelta bond is only weakened in 2R but is definitely cleaved in the oxidized species 2O. Also the mobility of the Im ligand seems to be reduced by the formation of a strong hydrogen bond that involves the Im Ndelta1-Hdelta1 bond and one carboxylate group. In 2O the interaction becomes so strong that a proton transfer occurs and the propionic acid is formed. Finally, the models 3 include a free N-methyl-acetamide molecule to mimic a portion of the protein backbone. This influences the orientation of carboxylate groups and limits the amount of their hydrogen bonding with the Im ligand. Residual electrostatic interactions are maintained, which are still able to modulate the dissociation of the methionine from the heme.
Siddick, M M; Ackland, G J; Morrison, C A
2006-08-14
We present a methodology for extracting phonon data from ab initio Born-Oppenheimer molecular dynamics calculations of molecular crystals. Conventional ab initio phonon methods based on perturbations are difficult to apply to lattice modes because the perturbation energy is dominated by intramolecular modes. We use constrained molecular dynamics to eliminate the effect of bond bends and stretches and then show how trajectories can be used to isolate and define in particular, the eigenvalues and eigenvectors of modes irrespective of their symmetry or wave vector. This is done by k-point and frequency filtering and projection onto plane wave states. The method is applied to crystalline ammonia: the constrained molecular dynamics allows a significant speed-up without affecting structural or vibrational modes. All Gamma point lattice modes are isolated: the frequencies are in agreement with previous studies; however, the mode assignments are different.
Khaliullin, Rustam Z; Kühne, Thomas D
2013-10-14
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.
Dissociation of NaCl in water from ab initio molecular dynamics simulations.
Timko, Jeff; Bucher, Denis; Kuyucak, Serdar
2010-03-21
We perform ab initio molecular dynamics simulations to study the dissociation of NaCl in water. The potential of mean force (PMF) between the two ions is determined using the constrained-force method. The simulation windows corresponding to the contact and solvent-separated minima, and the transition state in between, are further analyzed to determine the changes in the properties of hydration waters such as coordination number, dipole moment, and orientation. The ab initio results are compared with those obtained from classical molecular dynamics simulations of aqueous NaCl using several common force fields. The ab initio PMF is found to have a shallower contact minimum and a smaller transition barrier compared with the classical ones. Also the binding free energy calculated from the ab initio PMF almost vanishes whereas it is negative for all the classical PMFs. Water dipole moments are observed to exhibit little change during dissociation, indicating that description of NaCl with a nonpolarizable force field may be feasible. However, overcoordination of the ion pair at all distances remains as a serious shortcoming of the current classical models. The ab initio results presented here provide useful guidance for alternative parametrizations of the nonpolarizable force fields as well as the polarizable ones currently under construction.
Classical and ab-initio molecular dynamic simulation of an amorphous silica surface
NASA Astrophysics Data System (ADS)
Mischler, C.; Kob, W.; Binder, K.
2002-08-01
We present the results of a classical molecular dynamic simulation as well as of an ab-initio molecular dynamic simulation of an amorphous silica surface. In the case of the classical simulation we use the potential proposed by van Beest et al. (BKS) whereas the ab-initio simulation is done with a Car-Parrinello method (CPMD). We find that the surfaces generated by BKS have a higher concentration of defects (e.g., concentration of two-membered rings) than those generated with CPMD. In addition also the distribution functions of the angles and of the distances are different for the short rings. Hence we conclude that whereas the BKS potential is able to correctly reproduce the surface on the length scale beyond ≈5 Å, it is necessary to use an ab-initio method to reliably predict the structure at small scales.
Iyengar, Srinivasan S; Jakowski, Jacek
2005-03-15
A methodology to efficiently conduct simultaneous dynamics of electrons and nuclei is presented. The approach involves quantum wave packet dynamics using an accurate banded, sparse and Toeplitz representation for the discrete free propagator, in conjunction with ab initio molecular dynamics treatment of the electronic and classical nuclear degree of freedom. The latter may be achieved either by using atom-centered density-matrix propagation or by using Born-Oppenheimer dynamics. The two components of the methodology, namely, quantum dynamics and ab initio molecular dynamics, are harnessed together using a time-dependent self-consistent field-like coupling procedure. The quantum wave packet dynamics is made computationally robust by using adaptive grids to achieve optimized sampling. One notable feature of the approach is that important quantum dynamical effects including zero-point effects, tunneling, as well as over-barrier reflections are treated accurately. The electronic degrees of freedom are simultaneously handled at accurate levels of density functional theory, including hybrid or gradient corrected approximations. Benchmark calculations are provided for proton transfer systems and the dynamics results are compared with exact calculations to determine the accuracy of the approach.
Ab initio Molecular Dynamics Simulations of Water Under Static and Shock Compressed Conditions
Goldman, N; Fried, L E; Mundy, C J; Kuo, I W; Curioni, A; Reed, E
2007-07-25
We report herein a series of ab initio simulations of water under both static and shocked conditions. We have calculated the coherent x-ray scattering intensity of several phases of water under high pressure, using ab initio Density Functional Theory (DFT). We provide new atomic scattering form factors for water at extreme conditions, which take into account frequently neglected changes in ionic charge and electron delocalization. We have also simulated liquid water undergoing shock loading of velocities from 5-11 km/s using the Multi-Scale Shock Technique (MSST). We show that Density Functional Theory (DFT) molecular dynamics results compare extremely well to experiments on the water shock Hugoniot.
X-ray absorption Debye-Waller factors from ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Vila, F. D.; Lindahl, V. E.; Rehr, J. J.
2012-01-01
An ab initio equation of motion method is introduced to calculate the temperature-dependent mean-square vibrational amplitudes σ2 which appear in the Debye-Waller factors in x-ray absorption, x-ray scattering, and related spectra. The approach avoids explicit calculations of phonon modes, and is based instead on calculations of the displacement-displacement time correlation function from ab initio density functional theory molecular dynamics simulations. The method also yields the vibrational density of states and thermal quantities such as the lattice free energy. Illustrations of the method are presented for a number of systems and compared with other methods and experiment.
NASA Astrophysics Data System (ADS)
Arntsen, Christopher; Chen, Chen; Voth, Gregory A.
2017-09-01
We present two new multiscale molecular dynamics (MS-RMD) models for the hydrated excess proton in water developed directly from ab initio molecular dynamics (AIMD) simulation data of the same system. The potential of mean force along the proton transfer reaction coordinate and radial distribution functions for the MS-RMD models are shown to faithfully reproduce those of AIMD. The models are developed using an algorithm based on relative entropy minimization, thus demonstrating the ability of the method to rapidly generate accurate and highly efficient reactive MD force fields.
Arntsen, Christopher; Chen, Chen; Voth, Gregory A
2017-09-01
We present two new multiscale molecular dynamics (MS-RMD) models for the hydrated excess proton in water developed directly from ab initio molecular dynamics (AIMD) simulation data of the same system. The potential of mean force along the proton transfer reaction coordinate and radial distribution functions for the MS-RMD models are shown faithfully reproduce those of AIMD. The models are developed using an algorithm based on relative entropy minimization, thus demonstrating the ability of the method to rapidly generate accurate and highly efficient reactive MD force fields.
Ab initio molecular dynamics simulations of a binary system of ionic liquids.
Brüssel, Marc; Brehm, Martin; Voigt, Thomas; Kirchner, Barbara
2011-08-14
This work presents first insights into the structural properties of a binary mixture of ionic liquids from the perspective of ab initio molecular dynamics simulations. Simulations were carried out for a one-to-one mixture of 1-ethyl-3-methyl-imidazolium thiocyanate and 1-ethyl-3-methyl-imidazolium chloride and compared to pure 1-ethyl-3-methyl-imidazolium thiocyanate.
Ab initio molecular dynamics study of collective dynamics in liquid Tl: Thermo-viscoelastic analysis
NASA Astrophysics Data System (ADS)
Bryk, Taras; Demchuk, Taras
2017-08-01
We studied collective dynamics of pure liquid metal Tl using a combination of ab initio molecular dynamics (AIMD) simulations and a thermoviscoelastic model applied to calculations of dynamic eigenmodes and dispersion of collective excitations in particular. We found that for liquid Tl at ambient pressure the transverse current spectral functions obtained directly in ab initio simulations for wave numbers larger than first pseudo-Brillouin-zone boundary contain two low-and high-frequency peaks that is an evidence of emergence of the unusually high-frequency transverse modes as it was observed before in liquid Li at very high pressures. The thermo-viscoelastic dynamic model shows perfect reproduction of the simulation-derived longitudinal current autocorrelation functions, and the acoustic eigenmodes are in nice agreement with the peaks of the longitudinal current spectral functions up to the first pseudo-Brillouin-zone boundary. The deviation of the dynamic eigenmodes from peak positions at higher wave numbers gives evidence of L-T coupling effects.
NASA Astrophysics Data System (ADS)
Tilocca, Antonio
2007-12-01
Ab initio (Car-Parrinello) molecular dynamics simulations were carried out to investigate the melt precursor of a modified phosphosilicate glass with bioactive properties, and to quench the melt to the vitreous state. The properties of the 3000K liquid were extensively compared with those of the final glass structure. The melt is characterized by a significant fraction of structural defects (small rings, undercoordinated and overcoordinated ions), often combined together. The creation or removal of these coordinative defects in the liquid (through Si-O bond formation or dissociation) reflects frequent exchanges within the silicate first coordination shell, which in turn dynamically modify the intertetrahedral connectivity of silicate groups. The observed dynamical variation in both the identity and the number of silicate groups linked to a tagged Si ( Qn speciation) are considered key processes in the viscous flow of silicate melts [I. Farnan and J. F. Stebbins, Science 265, 1206 (1994)]. On the other hand, phosphate groups do not show an equally marked exchange activity in the coordination shell, but can still form links with Si. Once formed, these Si-O-P bridges are rather stable, and in fact they are retained in the glass phase obtained after cooling; their formation within the present full ab initio melt-and-quench approach strongly supports their presence in melt-derived phosphosilicate glasses with bioactive applications. On the other hand, the simulations show that the fraction of structural defects rapidly decreases during the cooling, and the glass is essentially free of miscoordinated ions and small rings.
Field theoretic approach to dynamical orbital localization in ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Thomas, Jordan W.; Iftimie, Radu; Tuckerman, Mark E.
2004-03-01
Techniques from gauge-field theory are employed to derive an alternative formulation of the Car-Parrinello ab initio molecular-dynamics method that allows maximally localized Wannier orbitals to be generated dynamically as the calculation proceeds. In particular, the Car-Parrinello Lagrangian is mapped onto an SU(n) non-Abelian gauge-field theory and the fictitious kinetic energy in the Car-Parrinello Lagrangian is modified to yield a fully gauge-invariant form. The Dirac gauge-fixing method is then employed to derive a set of equations of motion that automatically maintain orbital locality by restricting the orbitals to remain in the “Wannier gauge.” An approximate algorithm for integrating the equations of motion that is stable and maintains orbital locality is then developed based on the exact equations of motion. It is shown in a realistic application (64 water molecules plus one hydrogen-chloride molecule in a periodic box) that orbital locality can be maintained with only a modest increase in CPU time. The ability to keep orbitals localized in an ab initio molecular-dynamics calculation is a crucial ingredient in the development of emerging linear scaling approaches.
Liquid Be, Ca and Ba. An orbital-free ab-initio molecular dynamics study
Rio, B. G. del; González, L. E.
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.
NASA Astrophysics Data System (ADS)
Curchod, Basile; Penfold, Thomas; Rothlisberger, Ursula; Tavernelli, Ivano
2013-09-01
We review our recent work on ab initio nonadiabatic molecular dynamics, based on linear-response timedependent density functional theory for the calculation of the nuclear forces, potential energy surfaces, and nonadiabatic couplings. Furthermore, we describe how nuclear quantum dynamics beyond the Born-Oppenheimer approximation can be performed using quantum trajectories. Finally, the coupling and control of an external electromagnetic field with mixed quantum/classical trajectory surface hopping is discussed.
Ab-initio surface hopping and multiphoton ionisation study of the photodissociation dynamics of CS2
NASA Astrophysics Data System (ADS)
Bellshaw, Darren; Horke, Daniel A.; Smith, Adam D.; Watts, Hannah M.; Jager, Edward; Springate, Emma; Alexander, Oliver; Cacho, Cephise; Chapman, Richard T.; Kirrander, Adam; Minns, Russell S.
2017-09-01
New ab initio surface hopping simulations of the excited state dynamics of CS2 including spin-orbit coupling are compared to new experimental measurements using a multiphoton ionisation probe in a photoelectron spectroscopy experiment. The calculations highlight the importance of the triplet states even in the very early time dynamics of the dissociation process and allow us to unravel the signatures in the experimental spectrum, linking the observed changes to both electronic and nuclear degrees of freedom within the molecule.
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.
NASA Astrophysics Data System (ADS)
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.
Pierce, Levi C T; Markwick, Phineus R L; McCammon, J Andrew; Doltsinis, Nikos L
2011-05-07
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.
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
Conformational space of clindamycin studied by ab initio and full-atom molecular dynamics.
Kulczycka-Mierzejewska, Katarzyna; Trylska, Joanna; Sadlej, Joanna
2016-01-01
Molecular dynamics (MD) simulations allow determining internal flexibility of molecules at atomic level. Using ab initio Born-Oppenheimer molecular dynamics (BOMD), one can simulate in a reasonable time frame small systems with hundreds of atoms, usually in vacuum. With quantum mechanics/molecular mechanics (QM/MM) or full-atom molecular dynamics (FAMD), the influence of the environment can also be simulated. Here, we compare three types of MD calculations: ab initio BOMD, hybrid QM/MM, and classical FAMD. As a model system, we use a small antibiotic molecule, clindamycin, which is one of the lincosamide antibiotics. Clindamycin acquires two energetically stable forms and we investigated the transition between these two experimentally known conformers. We performed 60-ps BOMD simulations in vacuum, 50-ps QM/MM, and 100-ns FAMD in explicit water. The transition between two antibiotic conformers was observed using both BOMD and FAMD methods but was not noted in the QM/MM simulations.
Ab initio molecular dynamics simulations of the adsorption of H2 on palladium surfaces.
Gross, Axel
2010-05-17
The interaction of hydrogen with palladium surfaces represents a model system for the study of the adsorption and absorption at metal surfaces. Theoretical gas-surface dynamics studies have usually concentrated on the adsorption dynamics on clean surfaces. Only recently has it become possible, based on advances in electronic structure codes and improvements in computer power, to address the much more complex problem of the adsorption dynamics on precovered surfaces. Herein, recent ab initio molecular dynamics studies are discussed that address the adsorption dynamics of hydrogen molecules on hydrogen- and sulfur-precovered Pd surfaces. In addition, the relaxation dynamics of the hydrogen atoms after the dissociation on clean Pd(100) are presented.
Li ion diffusion mechanisms in LiFePO4: an ab initio molecular dynamics study.
Yang, Jianjun; Tse, John S
2011-11-17
The mechanisms for thermal (self) diffusion of Li ions in fully lithiated LiFePO(4) have been investigated with spin polarized ab initio molecular dynamics calculations. The effect of electron correlation is taken into account with the GGA+U formalism. It was found that Li ion diffusion is not a continuous process but through a series of jumps from one site to another. A dominant process is the hopping between neighboring Li sites around the PO(4) groups, which results in a zigzag pathway along the crystallographic b-axis. This observation is in agreement with a recent neutron diffraction experiment. A second process involves the collaborative movements of the Fe ions leading to the formation of antisite defects and promotes Li diffusion across the Li ion channels. The finding of the second mechanism demonstrates the benefit of ab initio molecular dynamics simulation in sampling diffusion pathways that may not be anticipated.
Ab initio molecular dynamics study on the excitation dynamics of psoralen compounds
NASA Astrophysics Data System (ADS)
Nakai, H.; Yamauchi, Y.; Nakata, A.; Baba, T.; Takahashi, H.
2003-08-01
Ab initio molecular dynamics (AIMD) simulations are performed for studying the S0→T1 excitation dynamics of psoralen compounds; namely, nonsubstituted psoralen, 5-methoxypsoralen (5-MOP), and 8-methoxypsoralen (8-MOP). The density functional theory calculations at the B3LYP/D95V level are used for evaluating the atomic forces in every AIMD step. The specific behavior of 8-MOP in the T1 state, which has been reported by the experimental study, is found to be due to a unique open-ring structure, which leads to a different spin distribution in comparison with the cases of psoralen and 5-MOP and further to a crossing between the S0 and T1 states.
NASA Astrophysics Data System (ADS)
Shimamura, K.; Shibuta, Y.; Ohmura, S.; Arifin, R.; Shimojo, F.
2016-04-01
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.
Ab initio potential energy surface for the highly nonlinear dynamics of the KCN molecule
Párraga, H.; Arranz, F. J. Benito, R. M.; Borondo, F.
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.
Sumner, Isaiah; Iyengar, Srinivasan S
2007-10-18
We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.
Rana, Malay Kumar; Chandra, Amalendu
2013-05-28
The behavior of water near a graphene sheet is investigated by means of ab initio and classical molecular dynamics simulations. The wetting of the graphene sheet by ab initio water and the relation of such behavior to the strength of classical dispersion interaction between surface atoms and water are explored. The first principles simulations reveal a layered solvation structure around the graphene sheet with a significant water density in the interfacial region implying no drying or cavitation effect. It is found that the ab initio results of water density at interfaces can be reproduced reasonably well by classical simulations with a tuned dispersion potential between the surface and water molecules. Calculations of vibrational power spectrum from ab initio simulations reveal a shift of the intramolecular stretch modes to higher frequencies for interfacial water molecules when compared with those of the second solvation later or bulk-like water due to the presence of free OH modes near the graphene sheet. Also, a weakening of the water-water hydrogen bonds in the vicinity of the graphene surface is found in our ab initio simulations as reflected in the shift of intermolecular vibrational modes to lower frequencies for interfacial water molecules. The first principles calculations also reveal that the residence and orientational dynamics of interfacial water are somewhat slower than those of the second layer or bulk-like molecules. However, the lateral diffusion and hydrogen bond relaxation of interfacial water molecules are found to occur at a somewhat faster rate than that of the bulk-like water molecules. The classical molecular dynamics simulations with tuned Lennard-Jones surface-water interaction are found to produce dynamical results that are qualitatively similar to those of ab initio molecular dynamics simulations.
Ab-initio study of several static and dynamic properties of liquid palladium and platinum
NASA Astrophysics Data System (ADS)
González, L. E.; González, D. J.; Molla, Mohammad Riazuddin; Ahmed, A. Z. Ziauddin; Bhuiyan, G. M.
2017-08-01
We report a study on several static and dynamic properties of liquid Pd and Pt metals at thermodynamic conditions near their respective triple points. The calculations have been carried out by an ab initio molecular dynamics simulation technique. Results are reported for several static structural magnitudes which are compared with the available X-ray diffraction. As for the dynamic properties, results have been obtained for both single and collective dynamical magnitudes as well as for some transport coeffcients which are compared with the corresponding experimental data.
Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo.
Zen, Andrea; Luo, Ye; Mazzola, Guglielmo; Guidoni, Leonardo; Sorella, Sandro
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.
NASA Astrophysics Data System (ADS)
Shibuta, Yasushi; Shimamura, Kohei; Oguri, Tomoya; Arifin, Rizal; Shimojo, Fuyuki; Yamaguchi, Shu
2015-03-01
The growth mechanism of carbon nanotubes (CNT) has been widely discussed both from experimental and computational studies. Regarding the computational studies, most of the studies focuses on the aggregation of isolate carbon atoms on the catalytic metal nanoparticle, whereas the initial dissociation of carbon source molecules should affect the yield and quality of the products. On the other hand, we have studied the dissociation process of carbon source molecules on the metal surface by the ab initio molecular dynamics simulation. In the study, we investigate the ethanol dissociation on Pt and Ni clusters by ab initio MD simulations to discuss the initial stage of CNT growth by alcohol CVD technique. Part of this research is supported by the Grant-in-Aid for Young Scientists (a) (No. 24686026) from MEXT, Japan.
Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo
Zen, Andrea; Luo, Ye Mazzola, Guglielmo Sorella, Sandro; Guidoni, Leonardo
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.
Study of atomic structure of liquid Hg-In alloys using ab-initio molecular dynamics
Sharma, Nalini; Ahluwalia, P. K.; Thakur, Anil
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.
Electronic properties of liquid Hg-In alloys : Ab-initio molecular dynamics study
Sharma, Nalini Ahluwalia, P. K.; Thakur, Anil
2016-05-23
Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-In alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Three liquid Hg-In alloys (Hg{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}Pb{sub 10}) 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.
Ab-initio molecular dynamics simulations of liquid Hg-Pb alloys
NASA Astrophysics Data System (ADS)
Sharma, Nalini; Thakur, Anil; Ahluwalia, P. K.
2014-04-01
Ab-initio molecular dynamics simulations are performed to study the structural properties of liquid Hg-Pb alloys. The interatomic interactions are described by ab-initio pseudopotentials given by Troullier and Martins. Three liquid Hg-Pb mixtures (Hg30Pb70, Hg50Pb50 and Hg90Pb10) at 600K 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 lead (l-Pb). 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 three alloys. Among the all considered alloys, Hg50Pb50 alloy shows presence of more chemical ordering and presence of hetero-coordination.
Study of atomic structure of liquid Hg-In alloys using ab-initio molecular dynamics
NASA Astrophysics Data System (ADS)
Sharma, Nalini; Thakur, Anil; Ahluwalia, P. K.
2015-05-01
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. 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.
Electronic properties of liquid Hg-In alloys : Ab-initio molecular dynamics study
NASA Astrophysics Data System (ADS)
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.
Low-temperature metallic liquid hydrogen: an ab-initio path-integral molecular dynamics perspective
NASA Astrophysics Data System (ADS)
Chen, Ji; Li, Xin-Zheng; Zhang, Qianfan; Probert, Matthew; Pickard, Chris; Needs, Richard; Michaelides, Angelos; Wang, Enge
2013-03-01
Experiments and computer simulations have shown that the melting temperature of solid hydrogen drops with pressure above about 65 GPa, suggesting that a low temperature liquid state might exist. It has also been suggested that this liquid state might be non-molecular and metallic, although evidence for such behaviour is lacking. Using a combination of ab initio path-integral molecular dynamics and the two-phase methods, we have simulated the melting of solid hydrogen under finite temperatures. We found an atomic solid phase from 500 to 800 GPa which melts at < 200 K. Beyond this and up to pressures of 1,200 GPa a metallic atomic liquid is stable at temperatures as low as 50 K. The quantum motion of the protons is critical to the low melting temperature in this system as ab initio simulations with classical nuclei lead to a considerably higher melting temperature of ~300 K across the entire pressure range considered.
Dynamic decomposition of aliphatic molecules on Al(111) from ab initio molecular dynamics
Zhong Jun; Hector, Louis G. Jr.; Adams, James B.
2009-03-15
Ab initio molecular dynamics based on density functional theory within the generalized gradient approximation was used to explore decomposition on Al(111) of butanol-alcohol and butanoic-acid, two important boundary additives in Al processing. Each molecule was oriented with its functional group closest to the surface and then given an initial velocity toward the surface. Decomposition occurred upon collision with Al(111) resulting in the formation of adhered fragments that represent the very initial stages in additive film formation during plastic deformation where nascent Al is liberated. Bonding interactions over the simulation time frames were explored with contours of the electron localization function. Results of the simulations were compared with existing experimental studies of chemical decomposition on clean Al surfaces and found to be in qualitative accord. The effects of other initial molecular orientations on decomposition were explored in ancillary calculations where the molecules were rotated through 90 deg. and 180 deg. prior to collision with Al(111)
Dynamic decomposition of aliphatic molecules on Al(111) from ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Zhong, Jun; Hector, Louis G., Jr.; Adams, James B.
2009-03-01
Ab initio molecular dynamics based on density functional theory within the generalized gradient approximation was used to explore decomposition on Al(111) of butanol-alcohol and butanoic-acid, two important boundary additives in Al processing. Each molecule was oriented with its functional group closest to the surface and then given an initial velocity toward the surface. Decomposition occurred upon collision with Al(111) resulting in the formation of adhered fragments that represent the very initial stages in additive film formation during plastic deformation where nascent Al is liberated. Bonding interactions over the simulation time frames were explored with contours of the electron localization function. Results of the simulations were compared with existing experimental studies of chemical decomposition on clean Al surfaces and found to be in qualitative accord. The effects of other initial molecular orientations on decomposition were explored in ancillary calculations where the molecules were rotated through 90° and 180° prior to collision with Al(111).
Geng, Hua Y.
2015-02-15
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model—the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of r{sub s}=0.912.
Ab initio molecular dynamics simulation of pressure-induced phase transformation in BeO
Xiao, Haiyan; Duan, G; Zu, X T; Weber, William J
2011-01-01
Ab initio molecular dynamics (MD) method has been used to study high pressure-induced phase transformation in BeO based on the local density approximation (LDA) and the generalized gradient approximation (GGA). Both methods show that the wurtzite (WZ) and zinc blende (ZB) BeO transforms to the rocksalt (RS) structure smoothly at high pressure. The transition pressures obtained from the LDA method are about 40 GPa larger than the GGA result for both WZ {yields} RS and ZB {yields} RS phase transformations, and the phase transformation mechanisms revealed by the LDA and GGA methods are different. For WZ {yields} RS phase transformations both mechanisms obtained from the LDA and GGA methods are not comparable to the previous ab initio MD simulations of WZ BeO at 700 GPa based on the GGA method. It is suggested that the phase transformation mechanisms of BeO revealed by the ab initio MD simulations are affected remarkably by the exchange-correlation functional employed and the way of applying pressure.
NASA Astrophysics Data System (ADS)
Geng, Hua Y.
2015-02-01
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model-the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate is about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of rs = 0.912.
Ab Initio Dynamics of Nuetral and Charged Solitons
NASA Astrophysics Data System (ADS)
Devore, Todd; Kawai, Ryoichi; Yeates, Todd; Dudis, Douglass
1997-03-01
Polyacetylene is a one-dimensional conjugate polymer that continues to attract interest because of its unique properties and possible future applications. The conductivity of this semiconductor can be changed with doping over many orders of magnitude and reaches metallic values with high dopant levels. The degenerate ground state permits soliton excitations which lead to intersting transport, optical and magnetic properties unexplainable in terms of ordinary spin 1/2 charge carriers. Charged solitons are known to be responsible for conductivity at low dopant levels. Dynamics of nuetral and charged solitons in one dimensional finite chains have been studied using model Hamiltonians such as the famous SSH Hamiltonian. Instead of using a semi-empirical approach we show soliton dynamics from first-principles calculations using the density functional and LDA. Simulations include dynamics of both nuetral and charged solitons subject to an external field. These simulations use the method of Car and Parinello to efficiently handle the updating of wavefunctions and are performed on massively parrallel computers.
Ab-initio vibrational dynamics study of silver nanoclusters
Mankad, Venu H.; Gupta, Sanjeev K.; Jha, Prafulla K.
2016-05-23
The size dependent structural, electronic and vibrational properties of silver metal clusters along with its bulk counterparts have been studied using the first principles calculations within density functional theory. The size effect was studied by calculating a series of clusters discussed in terms of the increase in band gap when going from the bulk to cluster. The phonon calculations show that the clusters with smaller size are dynamically stable. Our findings will give some reference to the insight understanding of the electronic and vibrational properties of size orientation dependent Ag metal cluster.
Dissipative Particle Dynamics interaction parameters from ab initio calculations
NASA Astrophysics Data System (ADS)
Sepehr, Fatemeh; Paddison, Stephen J.
2016-02-01
Dissipative Particle Dynamics (DPD) is a commonly employed coarse-grained method to model complex systems. Presented here is a pragmatic approach to connect atomic-scale information to the meso-scale interactions defined between the DPD particles or beads. Specifically, electronic structure calculations were utilized for the calculation of the DPD pair-wise interaction parameters. An implicit treatment of the electrostatic interactions for charged beads is introduced. The method is successfully applied to derive the parameters for a hydrated perfluorosulfonic acid ionomer with absorbed vanadium cations.
Orbital free ab initio study of static and dynamic properties of some liquid transition metals
NASA Astrophysics Data System (ADS)
Bhuiyan, G. M.; Molla, Mohammad Riazuddin; Ziauddin Ahmed, A. Z.; Gonzalez, L. E.; Gonzalez, D. J.
2017-08-01
Several static and dynamic properties of liquid transition metals Cr, Mn and Co are studied for the first time using the orbital free ab-initio molecular dynamics simulation (OF-AIMD). This method is based on the density functional theory (DFT) which accounts for the electronic energy of the system whereas the interionic forces are derived from the electronic energy via the Hellman-Feynman theorem. The external energy functional is treated with a local pseudopotential. Results are reported for static structure factors, isothermal compressibility, diffusion coeffcients, sound velocity and viscosity and comparison is performed with the available experimental data and other theoretical calculations.
Communication: Multiple-timestep ab initio molecular dynamics with electron correlation.
Steele, Ryan P
2013-07-07
A time-reversible, multiple-timestep protocol is presented for ab initio molecular dynamics simulations using correlated, wavefunction-based underlying potentials. The method is motivated by the observation that electron correlation contributions to forces vary on a slower timescale than their Hartree-Fock counterparts. An efficient dynamics algorithm, involving short-timestep Hartree-Fock and long-timestep Moøller-Plesset perturbation theory, is presented and tested. Results indicate stable trajectories and relative speedups comparable to those seen in force field-based multiple-timestep schemes, with the highest efficiency improvement occurring for large systems.
Communication: Multiple-timestep ab initio molecular dynamics with electron correlation
NASA Astrophysics Data System (ADS)
Steele, Ryan P.
2013-07-01
A time-reversible, multiple-timestep protocol is presented for ab initio molecular dynamics simulations using correlated, wavefunction-based underlying potentials. The method is motivated by the observation that electron correlation contributions to forces vary on a slower timescale than their Hartree-Fock counterparts. An efficient dynamics algorithm, involving short-timestep Hartree-Fock and long-timestep Møller-Plesset perturbation theory, is presented and tested. Results indicate stable trajectories and relative speedups comparable to those seen in force field-based multiple-timestep schemes, with the highest efficiency improvement occurring for large systems.
Experimental and Ab Initio Ultrafast Carrier Dynamics in Plasmonic Nanoparticles
NASA Astrophysics Data System (ADS)
Brown, Ana M.; Sundararaman, Ravishankar; Narang, Prineha; Schwartzberg, Adam M.; Goddard, William A.; Atwater, Harry A.
2017-02-01
Ultrafast pump-probe measurements of plasmonic nanostructures probe the nonequilibrium behavior of excited carriers, which involves several competing effects obscured in typical empirical analyses. Here we present pump-probe measurements of plasmonic nanoparticles along with a complete theoretical description based on first-principles calculations of carrier dynamics and optical response, free of any fitting parameters. We account for detailed electronic-structure effects in the density of states, excited carrier distributions, electron-phonon coupling, and dielectric functions that allow us to avoid effective electron temperature approximations. Using this calculation method, we obtain excellent quantitative agreement with spectral and temporal features in transient-absorption measurements. In both our experiments and calculations, we identify the two major contributions of the initial response with distinct signatures: short-lived highly nonthermal excited carriers and longer-lived thermalizing carriers.
Exploring the free energy surface using ab initio molecular dynamics
Samanta, Amit; Morales, Miguel A.; Schwegler, Eric
2016-04-22
Efficient exploration of the configuration space and identification of metastable structures are challenging from both computational as well as algorithmic perspectives. Here, we extend the recently proposed orderparameter aided temperature accelerated sampling schemes to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways within the framework of density functional theory based molecular dynamics. The sampling method is applied to explore the relevant parts of the configuration space in prototypical materials SiO_{2} and Ti to identify the different metastable structures corresponding to different phases in these materials. In addition, we use the string method in collective variables to study the melting pathways in the high pressure cotunnite phase of SiO_{2} and the hcp to fcc phase transition in Ti.
Ab initio sampling of transition paths by conditioned Langevin dynamics
NASA Astrophysics Data System (ADS)
Delarue, Marc; Koehl, Patrice; Orland, Henri
2017-10-01
We propose a novel stochastic method to generate Brownian paths conditioned to start at an initial point and end at a given final point during a fixed time tf under a given potential U(x). These paths are sampled with a probability given by the overdamped Langevin dynamics. We show that these paths can be exactly generated by a local stochastic partial differential equation. This equation cannot be solved in general but we present several approximations that are valid either in the low temperature regime or in the presence of barrier crossing. We show that this method warrants the generation of statistically independent transition paths. It is computationally very efficient. We illustrate the method first on two simple potentials, the two-dimensional Mueller potential and the Mexican hat potential, and then on the multi-dimensional problem of conformational transitions in proteins using the "Mixed Elastic Network Model" as a benchmark.
Exploring the free energy surface using ab initio molecular dynamics
Samanta, Amit; Morales, Miguel A.; Schwegler, Eric
2016-04-22
Efficient exploration of the configuration space and identification of metastable structures are challenging from both computational as well as algorithmic perspectives. Here, we extend the recently proposed orderparameter aided temperature accelerated sampling schemes to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways within the framework of density functional theory based molecular dynamics. The sampling method is applied to explore the relevant parts of the configuration space in prototypical materials SiO_{2} and Ti to identify the different metastable structures corresponding to different phases in these materials. In addition, we use the string method in collective variables to study the melting pathways in the high pressure cotunnite phase of SiO_{2} and the hcp to fcc phase transition in Ti.
Exploring the free energy surface using ab initio molecular dynamics
Samanta, Amit; Morales, Miguel A.; Schwegler, Eric
2016-04-22
Efficient exploration of the configuration space and identification of metastable structures are challenging from both computational as well as algorithmic perspectives. Here, we extend the recently proposed orderparameter aided temperature accelerated sampling schemes to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways within the framework of density functional theory based molecular dynamics. The sampling method is applied to explore the relevant parts of the configuration space in prototypical materials SiO2 and Ti to identify the different metastable structures corresponding to different phases in these materials. In addition, we use the string method inmore » collective variables to study the melting pathways in the high pressure cotunnite phase of SiO2 and the hcp to fcc phase transition in Ti.« less
Hydration structure of salt solutions from ab initio molecular dynamics
Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L.
2013-01-07
The solvation structures of Na{sup +}, K{sup +}, and Cl{sup -} ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na{sup +}, K{sup +}, and Cl{sup -}, respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.
Hydration structure of salt solutions from ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L.
2013-01-01
The solvation structures of Na^+, K^+, and Cl^- ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na^+, K^+, and Cl^-, respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.
Hydration structure of salt solutions from ab initio molecular dynamics.
Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L
2013-01-07
The solvation structures of Na(+), K(+), and Cl(-) ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na(+), K(+), and Cl(-), respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.
Ab initio study of the structure and dynamics of bulk liquid Fe
NASA Astrophysics Data System (ADS)
Marqués, M.; González, L. E.; González, D. J.
2015-10-01
Several static and dynamic properties of bulk liquid Fe at a thermodynamic state near its triple point have been evaluated by ab initio molecular dynamics simulations. The calculated static structure shows very good agreement with the available experimental data, including an asymmetric second peak in the structure factor which underlines a substantial local icosahedral short-range order in the liquid. The dynamical structure reveals propagating density fluctuations, with an associated dispersion relation which closely follows the experimental data. The dynamic structure factors S (q ,ω ) show a good agreement with their experimental counterparts which have been recently measured by an inelastic x-ray scattering experiment. The dynamical processes behind the S (q ,ω ) have been analyzed by using a model with two decay channels (a fast and a slow) associated with the relaxations of the collective excitations. The recent finding of transverselike excitation modes in the IXS data is analyzed by using the present ab initio simulation results. Several transport coefficients have been evaluated and the results are compared with the available experimental data.
NASA Astrophysics Data System (ADS)
Makhov, Dmitry V.; Symonds, Christopher; Fernandez-Alberti, Sebastian; Shalashilin, Dmitrii V.
2017-08-01
The Multiconfigurational Ehrenfest (MCE) method is a quantum dynamics technique which allows treatment of a large number of quantum nuclear degrees of freedom. This paper presents a review of MCE and its recent applications, providing a summary of the formalisms, including its ab initio direct dynamics versions and also giving a summary of recent results. Firstly, we describe the Multiconfigurational Ehrenfest version 2 (MCEv2) method and its applicability to direct dynamics and report new calculations which show that the approach converges to the exact result in model systems with tens of degrees of freedom. Secondly, we review previous ;on the fly; ab initio Multiple Cloning (AIMC-MCE) MCE dynamics results obtained for systems of a similar size, in which the calculations treat every electron and every nucleus of a polyatomic molecule on a fully quantum basis. We also review the Time Dependent Diabatic Basis (TDDB) version of the technique and give an example of its application. We summarise the details of the sampling techniques and interpolations used for calculation of the matrix elements, which make our approach efficient. Future directions of work are outlined.
Multiple-Time Step Ab Initio Molecular Dynamics Based on Two-Electron Integral Screening.
Fatehi, Shervin; Steele, Ryan P
2015-03-10
A multiple-timestep ab initio molecular dynamics scheme based on varying the two-electron integral screening method used in Hartree-Fock or density functional theory calculations is presented. Although screening is motivated by numerical considerations, it is also related to separations in the length- and timescales characterizing forces in a molecular system: Loose thresholds are sufficient to describe fast motions over short distances, while tight thresholds may be employed for larger length scales and longer times, leading to a practical acceleration of ab initio molecular dynamics simulations. Standard screening approaches can lead, however, to significant discontinuities in (and inconsistencies between) the energy and gradient when the screening threshold is loose, making them inappropriate for use in dynamics. To remedy this problem, a consistent window-screening method that smooths these discontinuities is devised. Further algorithmic improvements reuse electronic-structure information within the dynamics step and enhance efficiency relative to a naı̈ve multiple-timestepping protocol. The resulting scheme is shown to realize meaningful reductions in the cost of Hartree-Fock and B3LYP simulations of a moderately large system, the protonated sarcosine/glycine dipeptide embedded in a 19-water cluster.
Renison, C Alicia; Fernandes, Kyle D; Naidoo, Kevin J
2015-07-05
This article describes an extension of the quantum supercharger library (QSL) to perform quantum mechanical (QM) gradient and optimization calculations as well as hybrid QM and molecular mechanical (QM/MM) molecular dynamics simulations. The integral derivatives are, after the two-electron integrals, the most computationally expensive part of the aforementioned calculations/simulations. Algorithms are presented for accelerating the one- and two-electron integral derivatives on a graphical processing unit (GPU). It is shown that a Hartree-Fock ab initio gradient calculation is up to 9.3X faster on a single GPU compared with a single central processing unit running an optimized serial version of GAMESS-UK, which uses the efficient Schlegel method for s- and l-orbitals. Benchmark QM and QM/MM molecular dynamics simulations are performed on cellobiose in vacuo and in a 39 Å water sphere (45 QM atoms and 24843 point charges, respectively) using the 6-31G basis set. The QSL can perform 9.7 ps/day of ab initio QM dynamics and 6.4 ps/day of QM/MM dynamics on a single GPU in full double precision. © 2015 Wiley Periodicals, Inc.
NASA Astrophysics Data System (ADS)
Kubota, Yoshiyuki; Ohnuma, Toshiharu; Bučko, Tomáš
2017-03-01
The reaction of carbon dioxide (CO2) with aqueous 2-aminoethanol (MEA) has been investigated using both blue moon ensemble and metadynamics approaches combined with ab initio molecular dynamics (AIMD) simulations. The AIMD simulations predicted the spontaneous deprotonation of the intermediate compound, MEA zwitterion, and they were used to study two possible routes for subsequent proton transfer reactions: the formation of the protonated MEA and the formation of MEA carbamic acid. The free-energy curve depicted by blue moon ensemble technique supported the favorable deprotonation of MEA zwitterion. The overall free-energy profile showed the favorable formation of the ionic products of MEA carbamate ion and protonated MEA.
Initial Chemical Events in CL-20 Under Extreme Conditions: An Ab Initio Molecular Dynamics Study
2006-11-01
1,3,4,7,8,10-hexanitro-5,2,6- (iminomethenimino)-1H-imidazo[4,5-b]- pyrazin , C6H6N12O12), is an emerging energetic chemical that may replace RDX, however...hexanitro-5,2,6- (iminomethenimino)-1H-imidazo[4,5-b]- pyrazin ) belongs to one of the most important classes of high energetic compounds – nitramines. It...1,5- and 1,7- dihydro- diimidazo[4,5-b:4’,5’-e] pyrazine has been carried out at using static and dynamic ab initio techniques of computational
NASA Astrophysics Data System (ADS)
Pham, Thi Nu; Ono, Shota; Ohno, Kaoru
2016-04-01
Doing ab initio molecular dynamics simulations, we demonstrate a possibility of hydrogenation of carbon monoxide producing methanol step by step. At first, the hydrogen atom reacts with the carbon monoxide molecule at the excited state forming the formyl radical. Formaldehyde was formed after adding one more hydrogen atom to the system. Finally, absorption of two hydrogen atoms to formaldehyde produces methanol molecule. This study is performed by using the all-electron mixed basis approach based on the time dependent density functional theory within the adiabatic local density approximation for an electronic ground-state configuration and the one-shot GW approximation for an electronic excited state configuration.
van der Spoel, D; Berendsen, H J
1996-01-01
In this work we give an overview of the methodologies required to compute the rate of proton transfer in hydrogen bonded systems in solution. Using ab initio or density functional methods we determine proton potentials of a truncated system as a function of proton-donor proton-acceptor distance as well as nonbonding parameters. By classical molecular dynamics we evaluate a swarm of proton potentials with the proton fixed in the reactant well. The rate of proton transfer is calculated perturbatively using the Density Matrix Evolution (DME) method, going beyond the Born Oppenheimer approximation. The method is illustrated by two examples: hydrogen malonate and the active center of HIV-1 protease.
Xiao, H. Y.; Weber, W. J.; Zhang, Y.; Zu, X. T.; Li, S.
2015-01-01
The response of titanate pyrochlores (A2Ti2O7, A = Y, Gd and Sm) to electronic excitation is investigated utilizing an ab initio molecular dynamics method. All the titanate pyrochlores are found to undergo a crystalline-to-amorphous structural transition under a low concentration of electronic excitations. The transition temperature at which structural amorphization starts to occur depends on the concentration of electronic excitations. During the structural transition, O2-like molecules are formed, and this anion disorder further drives cation disorder that leads to an amorphous state. This study provides new insights into the mechanisms of amorphization in titanate pyrochlores under laser, electron and ion irradiations. PMID:25660219
The hydrogen diffusion in liquid aluminum alloys from ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Jakse, N.; Pasturel, A.
2014-09-01
We study the hydrogen diffusion in liquid aluminum alloys through extensive ab initio molecular dynamics simulations. At the microscopic scale, we show that the hydrogen motion is characterized by a broad distribution of spatial jumps that does not correspond to a Brownian motion. To determine the self-diffusion coefficient of hydrogen in liquid aluminum alloys, we use a generalized continuous time random walk model recently developed to describe the hydrogen diffusion in pure aluminum. In particular, we show that the model successfully accounts the effects of alloying elements on the hydrogen diffusion in agreement with experimental features.
Dissolution of cellulose in ionic liquids: an ab initio molecular dynamics simulation study.
Payal, Rajdeep Singh; Balasubramanian, Sundaram
2014-09-07
Interactions determining the dissolution of a monomer of β-cellulose, i.e., cellobiose in a room temperature ionic liquid, [Emim][OAc], have been studied using ab initio molecular dynamics simulations. Although anions are the predominant species in the first coordination shell of cellobiose, cations too are present to a minor extent around it. The presence of low concentration of water in the solution does not significantly alter the nature of the coordination environment of cellobiose. All intra-molecular hydrogen bonds of anti-syn cellobiose are replaced by inter-molecular hydrogen bonds formed with the anions, whereas the anti-anti conformer retains an intramolecular hydrogen bond.
The hydrogen diffusion in liquid aluminum alloys from ab initio molecular dynamics.
Jakse, N; Pasturel, A
2014-09-07
We study the hydrogen diffusion in liquid aluminum alloys through extensive ab initio molecular dynamics simulations. At the microscopic scale, we show that the hydrogen motion is characterized by a broad distribution of spatial jumps that does not correspond to a Brownian motion. To determine the self-diffusion coefficient of hydrogen in liquid aluminum alloys, we use a generalized continuous time random walk model recently developed to describe the hydrogen diffusion in pure aluminum. In particular, we show that the model successfully accounts the effects of alloying elements on the hydrogen diffusion in agreement with experimental features.
Debela, T. T.; Wang, X. D.; Cao, Q. P.; Zhang, D. X.; Wang, S. Y.; Wang, Cai-Zhuang; Jiang, J. Z.
2013-12-12
Atomic structure transitions of liquid niobium during solidification, at different temperatures from 3200 to 1500 K, were studied by using ab initio molecular dynamics simulations. The local atomic structure variations with temperature are investigated by using the pair-correlation function, the structure factor, the bond-angle distribution function, the Honeycutt–Anderson index, Voronoi tessellation and the cluster alignment methods. Our results clearly show that, upon quenching, the icosahedral short-range order dominates in the stable liquid and supercooled liquid states before the system transforms to crystalline body-center cubic phase at a temperature of about 1830 K.
Ab initio Path Integral Molecular Dynamics Based on Fragment Molecular Orbital Method
NASA Astrophysics Data System (ADS)
Fujita, Takatoshi; Watanabe, Hirofumi; Tanaka, Shigenori
2009-10-01
We have developed an ab initio path integral molecular dynamics method based on the fragment molecular orbital method. This “FMO-PIMD” method can treat both nuclei and electrons quantum mechanically, and is useful to simulate large hydrogen-bonded systems with high accuracy. After a benchmark calculation for water monomer, water trimer and glycine pentamer have been studied using the FMO-PIMD method to investigate nuclear quantum effects on structure and molecular interactions. The applicability of the present approach is demonstrated through a number of test calculations.
Hayashi, Shigehiko; Tajkhorshid, Emad; Schulten, Klaus
2003-01-01
Retinal proteins are photoreceptors found in many living organisms. They possess a common chromophore, retinal, that upon absorption of light isomerizes and thereby triggers biological functions ranging from light energy conversion to phototaxis and vision. The photoisomerization of retinal is extremely fast, highly selective inside the protein matrix, and characterized through optimal sensitivity to incoming light. This article describes the first report of an ab initio quantum mechanical description of the in situ isomerization dynamics of retinal in bacteriorhodopsin, a microbial retinal protein that functions as a light-driven proton pump. The description combines ab initio multi-electronic state molecular dynamics of a truncated retinal chromophore model (N-methyl-γ-methylpenta-2,4-dieniminium cation fragment) with molecular mechanics of the protein motion and unveils in complete detail the photoisomerization process. The results illustrate the essential role of the protein for the characteristic kinetics and high selectivity of the photoisomerization: the protein arrests inhomogeneous photoisomerization paths and funnels them into a single path that initiates the functional process. Supported by comparison with dynamic spectral modulations observed in femtosecond spectroscopy, the results identify the principal molecular motion during photoisomerization. PMID:12944261
Time-domain ab initio modeling of photoinduced dynamics at nanoscale interfaces.
Wang, Linjun; Long, Run; Prezhdo, Oleg V
2015-04-01
Nonequilibrium processes involving electronic and vibrational degrees of freedom in nanoscale materials are under active experimental investigation. Corresponding theoretical studies are much scarcer. The review starts with the basics of time-dependent density functional theory, recent developments in nonadiabatic molecular dynamics, and the fusion of the two techniques. Ab initio simulations of this kind allow us to directly mimic a great variety of time-resolved experiments performed with pump-probe laser spectroscopies. The focus is on the ultrafast photoinduced charge and exciton dynamics at interfaces formed by two complementary materials. We consider purely inorganic materials, inorganic-organic hybrids, and all organic interfaces, involving bulk semiconductors, metallic and semiconducting nanoclusters, graphene, carbon nanotubes, fullerenes, polymers, molecular crystals, molecules, and solvent. The detailed atomistic insights available from time-domain ab initio studies provide a unique description and a comprehensive understanding of the competition between electron transfer, thermal relaxation, energy transfer, and charge recombination processes. These advances now make it possible to directly guide the development of organic and hybrid solar cells, as well as photocatalytic, electronic, spintronic, and other devices relying on complex interfacial dynamics.
Time-Domain Ab Initio Modeling of Photoinduced Dynamics at Nanoscale Interfaces
NASA Astrophysics Data System (ADS)
Wang, Linjun; Long, Run; Prezhdo, Oleg V.
2015-04-01
Nonequilibrium processes involving electronic and vibrational degrees of freedom in nanoscale materials are under active experimental investigation. Corresponding theoretical studies are much scarcer. The review starts with the basics of time-dependent density functional theory, recent developments in nonadiabatic molecular dynamics, and the fusion of the two techniques. Ab initio simulations of this kind allow us to directly mimic a great variety of time-resolved experiments performed with pump-probe laser spectroscopies. The focus is on the ultrafast photoinduced charge and exciton dynamics at interfaces formed by two complementary materials. We consider purely inorganic materials, inorganic-organic hybrids, and all organic interfaces, involving bulk semiconductors, metallic and semiconducting nanoclusters, graphene, carbon nanotubes, fullerenes, polymers, molecular crystals, molecules, and solvent. The detailed atomistic insights available from time-domain ab initio studies provide a unique description and a comprehensive understanding of the competition between electron transfer, thermal relaxation, energy transfer, and charge recombination processes. These advances now make it possible to directly guide the development of organic and hybrid solar cells, as well as photocatalytic, electronic, spintronic, and other devices relying on complex interfacial dynamics.
NASA Astrophysics Data System (ADS)
Clementi, Enrico; Corongiu, Giorgina; Sciortino, Francesco
1993-08-01
Results are presented on the reliability of the ab initio, polarizable and flexible Nieser—Corongiu—Clementi potential at describing the structure and dynamics of the liquid and solid phases of water. For both structural and dynamic quantities the agreement between experimental and numerical results is good. A "substance" very similar to "real water" has indeed been created on the basis of ab initio quantum mechanical calculations. This gives confidence in the use of the simulations to examine features that are not directly measurable, but are of central importance in the understanding of water structure and dynamics.
Ab initio molecular dynamics simulations of ion-solid interactions in zirconate pyrochlores
Xiao, Haiyan Y.; Weber, William J.; Zhang, Yanwen; ...
2015-01-31
In this paper, an ab initio molecular dynamics method is employed to study low energy recoil events in zirconate pyrochlores (A2Zr2O7, A = La, Nd and Sm). It shows that both cations and anions in Nd2Zr2O7 and Sm2Zr2O7 are generally more likely to be displaced than those in La2Zr2O7. The damage end states mainly consist of Frenkel pair defects, and the Frenkel pair formation energies in Nd2Zr2O7 and Sm2Zr2O7 are lower than those in La2Zr2O7. These results suggest that the order–disorder structural transition more easily occurs in Nd2Zr2O7 and Sm2Zr2O7 resulting in a defect-fluorite structure, which agrees well with experimentalmore » observations. Our calculations indicate that oxygen migration from 48f and 8b to 8a sites is dominant under low energy irradiation. A number of new defects, including four types of cation Frenkel pairs and six types of anion Frenkel pairs, are revealed by ab initio molecular dynamics simulations. The present findings may help to advance the fundamental understanding of the irradiation response behavior of zirconate pyrochlores.« less
NASA Astrophysics Data System (ADS)
Galler, Anna; Gunacker, Patrik; Tomczak, Jan; Thunström, Patrik; Held, Karsten
Recently, approaches such as the dynamical vertex approximation (D ΓA) or the dual-fermion method have been developed. These diagrammatic approaches are going beyond dynamical mean field theory (DMFT) by including nonlocal electronic correlations on all length scales as well as the local DMFT correlations. Here we present our efforts to extend the D ΓA methodology to ab-initio materials calculations (ab-initio D ΓA). Our approach is a unifying framework which includes both GW and DMFT-type of diagrams, but also important nonlocal correlations beyond, e.g. nonlocal spin fluctuations. In our multi-band implementation we are using a worm sampling technique within continuous-time quantum Monte Carlo in the hybridization expansion to obtain the DMFT vertex, from which we construct the reducible vertex function using the two particle-hole ladders. As a first application we show results for transition metal oxides. Support by the ERC project AbinitioDGA (306447) is acknowledged.
Ab initio molecular dynamics of solvation effects on reactivity at electrified interfaces
NASA Astrophysics Data System (ADS)
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.
Ab Initio Molecular Dynamics Study of Dissociation of Water under an Electric Field
NASA Astrophysics Data System (ADS)
Saitta, A. Marco; Saija, Franz; Giaquinta, Paolo V.
2012-05-01
The behavior of liquid water under an electric field is a crucial phenomenon in science and engineering. However, its detailed description at a microscopic level is difficult to achieve experimentally. Here we report on the first ab initio molecular-dynamics study on water under an electric field. We observe that the hydrogen-bond length and the molecular orientation are significantly modified at low-to-moderate field intensities. Fields beyond a threshold of about 0.35V/Å are able to dissociate molecules and sustain an ionic current via a series of correlated proton jumps. Upon applying even more intense fields (˜1.0V/Å), a 15%-20% fraction of molecules are instantaneously dissociated and the resulting ionic flow yields a conductance of about 7.8Ω-1cm-1, in good agreement with experimental values. This result paves the way to quantum-accurate microscopic studies of the effect of electric fields on aqueous solutions and, thus, to massive applications of ab initio molecular dynamics in neurobiology, electrochemistry, and hydrogen economy.
Ab initio molecular dynamics of solvation effects on reactivity at electrified interfaces
Herron, Jeffrey A.; Morikawa, Yoshitada; Mavrikakis, Manos
2016-01-01
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. PMID:27503889
Xiong, L H; Yoo, H; Lou, H B; Wang, X D; Cao, Q P; Zhang, D X; Jiang, J Z; Xie, H L; Xiao, T Q; Jeon, S; Lee, G W
2015-01-28
X-ray diffraction and electrostatic levitation measurements, together with the ab initio molecular dynamics simulation of liquid Al(75)Cu(25) alloy have been performed from 800 to 1600 K. Experimental and ab initio molecular dynamics simulation results match well with each other. No abnormal changes were experimentally detected in the specific heat capacity over total hemispheric emissivity and density curves in the studied temperature range for a bulk liquid Al(75)Cu(25) alloy measured by the electrostatic levitation technique. The structure factors gained by the ab initio molecular dynamics simulation precisely coincide with the experimental data. The atomic structure analyzed by the Honeycutt-Andersen index and Voronoi tessellation methods shows that icosahedral-like atomic clusters prevail in the liquid Al(75)Cu(25) alloy and the atomic clusters evolve continuously. All results obtained here suggest that no liquid-liquid transition appears in the bulk liquid Al(75)Cu(25) alloy in the studied temperature range.
Ab Initio Molecular Dynamics Studies of Pb m Sb n (m + n ≤ 9) Alloy Clusters
NASA Astrophysics Data System (ADS)
Song, Bingyi; Xu, Baoqiang; Yang, Bin; Jiang, Wenlong; Chen, Xiumin; Xu, Na; Liu, Dachun; Dai, Yongnian
2017-07-01
Structure, stability, and dynamics of Pb m Sb n (m + n ≤ 9) clusters were investigated using ab initio molecular dynamics. Size dependence of binding energies, the second-order energy difference of clusters, dissociation energy, HOMO-LUMO gaps, Mayer bond order, and the diffusion coefficient of Pb m Sb n clusters were discussed. Results suggest that Pb3Sb2, Pb4Sb2, and Pb5Sb4 (n = 2 or 4) clusters have higher stability than other clusters, which is consistent with previous findings. In case of Pb-Sb alloy, the dynamics results show that Pb4Sb2 (Pb-22.71 wt pct Sb) can exist in gas phase at 1073 K (800 °C), which reasonably explains the azeotropic phenomenon, and the calculated values are in agreement with the experimental results (Pb-22 wt pct Sb).
An Efficient Local Molecular Dynamics Polymerization Simulation Combined with an Ab Initio MO Method
Xie, Peng; Orimoto, Yuuichi; Aoki, Yuriko
2013-01-01
A new local ab initio molecular dynamics method, namely elongation molecular dynamics (ELG-MD) is proposed for highly efficient simulations of aperiodic polymer systems. ELG-MD combines the elongation method (ELG) with the Gear predictor corrector (GPC) algorithm of molecular dynamics simulation. In this method, the local gradients acting on the atom’s nucleus in the active region are calculated by the ELG method while the equations of the nucleus’s motion are solved by the GPC algorithm. In this work, the first application of this ELG-MD method is described to investigate the stable conformation of polyglycine with surrounding water molecules. The water effects on the structure of polyglycine are examined. The ELG-MD simulations show that the formation of the polyglycine helix is strongly induced by the hydrogen bonds observed in two types of H-bond rings. PMID:28809345
Ab initio molecular dynamics and quasichemical study of H+(aq)
Asthagiri, D.; Pratt, L. R.; Kress, J. D.
2005-01-01
The excess proton in water, H+(aq), plays a fundamental role in aqueous solution chemistry. Its solution thermodynamic properties are essential to molecular descriptions of that chemistry and for validation of dynamical calculations. Within the quasichemical theory of solutions those thermodynamic properties are conditional on recognizing underlying solution structures. The quasichemical treatment identifies H3O+ and H2O5+ as natural inner-shell complexes, corresponding to the cases of n = 1, 2 water molecule ligands, respectively, of a distinguished H+ ion. A quantum-mechanical treatment of the inner-shell complex with both a dielectric continuum and a classical molecular dynamics treatment of the outer-shell contribution identifies the latter case (the Zundel complex) as the more numerous species. Ab initio molecular dynamics simulations, with two different electron density functionals, suggest a preponderance of Zundel-like structures, but a symmetrical ideal Zundel cation is not observed. PMID:15831590
Ab Initio Molecular Dynamics Studies of Pb m Sb n ( m + n ≤ 9) Alloy Clusters
NASA Astrophysics Data System (ADS)
Song, Bingyi; Xu, Baoqiang; Yang, Bin; Jiang, Wenlong; Chen, Xiumin; Xu, Na; Liu, Dachun; Dai, Yongnian
2017-10-01
Structure, stability, and dynamics of Pb m Sb n ( m + n ≤ 9) clusters were investigated using ab initio molecular dynamics. Size dependence of binding energies, the second-order energy difference of clusters, dissociation energy, HOMO-LUMO gaps, Mayer bond order, and the diffusion coefficient of Pb m Sb n clusters were discussed. Results suggest that Pb3Sb2, Pb4Sb2, and Pb5Sb4 ( n = 2 or 4) clusters have higher stability than other clusters, which is consistent with previous findings. In case of Pb-Sb alloy, the dynamics results show that Pb4Sb2 (Pb-22.71 wt pct Sb) can exist in gas phase at 1073 K (800 °C), which reasonably explains the azeotropic phenomenon, and the calculated values are in agreement with the experimental results (Pb-22 wt pct Sb).
Ab initio study on the dynamics of furfural at the liquid-solid interfaces
NASA Astrophysics Data System (ADS)
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
NASA Astrophysics Data System (ADS)
Kawashima, Yukio; Tachikawa, Masanori
2013-05-01
Ab initio path integral molecular dynamics simulation was performed to understand the nuclear quantum effect on the hydrogen bond of hydrogen malonate anion. Static calculation predicted the proton transfer barrier as 0.12 kcal/mol. Conventional ab initio molecular dynamics simulation at 300 K found proton distribution with a double peak on the proton transfer coordinate. Inclusion of thermal effect alone elongates the hydrogen bond length, which increases the barrier height. Inclusion of nuclear quantum effect washes out this barrier, and distributes a single broad peak in the center. H/D isotope effect on the proton transfer is also discussed.
i-PI: A Python interface for ab initio path integral molecular dynamics simulations
NASA Astrophysics Data System (ADS)
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
Three-cluster dynamics within an ab initio framework
Quaglioni, Sofia; Romero-Redondo, Carolina; Navratil, Petr
2013-09-26
In this study, we introduce a fully antisymmetrized treatment of three-cluster dynamics within the ab initio framework of the no-core shell model/resonating-group method. Energy-independent nonlocal 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 Schrödinger 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 a ^{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 no-core shell model. Differences between the two calculations provide a measure of core (^{4}He) polarization effects.
Structural phase transition of BeTe: an ab initio molecular dynamics study.
Alptekin, Sebahaddin
2017-08-11
Beryllium telluride (BeTe) with cubic zinc-blende (ZB) structure was studied using ab initio constant pressure method under high pressure. The ab initio molecular dynamics (MD) approach for constant pressure was studied and it was found that the first order phase transition occurs from the ZB structure to the nickel arsenide (NiAs) structure. It has been shown that the MD simulation predicts the transition pressure P T more than the value obtained by the static enthalpy and experimental data. The structural pathway reveals MD simulation such as cubic → tetragonal → orthorhombic → monoclinic → orthorhombic → hexagonal, leading the ZB to NiAs phase. The phase transformation is accompanied by a 10% volume drop and at 80 GPa is likely to be around 35 GPa in the experiment. In the present study, our obtained values can be compared with the experimental and theoretical results. Graphical abstract The energy-volume relation and ZB phase for the BeTe.
Ab initio study of the anharmonic lattice dynamics of iron at the γ -δ phase transition
NASA Astrophysics Data System (ADS)
Lian, Chao-Sheng; Wang, Jian-Tao; Chen, Changfeng
2015-11-01
We report calculations of phonon dispersions of iron (Fe) at its γ -δ phase transition using a self-consistent ab initio lattice dynamical method in conjunction with an effective magnetic force approach via the antiferromagnetic approximation. Our results show that anharmonic phonon-phonon interactions play a crucial role in stabilizing the δ -Fe phase in the open bcc lattice. In contrast, the lattice dynamics of the close-packed fcc γ -Fe phase are dominated by magnetic interactions. Simultaneous considerations of the lattice anharmonic and magnetic interactions produced temperature-dependent phonon dispersions for δ -Fe and γ -Fe phases in excellent agreement with recent experimental measurements. The present results highlight the key role of lattice anharmonicity in determining the structural stability of iron at high temperatures, which has significant implications for other high-temperature paramagnetic metals like Ce and Pu.
An ab initio approach to free-energy reconstruction using logarithmic mean force dynamics
Nakamura, Makoto Obata, Masao; Morishita, Tetsuya; Oda, Tatsuki
2014-05-14
We present an ab initio approach for evaluating a free energy profile along a reaction coordinate by combining logarithmic mean force dynamics (LogMFD) and first-principles molecular dynamics. The mean force, which is the derivative of the free energy with respect to the reaction coordinate, is estimated using density functional theory (DFT) in the present approach, which is expected to provide an accurate free energy profile along the reaction coordinate. We apply this new method, first-principles LogMFD (FP-LogMFD), to a glycine dipeptide molecule and reconstruct one- and two-dimensional free energy profiles in the framework of DFT. The resultant free energy profile is compared with that obtained by the thermodynamic integration method and by the previous LogMFD calculation using an empirical force-field, showing that FP-LogMFD is a promising method to calculate free energy without empirical force-fields.
An ab initio approach to free-energy reconstruction using logarithmic mean force dynamics
NASA Astrophysics Data System (ADS)
Nakamura, Makoto; Obata, Masao; Morishita, Tetsuya; Oda, Tatsuki
2014-05-01
We present an ab initio approach for evaluating a free energy profile along a reaction coordinate by combining logarithmic mean force dynamics (LogMFD) and first-principles molecular dynamics. The mean force, which is the derivative of the free energy with respect to the reaction coordinate, is estimated using density functional theory (DFT) in the present approach, which is expected to provide an accurate free energy profile along the reaction coordinate. We apply this new method, first-principles LogMFD (FP-LogMFD), to a glycine dipeptide molecule and reconstruct one- and two-dimensional free energy profiles in the framework of DFT. The resultant free energy profile is compared with that obtained by the thermodynamic integration method and by the previous LogMFD calculation using an empirical force-field, showing that FP-LogMFD is a promising method to calculate free energy without empirical force-fields.
NASA Astrophysics Data System (ADS)
Mazzola, Guglielmo; Sorella, Sandro
2017-01-01
We propose an ab initio molecular dynamics method, capable of dramatically reducing the autocorrelation time required for the simulation of classical and quantum particles at finite temperatures. 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 to both Lennard-Jones models, to demonstrate the accuracy and speeding-up of the sampling, and within a quantum Monte Carlo based wave function approach, 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 a few hundred 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 pressure when the long range dispersive forces are taken into account.
Muchová, Eva; Slavícek, Petr; Sobolewski, Andrzej L; Hobza, Pavel
2007-06-21
The goal of this study is to explore the photochemical processes following optical excitation of the glycine molecule into its two low-lying excited states. We employed electronic structure methods at various levels to map the PES of the ground state and the two low-lying excited states of glycine. It follows from our calculations that the photochemistry of glycine can be regarded as a combination of photochemical behavior of amines and carboxylic acid. The first channel (connected to the presence of amino group) results in ultrafast decay, while the channels characteristic for the carboxylic group occur on a longer time scale. Dynamical calculations provided the branching ratio for these channels. We also addressed the question whether conformationally dependent photochemistry can be observed for glycine. While electronic structure calculations favor this possibility, the ab initio multiple spawning (AIMS) calculations showed only minor relevance of the reaction path resulting in conformationally dependent dynamics.
Decarboxylation of furfural on Pd(111): Ab initio molecular dynamics simulations
NASA Astrophysics Data System (ADS)
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.
Insights into H2 formation in space from ab initio molecular dynamics.
Casolo, Simone; Tantardini, Gian Franco; Martinazzo, Rocco
2013-04-23
Hydrogen formation is a key process for the physics and the chemistry of interstellar clouds. Molecular hydrogen is believed to form on the carbonaceous surface of dust grains, and several mechanisms have been invoked to explain its abundance in different regions of space, from cold interstellar clouds to warm photon-dominated regions. Here, we investigate direct (Eley-Rideal) recombination including lattice dynamics, surface corrugation, and competing H-dimers formation by means of ab initio molecular dynamics. We find that Eley-Rideal reaction dominates at energies relevant for the interstellar medium and alone may explain observations if the possibility of facile sticking at special sites (edges, point defects, etc.) on the surface of the dust grains is taken into account.
NASA Astrophysics Data System (ADS)
Michel, K. H.; ćakır, D.; Sevik, C.; Peeters, F. M.
2017-03-01
The elastic constant C11 and piezoelectric stress constant e1 ,11 of two-dimensional (2D) dielectric materials comprising h-BN, 2 H -MoS2 , and other transition-metal dichalcogenides and dioxides are calculated using lattice dynamical theory. The results are compared with corresponding quantities obtained with ab initio calculations. We identify the difference between clamped-ion and relaxed-ion contributions with the dependence on inner strains which are due to the relative displacements of the ions in the unit cell. Lattice dynamics allows us to express the inner-strain contributions in terms of microscopic quantities such as effective ionic charges and optoacoustical couplings, which allows us to clarify differences in the piezoelectric behavior between h-BN and MoS2. Trends in the different microscopic quantities as functions of atomic composition are discussed.
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. (c) 2004 American Institute of Physics.
An ab initio approach to free-energy reconstruction using logarithmic mean force dynamics.
Nakamura, Makoto; Obata, Masao; Morishita, Tetsuya; Oda, Tatsuki
2014-05-14
We present an ab initio approach for evaluating a free energy profile along a reaction coordinate by combining logarithmic mean force dynamics (LogMFD) and first-principles molecular dynamics. The mean force, which is the derivative of the free energy with respect to the reaction coordinate, is estimated using density functional theory (DFT) in the present approach, which is expected to provide an accurate free energy profile along the reaction coordinate. We apply this new method, first-principles LogMFD (FP-LogMFD), to a glycine dipeptide molecule and reconstruct one- and two-dimensional free energy profiles in the framework of DFT. The resultant free energy profile is compared with that obtained by the thermodynamic integration method and by the previous LogMFD calculation using an empirical force-field, showing that FP-LogMFD is a promising method to calculate free energy without empirical force-fields.
Ab Initio Excited State Properties and Dynamics of a Prototype σ-Bridged-Donor-Acceptor Molecule
NASA Astrophysics Data System (ADS)
Tapavicza, Enrico; Tavernelli, Ivano; Rothlisberger, Ursula
2009-08-01
The photophysical and dynamical properties of the donor-(σ-bridge)-acceptor molecule N-phenylpiperindone-malondinitrile are investigated by second-order approximate coupled cluster (CC2) and time-dependent density functional theory (TDDFT). The study is based on optimized equilibrium geometries for ground and excited states as well as on ab initio molecular dynamics simulations. While CC2 and DFT both predict ground state geometries that are consistent with the crystal structure, equilibrium geometries for the fluorescent charge transfer (CT) state are qualitatively different between CC2 and TDDFT. CC2 reproduces the experimental results for vertical excitations (within 0.3 eV) and provides an orbital assignment of the experimental absorption bands that is supported by experiments. Using CC2, a good agreement is also found for fluorescence energies (within 0.1-0.6 eV). At contrast, CT absorption and fluorescence energies are strongly underestimated by TDDFT using the semi-local functional PBE but improved agreement is found for the hybrid functional PBE0. However, for both functionals, TDDFT fails to predict an equilibrium geometry of the intradonor excited state because of mixing between this state and an artificially low-lying CT state during the optimization. This is an example where the well documented CT failure of TDDFT affects properties of other locally excited states. The minimum of the intradonor locally excited state was therefore only located by the CC2 method. The internal conversion (IC) process from a locally excited donor state to the CT state is simulated by excited state ab initio molecular dynamics based on CC2 and where nonadiabatic transitions are described using the Landau-Zener approximation. We find the IC process to occur a few tens of femtoseconds after excitation. The simulation provides a detailed description of the atomic rearrangements in electron donor and acceptor that drive the interconversion process.
NASA Astrophysics Data System (ADS)
Chen, Jiangchao
Dissociative laser-driven photoreactions of open-shell lanthanide metal-organic complexes are analyzed from experimental and computational aspects. Experimental analysis, based on time-of-flight mass spectrometry suggests the most probable pathway for the photoreactions. A sequence of intermediates and the distribution of final products are identified. The computational analysis, based on excited-state ab initio molecular dynamics with surface hopping, is implemented at the DFT level of theory. Computational treatment prompts the mechanism of laser-driven photoreactions at time ranges from femtoseconds to picoseconds. The experimental and computational analyses agree on several key products of photoreactions. Branching between two reaction pathways, ligand ejection versus cracking, is observed and explained. The results obtained are of importance for basic studies of processes beyond the Born-Oppenheimer approximation and for nano-electronics application of laser-assisted chemical vapor deposition of insulators with super-high dielectric constant.
Ortiz-Sánchez, Juan Manuel; Bucher, Denis; Pierce, Levi C T; Markwick, Phineus R L; McCammon, J Andrew
2012-08-14
In the present work, we employ excited state accelerated ab initio molecular dynamics (A-AIMD) to efficiently study the excited state energy landscape and photophysical topology of a variety of molecular systems. In particular, we focus on two important challenges for the modeling of excited electronic states: (i) the identification and characterization of conical intersections and crossing seams, in order to predict different and often competing radiationless decay mechanisms, and (ii) the description of the solvent effect on the absorption and emission spectra of chemical species in solution. In particular, using as examples the Schiff bases formaldimine and salicylidenaniline, we show that A-AIMD can be readily employed to explore the conformational space around crossing seams in molecular systems with very different photochemistry. Using acetone in water as an example, we demonstrate that the enhanced configurational space sampling may be used to accurately and efficiently describe both the prominent features and line-shapes of absorption and emission spectra.
Communication: Improved ab initio molecular dynamics by minimally biasing with experimental data
NASA Astrophysics Data System (ADS)
White, Andrew D.; Knight, Chris; Hocky, Glen M.; Voth, Gregory A.
2017-01-01
Accounting for electrons and nuclei simultaneously is a powerful capability of ab initio molecular dynamics (AIMD). However, AIMD is often unable to accurately reproduce properties of systems such as water due to inaccuracies in the underlying electronic density functionals. This shortcoming is often addressed by added empirical corrections and/or increasing the simulation temperature. We present here a maximum-entropy approach to directly incorporate limited experimental data via a minimal bias. Biased AIMD simulations of water and an excess proton in water are shown to give significantly improved properties both for observables which were biased to match experimental data and for unbiased observables. This approach also yields new physical insight into inaccuracies in the underlying density functional theory as utilized in the unbiased AIMD.
Thermal transmission at Si/Ge interface: ab initio lattice dynamics calculation
NASA Astrophysics Data System (ADS)
Alkurdi, A.; Merabia, S.
2017-01-01
We perform lattice dynamics calculations (LD) on silicon/germanium interfaces using ab initio interatomic force constants to predict the interfacial phonon transmission as a function of both phonon frequency and the transmission angle. We carry out a spectral and angular analysis to quantify the contribution of each phonon mode in a given scattering direction. The effect of the interaction range was studied at this interface by taking account of more or less atom layers across the interface. Moreover, we were able to predict the thermal boundary conductance (TBC) as a function of the transmission angle and temperature as well. Our results show that, the thermal energy transmission is highly anisotropic while thermal energy reflection is almost isotropic. In addition, we found that it seems there is a global critical angle of transmission beyond which almost no thermal energy is transmitted. This can be used to device high pass phonon filter via changing the orientation of the interface.
Gor, Gennady Y; Bernstein, Noam
2016-05-31
Adsorption-induced deformation is expansion or contraction of a solid due to adsorption on its surface. This phenomenon is important for a wide range of applications, from chemomechanical sensors to methane recovery from geological formations. The strain of the solid is driven by the change of the surface stress due to adsorption. Using ab initio molecular dynamics, we calculate the surface stresses for the dry α-quartz surfaces, and investigate how these stresses change when the surfaces are exposed to water. We find that the nonhydroxylated surface shows small and approximately isotropic changes in stress, while the hydroxylated surface, which interacts more strongly with the polar water molecules, shows larger and qualitatively anisotropic (opposite sign in xx and yy) surface stress changes. All of these changes are several times larger than the surface tension of water itself. The anisotropy and possibility of positive surface stress change can explain experimentally observed surface area contraction due to adsorption.
Chaban, Vitaly V; Prezhdo, Oleg V
2016-07-07
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.
Ab-initio molecular dynamics study of lanthanides in liquid sodium
NASA Astrophysics Data System (ADS)
Li, Xiang; Samin, Adib; Zhang, Jinsuo; Unal, C.; Mariani, R. D.
2017-02-01
To mitigate the fuel cladding chemical interaction (FCCI) phenomena in liquid sodium cooled fast reactors, a fundamental understanding of the lanthanide (Ln) transport through liquid Nasbnd Cs filled pores in Usbnd Zr fuel is necessary. In this study, we investigate three abundant Ln fission products diffusion coefficients in liquid Na at multiple temperatures. By utilization of Ab-initio Molecular Dynamics, the Ln diffusivities are found to be in the magnitude order of liquid diffusion (10-5cm2 /s) and the temperature dependence of the diffusivity for different lanthanides in liquid sodium was explored. It is also observed that dilute concentration of Pr and Nd led to a significant change in Na diffusivity. The structural and electronic properties of Nasbnd Ln metallic systems have been investigated. The total coordination number shows dependence on both the temperature and the composition.
Ab Initio Molecular-Dynamics Simulation of Neuromorphic Computing in Phase-Change Memory Materials.
Skelton, Jonathan M; Loke, Desmond; Lee, Taehoon; Elliott, Stephen R
2015-07-08
We present an in silico study of the neuromorphic-computing behavior of the prototypical phase-change material, Ge2Sb2Te5, using ab initio molecular-dynamics simulations. Stepwise changes in structural order in response to temperature pulses of varying length and duration are observed, and a good reproduction of the spike-timing-dependent plasticity observed in nanoelectronic synapses is demonstrated. Short above-melting pulses lead to instantaneous loss of structural and chemical order, followed by delayed partial recovery upon structural relaxation. We also investigate the link between structural order and electrical and optical properties. These results pave the way toward a first-principles understanding of phase-change physics beyond binary switching.
Habenicht, Bradley F; Paddison, Stephen J; Tuckerman, Mark E
2010-08-21
Proton dissociation and transfer were examined with ab initio molecular dynamics (AIMD) simulations of carbon nanotubes (CNT) functionalized with perfluorosulfonic acid (-CF(2)SO(3)H) groups with 1-3 H(2)O/SO(3)H. The CNT systems were constructed both with and without fluorine atoms covalently bound to the walls to elucidate the effects of the presence of a strongly hydrophobic environment, the fluorine, on proton dissociation, hydration, and stabilization. The simulations revealed that the dissociated proton was preferentially stabilized as a hydrated hydronium cation (i.e., Eigen like) in the fluorinated CNTs but as a Zundel (H(5)O(2)(+)) cation in the nonfluorinated CNTs. This feature is attributed to the fluorine atoms forming hydrogen bonds with the water molecules coordinated to the central hydronium ion.
Xiao, Haiyan Y.; Weber, William J.; Zhang, Yanwen; ...
2015-02-09
In this study, the response of titanate pyrochlores (A2Ti2O7, A = Y, Gd and Sm) to electronic excitation is investigated utilizing an ab initio molecular dynamics method. All the titanate pyrochlores are found to undergo a crystalline-to-amorphous structural transition under a low concentration of electronic excitations. The transition temperature at which structural amorphization starts to occur depends on the concentration of electronic excitations. During the structural transition, O2-like molecules are formed, and this anion disorder further drives cation disorder that leads to an amorphous state. This study provides new insights into the mechanisms of amorphization in titanate pyrochlores under laser,more » electron and ion irradiations.« less
Ab initio molecular dynamics simulation of pressure-induced phase transition in MgS
NASA Astrophysics Data System (ADS)
Begeç, Ebru; Eker, Sıtkı; Bozdemir, Süleyman
2017-08-01
Pressure-induced phase transition in MgS is studied using a constant pressure ab initio molecular dynamics method, and a solid evidence of existence of its high-pressure phase is provided. As predicted by total energy calculations, MgS undergoes a structural phase transformation from the rocksalt structure to a CsCl-type structure under hydrostatic pressure. The transformation mechanism is characterized, and two intermediate phases having P4/ nmm and P21/ m symmetries for the rocksalt-to-CsCl-type phase transformation of MgS are proposed, which is different from the previously proposed mechanisms. We also study this phase transition using the total energy calculations. Our predicted transition parameters and bulk properties are in good agreement with the earlier first principle simulations.
Brandt, Erik G; Agosta, Lorenzo; Lyubartsev, Alexander P
2016-07-21
Small-sized wet TiO2 nanoparticles have been investigated by ab initio molecular dynamics simulations. Chemical and physical adsorption of water on the TiO2-water interface was studied as a function of water content, ranging from dry nanoparticles to wet nanoparticles with monolayer coverage of water. The surface reactivity was shown to be a concave function of water content and driven by surface defects. The local coordination number at the defect was identified as the key factor to decide whether water adsorption proceeds through dissociation or physisorption on the surface. A consistent picture of TiO2 nanoparticle wetting at the microscopic level emerges, which corroborates existing experimental data and gives further insight into the molecular mechanisms behind nanoparticle wetting. These calculations will facilitate the engineering of metal oxide nanoparticles with a controlled catalytic water activity.
Ab initio molecular dynamic study of solid-state transitions of ammonium nitrate
Yu, Hongyu; Duan, Defang; Liu, Hanyu; Yang, Ting; Tian, Fubo; Bao, Kuo; Li, Da; Zhao, Zhonglong; Liu, Bingbing; Cui, Tian
2016-01-01
High-pressure polymorphism and phase transitions have wide ranging consequences on the basic properties of ammonium nitrate. However, the phase diagram of ammonium nitrate at high pressure and high temperature is still under debate. This study systematically investigates the phase transitions and structural properties of ammonium nitrate at a pressure range of 5–60 GPa and temperature range of 250–400 K by ab initio molecular dynamics simulations. Two new phases are identified: one corresponds to the experimentally observed phase IV’ and the other is named AN-X. Simultaneously, the lattice strains play a significant role in the formation and stabilization of phase IV’, providing a reasonable explanation for experimental observation of phase IV-IV’ transition which only appears under nonhydrostatic pressure. In addition, 12 O atoms neighboring the NH (N atom in ammonium cation) atom are selected as reference system to clearly display the tanglesome rotation of ammonium cation. PMID:26754622
Threshold displacement energy in GaN; Ab initio molecular dynamics study
Xiao, H. Y.; Gao, Fei; Zu, Xiaotao T.; Weber, William J.
2009-06-25
Large-scale ab initio molecular dynamics method has been used to determine the threshold displacement energies, Ed, along five specific directions and to determine the defect configurations created during low energy events. The Ed shows a significant dependence on direction. The minimum Ed is determined to be 39 eV along the <-1010> direction for a gallium atom and 17.0 eV along the <-1010> direction for a nitrogen atom, which are in reasonable agreement with the experimental measurements. The average Ed values determined are 73.2 and 32.4 eV for gallium and nitrogen atoms, respectively. The N defects created at low energy events along different crystallographic directions have a similar configuration (a N-N dumbbell configuration), but various configurations for Ga defects are formed in GaN.
NASA Technical Reports Server (NTRS)
Jaffe, Richard L.; Pattengill, Merle D.; Schwenke, David W.
1989-01-01
Strategies for constructing global potential energy surfaces from a limited number of accurate ab initio electronic energy calculations are discussed. Generally, these data are concentrated in small regions of configuration space (e.g., in the vicinity of saddle points and energy minima) and difficulties arise in generating a potential function that is globally well-behaved. Efficient computer codes for carrying out classical trajectory calculations on vector and parallel processors are also described. Illustrations are given from recent work on the following chemical systems: Ca + HF yields CaF + H, H + H + H2 yields H2 + H2, N + O2 yields NO + O and O + N2 yields NO + N. The dynamics and kinetics of metathesis, dissociation, recombination, energy transfer and complex formation processes will be discussed.
Initial stages of salt crystal dissolution determined with ab initio molecular dynamics.
Liu, Li-Min; Laio, Alessandro; Michaelides, Angelos
2011-08-07
The initial stages of NaCl dissolution in liquid water have been examined with state-of-the-art ab initio molecular dynamics and free energy sampling techniques. Our simulations reveal a complex multi-step process triggered by the departure of Cl ions from the lattice, with a well-defined intermediate state wherein departing ions are partially solvated but remain in contact with the crystal. The polarizability of Cl(-) is identified as the source of the anion's preferential initial dissolution, an effect which leads a forcefield based description of NaCl dissolution to fail to identify a preference for Cl over Na dissolution. This journal is © the Owner Societies 2011
Ab initio molecular dynamic study of solid-state transitions of ammonium nitrate
NASA Astrophysics Data System (ADS)
Yu, Hongyu; Duan, Defang; Liu, Hanyu; Yang, Ting; Tian, Fubo; Bao, Kuo; Li, Da; Zhao, Zhonglong; Liu, Bingbing; Cui, Tian
2016-01-01
High-pressure polymorphism and phase transitions have wide ranging consequences on the basic properties of ammonium nitrate. However, the phase diagram of ammonium nitrate at high pressure and high temperature is still under debate. This study systematically investigates the phase transitions and structural properties of ammonium nitrate at a pressure range of 5–60 GPa and temperature range of 250–400 K by ab initio molecular dynamics simulations. Two new phases are identified: one corresponds to the experimentally observed phase IV’ and the other is named AN-X. Simultaneously, the lattice strains play a significant role in the formation and stabilization of phase IV’, providing a reasonable explanation for experimental observation of phase IV-IV’ transition which only appears under nonhydrostatic pressure. In addition, 12 O atoms neighboring the NH (N atom in ammonium cation) atom are selected as reference system to clearly display the tanglesome rotation of ammonium cation.
Hydration and coordination of K+ solvation in water from ab initio molecular-dynamics simulation.
Liu, Yi; Lu, Haigang; Wu, Yanbo; Hu, Tuoping; Li, Qiaoling
2010-03-28
Potassium ion in water plays a very important role in chemistry and biology. In this paper, we investigated the hydration structure and coordination of K(+) solvation in water at 300 and 450 K using ab initio Car-Parrinello molecular dynamics. The K(+)-oxygen radial distribution function indicated that the perturbation of K(+) on the water structure is strong in the first hydration shells, while it is mild outside of this region in normal liquid. According to our natural geometric criterion for the coordinated oxygen atom, the average coordination number of K(+) is 6.24 and 6.53 at 300 and 450 K, respectively, which agrees with the experimental value (6.1). This geometric criterion can also be used to define strong, moderate and weak hydrogen bonds in liquid.
NASA Technical Reports Server (NTRS)
Jaffe, Richard L.; Pattengill, Merle D.; Schwenke, David W.
1989-01-01
Strategies for constructing global potential energy surfaces from a limited number of accurate ab initio electronic energy calculations are discussed. Generally, these data are concentrated in small regions of configuration space (e.g., in the vicinity of saddle points and energy minima) and difficulties arise in generating a potential function that is globally well-behaved. Efficient computer codes for carrying out classical trajectory calculations on vector and parallel processors are also described. Illustrations are given from recent work on the following chemical systems: Ca + HF yields CaF + H, H + H + H2 yields H2 + H2, N + O2 yields NO + O and O + N2 yields NO + N. The dynamics and kinetics of metathesis, dissociation, recombination, energy transfer and complex formation processes will be discussed.
A unified scheme for ab initio molecular orbital theory and path integral molecular dynamics
NASA Astrophysics Data System (ADS)
Shiga, Motoyuki; Tachikawa, Masanori; Miura, Shinichi
2001-11-01
We present a general approach for accurate calculation of chemical substances which treats both nuclei and electrons quantum mechanically, adopting ab initio molecular orbital theory for the electronic structure and path integral molecular dynamics for the nuclei. The present approach enables the evaluation of physical quantities dependent on the nuclear configuration as well as the electronic structure, within the framework of Born-Oppenheimer adiabatic approximation. As an application, we give the path integral formulation of electric response properties—dipole moment and polarizability, which characterize the changes both in electronic structure and nuclear configuration at a given temperature when uniform electrostatic field is present. We also demonstrate the calculation of a water molecule using the present approach and the result of temperature and isotope effects is discussed.
NASA Astrophysics Data System (ADS)
Shiga, Motoyuki; Tachikawa, Masanori; Miura, Shinichi
2000-12-01
We present an accurate calculational scheme for many-body systems composed of electrons and nuclei, by path integral molecular dynamics technique combined with the ab initio molecular orbital theory. Based upon the scheme, the simulation of a water molecule at room temperature is demonstrated, applying all-electron calculation at the Hartree-Fock level of theory.
Ludwig, Jeffery; Vlachos, Dionisios G
2007-10-21
We outline a hybrid multiscale approach for the construction of ab initio potential energy surfaces (PESs) useful for performing six-dimensional (6D) classical or quantum mechanical molecular dynamics (MD) simulations of diatomic molecules reacting at single crystal surfaces. The algorithm implements concepts from the corrugation reduction procedure, which reduces energetic variation in the PES, and uses neural networks for interpolation of smoothed ab initio data. A novelty sampling scheme is implemented and used to identify configurations that are most likely to be predicted inaccurately by the neural network. This hybrid multiscale approach, which couples PES construction at the electronic structure level to MD simulations at the atomistic scale, reduces the number of density functional theory (DFT) calculations needed to specify an accurate PES. Due to the iterative nature of the novelty sampling algorithm, it is possible to obtain a quantitative measure of the convergence of the PES with respect to the number of ab initio calculations used to train the neural network. We demonstrate the algorithm by first applying it to two analytic potentials, which model the H2/Pt(111) and H2/Cu(111) systems. These potentials are of the corrugated London-Eyring-Polanyi-Sato form, which are based on DFT calculations, but are not globally accurate. After demonstrating the convergence of the PES using these simple potentials, we use DFT calculations directly and obtain converged semiclassical trajectories for the H2/Pt(111) system at the PW91/generalized gradient approximation level. We obtain a converged PES for a 6D hydrogen-surface dissociation reaction using novelty sampling coupled directly to DFT. These results, in excellent agreement with experiments and previous theoretical work, are compared to previous simulations in order to explore the sensitivity of the PES (and therefore MD) to the choice of exchange and correlation functional. Despite having a lower energetic
NASA Astrophysics Data System (ADS)
Ludwig, Jeffery; Vlachos, Dionisios G.
2007-10-01
We outline a hybrid multiscale approach for the construction of ab initio potential energy surfaces (PESs) useful for performing six-dimensional (6D) classical or quantum mechanical molecular dynamics (MD) simulations of diatomic molecules reacting at single crystal surfaces. The algorithm implements concepts from the corrugation reduction procedure, which reduces energetic variation in the PES, and uses neural networks for interpolation of smoothed ab initio data. A novelty sampling scheme is implemented and used to identify configurations that are most likely to be predicted inaccurately by the neural network. This hybrid multiscale approach, which couples PES construction at the electronic structure level to MD simulations at the atomistic scale, reduces the number of density functional theory (DFT) calculations needed to specify an accurate PES. Due to the iterative nature of the novelty sampling algorithm, it is possible to obtain a quantitative measure of the convergence of the PES with respect to the number of ab initio calculations used to train the neural network. We demonstrate the algorithm by first applying it to two analytic potentials, which model the H2/Pt(111) and H2/Cu(111) systems. These potentials are of the corrugated London-Eyring-Polanyi-Sato form, which are based on DFT calculations, but are not globally accurate. After demonstrating the convergence of the PES using these simple potentials, we use DFT calculations directly and obtain converged semiclassical trajectories for the H2/Pt(111) system at the PW91/generalized gradient approximation level. We obtain a converged PES for a 6D hydrogen-surface dissociation reaction using novelty sampling coupled directly to DFT. These results, in excellent agreement with experiments and previous theoretical work, are compared to previous simulations in order to explore the sensitivity of the PES (and therefore MD) to the choice of exchange and correlation functional. Despite having a lower energetic
Ab initio study of several static and dynamic properties of bulk liquid Ni near melting
NASA Astrophysics Data System (ADS)
del Rio, B. G.; González, L. E.; González, D. J.
2017-01-01
Several static and dynamic properties of bulk liquid Ni at a thermodynamic state near its triple point have been evaluated by ab initio molecular dynamics simulations. The calculated static structure shows very good agreement with the available experimental data, including an asymmetric second peak in the static structure factor, which underlines a marked local icosahedral short-range order in the liquid. The dynamical structure reveals propagating density fluctuations, and the calculated dynamic structure factors, S (q ,ω ) , show a good agreement with the inelastic x-ray scattering measurements. The obtained dispersion relation closely follows that obtained from the inelastic x-ray scattering measurements; moreover we analyze the possible reasons behind its discrepancy with respect to the dispersion relation derived from the inelastic neutron scattering data. The dynamical processes behind the S (q ,ω ) have been analyzed by using a model with two decay channels (a fast and a slow) associated with the relaxations of the collective excitations. We have found that the transverse current spectral functions exhibit some features which, so far, had previously been shown by high pressure liquid metals only. Furthermore, the calculated S (q ,ω ) show, within some q-range, the appearance of transverse-like excitation modes, similar to those recently found in other liquid metals. Finally, results are also reported for several transport coefficients.
NASA Astrophysics Data System (ADS)
del Rio, B. G.; González, L. E.
2017-06-01
We perform ab initio molecular dynamics simulations of liquid Zn near the melting point in order to study the longitudinal and transverse dynamic properties of the system. We find two propagating excitations in both of them in a wide range of wave vectors. This is in agreement with some experimental observations of the dynamic structure factor in the region around half the position of the main peak. Moreover, the two-mode structure in the transverse and longitudinal current correlation functions had also been previously observed in high pressure liquid metallic systems. We perform a theoretical analysis in order to investigate the possible origin of such two components by resorting to mode-coupling theories. They are found to describe qualitatively the appearance of two modes in the dynamics, but their relative intensities are not quantitatively reproduced. We suggest some possible improvements of the theory through the analysis of the structure of the memory functions. We also analyze the single-particle dynamics embedded in the velocity autocorrelation function, and explain its characteristics through mode-coupling concepts.
Marsalek, Ondrej; Markland, Thomas E
2016-02-07
Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.
Marsalek, Ondrej; Markland, Thomas E.
2016-02-07
Path integral molecular dynamics simulations, combined with an ab initio evaluation of interactions using electronic structure theory, incorporate the quantum mechanical nature of both the electrons and nuclei, which are essential to accurately describe systems containing light nuclei. However, path integral simulations have traditionally required a computational cost around two orders of magnitude greater than treating the nuclei classically, making them prohibitively costly for most applications. Here we show that the cost of path integral simulations can be dramatically reduced by extending our ring polymer contraction approach to ab initio molecular dynamics simulations. By using density functional tight binding as a reference system, we show that our ring polymer contraction scheme gives rapid and systematic convergence to the full path integral density functional theory result. We demonstrate the efficiency of this approach in ab initio simulations of liquid water and the reactive protonated and deprotonated water dimer systems. We find that the vast majority of the nuclear quantum effects are accurately captured using contraction to just the ring polymer centroid, which requires the same number of density functional theory calculations as a classical simulation. Combined with a multiple time step scheme using the same reference system, which allows the time step to be increased, this approach is as fast as a typical classical ab initio molecular dynamics simulation and 35× faster than a full path integral calculation, while still exactly including the quantum sampling of nuclei. This development thus offers a route to routinely include nuclear quantum effects in ab initio molecular dynamics simulations at negligible computational cost.
New Developments in Ab Initio Multiple Spawning for Efficient Nonadiabatic Molecular Dynamics
NASA Astrophysics Data System (ADS)
Curchod, Basile F. E.; Sisto, Aaron; Glowacki, David R.; Martínez, Todd J.
Ab initio multiple spawning (AIMS) describes the nonadiabatic dynamics of nuclear wavepackets by means of a linear combination of frozen Gaussians. While the Gaussian centers follow classical trajectories, the expansion coefficients are propagated according to the time-dependent Schrödinger equation. As a result of the coupling between Gaussian functions, AIMS accurately describes coherence and decoherence effects close to nonadiabatic regions. This accuracy has further been validated by the excellent agreement reported between AIMS dynamics and experimental observations. In this Contribution, we will discuss new techniques used to extend the applicability of AIMS to (i) larger molecules, (ii) long-time simulations, and (iii) dynamics involving an important number of electronic states. We will present different examples of nonadiabatic molecular dynamics in organic and atmospheric photochemistry, resulting from the interface between AIMS and the GPU-accelerated electronic structure code TeraChem. New methods improving the AIMS efficiency for larger systems will be discussed, such as the stochastic-selection AIMS. Finally, we will highlight early results on the extension of AIMS to the combined description of both internal conversion and intersystem crossing phenomena. B.F.E.C. acknowledges the Swiss National Science Foundation (fellowship P2ELP2_151927) for financial support.
Lasoroski, Aurélie; Vuilleumier, Rodolphe; Pollet, Rodolphe
2014-07-07
The electronic relaxation of gadolinium complexes used as MRI contrast agents was studied theoretically by following the short time evolution of zero-field-splitting parameters. The statistical analysis of ab initio molecular dynamics trajectories provided a clear separation between static and transient contributions to the zero-field-splitting. For the latter, the correlation time was estimated at approximately 0.1 ps. The influence of the ligand was also probed by replacing one pendant arm of our reference macrocyclic complex by a bulkier phosphonate arm. In contrast to the transient contribution, the static zero-field-splitting was significantly influenced by this substitution.
Aqueous solutions: state of the art in ab initio molecular dynamics.
Hassanali, Ali A; Cuny, Jérôme; Verdolino, Vincenzo; Parrinello, Michele
2014-03-13
The simulation of liquids by ab initio molecular dynamics (AIMD) has been a subject of intense activity over the last two decades. The significant increase in computational resources as well as the development of new and efficient algorithms has elevated this method to the status of a standard quantum mechanical tool that is used by both experimentalists and theoreticians. As AIMD computes the electronic structure from first principles, it is free of ad hoc parametrizations and has thus been applied to a large variety of physical and chemical problems. In particular, AIMD has provided microscopic insight into the structural and dynamical properties of aqueous solutions which are often challenging to probe experimentally. In this review, after a brief theoretical description of the Born-Oppenheimer and Car-Parrinello molecular dynamics formalisms, we show how AIMD has enhanced our understanding of the properties of liquid water and its constituent ions: the proton and the hydroxide ion. Thereafter, a broad overview of the application of AIMD to other aqueous systems, such as solvated organic molecules and inorganic ions, is presented. We also briefly describe the latest theoretical developments made in AIMD, such as methods for enhanced sampling and the inclusion of nuclear quantum effects.
Fischer, Sean A; Aprà, Edoardo; Govind, Niranjan; Hess, Wayne P; El-Khoury, Patrick Z
2017-02-16
Recent developments in nanophotonics have paved the way for achieving significant advances in the realm of single-molecule chemical detection, imaging, and dynamics. In particular, surface-enhanced Raman scattering (SERS) is a powerful analytical technique that is now routinely used to identify the chemical identity of single molecules. Understanding how nanoscale physical and chemical processes affect single-molecule SERS spectra and selection rules is a challenging task and is still actively debated. Herein, we explore underappreciated chemical phenomena in ultrasensitive SERS. We observe a fluctuating excited electronic state manifold, governed by the conformational dynamics of a molecule (4,4'-dimercaptostilbene, DMS) interacting with a metallic cluster (Ag20). This affects our simulated single-molecule SERS spectra; the time trajectories of a molecule interacting with its unique local environment dictates the relative intensities of the observable Raman-active vibrational states. Ab initio molecular dynamics of a model Ag20-DMS system are used to illustrate both concepts in light of recent experimental results.
Multiple-Timestep ab Initio Molecular Dynamics Using an Atomic Basis Set Partitioning.
Steele, Ryan P
2015-12-17
This work describes an approach to accelerate ab initio Born-Oppenheimer molecular dynamics (MD) simulations by exploiting the inherent timescale separation between contributions from different atom-centered Gaussian basis sets. Several MD steps are propagated with a cost-efficient, low-level basis set, after which a dynamical correction accounts for large basis set relaxation effects in a time-reversible fashion. This multiple-timestep scheme is shown to generate valid MD trajectories, on the basis of rigorous testing for water clusters, the methanol dimer, an alanine polypeptide, protonated hydrazine, and the oxidized water dimer. This new approach generates observables that are consistent with those of target basis set trajectories, including MD-based vibrational spectra. This protocol is shown to be valid for Hartree-Fock, density functional theory, and second-order Møller-Plesset perturbation theory approaches. Recommended pairings include 6-31G as a low-level basis set for 6-31G** or 6-311G**, as well as cc-pVDZ as the subset for accurate dynamics with aug-cc-pVTZ. Demonstrated cost savings include factors of 2.6-7.3 on the systems tested and are expected to remain valid across system sizes.
Moin, Syed Tarique; Hofer, Thomas S
2014-01-01
Ab initio QMCF-MD simulations were performed for porphyrin (POR) and magnesium-porphyrin (Mg-POR) immersed in water to study their structural and dynamical properties. The observed hydration behaviour of these solutes representing biomimetic models is in fair agreement with structural and dynamical features of their biological analogues, protoporphyrin IX (PPIX) and chlorophyll (CHl). Structural data obtained from the radial, angular and spatial distribution functions as well as the angular-radial distributions have a consensus on possessing a contrasting hydration behaviour of POR and Mg-POR. Flexibility of the ring in both solutes described by the improper torsional distribution and root mean square fluctuation showed an influence on H-bond interactions between the nitrogen atoms and water molecules that are also reflected in the respective dynamics. An axial water molecule coordinated to the Mg(ii) ion indicates the penta-coordinated Mg-POR to be stable along the simulation. It was also shown that complexation of the Mg(ii) ion to the porphyrin influences the hydration patterns significantly compared to the porphyrin itself, which is further supported by the vibrational power spectra evaluated for both solutes. Free energy of binding and solvent accessible surface area calculations also confirmed that these two solutes have distinct hydration behaviour. Detailed knowledge of the individual hydration patterns is expected to be of particular benefit.
NASA Astrophysics Data System (ADS)
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
Algorithms and novel applications based on the isokinetic ensemble. II. Ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Minary, Peter; Martyna, Glenn J.; Tuckerman, Mark E.
2003-02-01
In this paper (Paper II), the isokinetic dynamics scheme described in Paper I is combined with the plane-wave based Car-Parrinello (CP) ab initio molecular dynamics (MD) method [R. Car and M. Parrinello, Phys. Rev. Lett. 55, 2471 (1985)] to enable the efficient study of chemical reactions and metallic systems. The Car-Parrinello approach employs "on the fly" electronic structure calculations as a means of generating accurate internuclear forces for use in a molecular dynamics simulation. This is accomplished by the introduction of an extended Lagrangian that contains the electronic orbitals as fictitious dynamical variables (often expressed directly in terms of the expansion coefficients of the orbitals in a particular basis set). Thus, rather than quench the expansion coefficients to obtain the ground state energy and nuclear forces at every time step, the orbitals are "propagated" under conditions that allow them to fluctuate rapidly around their global minimum and, hence, generate an accurate approximation to the nuclear forces as the simulation proceeds. Indeed, the CP technique requires the dynamics of the orbitals to be both fast compared to the nuclear degrees of freedom while keeping the fictitious kinetic energy that allows them to be propagated dynamically as small as possible. While these conditions can be easy to achieve in many types of systems, in metals and highly exothermic chemical reactions difficulties arise. (Note, the CP dynamics of metals is incorrect because the nuclear motion does not occur on the ground state electronic surface but it can, nonetheless, provide useful information.) In order to alleviate these difficulties the isokinetic methods of Paper I are applied to derive isokinetic CP equations of motion. The efficacy of the new isokinetic CPMD method is demonstrated on model and realistic systems. The latter include, metallic systems, liquid aluminum, a small silicon sample, the 2×1 reconstruction of the silicon 100 surface, and the
Nucleation of aluminum nanoclusters on graphene: an ab-initio molecular dynamics study
NASA Astrophysics Data System (ADS)
Alnemrat, Sufian; Mayo, Dennis; de Carlo, Samantha; Eichhorn, Bryan; Hooper, Joseph
2015-06-01
Recent experimental results have shown that liquid AlCl and AlBr can, in the presence of a reducing agent, nucleate and grow 10-20 nm aluminum nanoparticles on functionalized graphene sheets. This may offer a route to patterned 2D structures of Al nanoparticles and clusters. Here we present DFT and ab initio molecular dynamics simulations of possible nucleation processes on defect-laden graphene beginning with the AlCl precursor. Static calculations show that AlCl weakly physisorbs on perfect graphene, with binding energies less than 0.5 eV and very small barriers for diffusion along the surface. Covalent bonding is seen on graphene only at vacancy sites. Car-Parrinello molecular dynamics is used to study possible cluster nucleation mechanisms near characteristic vacancies. Simulations at 500 and 1000 K show that the AlCl is very reactive in the presence of the defect, quickly agglomerating and forming long AlCl chains with strong Al-Al bonds.
Ab initio molecular dynamics simulations of low energy recoil events in MgO
Petersen, B. A.; Liu, B.; Weber, W. J.; ...
2017-01-11
In this paper, low-energy recoil events in MgO are studied using ab initio molecular dynamics simulations to reveal the dynamic displacement processes and final defect configurations. Threshold displacement energies, Ed, are obtained for Mg and O along three low-index crystallographic directions, [100], [110], and [111]. The minimum values for Ed are found along the [110] direction consisting of the same element, either Mg or O atoms. Minimum threshold values of 29.5 eV for Mg and 25.5 eV for O, respectively, are suggested from the calculations. For other directions, the threshold energies are considerably higher, 65.5 and 150.0 eV for Omore » along [111] and [100], and 122.5 eV for Mg along both [111] and [100] directions, respectively. These results show that the recoil events in MgO are partial-charge transfer assisted processes where the charge transfer plays an important role. Finally, there is a similar trend found in other oxide materials, where the threshold displacement energy correlates linearly with the peak partial-charge transfer, suggesting this behavior might be universal in ceramic oxides.« less
Equation of state of paramagnetic CrN from ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Steneteg, Peter; Alling, Björn; Abrikosov, Igor A.
2012-04-01
The equation of state for chromium nitride has been debated in the literature in connection with a proposed collapse of its bulk modulus following the pressure-induced transition from the paramagnetic cubic phase to the antiferromagnetic orthorhombic phase [F. Rivadulla , Nature Mater.1476-112210.1038/nmat2549 8, 947 (2009); B. Alling , Nature Mater.1476-112210.1038/nmat2722 9, 283 (2010)]. Experimentally the measurements are complicated due to the low transition pressure, while theoretically the simulation of magnetic disorder represents a major challenge. Here a first-principles method is suggested for the calculation of thermodynamic properties of magnetic materials in their high-temperature paramagnetic phase. It is based on ab initio molecular dynamics and simultaneous redistributions of the disordered but finite local magnetic moments. We apply this disordered local moments molecular dynamics method to the case of CrN and simulate its equation of state. In particular the debated bulk modulus is calculated in the paramagnetic cubic phase and is shown to be very similar to that of the antiferromagnetic orthorhombic CrN phase for all considered temperatures.
Liquid boron: x-ray measurements and ab initio molecular dynamics simulations.
Price, D. L.; Alatas, A.; Hennet, L.; Jakse, N.; Krishnan, S.; Pasturel, A.; Pozdnyakova, I.; Saboungi, M. L.; Said, A.; Scheunemann, R.; Schirmacher, W.; Sinn, H.; Centre de Recherche sure les Conditions Extremes et Materiaux; Lab. de Physique ed Modelisantion des Milieux Condensees; KLA-Tencor; Containerless Research, Inc.; Univ. Munchen; DESY
2009-01-01
We report results of a comprehensive study of liquid boron with x-ray measurements of the atomic structure and dynamics coupled with ab initio molecular dynamics simulations. There is no evidence of survival into the liquid of the icosahedral arrangements that characterize the crystal structures of boron but many atoms appear to adopt a geometry corresponding to the pentagonal pyramids of the crystalline phases. Despite similarities in the melting behavior of boron and silicon, there is little evidence of a significant structural shift with temperature that might suggest an eventual liquid-liquid phase transition. Relatively poor agreement with the observed damping of the sound excitations is obtained with the simple form of mode-coupling theory that has proved successful with other monatomic liquids, indicating that higher-order correlation functions arising from directional bonding and short-lived local structures are playing a crucial role. The large ratio of the high frequency to the isothermal sound velocity indicates a much stronger viscoelastic stiffening than in other monatomic liquids.
Hiratsuka, Masaki; Ohmura, Ryo; Sum, Amadeu K; Yasuoka, Kenji
2012-10-14
Vibrational spectra of guest molecules in clathrate hydrates are frequently measured to determine the characteristic signatures of the molecular environment and dynamical properties of guest-host interactions. Here, we present results of our study on the vibrational frequencies of methane molecules in structure H clathrate hydrates, namely, in the 5(12) and 4(3)5(6)6(3) cages, as the frequencies of stretching vibrational modes in these environments are still unclear. The vibrational spectra of methane molecules in structure H clathrate hydrate were obtained from ab initio molecular dynamics simulation and computed from Fourier transform of autocorrelation functions for each distinct vibrational mode. The calculated symmetric and asymmetric stretching vibrational frequencies of methane molecules were found to be lower in the 4(3)5(6)6(3) cages than in the 5(12) cages (3.8 cm(-1) for symmetric stretching and 6.0 cm(-1) for asymmetric stretching). The C-H bond length and average distance between methane molecules and host-water molecules in 4(3)5(6)6(3) cages were slightly longer than those in the 5(12) cages.
Ab initio molecular dynamics simulations of nitromethane under shock initiation conditions
NASA Astrophysics Data System (ADS)
Decker, S. A.; Chau, D.; Woo, T. K.; Zhang, F.
Detonation theories for homogeneous, condensed energetic materials have focused on 1-d analysis in which the detonation ignition physics forms the most difficult part. The classic ZND model considers detonation ignition through a frozen shock transition followed by an induction period, in which the shock temperature induces vibrational, rotational and electronic excitation followed by molecular dissociation (i.e., thermal decomposition). The frozen shock assumption has been the topic of debate and an alternative model has been proposed whereby detonation ignition arises from excitation of the translational degrees of freedom in the shock front [1]. This raises an important postulation of detonation ignition of molecular condensed matter being initiated by non-equilibrium kinetic events within the shock front rather than equilibrium thermal molecular dissociation due to the shock temperature. Experimental support for this hypothesis must be derived from observations inside the shock front thereby requiring measurements on the time scale of 10-2-1 ps, which remains beyond the scope of current experimental techniques. However, the recent development of ab initio molecular dynamics simulations offers an alternative approach to elucidate possible mechanisms of detonation ignition. These methods are based on first-principle quantum mechanical calculations that allow for the simulation of chemical processes at the atomic level. Molecular dynamics simulations of bimolecular collisions using density functional theories serve as a most simplified model for shock-induced dissociation [2-3], while multimolecular collisions including neighbourhood molecules serve as a simple model for shock dissociation in bulk liquid [4].
Ab initio molecular dynamics study of the structural and electronic transition in VO2
NASA Astrophysics Data System (ADS)
Plašienka, Dušan; MartoÅák, Roman; Newton, Marcus C.
2017-08-01
The temperature-induced structural and electronic transformation in VO2 between the monoclinic M1 and tetragonal rutile phases was studied by means of ab initio molecular dynamics, based on density functional theory with Hubbard correction (DFT+U ). We compare the structure of both phases, transition temperature and atomic fluctuations both above and below the transition, as well as the phonon density of states and scattering intensity of centroid position, with experimental data. The good quantitative agreement indicates that the chosen DFT+U scheme is able to provide a fairly good description of the energetics of the system. Analysis of the dynamical processes associated with the structural transformation was carried out on the atomic scale by following the time evolution of dimerization amplitudes of vanadium atom chains and the twisting angle of vanadium dimers. The electronic transition was studied by tracing the changes in projected densities of states and their correlation with the evolution of the structural transformation. Our results reveal a strong interconnection between the structural and electronic transformations and show that they take place on the same time scale.
Resolving the HONO formation mechanism in the ionosphere via ab initio molecular dynamic simulations
He, Rongxing; Li, Lei; Zhong, Jie; Zhu, Chongqin; Francisco, Joseph S.; Zeng, Xiao Cheng
2016-01-01
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
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.
NASA Astrophysics Data System (ADS)
Chen, Chen; Arntsen, Christopher; Voth, Gregory A.
2017-10-01
Incorporation of quantum mechanical electronic structure data is necessary to properly capture the physics of many chemical processes. Proton hopping in water, which involves rearrangement of chemical and hydrogen bonds, is one such example of an inherently quantum mechanical process. Standard ab initio molecular dynamics (AIMD) methods, however, do not yet accurately predict the structure of water and are therefore less than optimal for developing force fields. We have instead utilized a recently developed method which minimally biases AIMD simulations to match limited experimental data to develop novel multiscale reactive molecular dynamics (MS-RMD) force fields by using relative entropy minimization. In this paper, we present two new MS-RMD models using such a parameterization: one which employs water with harmonic internal vibrations and another which uses anharmonic water. We show that the newly developed MS-RMD models very closely reproduce the solvation structure of the hydrated excess proton in the target AIMD data. We also find that the use of anharmonic water increases proton hopping, thereby increasing the proton diffusion constant.
Kritayakornupong, Chinapong; Vchirawongkwin, Viwat; Rode, Bernd M
2010-06-01
An ab initio quantum mechanical charge field (QMCF) molecular dynamics simulation has been performed to study the structural and dynamical properties of a dilute aqueous HCl solution. The solute molecule HCl and its surrounding water molecules were treated at Hartree-Fock level in conjunction with Dunning double-zeta plus polarization function basis sets. The simulation predicts an average H-Cl bond distance of 1.28 A, which is in good agreement with the experimental value. The H(HCl)...O(w) and Cl(HCl)...H(w) distances of 1.84 and 3.51 A were found for the first hydration shell. At the hydrogen site of HCl, a single water molecule is the most preferred coordination, whereas an average coordination number of 12 water molecules of the full first shell was observed for the chloride site. The hydrogen bonding at the hydrogen site of HCl is weakened by proton transfer reactions and an associated lability of ligand binding. Two proton transfer processes were observed in the QMCF MD simulation, demonstrating acid dissociation of HCl. A weak structure-making/breaking effect of HCl in water is recognized from the mean residence times of 2.1 and 0.8 ps for ligands in the neighborhood of Cl and H sites of HCl, respectively. Copyright 2009 Wiley Periodicals, Inc.
Hydration of the cyanide ion: an ab initio quantum mechanical charge field molecular dynamics study.
Moin, Syed Tarique; Hofer, Thomas S
2014-12-21
This paper presents an ab initio quantum mechanical charge field molecular dynamics simulation study of the cyanide anion (CN(-)) in aqueous solution where hydrogen bond formation plays a dominant role in the hydration process. Preferential orientation of water hydrogens compared to oxygen atoms was quantified in terms of radial, angular as well as coordination number distributions. All structural results indicate that the water hydrogens are attracted towards CN(-) atoms, thus contributing to the formation of the hydration layer. Moreover, a clear picture of the local arrangement of water molecules around the ellipsoidal CN(-) ion is provided via angular-radial distribution and spatial distribution functions. Apart from the structural analysis, the evaluation of water dynamics in terms of ligand mean residence times and H-bond correlation functions indicates the weak structure making capacity of the CN(-) ion. The similar values of H-bond lifetimes obtained for the NHwat and CHwat bonds indicate an isokinetic behaviour of these H-bonds, since there is a very small difference in the magnitude of the lifetimes. On the other hand, the H-bond lifetimes between water molecules of the hydration shell, and between solute and solvent evidence the slightly stable hydration of the CN(-). Overall, the H-bonding dominates in the hydration process of the cyanide anion enabling it to become soluble in the aqueous environment associated to chemical and biological processes.
Hayes, Robin L; Paddison, Stephen J; Tuckerman, Mark E
2011-06-16
Trifluoromethanesulfonic acid hydrates provide a well-defined system to study proton dissociation and transport in perfluorosulfonic acid membranes, typically used as the electrolyte in hydrogen fuel cells, in the limit of minimal water. The triflic acid pentahydrate crystal (CF(3)SO(3)H·5H(2)O) is sufficiently aqueous that it contains an extended three-dimensional water network. Despite it being extended, however, long-range proton transport along the network is structurally unfavorable and would require considerable rearrangement. Nevertheless, the triflic acid pentahydrate crystal system can provide a clear picture of the preferred locations of local protonic defects in the water network, which provides insights about related structures in the disordered, low-hydration environment of perfluorosulfonic acid membranes. Ab initio molecular dynamics simulations reveal that the proton defect is most likely to transfer to the closest water that has the expected presolvation and only contains water in its first solvation shell. Unlike the tetrahydrate of triflic acid (CF(3)SO(3)H·4H(2)O), there is no evidence of the proton preferentially transferring to a water molecule bridging two of the sulfonate groups. However, this could be an artifact of the crystal structure since the only such water molecule is separated from the proton by long O-O distances. Hydrogen bonding criteria, using the two-dimensional potential of mean force, are extracted. Radial distribution functions, free energy profiles, radii of gyration, and the root-mean-square displacement computed from ab initio path integral molecular dynamics simulations reveal that quantum effects do significantly extend the size of the protonic defect and increase the frequency of proton transfer events by nearly 15%. The calculated IR spectra confirm that the dominant protonic defect mostly exists as an Eigen cation but contains some Zundel ion characteristics. Chain lengths and ring sizes determined from the
Zhao, Jing; Wang, Mei; Fu, Aiyun; Yang, Hongfang; Bu, Yuxiang
2015-08-03
We present an ab initio molecular dynamics (AIMD) simulation study into the transfer dynamics of an excess electron from its cavity-shaped hydrated electron state to a hydrated nucleobase (NB)-bound state. In contrast to the traditional view that electron localization at NBs (G/A/C/T), which is the first step for electron-induced DNA damage, is related only to dry or prehydrated electrons, and a fully hydrated electron no longer transfers to NBs, our AIMD simulations indicate that a fully hydrated electron can still transfer to NBs. We monitored the transfer dynamics of fully hydrated electrons towards hydrated NBs in aqueous solutions by using AIMD simulations and found that due to solution-structure fluctuation and attraction of NBs, a fully hydrated electron can transfer to a NB gradually over time. Concurrently, the hydrated electron cavity gradually reorganizes, distorts, and even breaks. The transfer could be completed in about 120-200 fs in four aqueous NB solutions, depending on the electron-binding ability of hydrated NBs and the structural fluctuation of the solution. The transferring electron resides in the π*-type lowest unoccupied molecular orbital of the NB, which leads to a hydrated NB anion. Clearly, the observed transfer of hydrated electrons can be attributed to the strong electron-binding ability of hydrated NBs over the hydrated electron cavity, which is the driving force, and the transfer dynamics is structure-fluctuation controlled. This work provides new insights into the evolution dynamics of hydrated electrons and provides some helpful information for understanding the DNA-damage mechanism in solution.
Armunanto, Ria; Schwenk, Christian F; Rode, Bernd M
2005-05-26
Structure and dynamics investigations of Ag(+) in 18.6% aqueous ammonia solution have been carried out by means of the ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulation method. The most important region, the first solvation shell, was treated by ab initio quantum mechanics at the Restricted Hartree-Fock (RHF) level using double-zeta plus polarization basis sets for ammonia and plus ECP for Ag(+). For the remaining region in the system, newly constructed three-body corrected potential functions were used. The average composition of the first solvation shell was found to be [Ag(NH(3))(2)(H(2)O)(2.8)](+). No ammonia exchange process was observed for the first solvation shell, whereas ligand exchange processes occurred with a very short mean residence time of 1.1 ps for the water ligands. No distinct second solvation shell was observed in this simulation.
Quarti, Claudio; Mosconi, Edoardo; De Angelis, Filippo
2015-04-14
The last two years have seen the unprecedentedly rapid emergence of a new class of solar cells, based on hybrid organic-inorganic halide perovskites. The success of this class of materials is due to their outstanding photoelectrochemical properties coupled to their low cost, mainly solution-based, fabrication techniques. Solution processed materials are however often characterized by an inherent flexible structure, which is hardly mapped into a single local minimum energy structure. In this perspective, we report on the interplay between structural and electronic properties of hybrid lead iodide perovskites investigated using ab initio molecular dynamics (AIMD) simulations, which allow the dynamical simulation of disordered systems at finite temperature. We compare the prototypical MAPbI3 (MA = methylammonium) perovskite in its cubic and tetragonal structure with the trigonal phase of FAPbI3 (FA = formamidinium), investigating different starting arrangements of the organic cations. Despite the relatively short time scale amenable to AIMD, typically a few tens of ps, this analysis demonstrates the sizable structural flexibility of this class of materials, showing that the instantaneous structure could significantly differ from the time and thermal averaged structure. We also highlight the importance of the organic-inorganic interactions in determining the fluxional properties of this class of materials. A peculiar spatial localization of the valence and conduction band edges is also found, with a dynamics in the range of 0.1 ps, which is associated with the positional dynamics of the organic cations within the cubo-octahedral perovskite cage. This asymmetry in the spatial localization of the band edges is expected to ease exciton dissociation and assist the initial stages of charge separation, possibly constituting one of the key factors for the impressive photovoltaic performances of hybrid lead-iodide perovskites.
NASA Astrophysics Data System (ADS)
Whitfield, T. W.; Crain, J.; Martyna, G. J.
2006-03-01
In order to better understand the physical interactions that stabilize protein secondary structure, the neat liquid state of a peptidic fragment, N-methylacetamide (NMA), was studied using computer simulation. Three different descriptions of the molecular liquid were examined: an empirical force field treatment with classical nuclei, an empirical force field treatment with quantum mechanical nuclei, and an ab initio density functional theory (DFT) treatment. The DFT electronic structure was evaluated using the BLYP approximate functional and a plane wave basis set. The different physical effects probed by the three models, such as quantum dispersion, many-body polarization, and nontrivial charge distributions on the liquid properties, were compared. Much of the structural ordering in the liquid is characterized by hydrogen bonded chains of NMA molecules. Modest structural differences are present among the three models of liquid NMA. The average molecular dipole in the liquid under the ab initio treatment, however, is enhanced by 60% over the gas phase value.
Ab Initio ONIOM-Molecular Dynamics (MD) Study on the Deamination Reaction by Cytidine Deaminase
Matsubara, Toshiaki; Dupuis, Michel; Aida, Misako
2007-08-23
We applied the ONIOM-molecular dynamics (MD) method to the hydrolytic deamination of cytidine by cytidine deaminase, which is an essential step of the activation process of the anticancer drug inside the human body. The direct MD simulations were performed for the realistic model of cytidine deaminase calculating the energy and its gradient by the ab initio ONIOM method on the fly. The ONIOM-MD calculations including the thermal motion show that the neighboring amino acid residue is an important factor of the environmental effects and significantly affects not only the geometry and energy of the substrate trapped in the pocket of the active site but also the elementary step of the catalytic reaction. We successfully simulate the second half of the catalytic cycle, which has been considered to involve the rate-determining step, and reveal that the rate-determing step is the release of the NH3 molecule. TM and MA were supported in part by grants from the Ministry of Education, Culture, Sports, Science and Technology of Japan. MD was supported by the Division of Chemical Sciences, Office of Basic Energy Sciences, and by the Office of Biological and Environmental Research of the U.S. Department of Energy DOE. Battelle operates Pacific Northwest National Laboratory for DOE.
How Is Acetylcholinesterase Phosphonylated by Soman? An Ab Initio QM/MM Molecular Dynamics Study
2015-01-01
Acetylcholinesterase (AChE) is a crucial enzyme in the cholinergic nerve system that hydrolyzes acetylcholine (ACh) and terminates synaptic signals by reducing the effective concentration of ACh in the synaptic clefts. Organophosphate compounds irreversibly inhibit AChEs, leading to irreparable damage to nerve cells. By employing Born–Oppenheimer ab initio QM/MM molecular dynamics simulations with umbrella sampling, a state-of-the-art approach to simulate enzyme reactions, we have characterized the covalent inhibition mechanism between AChE and the nerve toxin soman and determined its free energy profile for the first time. Our results indicate that phosphonylation of the catalytic serine by soman employs an addition–elimination mechanism, which is highly associative and stepwise: in the initial addition step, which is also rate-limiting, His440 acts as a general base to facilitate the nucleophilic attack of Ser200 on the soman’s phosphorus atom to form a trigonal bipyrimidal pentacovalent intermediate; in the subsequent elimination step, Try121 of the catalytic gorge stabilizes the leaving fluorine atom prior to its dissociation from the active site. Together with our previous characterization of the aging mechanism of soman inhibited AChE, our simulations have revealed detailed molecular mechanistic insights into the damaging function of the nerve agent soman. PMID:24786171
Mei, J.; Cooper, B.R.; Hao, Y.G.; Scoy, F.L. Van
1994-12-31
Molecular dynamics simulations have been performed to study thermal expansions of Ni-rich (fcc structure) Ni/Cr alloys (which serve as the basis for practical superalloy systems). This has been done using ab initio interatomic potentials with no experimental input. The coefficient of thermal expansion (CTE) as a function of temperature has been calculated. By admixing Re and Me atoms into fee Ni and the fee alloy system Ni/Cr, additive effects on the thermal expansion have been predicted. While addition of Cr lowers the CTE of Ni, and moderate addition of Mo lowers the CTE of Ni over a wide temperature range, moderate addition of Re raises the CTE of both Ni and Ni/Cr alloys over a significant temperature range. An explanation for the contrasting effect of additive Re on the CTE, based on a one-dimensional atomic chain model, is that the trade-off, between atomic volume effects increasing the CTE over that of pure Ni and pair-potential effects (exemplified by the Grueneisen parameter) decreasing the CTE from that of pure nickel, changes for Re compared to Cr and Mo.
Ab initio path-integral molecular dynamics and the quantum nature of hydrogen bonds
NASA Astrophysics Data System (ADS)
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).
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.
Shimamura, Kohei; Shimojo, Fuyuki; Nakano, Aiichiro; Tanaka, Shigenori
2016-12-14
NH3 is an essential molecule as a nitrogen source for prebiotic amino acid syntheses such as the Strecker reaction. Previous shock experiments demonstrated that meteorite impacts on ancient oceans would have provided a considerable amount of NH3 from atmospheric N2 and oceanic H2O through reduction by meteoritic iron. However, specific production mechanisms remain unclear, and impact velocities employed in the experiments were substantially lower than typical impact velocities of meteorites on the early Earth. Here, to investigate the issues from the atomistic viewpoint, we performed multi-scale shock technique-based ab initio molecular dynamics simulations. The results revealed a rapid production of NH3 within several picoseconds after the shock, indicating that shocks with greater impact velocities would provide further increase in the yield of NH3. Meanwhile, the picosecond-order production makes one expect that the important nitrogen source precursors of amino acids were obtained immediately after the impact. It was also observed that the reduction of N2 proceeded according to an associative mechanism, rather than a dissociative mechanism as in the Haber-Bosch process.
Simulating ionic thermal trasport by equilibrium ab-initio molecular dynamics
NASA Astrophysics Data System (ADS)
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.
SPASER as a complex system: femtosecond dynamics traced by ab-initio simulations
NASA Astrophysics Data System (ADS)
Totero Gongora, Juan Sebastian; Miroshnichenko, Andrey E.; Kivshar, Yuri S.; Fratalocchi, Andrea
2016-03-01
Integrating coherent light sources at the nanoscale with spasers is one of the most promising applications of plasmonics. A spaser is a nano-plasmonic counterpart of a laser, with photons replaced by surface plasmon polaritons and the resonant cavity replaced by a nanoparticle supporting localized plasmonic modes. Despite the large body of experimental and theoretical studies, the understanding of the fundamental properties of the spaser emission is still challenging. In this work, we investigated the ultrafast dynamics of the emission from a core-shell spaser by developing a rigorous first-principle numerical model. Our results show that the spaser is a highly nonlinear system with many interacting degrees of freedom, whose emission sustain a rich manifold of different spatial phases. In the regime of strong interaction we observed that the spaser emission manifests an irreversible ergodic evolution, where energy is equally shared among all the available degrees of freedom. Under this condition, the spaser generates ultrafast vortex lasing modes that are spinning on the femtosecond scale, acquiring the character of a nanoparticle with an effective spin. Interestingly, the spin orientation is defined by spontaneous symmetry breaking induced by quantum noise, which is a fundamental component of our ab-initio model. This opens up interesting possibilities of achieving unidirectional emission from a perfectly spherical nanoparticle, stimulating a broad range of applications for nano-plasmonic lasers as unidirectional couplers, random information sources and novel form of photonics neural-networks.
Ab initio molecular dynamics simulations of liquid water using high quality meta-GGA functionals
Ruiz Pestana, Luis; Mardirossian, Narbe; Head-Gordon, Martin; ...
2017-02-27
We have used ab initio molecular dynamics (AIMD) to characterize water properties using two meta-generalized gradient approximation (meta-GGA) functionals, M06-L-D3 and B97M-rV, and compared their performance against a standard GGA corrected for dispersion, revPBE-D3, at ambient conditions (298 K, and 1 g cm–3 or 1 atm). Simulations of the equilibrium density, radial distribution functions, self-diffusivity, the infrared spectrum, liquid dipole moments, and characterizations of the hydrogen bond network show that all three functionals have overcome the problem of the early AIMD simulations that erroneously found ambient water to be highly structured, but they differ substantially among themselves in agreement withmore » experiment on this range of water properties. We show directly using water cluster data up through the pentamer that revPBE-D3 benefits from a cancellation of its intrinsic functional error by running classical trajectories, whereas the meta-GGA functionals are demonstrably more accurate and would require the simulation of nuclear quantum effects to realize better agreement with all cluster and condensed phase properties.« less
Debela, Tekalign T; Wang, X D; Cao, Q P; Zhang, D X; Jiang, J Z
2017-03-14
The crystallization process of liquid metals is studied using ab initio molecular dynamics simulations. The evolution of short-range order during quenching in Pb and Zn liquids is compared with body-centered cubic (bcc) Nb and V, and hexagonal closed-packed (hcp) Mg. We found that the fraction and type of the short-range order depends on the system under consideration, in which the icosahedral symmetry seems to dominate in the body-centered cubic metals. Although the local atomic structures in stable liquids are similar, liquid hcp-like Zn, bcc-like Nb and V can be deeply supercooled far below its melting point before crystallization while the supercooled temperature range in liquid Pb is limited. Further investigations into the nucleation process reveal the process of polymorph selection. In the body-centered cubic systems, the polymorph selection occurs in the supercooled state before the nucleation is initiated, while in the closed-packed systems it starts at the time of onset of crystallization. Atoms with bcc-like lattices in all studied supercooled liquids are always detected before the polymorph selection. It is also found that the bond orientational ordering is strongly correlated with the crystallization process in supercooled Zn and Pb liquids.
Ab Initio Molecular Dynamics of Dimerization and Clustering in Alkali Metal Vapors.
Chaban, Vitaly V; Prezhdo, Oleg V
2016-06-30
Alkali metals are known to form dimers, trimers, and tetramers in their vapors. The mechanism and regularities of this phenomenon characterize the chemical behavior of the first group elements. We report ab initio molecular dynamics (AIMD) simulations of the alkali metal vapors and characterize their structural properties, including radial distribution functions and atomic cluster size distributions. AIMD confirms formation of Men, where n ranges from 2 to 4. High pressure sharply favors larger structures, whereas high temperature decreases their fraction. Heavier alkali metals maintain somewhat larger fractions of Me2, Me3, and Me4, relative to isolated atoms. A single atom is the most frequently observed structure in vapors, irrespective of the element and temperature. Due to technical difficulties of working with high temperatures and pressures in experiments, AIMD is the most affordable method of research. It provides valuable understanding of the chemical behavior of Li, Na, K, Rb, and Cs, which can lead to development of new chemical reactions involving these metals.
Ab initio molecular dynamics of the reaction of quercetin with superoxide radical
NASA Astrophysics Data System (ADS)
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.
Xu, Cong-Qiao; Lee, Mal-Soon; Wang, Yang-Gang; Cantu, David C; Li, Jun; Glezakou, Vassiliki-Alexandra; Rousseau, Roger
2017-02-28
The structure, composition, and atomic distribution of nanoalloys under operating conditions are of significant importance for their catalytic activity. In the present work, we use ab initio molecular dynamics simulations to understand the structural behavior of Au-Pd nanoalloys supported on rutile TiO2 under different conditions. We find that the Au-Pd structure is strongly dependent on the redox properties of the support, originating from strong metal-support interactions. Under reducing conditions, Pd atoms are inclined to move toward the metal/oxide interface, as indicated by a significant increase of Pd-Ti bonds. This could be attributed to the charge localization at the interface that leads to Coulomb attractions to positively charged Pd atoms. In contrast, under oxidizing conditions, Pd atoms would rather stay inside or on the exterior of the nanoparticle. Moreover, Pd atoms on the alloy surface can be stabilized by hydrogen adsorption, forming Pd-H bonds, which are stronger than Au-H bonds. Our work offers critical insights into the structure and redox properties of Au-Pd nanoalloy catalysts under working conditions.
NASA Astrophysics Data System (ADS)
Shimamura, Kohei; Shimojo, Fuyuki; Nakano, Aiichiro; Tanaka, Shigenori
2016-12-01
NH3 is an essential molecule as a nitrogen source for prebiotic amino acid syntheses such as the Strecker reaction. Previous shock experiments demonstrated that meteorite impacts on ancient oceans would have provided a considerable amount of NH3 from atmospheric N2 and oceanic H2O through reduction by meteoritic iron. However, specific production mechanisms remain unclear, and impact velocities employed in the experiments were substantially lower than typical impact velocities of meteorites on the early Earth. Here, to investigate the issues from the atomistic viewpoint, we performed multi-scale shock technique-based ab initio molecular dynamics simulations. The results revealed a rapid production of NH3 within several picoseconds after the shock, indicating that shocks with greater impact velocities would provide further increase in the yield of NH3. Meanwhile, the picosecond-order production makes one expect that the important nitrogen source precursors of amino acids were obtained immediately after the impact. It was also observed that the reduction of N2 proceeded according to an associative mechanism, rather than a dissociative mechanism as in the Haber-Bosch process.
Surface electron density models for accurate ab initio molecular dynamics with electronic friction
NASA Astrophysics Data System (ADS)
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.
An ab initio molecular dynamics study of iron phases at high pressure and temperature
NASA Astrophysics Data System (ADS)
Belonoshko, A. B.; Arapan, S.; Rosengren, A.
2011-12-01
The crystal structure of iron, the major component of the Earth’s inner core (IC), is unknown for the IC high pressure (P; 3.3-3.6 Mbar) and temperature (T; 5000-7000 K). There is mounting evidence that the hexagonal close-packed (hcp) phase of iron, stable at the high P of the IC and a low T, might be unstable under the IC conditions due to the impact of high T and impurities. Experiments at the IC P and T are difficult and do not provide a conclusive answer as regards the iron stability at the pressure of the IC and temperatures close to the iron melting curve. Recent theory provides contradictory results regarding the nature of the stable Fe phase. We investigated the possibility of body-centered cubic (bcc) phase stabilization at the P and T in the vicinity of the Fe melting curve by using ab initio molecular dynamics. Thermodynamic calculations, relying on the model of uncorrelated harmonic oscillators, provide nearly identical free energies within the error bars of our calculations. However, direct simulation of iron crystallization demonstrates that liquid iron freezes in the bcc structure at the P of the IC and T = 6000 K. All attempts to grow the hcp phase from the liquid failed. The mechanism of bcc stabilization is explained. This resolves most of the earlier confusion.
Philips, Adam; Marchenko, Alex; Truflandier, Lionel A; Autschbach, Jochen
2017-09-12
Quadrupolar NMR relaxation rates are computed for (17)O and (2)H nuclei of liquid water, and of (23)Na(+), and (35)Cl(-) in aqueous solution via Kohn-Sham (KS) density functional theory ab initio molecular dynamics (aiMD) and subsequent KS electric field gradient (EFG) calculations along the trajectories. The calculated relaxation rates are within about a factor of 2 of experimental results and improved over previous aiMD simulations. The relaxation rates are assessed with regard to the lengths of the simulations as well as configurational sampling. The latter is found to be the more limiting factor in obtaining good statistical sampling and is improved by averaging over many equivalent nuclei of a system or over several independent trajectories. Further, full periodic plane-wave basis calculations of the EFGs are compared with molecular-cluster atomic-orbital basis calculations. The two methods deliver comparable results with nonhybrid functionals. With the molecular-cluster approach, a larger variety of electronic structure methods is available. For chloride, the EFG computations benefit from using a hybrid KS functional.
NASA Astrophysics Data System (ADS)
Debela, Tekalign T.; Wang, X. D.; Cao, Q. P.; Zhang, D. X.; Jiang, J. Z.
2017-05-01
The crystallization process of liquid metals is studied using ab initio molecular dynamics simulations. The evolution of short-range order during quenching in Pb and Zn liquids is compared with body-centered cubic (bcc) Nb and V, and hexagonal closed-packed (hcp) Mg. We found that the fraction and type of the short-range order depends on the system under consideration, in which the icosahedral symmetry seems to dominate in the body-centered cubic metals. Although the local atomic structures in stable liquids are similar, liquid hcp-like Zn, bcc-like Nb and V can be deeply supercooled far below its melting point before crystallization while the supercooled temperature range in liquid Pb is limited. Further investigations into the nucleation process reveal the process of polymorph selection. In the body-centered cubic systems, the polymorph selection occurs in the supercooled state before the nucleation is initiated, while in the closed-packed systems it starts at the time of onset of crystallization. Atoms with bcc-like lattices in all studied supercooled liquids are always detected before the polymorph selection. It is also found that the bond orientational ordering is strongly correlated with the crystallization process in supercooled Zn and Pb liquids.
HCO3(-) formation from CO2 at high pH: ab initio molecular dynamics study.
Stirling, András
2011-12-15
Ab initio molecular dynamics simulations have been performed to study the dissolution of CO2 in water at high pH. The CO2 + OH(-) --> HCO3(-) forward and the HCO3(-) --> CO2 + OH(-) reverse paths have been simulated by employing the metadynamics technics. We have found that the free energy barrier along the forward direction is predominantly hydration related and significantly entropic in origin, whereas the backward barrier is primarily enthalpic. The main motifs in the forward mechanism are the structural diffusion of the hydroxyl ion to the first hydration sphere of CO2, its desolvation, and the C-O bond formation in concert with the CO2 bending within the hydrate cavity. In the reverse reaction, the origin of the barrier is the rupture of the strong C-O(H) bond. The present findings support the notion that the free energy barrier of the bicarbonate formation is strongly solvation related but provide also additional mechanistic details at the molecular level.
Shimamura, Kohei; Shimojo, Fuyuki; Nakano, Aiichiro; Tanaka, Shigenori
2016-01-01
NH3 is an essential molecule as a nitrogen source for prebiotic amino acid syntheses such as the Strecker reaction. Previous shock experiments demonstrated that meteorite impacts on ancient oceans would have provided a considerable amount of NH3 from atmospheric N2 and oceanic H2O through reduction by meteoritic iron. However, specific production mechanisms remain unclear, and impact velocities employed in the experiments were substantially lower than typical impact velocities of meteorites on the early Earth. Here, to investigate the issues from the atomistic viewpoint, we performed multi-scale shock technique-based ab initio molecular dynamics simulations. The results revealed a rapid production of NH3 within several picoseconds after the shock, indicating that shocks with greater impact velocities would provide further increase in the yield of NH3. Meanwhile, the picosecond-order production makes one expect that the important nitrogen source precursors of amino acids were obtained immediately after the impact. It was also observed that the reduction of N2 proceeded according to an associative mechanism, rather than a dissociative mechanism as in the Haber-Bosch process. PMID:27966594
Ab initio molecular dynamics study of liquid sodium and cesium up to critical point
Yuryev, Anatoly A.; Gelchinski, Boris R.
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.
Ab initio molecular dynamics study of liquid sodium and cesium up to critical point
NASA Astrophysics Data System (ADS)
Yuryev, Anatoly A.; Gelchinski, Boris R.
2015-08-01
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.
Rowley, Christopher N; Woo, Tom K
2007-01-14
Transition path sampling is an innovative method for focusing a molecular dynamics simulation on a reactive event. Although transition path sampling methods can generate an ensemble of reactive trajectories, an initial reactive trajectory must be generated by some other means. In this paper, the authors have evaluated three methods for generating initial reactive trajectories for transition path sampling with ab initio molecular dynamics. The authors have tested each of these methods on a set of chemical reactions involving the breaking and making of covalent bonds: the 1,2-hydrogen elimination in the borane-ammonia adduct, a tautomerization, and the Claisen rearrangement. The first method is to initiate trajectories from the potential energy transition state, which was effective for all reactions in the test set. Assigning atomic velocities found using normal mode analysis greatly improved the success of this method. The second method uses a high temperature molecular dynamics simulation and then iteratively reduces the total energy of the simulation until a low temperature reactive trajectory is found. This was effective in generating a low temperature trajectory from an initial trajectory run at 3000 K of the tautomerization reaction, although it failed for the other two. The third uses an orbital based bias potential to find a reactive trajectory and uses this trajectory to initiate an unbiased trajectory. The authors found that a highest occupied molecular orbital-lowest unoccupied molecular orbital bias could be used to find a reactive trajectory for the Claisen rearrangement, although it failed for the other two reactions. These techniques will help make it practical to use transition path sampling to study chemical reaction mechanisms that involve bond breaking and forming.
Closser, Kristina D; Gessner, Oliver; Head-Gordon, Martin
2014-04-07
The dynamics resulting from electronic excitations of helium clusters were explored using ab initio molecular dynamics. The simulations were performed with configuration interaction singles and adiabatic classical dynamics coupled to a state-following algorithm. 100 different configurations of He7 were excited into the 2s and 2p manifold for a total of 2800 trajectories. While the most common outcome (90%) was complete fragmentation to 6 ground state atoms and 1 excited state atom, 3% of trajectories yielded bound, He2(*), and <0.5% yielded an excited helium trimer. The nature of the dynamics, kinetic energy release, and connections to experiments are discussed.
NASA Astrophysics Data System (ADS)
Sun, Tao; Zhang, Dong-Bo; Wentzcovitch, Renata M.
2014-03-01
The stability of cubic CaSiO3 perovskite (CaPv) at high temperatures and pressures is investigated by vibrational normal-mode analysis. We compute power spectra of mode autocorrelation functions using a recently developed hybrid approach combining ab initio molecular dynamics with lattice dynamics. These power spectra, together with the probability distributions of atomic displacements, indicate that cubic CaPv is stabilized at T ˜600 K and P ˜ 26 GPa. We then utilize the concept of phonon quasiparticles to characterize the vibrational properties of cubic CaPv at high temperature and obtain anharmonic phonon dispersions through the whole Brillouin zone. Such temperature-dependent phonon dispersions pave the way for more accurate calculations of free-energy, thermodynamic, and thermoelastic properties of cubic CaPv at Earth's lower mantle conditions.
NASA Astrophysics Data System (ADS)
Lahnsteiner, Jonathan; Kresse, Georg; Kumar, Abhinav; Sarma, D. D.; Franchini, Cesare; Bokdam, Menno
2016-12-01
The high efficiency of lead organo-metal-halide perovskite solar cells has raised many questions about the role of the methylammonium (MA) molecules in the Pb-I framework. Experiments indicate that the MA molecules are able to "freely" spin around at room temperature even though they carry an intrinsic dipole moment. We have performed large supercell (2592 atoms) finite-temperature ab initio molecular dynamics calculations to study the correlation between the molecules in the framework. An underlying long-range antiferroelectric ordering of the molecular dipoles is observed. The dynamical correlation between neighboring molecules shows a maximum around room temperature in the mid-temperature phase. In this phase, the rotations are slow enough to (partially) couple to neighbors via the Pb-I cage. This results in a collective motion of neighboring molecules in which the cage acts as the mediator. At lower and higher temperatures, the motions are less correlated.
Jakse, N.; Pasturel, A.
2014-12-21
In the present work, the structural and dynamic properties of liquid and undercooled boron are investigated by means of ab initio molecular dynamics simulation. Our results show that both liquid and undercooled states present a well pronounced short-range order (SRO) mainly due to the formation of inverted umbrella structural units. Moreover, we observe the development of a medium-range order (MRO) in the undercooling regime related to the increase of inverted umbrella structural units and of their interconnection as the temperature decreases. We also evidence that this MRO leads to a partial crystallization in the β-rhombohedral crystal below T = 1900 K. Finally, we discuss the role played by the SRO and MRO in the nearly Arrhenius evolution of the diffusion and the non-Arrhenius temperature dependence of the shear viscosity, in agreement with the experiment.
An analysis of hydrated proton diffusion in ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Tse, Ying-Lung Steve; Knight, Chris; Voth, Gregory A.
2015-01-01
A detailed understanding of the inherently multiscale proton transport process raises a number of scientifically challenging questions. For example, there remain many (partially addressed) questions on the molecular mechanism for long-range proton migration and the potential for the formation of long-lived traps giving rise to burst-and-rest proton dynamics. Using results from a sizeable collection of ab initio molecular dynamics (AIMD) simulations (totaling ˜2.7 ns) with various density functional approximations (Becke-Lee-Yang-Parr (BLYP), BLYP-D3, Hamprecht-Cohen-Tozer-Handy, B3LYP) and temperatures (300-330 K), equilibrium and dynamical properties of one excess proton and 128 water molecules are studied. Two features in particular (concerted hops and weak hydrogen-bond donors) are investigated to identify modes in the system that are strongly correlated with the onset of periods of burst-and-rest dynamics. The question of concerted hops seeks to identify those time scales over which long-range proton transport can be classified as a series of sequential water hopping events or as a near-simultaneous concerted process along compressed water wires. The coupling of the observed burst-and-rest dynamics with motions of a fourth neighboring water molecule (a weak hydrogen-bond donor) solvating the protonated water molecule is also investigated. The presence (absence) of hydrogen bonds involving this fourth water molecule before and after successful proton hopping events is found to be strongly correlated with periods of burst (rest) dynamics (and consistent with pre-solvation concepts). By analyzing several realizations of the AIMD trajectories on the 100-ps time scale, convergence of statistics can be assessed. For instance, it was observed that the probability for a fourth water molecule to approach the hydronium, if not already proximal at the beginning of the lifetime of the hydronium, is very low, indicative of the formation of stable void regions. Furthermore
An analysis of hydrated proton diffusion in ab initio molecular dynamics
Tse, Ying-Lung Steve; Voth, Gregory A.; Knight, Chris
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
NASA Astrophysics Data System (ADS)
Sun, Bo; Liu, Haifeng; Song, Haifeng
2015-06-01
Based on the non-local van der Waals density functional (vdW-DF)+ U scheme, we carry out the ab initio molecular dynamics study of the interaction dynamics for H2 molecules impingement against Pu-oxides and mononitride surfaces. We show that except for the weak physisorption, both PuO2 and PuN surfaces are so difficult of access that almost all of H2 molecules will bounce back to the vacuum when their initial kinetic energies are not sufficient. Although the dissociative adsorption of H2 on PuO2 surfaces is found to be exothermic, the collision-induced dissociation barriers of H2 are very high (up to 2.2 eV). However, PuO2 overlayer on Pu-metal can be reduced to α-Pu2O3 drived by oxygen-lean conditions, and H2 can penetrate and diffuse in α-Pu2O3 easily. As a result, α-Pu2O3 can promote the hydriding process of Pu. Unlike PuO2, PuN is found to be one kind of stable and uniform passivation layer against Pu-hydriding. Specifically, the incorporation of PuN and H-atom is proven to be thermodynamically unstable. Overall, our current study reveals the mechanical and chemical resistances of Pu-oxide and Pu-nitride to hydrogen corrosion, which have strong implications to the understanding of the surface corrosion and passivation of Pu metal. This work was supported by the FDST of CAEP under Grant No. 9090707.
Diffusion within α-CuI studied using ab initio molecular dynamics simulations
NASA Astrophysics Data System (ADS)
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.
Han, Chen; Zhao, Juan; Yang, Fan; Wang, Jianping
2013-07-25
N-Acylglucosamine is an important component in many oligosaccharides in eukaryotes, where it plays a very important biological role. Located between a glucose ring and an alkyl group of such species is an amide unit (-CONH-), which exhibits an infrared absorption band, mainly due to the C═O stretching, in the region of 1600-1700 cm(-1), similar to the amide-I band found in polypeptides. In this work, vibrational properties of such an "amide-I mode" in N-propionyl-d-glucosamine (GlcNPr) are examined in three typical solvents (water, methanol, and dimethylsulfoxide) by using steady-state infrared and femtosecond infrared dispersed pump-probe spectroscopies. As a result of solute-solvent interactions, multiple structured GlcNPr-solvent clusters are formed in water and methanol but are unlikely in dimethylsulfoxide. The vibrational relaxation rate of the amide-I mode is slightly frequency-dependent, supporting the presence of multiple solvated structures. Further, the amide-I lifetime is significantly shorter in GlcNPr than that in a well-known monopeptide, N-methylacetamide, which can be attributed to the presence of additional downstream vibrational modes caused by the sugar unit. Ab initio molecular dynamics simulations are used to reveal microscopic details of the first solvation shell of GlcNPr. Our results demonstrate that the amide-I mode in glucosamine exhibits both structural and solvent sensitivities that can be used to characterize the three-dimensional arrangement of sugar residues and their structural dynamics in glycopeptides.
Tachikawa, Hiroto
2006-01-12
Ionization processes of chlorobenzene-ammonia 1:1 complex (PhCl-NH3) have been investigated by means of full dimensional direct ab initio molecular dynamics (MD) method, static ab initio calculations, and density functional theory (DFT) calculations. The static ab initio and DFT calculations of neutral PhCl-NH3 complex showed that one of the hydrogen atoms of NH3 orients toward a carbon atom in the para-position of PhCl. The dynamics calculation for ionization of PhCl-NH3 indicated that two reaction channels are competitive with each other as product channels: one is an intramolecular SN2 reaction expressed by a reaction scheme [PhCl-NH3]+-->SN2 intermediate complex-->PhNH3++Cl, and the other is ortho-NH3 addition complex (ortho complex) in which NH3 attacks the ortho-carbon of PhCl+ and the trajectory leads to a bound complex expressed by (PhCl-NH3)+. The mechanism of the ionization of PhCl-NH3 is discussed on the basis of the theoretical results.
Alonso, J L; Andrade, X; Echenique, P; Falceto, F; Prada-Gracia, D; Rubio, A
2008-08-29
A new "on the fly" method to perform Born-Oppenheimer ab initio molecular dynamics (AIMD) simulations is presented. Inspired by Ehrenfest dynamics in time-dependent density functional theory, the electronic orbitals are evolved by a Schrödinger-like equation, where the orbital time derivative is multiplied by a parameter. This parameter controls the time scale of the fictitious electronic motion and speeds up the calculations with respect to standard Ehrenfest dynamics. In contrast with other methods, wave function orthogonality needs not be imposed as it is automatically preserved, which is of paramount relevance for large-scale AIMD simulations.
An ab initio study of the structure and dynamics of bulk liquid Ag and its liquid-vapor interface
NASA Astrophysics Data System (ADS)
Gonzalez Del Rio, Beatriz; Gonzalez Tesedo, Luis Enrique; Gonzalez Fernandez, David Jose
Several static and dynamic properties of bulk liquid Ag at a thermodynamic state near its triple point have been calculated by means of ab initio molecular dynamics simulations. The calculated static structure shows a very good agreement with the available experimental data. The dynamical structure reveals collective density excitations with an associated dispersion relation which points to a small positive dispersion. Results are also reported at a slightly higher temperature in order to study the structure of the free liquid surface. The ionic density profile shows an oscillatory behaviour with two different wavelenghts, as the spacing between the outer and first inner layer is different from that between the other inner layers.
Pluharova, Eva; Baer, Marcel D.; Mundy, Christopher J.; Schmidt, Burkhard; Jungwirth, Pavel
2014-07-03
Understanding specific ion effects on proteins remains a considerable challenge. N-methylacetamide serves as a useful proxy for the protein backbone that can be well characterized both experimentally and theoretically. The spectroscopic signatures in the amide I band reflecting the strength of the interaction of alkali cations and alkali earth dications with the carbonyl group remain difficult to assign and controversial to interpret. Herein, we directly compute the IR shifts corresponding to the binding of either sodium or calcium to aqueous N-methylacetamide using ab initio molecular dynamics simulations. We show that the two cations interact with aqueous N-methylacetamide with different affinities and in different geometries. Since sodium exhibits a weak interaction with the carbonyl group, the resulting amide I band is similar to an unperturbed carbonyl group undergoing aqueous solvation. In contrast, the stronger calcium binding results in a clear IR shift with respect to N-methylacetamide in pure water. Support from the Czech Ministry of Education (grant LH12001) is gratefully acknowledged. EP thanks the International Max-Planck Research School for support and the Alternative Sponsored Fellowship program at Pacific Northwest National Laboratory (PNNL). PJ acknowledges the Praemium Academie award from the Academy of Sciences. Calculations of the free energy profiles were made possible through generous allocation of computer time from the North-German Supercomputing Alliance (HLRN). Calculations of vibrational spectra were performed in part using the computational resources in the National Energy Research Supercomputing Center (NERSC) at Lawrence Berkeley National Laboratory. This work was supported by National Science Foundation grant CHE-0431312. CJM is supported by the U.S. Department of Energy`s (DOE) Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. PNNL is operated for the Department of Energy by Battelle. MDB is
NASA Astrophysics Data System (ADS)
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.
Nesbitt, David J; Dong, Feng
2008-04-21
Large-amplitude tunneling in vinyl radical over a C2v planar transition state involves CCH bending excitation coupled to all other internal coordinates, resulting in a significant dependence of barrier height and shape on vibrational degrees of freedom at the zero-point level. An ab initio potential surface for vinyl radical has been calculated at the CCSD(T) level (AVnZ; n=2, 3, 4, 5) for vibrationally adiabatic 1D motion along the planar CCH bending tunneling coordinate, extrapolated to the complete basis set (CBS) limit and corrected for anharmonic zero-point effects. The polyatomic reduced moment of inertia is calculated explicitly as a function of tunneling coordinate, with eigenvalues and tunneling splittings obtained from numerical solution of the resulting 1D Schrödinger equation. Linear scaling of the CBS potential to match predicted and observed tunneling splittings empirically yields an adiabatic barrier height of DeltaEadiab=1696(20) cm(-1) which, when corrected for zero-point energy contributions, translates into an effective barrier of DeltaEeff=1602(20) cm(-1) consistent with estimates (DeltaE=1580(100) cm(-1)) by Tanaka and coworkers [J. Chem. Phys., 2004, 120, 3604-3618]. These zero-point-corrected potential surfaces are used to predict tunneling dynamics in vibrationally excited states of vinyl radical, providing strong support for previous jet-cooled high-resolution infrared studies [Dong et al., J. Phys. Chem. A, 2006, 110, 3059-3070] in the symmetric CH2 stretch mode.
Silicate-Metal Partitioning of Trace Elements: An Exploratory Ab Initio Molecular Dynamics Study
NASA Astrophysics Data System (ADS)
Künzel, D.; Jahn, S.
2014-12-01
Partition coefficients of trace elements are very important for the reconstruction of Earth formation and evolution processes. As such processes typically take place at extreme conditions of pressure and temperature, it is still challenging to obtain experimental data. However, recent developments in super-computing facilities and in computational methods have made it possible to obtain supplementing information on melts and element partitioning from ab initio atomistic calculations. The model system used in this pilot study consists of two different melts: a simple Fe-Ni alloy representing the metal and a silicate phase with a varying ratio of Fe and Mg ((Fe,Mg)2SiO4). Traces of Ni or Cr are added to each system. Molecular dynamics simulations based on density functional theory are initially run at 2500 K and ambient pressure, using the CPMD and CP2K software packages. Conditions are chosen so that the results can be compared to available experimental data in order to assess the feasibility of the approach and the quality of its results. However, preliminary results at increased pressure and temperature conditions that are more relevant for core formation will be presented as well. The results of the calculations include information on the melt structure, such as coordination environment, nearest neighbor distance and x-ray diffraction structure factors. The calculations at ambient pressure show that the behavior of Ni atoms in the silicate melt shows similarities to Mg and differs clearly from Fe. First results with a Cr trace show that it resembles Fe rather than Ni. Furthermore, thermodynamic integration is able to provide thermodynamic information about the exchange of trace elements between both phases. It is possible to obtain the energy difference connected to this exchange, which can then be used to estimate partition factors. First results on the Ni partitioning will be presented.
2011-01-01
We have implemented the accelerated molecular dynamics approach (Hamelberg, D.; Mongan, J.; McCammon, J. A. J. Chem. Phys. 2004, 120 (24), 11919) in the framework of ab initio MD (AIMD). Using three simple examples, we demonstrate that accelerated AIMD (A-AIMD) can be used to accelerate solvent relaxation in AIMD simulations and facilitate the detection of reaction coordinates: (i) We show, for one cyclohexane molecule in the gas phase, that the method can be used to accelerate the rate of the chair-to-chair interconversion by a factor of ∼1 × 105, while allowing for the reconstruction of the correct canonical distribution of low-energy states; (ii) We then show, for a water box of 64 H2O molecules, that A-AIMD can also be used in the condensed phase to accelerate the sampling of water conformations, without affecting the structural properties of the solvent; and (iii) The method is then used to compute the potential of mean force (PMF) for the dissociation of Na−Cl in water, accelerating the convergence by a factor of ∼3−4 compared to conventional AIMD simulations.(2) These results suggest that A-AIMD is a useful addition to existing methods for enhanced conformational and phase-space sampling in solution. While the method does not make the use of collective variables superfluous, it also does not require the user to define a set of collective variables that can capture all the low-energy minima on the potential energy surface. This property may prove very useful when dealing with highly complex multidimensional systems that require a quantum mechanical treatment. PMID:21494425
Self-Assembly and Dynamics of Organic 2D Molecular Sieves: Ab Initio and Molecular Dynamics Studies
NASA Astrophysics Data System (ADS)
St. John, Alexander; Wexler, Carlos
2015-03-01
Spontaneous molecular self-assembly is a promising route for bottom-up manufacturing of two-dimensional (2D) nanostructures with specific topologies on atomically flat surfaces. Of particular interest is the possibility of selective lock-and-key interaction of guest molecules inside cavities formed by complex self-assembled host structures. Our host structure is a monolayer consisting of interdigitated 1,3,5-tristyrylbenzene substituted by alkoxy peripheral chains containing n = 6, 8, 10, 12, or 14 carbon atoms (TSB3,5-C n) deposited on a highly ordered pyrolytic graphite (HOPG) surface. Using ab initio methods from quantum chemistry and molecular dynamics simulations, we construct and analyze the structure and functionality of the TSB3,5-C n monolayer as a molecular sieve. Supported by ACS-PRF 52696-ND5.
NASA Astrophysics Data System (ADS)
Pietrucci, Fabio; Andreoni, Wanda
2011-08-01
Social permutation invariant coordinates are introduced describing the bond network around a given atom. They originate from the largest eigenvalue and the corresponding eigenvector of the contact matrix, are invariant under permutation of identical atoms, and bear a clear signature of an order-disorder transition. Once combined with ab initio metadynamics, these coordinates are shown to be a powerful tool for the discovery of low-energy isomers of molecules and nanoclusters as well as for a blind exploration of isomerization, association, and dissociation reactions.
Structure and dynamics of the Lu2Si2O7 lattice: Ab initio calculation
NASA Astrophysics Data System (ADS)
Nazipov, D. V.; Nikiforov, A. E.
2017-01-01
The ab initio calculations have been carried out for the crystal structure and Raman spectrum of a single crystal of lutetium pyrosilicate Lu2Si2O7. The types of fundamental vibrations and their frequencies and intensities in the Raman spectrum for two polarizations of the crystal have been determined. The calculations have been performed within the framework of the density functional theory (DFT) using the hybrid functionals. The ions involved in the vibrations have been identified using the method of isotopic substitution. The results of the calculations are in good agreement with the experiment.
Pietrucci, Fabio; Andreoni, Wanda
2011-08-19
Social permutation invariant coordinates are introduced describing the bond network around a given atom. They originate from the largest eigenvalue and the corresponding eigenvector of the contact matrix, are invariant under permutation of identical atoms, and bear a clear signature of an order-disorder transition. Once combined with ab initio metadynamics, these coordinates are shown to be a powerful tool for the discovery of low-energy isomers of molecules and nanoclusters as well as for a blind exploration of isomerization, association, and dissociation reactions.
Icosahedral short-range order in amorphous Cu80Si20 by ab initio molecular dynamics simulation study
Wu, S.; Kramer, Matthew J.; Fang, Xiaowei; Wang, Shy-Guey; Wang, Cai-Zhuang; Ho, Kai-Ming; Ding, Z.J.; Chen, L.Y.
2012-04-26
Short-range order in liquid and amorphous structures of Cu80Si20 is studied by ab initio molecular dynamics simulations. We performed the simulations at 1140 and 300 K respectively to investigate the local structure change from liquid to amorphous. The result of structure factor in comparison with experimental data indicates that our simulation of amorphous Cu80Si20 is reliable. By using the bond-angle distribution function, Honeycutt–Andersen index, Voronoi tessellation method, and the atomistic cluster alignment method, the icosahedral short-range order in the system is revealed. Strong Cu–Si interaction was also observed.
NASA Astrophysics Data System (ADS)
Chakraborty, S.; Boolchand, P.; Micoulaut, M.
2017-09-01
We investigate the amorphous GexS100 -x (with 10 ≤x ≤40 ) system from ab initio simulations. Results show a very good agreement with experimental findings from diffraction and the topology of the obtained structural models is further analyzed and compared with the selenide analog. Differences emerge, however, from a detailed molecular dynamics analysis showing that the ring statistics and the homopolar defects do not evolve similarly. The findings are also connected to rigidity theory, which provides a topological approach to decoding the physics of network glasses, and the effects of composition and temperature are analyzed.
Bylaska, Eric J.; Glass, Kevin A.; Baxter, Douglas J.; Baden, Scott B.; Weare, John H.
2010-09-16
An overview of the parallel algorithms for ab initio molecular dynamics (AIMD) used in the NWChem program package is presented, including recent developments for computing exact exchange. These algorithms make use of a two-dimensional processor geometry proposed by Gygi et al for use in AIMD algorithms. Using this strategy, a highly scalable algorithm for exact exchange has been developed and incorporated it into AIMD. This new algorithm for exact exchange employs an incomplete butterfly to overcome the bottleneck associated with exact exchange term, and it makes judicious use of data replication. Initial testing has shown that this algorithm can scale to over 20,000 CPUs even for modest size simulation.
NASA Astrophysics Data System (ADS)
Koura, Akihide; Shimojo, Fuyuki
2017-08-01
We have investigated the pressure dependence of the static structure of liquid GeTe based on ab initio molecular dynamics simulations. The pressure range is between ambient pressure and 250 GPa, and their temperatures between 1000 K and 4000 K, which keep the liquid state. In this study, we found two transition stages caused by the compression. At the first stage, below 12 GPa, atomic distances elongate and Peierls-type distortion is dissolved with increasing pressure. At the second stage, above 12 GPa, atomic distances shorten and the electronic states shows metallic.
NASA Astrophysics Data System (ADS)
Kakizaki, Akira; Takayanagi, Toshiyuki; Shiga, Motoyuki
2007-11-01
Path integral molecular dynamics simulations for the H6+ and D6+ cluster cations have been carried out in order to understand the floppy nature of their molecular structure due to quantum-mechanical fluctuation. A full-dimensional analytical potential energy surface for the ground electronic state of H6+ has been developed on the basis of accurate ab initio electronic structure calculations at the CCSD(T)/cc-pVTZ level. It is found that the outer H 2(D 2) nuclei rotate almost freely and that the probability density distributions of the central H 2(D 2) nuclei show strong spatial delocalization.
Moin, Syed Tarique; Lim, Len Herald V; Hofer, Thomas S; Randolf, Bernhard R; Rode, Bernd M
2011-04-18
An ab initio Quantum Mechanical Charge Field Molecular Dynamics Simulation (QMCF MD) was performed to investigate structure and dynamics behavior of hydrated sulfur dioxide (SO(2)) at the Hartree-Fock level of theory employing Dunning DZP basis sets for solute and solvent molecules. The intramolecular structural characteristics of SO(2), such as S═O bond lengths and O═S═O bond angle, are in good agreement with the data available from a number of different experiments. The structural features of the hydrated SO(2) were primarily evaluated in the form of S-O(wat) and O(SO(2))-H(wat) radial distribution functions (RDFs) which gave mean distances of 2.9 and 2.2 Å, respectively. The dynamical behavior characterizes the solute molecule to have structure making properties in aqueous solution or water aerosols, where the hydrated SO(2) can easily get oxidized to form a number of sulfur(VI) species, which are believed to play an important role in the atmospheric processes.
Cragnolini, Tristan; Derreumaux, Philippe; Pasquali, Samuela
2015-06-17
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, the experimental determination of RNA structures through x-ray crystallography and NMR seems to have reached a plateau in the number of structures resolved each year, but as more and more RNA sequences are being discovered, the need for structure prediction tools to complement experimental data is strong. Theoretical approaches to RNA folding have been developed since the late nineties, when the first algorithms for secondary structure prediction appeared. Over the last 10 years a number of prediction methods for 3D structures have been developed, first based on bioinformatics and data-mining, and more recently based on a coarse-grained physical representation of the systems. In this review we are going to present the challenges of RNA structure prediction and the main ideas behind bioinformatic approaches and physics-based approaches. We will focus on the description of the more recent physics-based phenomenological models and on how they are built to include the specificity of the interactions of RNA bases, whose role is critical in folding. Through examples from different models, we will point out the strengths of physics-based approaches, which are able not only to predict equilibrium structures, but also to investigate dynamical and thermodynamical behavior, and the open challenges to include more key interactions ruling RNA folding.
NASA Astrophysics Data System (ADS)
Cragnolini, Tristan; Derreumaux, Philippe; Pasquali, Samuela
2015-06-01
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, the experimental determination of RNA structures through x-ray crystallography and NMR seems to have reached a plateau in the number of structures resolved each year, but as more and more RNA sequences are being discovered, the need for structure prediction tools to complement experimental data is strong. Theoretical approaches to RNA folding have been developed since the late nineties, when the first algorithms for secondary structure prediction appeared. Over the last 10 years a number of prediction methods for 3D structures have been developed, first based on bioinformatics and data-mining, and more recently based on a coarse-grained physical representation of the systems. In this review we are going to present the challenges of RNA structure prediction and the main ideas behind bioinformatic approaches and physics-based approaches. We will focus on the description of the more recent physics-based phenomenological models and on how they are built to include the specificity of the interactions of RNA bases, whose role is critical in folding. Through examples from different models, we will point out the strengths of physics-based approaches, which are able not only to predict equilibrium structures, but also to investigate dynamical and thermodynamical behavior, and the open challenges to include more key interactions ruling RNA folding.
NASA Technical Reports Server (NTRS)
Smith, Grant D.; Jaffe, R. L.; Yoon, D. Y.; Arnold, James O. (Technical Monitor)
1994-01-01
Molecular dynamics simulations of POE melts have been performed utilizing a potential force field parameterized to reproduce conformer energies and rotational energy barriers in dimethoxyethane as determined from ab initio electronic structure calculations. Chain conformations and dimensions of POE from the simulations were found to be in good agreement with predictions of a rotational isomeric state (RIS) model based upon the ab initio conformational. energies. The melt chains were found to be somewhat extended relative to chains at theta conditions. This effect will be discussed in light of neutron scattering experiments which indicate that POE chains are extended in the melt relative to theta solutions. The conformational characteristics of POE chains will also be compared with those of other poly (alkylethers), namely poly(oxymethylene), poly(oxytrimethylene) and poly(oxytetramethylene). Local conformational dynamics were found to be more rapid than in polymethylene. Calculated C-H vector correlation times were found to be in reasonable agreement with experimental values from C-13 NMR spin-lattice relaxation times. The influence of ionic salts on local conformations and dynamics will also be discussed.
Rio, Beatriz G del; González, Luis E
2014-11-19
We have performed a comprehensive study of the properties of liquid Be, Ca and Ba, through the use of orbital free ab initio simulations. To this end we have developed a force-matching method to construct the necessary local pseudopotentials from standard ab initio calculations. The structural magnitudes are analyzed, including the average and local structures and the dynamic properties are studied. We find several common features, like an asymmetric second peak in the structure factor, a large amount of local structures with five-fold symmetry, a quasi-universal behaviour of the single-particle dynamic properties and a large degree of positive dispersion in the propagation of collective density fluctuations, whose damping is dictated by slow thermal relaxations and fast viscoelastic ones. Some peculiarities in the dynamic properties are however observed, like a very high sound velocity and a large violation of the Stokes-Einstein relation for Be, or an extremely high positive dispersion and a large slope in the dispersion relation of shear waves at the onset of the wavevector region where they are supported for Ba.
Ab initio infrared and Raman spectra
NASA Astrophysics Data System (ADS)
Fredkin, Donald R.; Komornicki, Andrew; White, Steven R.; Wilson, Kent R.
1983-06-01
We discuss several ways in which molecular absorption and scattering spectra can be computed ab initio, from the fundamental constants of nature. These methods can be divided into two general categories. In the first, or sequential, type of approach, one first solves the electronic part of the Schrödinger equation in the Born-Oppenheimer approximation, mapping out the potential energy, dipole moment vector (for infrared absorption) and polarizability tensor (for Raman scattering) as functions of nuclear coordinates. Having completed the electronic part of the calculation, one then solves the nuclear part of the problem either classically or quantum mechanically. As an example of the sequential ab initio approach, the infrared and Raman rotational and vibrational-rotational spectral band contours for the water molecule are computed in the simplest rigid rotor, normal mode approximation. Quantum techniques are used to calculate the necessary potential energy, dipole moment, and polarizability information at the equilibrium geometry. A new quick, accurate, and easy to program classical technique involving no reference to Euler angles or special functions is developed to compute the infrared and Raman band contours for any rigid rotor, including asymmetric tops. A second, or simultaneous, type of ab initio approach is suggested for large systems, particularly those for which normal mode analysis is inappropriate, such as liquids, clusters, or floppy molecules. Then the curse of dimensionality prevents mapping out in advance the complete potential, dipole moment, and polarizability functions over the whole space of nuclear positions of all atoms, and a solution in which the electronic and nuclear parts of the Born-Oppenheimer approximation are simultaneously solved is needed. A quantum force classical trajectory (QFCT) molecular dynamic method, based on linear response theory, is described, in which the forces, dipole moment, and polarizability are computed quantum
AB INITIO AND CALPHAD THERMODYNAMICS OF MATERIALS
Turchi, P A
2004-04-14
Ab initio electronic structure methods can supplement CALPHAD in two major ways for subsequent applications to stability in complex alloys. The first one is rather immediate and concerns the direct input of ab initio energetics in CALPHAD databases. The other way, more involved, is the assessment of ab initio thermodynamics {acute a} la CALPHAD. It will be shown how these results can be used within CALPHAD to predict the equilibrium properties of multi-component alloys.
Hammond, Philip S; Wu, Yudong; Harris, Rebecca; Minehardt, Todd J; Car, Roberto; Schmitt, Jeffrey D
2005-01-01
A variety of biologically active small molecules contain prochiral tertiary amines, which become chiral centers upon protonation. S-nicotine, the prototypical nicotinic acetylcholine receptor agonist, produces two diastereomers on protonation. Results, using both classical (AMBER) and ab initio (Car-Parrinello) molecular dynamical studies, illustrate the significant differences in conformational space explored by each diastereomer. As is expected, this phenomenon has an appreciable effect on nicotine's energy hypersurface and leads to differentiation in molecular shape and divergent sampling. Thus, protonation induced isomerism can produce dynamic effects that may influence the behavior of a molecule in its interaction with a target protein. We also examine differences in the conformational dynamics for each diastereomer as quantified by both molecular dynamics methods.
Lee, Mal-Soon; Peter McGrail, B.; Rousseau, Roger; Glezakou, Vassiliki-Alexandra
2015-01-01
The boundary layer at solid-liquid interfaces is a unique reaction environment that poses significant scientific challenges to characterize and understand by experimentation alone. Using ab initio molecular dynamics (AIMD) methods, we report on the structure and dynamics of boundary layer formation, cation mobilization and carbonation under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar) on a prototypical anorthite (001) surface. At low coverage, water film formation is enthalpically favored, but entropically hindered. Simulated adsorption isotherms show that a water monolayer will form even at the low water concentrations of water-saturated scCO2. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies that readily form in the presence of a water monolayer. These results point to a carbonation mechanism that does not require prior carbonic acid formation in the bulk liquid. This work also highlights the modern capabilities of theoretical methods to address structure and reactivity at interfaces of high chemical complexity. PMID:26456362
Kritayakornupong, Chinapong; Vchirawongkwin, Viwat; Hofer, Thomas S; Rode, Bernd M
2008-09-25
The novel ab initio quantum mechanical charge field (QMCF) molecular dynamics simulation at the Hartree-Fock level has been employed to investigate hydration structure and dynamics of hydrogen fluoride in aqueous solution. The average H-F bond length of 0.93 A obtained from the QMCF MD simulation is in good agreement with the experimental data. The HHF...Ow distance of 1.62 A was evaluated for the first hydration shell, and 2.00 A was observed for the FHF...Hw distance. The stability of hydrogen bonding is more pronounced in the hydrogen site of hydrogen fluoride, with a single water molecule in this part of the first hydration shell. A wide range of coordination numbers between 3 and 9 with an average value of 5.6 was obtained for the fluorine site. The force constants of 819.1 and 5.9 N/m were obtained for the HHF-FHF and HHF...Ow interactions, respectively, proving the stability of the nondissociated form of hydrogen fluoride in aqueous solution. The mean residence times of 2.1 and 2.5 ps were determined for ligand exchange processes in the neighborhood of fluorine and hydrogen atoms of hydrogen fluoride, respectively, indicating a weak structure-making effect of hydrogen fluoride in water. The corresponding H-bond lifetimes attribute this effect to the H atom site of HF.
Ganesh, P.; Jiang, D.; Kent, P.R.C.
2011-03-31
Lithium-ion batteries have the potential to revolutionize the transportation industry, as they did for wireless communication. A judicious choice of the liquid electrolytes used in these systems is required to achieve a good balance among high-energy storage, long cycle life and stability, and fast charging. Ethylene-carbonate (EC) and propylene-carbonate (PC) are popular electrolytes. However, to date, almost all molecular-dynamics simulations of these fluids rely on classical force fields, while a complete description of the functionality of Li-ion batteries will eventually require quantum mechanics. We perform accurate ab initio molecular-dynamics simulations of ethylene- and propylene-carbonate with LiPF6 at experimental concentrations to build solvation models which explain available neutron scattering and nuclear magnetic resonance (NMR) results and to compute Li-ion solvation energies and diffusion constants. Our results suggest some similarities between the two liquids as well as some important differences. Simulations also provide useful insights into formation of solid-electrolyte interphases in the presence of electrodes in conventional Li-ion batteries.
Ganesh, Panchapakesan; Jiang, Deen; Kent, Paul R
2011-01-01
Lithium-ion batteries have the potential to revolutionize the transportation industry, as they did for wireless communication. A judicious choice of the liquid electrolytes used in these systems is required to achieve a good balance among high-energy storage, long cycle life and stability, and fast charging. Ethylene-carbonate (EC) and propylene-carbonate (PC) are popular electrolytes. However, to date, almost all molecular-dynamics simulations of these fluids rely on classical force fields, while a complete description of the functionality of Li-ion batteries will eventually require quantum mechanics. We perform accurate ab initio molecular-dynamics simulations of ethylene- and propylene-carbonate with LiPF6 at experimental concentrations to build solvation models which explain available neutron scattering and nuclear magnetic resonance (NMR) results and to compute Li-ion solvation energies and diffusion constants. Our results suggest some similarities between the two liquids as well as some important differences. Simulations also provide useful insights into formation of solid-electrolyte interphases in the presence of electrodes in conventional Li-ion batteries.
Ganesh, P; Jiang, De-en; Kent, P R C
2011-03-31
Lithium-ion batteries have the potential to revolutionize the transportation industry, as they did for wireless communication. A judicious choice of the liquid electrolytes used in these systems is required to achieve a good balance among high-energy storage, long cycle life and stability, and fast charging. Ethylene-carbonate (EC) and propylene-carbonate (PC) are popular electrolytes. However, to date, almost all molecular-dynamics simulations of these fluids rely on classical force fields, while a complete description of the functionality of Li-ion batteries will eventually require quantum mechanics. We perform accurate ab initio molecular-dynamics simulations of ethylene- and propylene-carbonate with LiPF(6) at experimental concentrations to build solvation models which explain available neutron scattering and nuclear magnetic resonance (NMR) results and to compute Li-ion solvation energies and diffusion constants. Our results suggest some similarities between the two liquids as well as some important differences. Simulations also provide useful insights into formation of solid-electrolyte interphases in the presence of electrodes in conventional Li-ion batteries.
NASA Astrophysics Data System (ADS)
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.
Guo, Xun; Zhang, Xitong; Zhao, Shijun; Huang, Qing; Xue, Jianming
2016-01-07
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.
Rodríguez-Santiago, Luis; Alí-Torres, Jorge; Vidossich, Pietro; Sodupe, Mariona
2015-05-28
Several lines of evidence supporting the role of metal ions in amyloid aggregation, one of the hallmarks of Alzheimer's disease (AD), have turned metal ion chelation into a promising therapeutic treatment. The design of efficient chelating ligands requires proper knowledge of the electronic and molecular structure of the complexes formed, including their hydration properties. Among various potential chelators, clioquinol (5-chloro-7-iodo-8-hydroxyquinoline, CQH) has been evaluated with relative success in in vitro experiments and even in phase 2 clinical trials. Clioquinol interacts with Zn(ii) to lead to a binary metal/ligand 1 : 2 stoichiometric complex in which the phenolic group of CQH is deprotonated, resulting in Zn(CQ)2 neutral complexes, to which additional water molecules may coordinate. In the present work, the coordinative properties of clioquinol in aqueous solution have been analyzed by means of static, minimal cluster based DFT calculations and explicit solvent ab initio molecular dynamics simulations. Results from static calculations accounting for solvent effects by means of polarized continuum models suggest that the preferred metal coordination environment is tetrahedral Zn(CQ)2, whereas ab initio molecular dynamics simulations point to quasi degenerate penta Zn(CQ)2(H2O) and hexa Zn(CQ)2(H2O)2 coordinated complexes. The possible reasons for these discrepant results are discussed.
NASA Astrophysics Data System (ADS)
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.
NASA Astrophysics Data System (ADS)
Wang, Liancheng; Tian, Fubo; Feng, Wanxiang; Chen, Changbo; He, Zhi; Ma, Yanming; Cui, Tian; Liu, Bingbing; Zou, Guangtian
2010-04-01
The structural and dynamical properties of phase IV and V of hydrogen sulfide were investigated by means of extensive ab initio molecular dynamics simulations. Starting from an experimental proposal for the structure of phase IV, an Ibca symmetry with a stable hydrogen bonding network is found at 15 GPa and 100 K. Molecular dynamics simulations at increasing temperature and at the pressure of 15 GPa suggest that phase IV will transform to a proton disordered structure at 15 GPa and 350 K. The newfound structure has a hexagonal lattice of P63/mmc symmetry, which is believed to be the remaining crystalline structure of phase V. The high mobility of protons in phase V is believed to be the key point to the dissociation and decomposition of hydrogen sulfide.
An ab initio study of the structure and dynamics of bulk liquid Cd and its liquid-vapor interface.
Calderín, L; González, L E; González, D J
2013-02-13
Several static and dynamic properties of bulk liquid Cd at a thermodynamic state near its triple point have been calculated by means of ab initio molecular dynamics simulations. The calculated static structure shows a very good agreement with the available experimental data. The dynamical structure reveals collective density excitations with an associated dispersion relation which points to a small positive dispersion. Results are also reported for several transport coefficients. Additional simulations have also been performed at a slightly higher temperature in order to study the structure of the free liquid surface. The ionic density profile shows an oscillatory behavior with two different wavelengths, as the spacing between the outer and first inner layer is different from that between the other inner layers. The calculated reflectivity shows a marked maximum whose origin is related to the surface layering, along with a shoulder located at a much smaller wavevector transfer.
NASA Astrophysics Data System (ADS)
Lee, Hee-Seung; Tuckerman, Mark E.
2007-04-01
Dynamical properties of liquid water were studied using Car-Parrinello [Phys. Rev. Lett. 55, 2471 (1985)] ab initio molecular dynamics (AIMD) simulations within the Kohn-Sham (KS) density functional theory employing the Becke-Lee-Yang-Parr exchange-correlation functional for the electronic structure. The KS orbitals were expanded in a discrete variable representation basis set, wherein the complete basis set limit can be easily reached and which, therefore, provides complete convergence of ionic forces. In order to minimize possible nonergodic behavior of the simulated water system in a constant energy (NVE) ensemble, a long equilibration run (30ps) preceded a 60ps long production run. The temperature drift during the entire 60ps trajectory was found to be minimal. The diffusion coefficient [0.055Å2/ps] obtained from the present work for 32 D2O molecules is a factor of 4 smaller than the most up to date experimental value, but significantly larger than those of other recent AIMD studies. Adjusting the experimental result so as to match the finite-sized system used in the present study brings the comparison between theory and experiment to within a factor of 3. More importantly, the system is not observed to become "glassy" as has been reported in previous AIMD studies. The computed infrared spectrum is in good agreement with experimental data, especially in the low frequency regime where the translational and librational motions of water are manifested. The long simulation length also made it possible to perform detailed studies of hydrogen bond dynamics. The relaxation dynamics of hydrogen bonds observed in the present AIMD simulation is slower than those of popular force fields, such as the TIP4P potential, but comparable to that of the TIP5P potential.
Jackson, Bret; Nattino, Francesco; Kroes, Geert-Jan
2014-08-07
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.
Li, Y Q; Zhang, P Y; Han, K L
2015-03-28
A global many-body expansion potential energy surface is reported for the electronic ground state of CH2 (+) by fitting high level ab initio energies calculated at the multireference configuration interaction level with the aug-cc-pV6Z basis set. The topographical features of the new global potential energy surface are examined in detail and found to be in good agreement with those calculated directly from the raw ab initio energies, as well as previous calculations available in the literature. In turn, in order to validate the potential energy surface, a test theoretical study of the reaction CH(+)(X(1)Σ(+))+H((2)S)→C(+)((2)P)+H2(X(1)Σg (+)) has been carried out with the method of time dependent wavepacket on the title potential energy surface. The total integral cross sections and the rate coefficients have been calculated; the results determined that the new potential energy surface can both be recommended for dynamics studies of any type and as building blocks for constructing the potential energy surfaces of larger C(+)/H containing systems.
Reduced dimensionality spin-orbit dynamics of CH3 + HCl ⇌ CH4 + Cl on ab initio surfaces.
Remmert, Sarah M; Banks, Simon T; Harvey, Jeremy N; Orr-Ewing, Andrew J; Clary, David C
2011-05-28
A reduced dimensionality quantum scattering method is extended to the study of spin-orbit nonadiabatic transitions in the CH(3) + HCl ⇌ CH(4) + Cl((2)P(J)) reaction. Three two-dimensional potential energy surfaces are developed by fitting a 29 parameter double-Morse function to CCSD(T)/IB//MP2/cc-pV(T+d)Z-dk ab initio data; interaction between surfaces is described by geometry-dependent spin-orbit coupling functions fit to MCSCF/cc-pV(T+d)Z-dk ab initio data. Spectator modes are treated adiabatically via inclusion of curvilinear projected frequencies. The total scattering wave function is expanded in a vibronic basis set and close-coupled equations are solved via R-matrix propagation. Ground state thermal rate constants for forward and reverse reactions agree well with experiment. Multi-surface reaction probabilities, integral cross sections, and initial-state selected branching ratios all highlight the importance of vibrational energy in mediating nonadiabatic transition. Electronically excited state dynamics are seen to play a small but significant role as consistent with experimental conclusions.
Castillo, J F; Aoiz, F J; Martínez-Haya, B
2011-05-14
We present a global full dimensional potential energy surface (PES) for the Cl + O(3)→ ClO + O(2) reaction, which is an elementary step in a catalytic cycle that leads to the destruction of ozone in the stratosphere. The PES is constructed by interpolation of quantum chemistry data using the method developed by Collins and co-workers. Ab initio data points (energy, gradients and Hessian matrix elements) have been calculated at the UQCISD/aug-cc-pVDZ (unrestricted quadratic configuration interaction with single and double excitations) level of theory. The ab initio calculations predict a markedly non-coplanar (dihedral angle of 80°) transition state for the reaction, located very early in the reactant valley and slightly below the energy of the reactants as long as the spin-orbit splitting is neglected. Quasiclassical trajectory (QCT) calculations have been carried out at several collision energies to investigate the reaction dynamics. The QCT excitation function shows no threshold, displays a minimum at a collision energy of 2.5 kcal mol(-1), and then increases monotonically at larger collision energies. This behaviour is consistent with a barrierless reaction dominated by an oxygen-abstraction mechanism. The calculated product vibrational distributions (strongly inverted for ClO) and rate constants are compared with experimental determinations. Differential cross sections (DCS) summed over all final states are found to be in fairly good agreement with those derived from crossed molecular beam experiments.
Ab Initio Crystal Field for Lanthanides.
Ungur, Liviu; Chibotaru, Liviu F
2017-03-13
An ab initio methodology for the first-principle derivation of crystal-field (CF) parameters for lanthanides is described. The methodology is applied to the analysis of CF parameters in [Tb(Pc)2 ](-) (Pc=phthalocyanine) and Dy4 K2 ([Dy(4) K(2) O(OtBu)(12) ]) complexes, and compared with often used approximate and model descriptions. It is found that the application of geometry symmetrization, and the use of electrostatic point-charge and phenomenological CF models, lead to unacceptably large deviations from predictions based on ab initio calculations for experimental geometry. It is shown how the predictions of standard CASSCF (Complete Active Space Self-Consistent Field) calculations (with 4f orbitals in the active space) can be systematically improved by including effects of dynamical electronic correlation (CASPT2 step) and by admixing electronic configurations of the 5d shell. This is exemplified for the well-studied Er-trensal complex (H3 trensal=2,2',2"-tris(salicylideneimido)trimethylamine). The electrostatic contributions to CF parameters in this complex, calculated with true charge distributions in the ligands, yield less than half of the total CF splitting, thus pointing to the dominant role of covalent effects. This analysis allows the conclusion that ab initio crystal field is an essential tool for the decent description of lanthanides.
Liu, Jinxiang; Cukier, Robert I; Bu, Yuxiang
2013-11-12
We report an ab initio molecular dynamics simulation study of the solvation and dynamics of an excess electron in liquid acetonitrile (ACN). Four families of states are observed: a diffusely solvated state and three ACN core-localized states with monomer core, quasi-dimer (π*-Rydberg mode) core, and dual-core/dimer core (a coupled dual-core). These core localized states cannot be simply described as the corresponding anions because only a part of the excess electron resides in the core molecule(s). The quasi-dimer core state actually is a mixture that features cooperative excess electron capture by the π* and Rydberg orbitals of two ACNs. Well-defined dimer anion and solvated electron cavity were not observed in the 5-10 ps simulations, which may be attributed to slow dynamics of the formation of the dimer anion and difficulty of the formation of a cavity in such a fluxional medium. All of the above observed states have near-IR absorptions and thus can be regarded as the solvated electron states but with different structures, which can interpret the experimentally observed IR band. These states undergo continuous conversions via a combination of long-lasting breathing oscillation and core switching, characterized by highly cooperative oscillations of the electron cloud volume and vertical detachment energy. The quasi-dimer core and diffusely solvated states dominate the time evolution, with the monomer core and dual-core/dimer core states occurring occasionally during the breathing and core switching processes, respectively. All these oscillations and core switchings are governed by a combination of the electron-impacted bending vibration of the core ACN molecule(s) and thermal fluctuations.
NASA Astrophysics Data System (ADS)
del Rio, B. G.; González, L. E.
2017-08-01
We report results of an orbital-free ab initio molecular dynamics (OF-AIMD) study of the free liquid surface (FLS) of Sn at 1000 K and 600 K. A key ingredient in the OF-AIMD method is the local pseudopotential describing the ions-valence electrons interaction. We have used a force-matching method to derive a local pseudopotential suitable to account for the variation of the forces from the bulk to the FLS. We obtain very good results for structural properties, such as the reflectivity, including the characteristic shoulder it presents in x-ray experiments. Moreover we have been able to study ab initio for the first time the evolution in some dynamical properties as we move from the central region, where the system behaves like the bulk liquid, to the FLS.
Mignolet, Benoit; Curchod, Basile F. E.; Martinez, Todd J.
2016-11-17
Attoscience is an emerging field where attosecond pulses or few cycle IR pulses are used to pump and probe the correlated electron-nuclear motion of molecules. We present the trajectory-guided eXternal Field Ab Initio Multiple Spawning (XFAIMS) method that models such experiments “on-the-fly,” from laser pulse excitation to fragmentation or nonadiabatic relaxation to the ground electronic state. For the photoexcitation of the LiH molecule, we show that XFAIMS gives results in close agreement with numerically exact quantum dynamics simulations, both for atto- and femtosecond laser pulses. As a result, we then show the ability of XFAIMS to model the dynamics in polyatomic molecules by studying the effect of nuclear motion on the photoexcitation of a sulfine (H_{2}CSO).
Mignolet, Benoit; Curchod, Basile F. E.; Martinez, Todd J.
2016-11-17
Attoscience is an emerging field where attosecond pulses or few cycle IR pulses are used to pump and probe the correlated electron-nuclear motion of molecules. We present the trajectory-guided eXternal Field Ab Initio Multiple Spawning (XFAIMS) method that models such experiments “on-the-fly,” from laser pulse excitation to fragmentation or nonadiabatic relaxation to the ground electronic state. For the photoexcitation of the LiH molecule, we show that XFAIMS gives results in close agreement with numerically exact quantum dynamics simulations, both for atto- and femtosecond laser pulses. As a result, we then show the ability of XFAIMS to model the dynamics inmore » polyatomic molecules by studying the effect of nuclear motion on the photoexcitation of a sulfine (H2CSO).« less
Ab initio treatment of ion-induced charge transfer dynamics of isolated 2-deoxy-D-ribose.
Bacchus-Montabonel, Marie-Christine
2014-08-21
Modeling-induced radiation damage in biological systems, in particular, in DNA building blocks, is of major concern in cancer therapy studies. Ion-induced charge-transfer dynamics may indeed be involved in proton and hadrontherapy treatments. We have thus performed a theoretical approach of the charge-transfer dynamics in collision of C(4+) ions and protons with isolated 2-deoxy-D-ribose in a wide collision energy range by means of ab initio quantum chemistry molecular methods. The comparison of both projectile ions has been performed with regard to previous theoretical and experimental results. The charge transfer appears markedly less efficient with the 2-deoxy-D-ribose target than that with pyrimidine nucleobases, which would induce an enhancement of the fragmentation process in agreement with experimental measurements. The mechanism has been analyzed with regard to inner orbital excitations, and qualitative tendencies have been pointed out for studies on DNA buiding block damage.
Taioli, Simone; Garberoglio, Giovanni; Simonucci, Stefano; a Beccara, Silvio; Aversa, Lucrezia; Nardi, Marco; Verucchi, Roberto; Iannotta, Salvatore; Dapor, Maurizio; Alfè, Dario
2013-01-28
In this work, we investigate the processes leading to the room-temperature growth of silicon carbide thin films by supersonic molecular beam epitaxy technique. We present experimental data showing that the collision of fullerene on a silicon surface induces strong chemical-physical perturbations and, for sufficient velocity, disruption of molecular bonds, and cage breaking with formation of nanostructures with different stoichiometric character. We show that in these out-of-equilibrium conditions, it is necessary to go beyond the standard implementations of density functional theory, as ab initio methods based on the Born-Oppenheimer approximation fail to capture the excited-state dynamics. In particular, we analyse the Si-C(60) collision within the non-adiabatic nuclear dynamics framework, where stochastic hops occur between adiabatic surfaces calculated with time-dependent density functional theory. This theoretical description of the C(60) impact on the Si surface is in good agreement with our experimental findings.
Taioli, Simone; Garberoglio, Giovanni; Simonucci, Stefano; Beccara, Silvio a; Aversa, Lucrezia; Nardi, Marco; Verucchi, Roberto; Iannotta, Salvatore; Dapor, Maurizio; and others
2013-01-28
In this work, we investigate the processes leading to the room-temperature growth of silicon carbide thin films by supersonic molecular beam epitaxy technique. We present experimental data showing that the collision of fullerene on a silicon surface induces strong chemical-physical perturbations and, for sufficient velocity, disruption of molecular bonds, and cage breaking with formation of nanostructures with different stoichiometric character. We show that in these out-of-equilibrium conditions, it is necessary to go beyond the standard implementations of density functional theory, as ab initio methods based on the Born-Oppenheimer approximation fail to capture the excited-state dynamics. In particular, we analyse the Si-C{sub 60} collision within the non-adiabatic nuclear dynamics framework, where stochastic hops occur between adiabatic surfaces calculated with time-dependent density functional theory. This theoretical description of the C{sub 60} impact on the Si surface is in good agreement with our experimental findings.
Ab initio path integral molecular dynamics simulation study on the dihydrogen bond of NH4+⋯BeH2
NASA Astrophysics Data System (ADS)
Hayashi, Aiko; Shiga, Motoyuki; Tachikawa, Masanori
2005-07-01
An ab initio path integral molecular dynamics simulation has been performed to study the quantum and thermal effects of a dihydrogen bonded cation, NH4+⋯BeH2. In this system, an attractive interaction exists between two neighboring hydrogen atoms as N δ- H δ+ ⋯H δ- Be δ+ involving large-amplitude of vibration. Some properties playing a key role for this dihydrogen bonded system, such as the bond length, bond angle, and distribution of atomic charges, are investigated in detail by comparing the results of path integral and classical molecular dynamics with those of the equilibrium structure. It was found that the atomic charges of H δ+ and H δ- are decreased and the dihydrogen H δ+ ⋯H δ- bond length is expanded as the thermal and zero-point quantum effects.
On the hierarchical parallelization of ab initio simulations
NASA Astrophysics Data System (ADS)
Ruiz-Barragan, Sergi; Ishimura, Kazuya; Shiga, Motoyuki
2016-02-01
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.
Martonak; Molteni; Parrinello
2000-01-24
We present a new constant-pressure ab initio molecular dynamics method suitable for studying, e.g., pressure-induced structural transformations in finite nonperiodic systems such as clusters. We immerse an ab initio treated cluster into a model classical liquid, described by a soft-sphere potential, which acts as a pressure reservoir. The pressure is varied by tuning the parameter of the liquid potential. We apply the method to a Si35H36 cluster, which undergoes a pressure-induced amorphization at approximately 35 GPa, and remains in a disordered state even upon pressure release.
Non-equilibrium dynamics in disordered materials: Ab initio molecular dynamics simulations
NASA Astrophysics Data System (ADS)
Ohmura, Satoshi; Nagaya, Kiyonobu; Shimojo, Fuyuki; Yao, Makoto
2015-08-01
The dynamic properties of liquid B2O3 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 B2O3 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).
NASA Astrophysics Data System (ADS)
Pacheco, Alexander B.; Iyengar, Srinivasan S.
2010-07-01
We propose a multistage quantum wavepacket dynamical treatment for the study of delocalized electronic systems as well as electron transport through donor-bridge-acceptor systems such as those found in molecular-wire/electrode networks. The full donor-bridge-acceptor system is treated through a rigorous partitioning scheme that utilizes judiciously placed offsetting absorbing and emitting boundary conditions. These facilitate a computationally efficient and potentially accurate treatment of the long-range coupling interactions between the bridge and donor/acceptor systems and the associated open system boundary conditions. Time-independent forms of the associated, partitioned equations are also derived. In the time-independent form corresponding to the bridge system, coupling to donor and acceptor, that is long-range interactions, is completely accounted. For the time-dependent study, the quantum dynamics of the electronic flux through the bridge-donor/acceptor interface is constructed using an accurate and efficient representation of the discretized quantum-mechanical free-propagator. A model for an electrode-molecular wire-electrode system is used to test the accuracy of the scheme proposed. Transmission probability is obtained directly from the probability density of the electronic flux in the acceptor region. Conductivity through the molecular wire is computed using a wavepacket flux correlation function.
Non-equilibrium dynamics in disordered materials: Ab initio molecular dynamics simulations
Ohmura, Satoshi; Nagaya, Kiyonobu; Yao, Makoto; Shimojo, Fuyuki
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)
NASA Astrophysics Data System (ADS)
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.
NASA Astrophysics Data System (ADS)
Ko, Hsin-Yu; Distasio, Robert A., Jr.; Santra, Biswajit; Car, Roberto
2014-03-01
Pyridine has recently been investigated as a potentially effective material for use in artificial light harvesting.In this work, we propose the use of ab initio molecular dynamics (AIMD) to gain valuable physical insight into the artificial photosynthetic processes occurring in condensed-phase pyridine, the study of which has been limited to semi-empirical force fields to date.For this purpose, we introduce an accurate and efficient AIMD method, based on density functional theory (DFT) and a self-consistent pairwise description of van der Waals (vdW) interactions, for use in finite temperature and pressure (NPT) simulations on pyridine and several pyridine-like molecular crystals (PLMCs). Utilizing this approach, we demonstrate that vdW forces play a crucial role in the theoretical prediction of the structure and density of pyridine and PLMCs, and therefore must be accounted for in studies of these potential alternative energy materials. DOE: DE-SC0008626, NSF: DMS-1065894.
Samin, Adib; Li, Xiang; Zhang, Jinsuo; Mariani, R. D.; Unal, Cetin
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.
NASA Astrophysics Data System (ADS)
Bankura, Arindam; Klein, Michael L.; Carnevale, Vincenzo
2013-08-01
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 Nɛ positions of the imidazole group to estimate the pKas. Anticipating our results, we will see that the estimated pKa 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.
Parkes, Marie V; Greathouse, Jeffery A; Hart, David B; Gallis, Dorina F Sava; Nenoff, Tina M
2016-04-28
The separation of oxygen from nitrogen using metal-organic frameworks (MOFs) is of great interest for potential pressure-swing adsorption processes for the generation of purified O2 on industrial scales. This study uses ab initio molecular dynamics (AIMD) simulations to examine for the first time the pure-gas and competitive gas adsorption of O2 and N2 in the M2(dobdc) (M = Cr, Mn, Fe) MOF series with coordinatively unsaturated metal centers. Effects of metal, temperature, and gas composition are explored. This unique application of AIMD allows us to study in detail the adsorption/desorption processes and to visualize the process of multiple guests competitively binding to coordinatively unsaturated metal sites of a MOF.
Anil Kumar, A V; Yashonath, S; Sluiter, Marcel; Kawazoe, Yoshiyuki
2002-01-01
Molecular dynamics simulation of a five-site model of methane within zeolite NaCaA and ab initio calculations have been reported. Methane shows a preferential orientation during its passage through the eight-ring window. Partial freezing of certain rotational degrees of freedom is observed during the passage of methane through the eight-ring window, which acts as a bottleneck for diffusion of methane. Both the orientation and the rotational motion of methane and its experimental verification can indicate the accuracy of the intermolecular potential between methane and zeolite employed in this study. Intracage motion of methane shows that methane performs a rolling motion rather than a sliding motion within the supercage.
Atomic structure of amorphous Mg40Cu35Ti25 alloy: An ab initio molecular dynamics study
NASA Astrophysics Data System (ADS)
Durandurdu, Murat
2013-01-01
Ab initio molecular dynamics simulations are carried out to model amorphous Mg40Cu35Ti25 and its local structural packing are investigated using a variety of analyzing techniques. Cu-atoms commonly form 12 fold coordinated clusters and some of which are perfect or defective types icosahedrons, implying an icosohedral short range order around Cu atoms. Mg and Ti atoms, on the other hand, favor to structure in higher coordinated polyhedrons. The coordination number of Ti atoms is slightly less than Mg atoms. The immiscibility effect between Ti and Mg is reflected by a low fraction of Mg-Ti bonding in the model. The atomic packing of Mg40Cu35Ti25 appears to be noticeably different from that of Mg-Cu-X (X=Y and Gd) metallic glasses even though all these materials exhibit primarily the same type of bonding natures.
Jin, K.; Xiao, H. Y.; Zhang, Y.; Weber, W. J.
2014-05-19
Ab initio molecular dynamics simulations are performed to investigate the effects of a boron nitride (BN) substrate on Stone-Wales (SW) defect formation and recovery in graphene. It is found that SW defects can be created by an off-plane recoil atom that interacts with the BN substrate. A mechanism with complete bond breakage for formation of SW defects in suspended graphene is also revealed for recoils at large displacement angles. In addition, further irradiation can result in recovery of the SW defects through a bond rotation mechanism in both graphene and graphene/BN, and the substrate has little effect on the recovery process. This study indicates that the BN substrate enhances the irradiation resistance of graphene.
The Fate of a Zwitterion in Water from ab Initio Molecular Dynamics: Monoethanolamine (MEA)-CO2.
Guido, Ciro A; Pietrucci, Fabio; Gallet, Grégoire A; Andreoni, Wanda
2013-01-08
Understanding the fundamental reactions accompanying the capture of carbon dioxide in amine solutions is critical for the design of high-performance solvents and requires an accurate modeling of the solute-solvent interaction. As a first step toward this goal, using ab initio molecular dynamics (Car-Parrinello) simulations, we investigate a zwitterionic carbamate, a species long proposed as intermediate in the formation of a stable carbamate, in a dilute aqueous solution. CO2 release and deprotonation are competitive routes for its dissociation and are both characterized by free-energy barriers of 6-8 kcal/mol. Water molecules play a crucial role in both pathways, resulting in large entropic effects. This is especially true in the case of CO2 release, which is accompanied by a strong reorganization of the solvent beyond the first coordination shell, leading to the formation of a water cage entrapping the solute (hydrophobic effect). Our results contrast with the assumptions of implicit solvent models.
Cicero, G; Grossman, J; Galli, G; Catellani, A
2005-01-28
We present a microscopic model of the interface between liquid water and a hydrophilic, solid surface, as obtained from ab-initio molecular dynamics simulations. In particular, we focused on the (100)surface of cubic SiC, a leading candidate semiconductor for bio-compatible devices. Our results show that, in the liquid in contact with the clean substrate, molecular dissociation occurs in a manner unexpectedly similar to that observed in the gas phase. After full hydroxylation takes place, the formation of a thin ({approx}3 {angstrom})interfacial layer is observed, which has higher density than bulk water and forms stable hydrogen bonds with the substrate. The liquid does not uniformly wet the surface, rather molecules preferably bind along directions parallel to the Si dimer rows. Our calculations also predict that one dimensional confinement between two hydrophilic surfaces at about 1.3 nm distance does not affect the structural and electronic properties of the whole water sample.
Koizumi, Kenichi; Nobusada, Katsuyuki; Boero, Mauro
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.
Ab initio molecular dynamics of Al irradiation-induced processes during Al{sub 2}O{sub 3} growth
Music, Denis; Nahif, Farwah; Friederichsen, Niklas; Schneider, Jochen M.; Sarakinos, Kostas
2011-03-14
Al bombardment induced structural changes in {alpha}-Al{sub 2}O{sub 3} (R-3c) and {gamma}-Al{sub 2}O{sub 3} (Fd-3m) were studied using ab initio molecular dynamics. Diffusion and irradiation damage occur for both polymorphs in the kinetic energy range from 3.5 to 40 eV. However, for {gamma}-Al{sub 2}O{sub 3}(001) subplantation of impinging Al causes significantly larger irradiation damage and hence larger mobility as compared to {alpha}-Al{sub 2}O{sub 3}. Consequently, fast diffusion along {gamma}-Al{sub 2}O{sub 3}(001) gives rise to preferential {alpha}-Al{sub 2}O{sub 3}(0001) growth, which is consistent with published structure evolution experiments.
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.
Ab initio molecular dynamics simulation on the formation process of He@C₆₀ synthesized by explosion.
Li, Jian-Ying; Liu, Li-Min; Jin, Bo; Liang, Hua; Yu, Hai-Jun; Zhang, Hong-Chang; Chu, Shi-Jin; Peng, Ru-Fang
2013-04-01
The applications of endohedral non-metallic fullerenes are limited by their low production rate. Recently, an explosive method developed in our group shows promise to prepare He@C₆₀ at fairly high yield, but the mechanism of He inserting into C₆₀ cage at explosive conditions was not clear. Here, ab initio molecular dynamics analysis has been used to simulate the collision between C₆₀ molecules at high-temperature and high-pressure induced by explosion. The results show that defects formed on the fullerene cage by collidsion can effectively decrease the reaction barrier for the insertion of He into C₆₀, and the self-healing capability of the defects was also observed.
Mundy, Christopher J.; Curioni, Alessandro; Kuo, I-F W.; Goldman, Nir; Reed, Evan; Fried, Larry; Ianuzzi, Marcella
2008-05-14
This work was performed while I was LLNL. We present an extremely large scale ab initio calculation of the transformation of graphite to diamond under shock compression utilizing Car-Parrinello Molecular Dynamics (CPMD) in conjunction with the Multi-scale Shock Method (MSSM). Our results indicate that the transition from graphite to diamond is Martensitic, in agreement with experimental observations. We find that a shock of 12 km/s forms a short-lived layered diamond phase that eventually relaxes to a cubic diamond state. Moreover, access to the electronic structure allows the computation of the x-ray absorption spectra (XAS) to characterize the final states. The XAS spectra and wide angle x-ray scattering spectra (WAXS) confirm the presence of a cubic diamond final state.
NASA Astrophysics Data System (ADS)
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.
Xiao, Haiyan Y.; Weber, William J.; Zhang, Yanwen; Zu, X. T.; Li, Sean
2015-02-09
In this study, the response of titanate pyrochlores (A_{2}Ti_{2}O_{7}, A = Y, Gd and Sm) to electronic excitation is investigated utilizing an ab initio molecular dynamics method. All the titanate pyrochlores are found to undergo a crystalline-to-amorphous structural transition under a low concentration of electronic excitations. The transition temperature at which structural amorphization starts to occur depends on the concentration of electronic excitations. During the structural transition, O_{2}-like molecules are formed, and this anion disorder further drives cation disorder that leads to an amorphous state. This study provides new insights into the mechanisms of amorphization in titanate pyrochlores under laser, electron and ion irradiations.
NASA Astrophysics Data System (ADS)
Thiering, Gergő; Gali, Adam
2017-08-01
Point defects in solids may realize solid state quantum bits. The spin-orbit coupling in these point defects plays a key role in the magneto-optical properties that determine the conditions of quantum bit operation. However, experimental data and methods do not directly yield these highly important data, particularly for such complex systems where the dynamic Jahn-Teller (DJT) effect damps the spin-orbit interaction. Here, we show for an exemplary quantum bit, the nitrogen-vacancy (NV) center in diamond, that ab initio supercell density functional theory provides a quantitative prediction for the spin-orbit coupling damped by DJT. We show that DJT is responsible for the multiple intersystem crossing rates of the NV center at cryogenic temperatures. Our results pave the way toward optimizing solid state quantum bits for quantum information processing and metrology applications.
Rowley, Christopher N; Roux, Benoıt
2012-10-09
Knowledge of the hydration structure of Na(+) and K(+) in the liquid phase has wide ranging implications in the field of biological chemistry. Despite numerous experimental and computational studies, even basic features such as the coordination number of these alkali ions in liquid water, thought to play a critical role in selectivity, continue to be the subject of intensive debates. Simulations based on accurate potential energy surfaces offer one approach to resolve these issues by providing reliable results on ion hydration. In this article, we report the results from molecular dynamics simulations of Na(+) and K(+) hydration based on a novel and rigorous strategy designed to overcome the challenges of QM/MM simulations of solvent molecules in the liquid phase. In this method, which we call Flexible Inner Region Ensemble Separator (FIRES), the ion and a fixed number of nearest water molecules form a dynamical and flexible inner region that is represented with high level ab initio quantum mechanical (QM) methods, while the water molecules from the surrounding bulk form an outer region that is represented by a polarizable molecular mechanical (MM) force field. Simulations yield rigorously correct thermodynamic averages as long as the solvent molecules in the flexible inner and outer regions are not allowed to exchange. Extensive FIRES simulations were carried out based on a QM/MM model in which the Na(+) or K(+) ion and the 12 nearest water molecules were represented by high level ab initio methods (RI-MP2/def2-TZVP and density functional theory with PBE/def2-TZVP), while the surrounding MM water molecules were represented by the polarizable SWM4-NDP potential. On the basis of these results, the ion coordination numbers are estimated to be within the range of 5.7-5.8 for Na(+) and 6.9-7.0 for K(+).
Ab initio molecular dynamics simulations of ion-solid interactions in zirconate pyrochlores
Xiao, Haiyan Y.; Weber, William J.; Zhang, Yanwen; Zu, X. T.
2015-01-31
In this paper, an ab initio molecular dynamics method is employed to study low energy recoil events in zirconate pyrochlores (A_{2}Zr_{2}O_{7}, A = La, Nd and Sm). It shows that both cations and anions in Nd_{2}Zr_{2}O_{7} and Sm_{2}Zr_{2}O_{7} are generally more likely to be displaced than those in La_{2}Zr_{2}O_{7}. The damage end states mainly consist of Frenkel pair defects, and the Frenkel pair formation energies in Nd_{2}Zr_{2}O_{7} and Sm_{2}Zr_{2}O_{7} are lower than those in La_{2}Zr_{2}O_{7}. These results suggest that the order–disorder structural transition more easily occurs in Nd_{2}Zr_{2}O_{7} and Sm_{2}Zr_{2}O_{7} resulting in a defect-fluorite structure, which agrees well with experimental observations. Our calculations indicate that oxygen migration from 48f and 8b to 8a sites is dominant under low energy irradiation. A number of new defects, including four types of cation Frenkel pairs and six types of anion Frenkel pairs, are revealed by ab initio molecular dynamics simulations. The present findings may help to advance the fundamental understanding of the irradiation response behavior of zirconate pyrochlores.
Lu, Zhenyu; Zhang, Yingkai
2009-01-01
In order to further improve the accuracy and applicability of combined quantum mechanical/molecular mechanical (QM/MM) methods, we have interfaced the ab initio QM method with the classical Drude oscillator polarizable MM force field (ai-QM/MM-Drude). Different coupling approaches have been employed and compared: 1. the conventional dual self-consistent-field (SCF) procedure; 2. the direct SCF scheme, in which QM densities and MM Drude positions are converged simultaneously; 3. the micro-iterative SCF scheme, in which the Drude positions of the polarizable model are fully converged during each self-consistent field (SCF) step of QM calculations; 4. the one-step-Drude-update scheme, in which the MM Drude positions are updated only once instead of fully converged during each molecular dynamics (MD) step. The last three coupling approaches are found to be efficient and can achieve the desired convergence in a similar number of QM SCF steps comparing with the corresponding QM method coupled to a non-polarizable force field. The feasibility and applicability of the implemented ai-QM/MM-Drude approach have been demonstrated by carrying out Born-Oppenheimer molecular dynamics simulations with the umbrella sampling method to determine potentials of mean force for both the methyl transfer reaction of the methyl chlorine-chlorine ion system and the glycine intra-molecular proton transfer reaction in aqueous solution. Our results indicate that the ai-QM/MM-Drude approach is very promising, which provides a better description of QM/MM interactions while can achieve quite similar computational efficiency in comparison with the corresponding conventional ab initio QM/MM method. PMID:19221605
Ab-initio Studies Of Lithium Oxide
NASA Astrophysics Data System (ADS)
Gupta, M. K.; Goel, Prabhatasree; Mittal, R.; Chaplot, S. L.
2010-12-01
Lithium oxide is an important material because of its high thermal conductivity and superionic behavior at high temperature. It behaves like a superionic conductor above 1200 K. Phonon frequencies have been calculated using ab-initio method. The calculations of phonon dispersion relation near unit cell volume corresponding to the superionic transition indicate softening of zone boundary transverse acoustic phonon mode along (110). The instability of phonon mode could lead to the dynamical disorder of lithium sub lattice. Thermal expansion and equation of states are also computed. The results compare well with our previous semi-empirical potential calculations.
Sumner, Isaiah; Iyengar, Srinivasan S
2008-08-07
We discuss hybrid quantum-mechanics/molecular-mechanics (QM/MM) and quantum mechanics/quantum mechanics (QM/QM) generalizations to our recently developed quantum wavepacket ab initio molecular dynamics methodology for simultaneous dynamics of electrons and nuclei. The approach is a synergy between a quantum wavepacket dynamics, ab initio molecular dynamics, and the ONIOM scheme. We utilize this method to include nuclear quantum effects arising from a portion of the system along with a simultaneous description of the electronic structure. The generalizations provided here make the approach a potentially viable alternative for large systems. The quantum wavepacket dynamics is performed on a grid using a banded, sparse, and Toeplitz representation of the discrete free propagator, known as the "distributed approximating functional." Grid-based potential surfaces for wavepacket dynamics are constructed using an empirical valence bond generalization of ONIOM and further computational gains are achieved through the use of our recently introduced time-dependent deterministic sampling technique. The ab initio molecular dynamics is achieved using Born-Oppenheimer dynamics. All components of the methodology, namely, quantum dynamics and ONIOM molecular dynamics, are harnessed together using a time-dependent Hartree-like procedure. We benchmark the approach through the study of structural and vibrational properties of molecular, hydrogen bonded clusters inclusive of electronic, dynamical, temperature, and critical quantum nuclear effects. The vibrational properties are constructed through a velocity/flux correlation function formalism introduced by us in an earlier publication.
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
Ab initio based polarizable force field parametrization
NASA Astrophysics Data System (ADS)
Masia, Marco
2008-05-01
Experimental and simulation studies of anion-water systems have pointed out the importance of molecular polarization for many phenomena ranging from hydrogen-bond dynamics to water interfaces structure. The study of such systems at molecular level is usually made with classical molecular dynamics simulations. Structural and dynamical features are deeply influenced by molecular and ionic polarizability, which parametrization in classical force field has been an object of long-standing efforts. Although when classical models are compared to ab initio calculations at condensed phase, it is found that the water dipole moments are underestimated by ˜30%, while the anion shows an overpolarization at short distances. A model for chloride-water polarizable interaction is parametrized here, making use of Car-Parrinello simulations at condensed phase. The results hint to an innovative approach in polarizable force fields development, based on ab initio simulations, which do not suffer for the mentioned drawbacks. The method is general and can be applied to the modeling of different systems ranging from biomolecular to solid state simulations.
Svoboda, Ondřej; Ončák, Milan; Slavíček, Petr
2011-10-21
We have applied ab initio based reflection principle to simulate photoelectron spectra of small water clusters, ranging from monomer to octamer. The role of quantum and thermal effects on the structure of the water photoelectron spectra is discussed within the ab initio path integral molecular dynamics (PIMD) framework. We have used the PIMD method with up to 40 beads to sample the ground state quantum distribution at temperature T = 180 K. We have thoroughly tested the performance of various density functionals (B3LYP, BHandHLYP, M06HF, BNL, LC-ωPBE, and CAM-B3LYP) for the ionization process description. The benchmarking based on a comparison of simulated photoelectron spectra to experimental data and high level equation-of-motion ionization potential coupled clusters with singles and doubles calculations has singled out the BHandHLYP and LC-ωPBE functionals as the most reliable ones for simulations of light induced processes in water. The good performance of the density functional theory functionals to model the water photoelectron spectra also reflects their ability to reliably describe open shell excited states. The width of the photoelectron spectrum converges quickly with the cluster size as it is controlled by specific interactions of local character. The peak position is, on the other hand, defined by long-range non-specific solvent effects; it therefore only slowly converges to the corresponding bulk value. We are able to reproduce the experimental valence photoelectron spectrum of liquid water within the combined model of the water octamer embedded in a polarizable dielectric continuum. We demonstrate that including the long-range polarization and the state-specific treatment of the solvent response are needed for a reliable liquid water ionization description. © 2011 American Institute of Physics
NASA Astrophysics Data System (ADS)
Svoboda, Ondřej; Ončák, Milan; Slavíček, Petr
2011-10-01
We have applied ab initio based reflection principle to simulate photoelectron spectra of small water clusters, ranging from monomer to octamer. The role of quantum and thermal effects on the structure of the water photoelectron spectra is discussed within the ab initio path integral molecular dynamics (PIMD) framework. We have used the PIMD method with up to 40 beads to sample the ground state quantum distribution at temperature T = 180 K. We have thoroughly tested the performance of various density functionals (B3LYP, BHandHLYP, M06HF, BNL, LC-ωPBE, and CAM-B3LYP) for the ionization process description. The benchmarking based on a comparison of simulated photoelectron spectra to experimental data and high level equation-of-motion ionization potential coupled clusters with singles and doubles calculations has singled out the BHandHLYP and LC-ωPBE functionals as the most reliable ones for simulations of light induced processes in water. The good performance of the density functional theory functionals to model the water photoelectron spectra also reflects their ability to reliably describe open shell excited states. The width of the photoelectron spectrum converges quickly with the cluster size as it is controlled by specific interactions of local character. The peak position is, on the other hand, defined by long-range non-specific solvent effects; it therefore only slowly converges to the corresponding bulk value. We are able to reproduce the experimental valence photoelectron spectrum of liquid water within the combined model of the water octamer embedded in a polarizable dielectric continuum. We demonstrate that including the long-range polarization and the state-specific treatment of the solvent response are needed for a reliable liquid water ionization description.
Chen, Ji; Ren, Xinguo; Li, Xin-Zheng; Alfè, Dario; Wang, Enge
2014-07-14
The finite-temperature phase diagram of hydrogen in the region of phase IV and its neighborhood was studied using the ab initio molecular dynamics (MD) and the ab initio path-integral molecular dynamics (PIMD). The electronic structures were analyzed using the density-functional theory (DFT), the random-phase approximation, and the diffusion Monte Carlo (DMC) methods. Taking the state-of-the-art DMC results as benchmark, comparisons of the energy differences between structures generated from the MD and PIMD simulations, with molecular and dissociated hydrogens, respectively, in the weak molecular layers of phase IV, indicate that standard functionals in DFT tend to underestimate the dissociation barrier of the weak molecular layers in this mixed phase. Because of this underestimation, inclusion of the quantum nuclear effects (QNEs) in PIMD using electronic structures generated with these functionals leads to artificially dissociated hydrogen layers in phase IV and an error compensation between the neglect of QNEs and the deficiencies of these functionals in standard ab initio MD simulations exists. This analysis partly rationalizes why earlier ab initio MD simulations complement so well the experimental observations. The temperature and pressure dependencies for the stability of phase IV were also studied in the end and compared with earlier results.
NASA Astrophysics Data System (ADS)
Chen, Ji; Ren, Xinguo; Li, Xin-Zheng; Alfè, Dario; Wang, Enge
2014-07-01
The finite-temperature phase diagram of hydrogen in the region of phase IV and its neighborhood was studied using the ab initio molecular dynamics (MD) and the ab initio path-integral molecular dynamics (PIMD). The electronic structures were analyzed using the density-functional theory (DFT), the random-phase approximation, and the diffusion Monte Carlo (DMC) methods. Taking the state-of-the-art DMC results as benchmark, comparisons of the energy differences between structures generated from the MD and PIMD simulations, with molecular and dissociated hydrogens, respectively, in the weak molecular layers of phase IV, indicate that standard functionals in DFT tend to underestimate the dissociation barrier of the weak molecular layers in this mixed phase. Because of this underestimation, inclusion of the quantum nuclear effects (QNEs) in PIMD using electronic structures generated with these functionals leads to artificially dissociated hydrogen layers in phase IV and an error compensation between the neglect of QNEs and the deficiencies of these functionals in standard ab initio MD simulations exists. This analysis partly rationalizes why earlier ab initio MD simulations complement so well the experimental observations. The temperature and pressure dependencies for the stability of phase IV were also studied in the end and compared with earlier results.
Kessler, Jan; Elgabarty, Hossam; Spura, Thomas; Karhan, Kristof; Partovi-Azar, Pouya; Hassanali, Ali A; Kühne, Thomas D
2015-08-06
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 [Willard, A. P.; Chandler, D. J. Phys. Chem. B 2010, 114, 1954]. 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.
Chen, Ying; Bylaska, Eric J.; Weare, John H.
2017-03-31
Many important geochemical and biogeochemical reactions occur in the mineral/formation water interface of the highly abundant mineral, goethite (α-Fe(OOH). Ab-initio molecular dynamics (AIMD) simulations of the goethite α-FeOOH (100) surface and the structure, water bond formation and dynamics of water molecules in the mineral/aqueous interface are presented. Here, several exchange correlation functionals were employed (PBE96, PBE96+Grimme, and PBE0) in the simulations of a (3 x 2) goethite surface with 65 absorbed water molecules in a 3D-periodic supercell (a=30 Å, FeOOH slab ~12 Å thick, solvation layer ~18 Å thick).
Ab initio phonon limited transport
NASA Astrophysics Data System (ADS)
Verstraete, Matthieu
We revisit the thermoelectric (TE) transport properties of two champion materials, PbTe and SnSe, using fully first principles methods. In both cases the performance of the material is due to subtle combinations of structural effects, scattering, and phase space reduction. In PbTe anharmonic effects are completely opposite to the predicted quasiharmonic evolution of phonon frequencies and to frequently (and incorrectly) cited extrapolations of experiments. This stabilizes the material at high T, but also tends to enhance its thermal conductivity, in a non linear manner, above 600 Kelvin. This explains why PbTe is in practice limited to room temperature applications. SnSe has recently been shown to be the most efficient TE material in bulk form. This is mainly due to a strongly enhanced carrier concentration and electrical conductivity, after going through a phase transition from 600 to 800 K. We calculate the transport coefficients as well as the defect concentrations ab initio, showing excellent agreement with experiment, and elucidating the origin of the double phase transition as well as the new charge carriers. AH Romero, EKU Gross, MJ Verstraete, and O Hellman PRB 91, 214310 (2015) O. Hellman, IA Abrikosov, and SI Simak, PRB 84 180301 (2011)
Gross, Axel
2011-11-07
The interaction of hydrogen with palladium surfaces represents one of the model systems for the study of the adsorption and absorption at metal surfaces. Theoretical gas-surface dynamics studies have usually concentrated on the adsorption dynamics on clean surfaces. Only recently it has become possible, based on advances in the electronic structure codes and improvements in the computer power, to address the much more complex problem of the adsorption dynamics on precovered surfaces. Here, I present ab initio molecular dynamics (AIMD) simulations based on periodic density functional theory (DFT) calculations of the adsorption of H(2) on hydrogen-precovered Pd(100) for a broad variety of different hydrogen coverage structures. The stability of the adsorbate structures and the adsorption dynamics are analyzed in detail. Calculated sticking probabilities are larger than expected for pure site-blocking consistent with experimental results. It turns out that the adsorption dynamics on the strongly corrugated surfaces depends sensitively on the dynamic response of the substrate atoms upon the impact of the impinging H(2) molecules. In addition, for some structures the adsorption probability was evaluated as a function of the kinetic energy. Adsorbate structures corresponding to the same coverage but with different arrangements of the adsorbed atoms can lead to a qualitatively different dependence of the adsorption probability on the kinetic energy changing also the order of the preferred structures, as far as the adsorption is concerned, as a function of the kinetic energy. This indicates that dynamical effects such as steering and dynamical trapping play an important role in the adsorption on these precovered substrates.
Ab initio molecular dynamics simulations of low energy recoil events in MgO
NASA Astrophysics Data System (ADS)
Petersen, B. A.; Liu, B.; Weber, W. J.; Zhang, Y.
2017-04-01
Low-energy recoil events in MgO are studied using ab intio molecular dynamics simulations to reveal the dynamic displacement processes and final defect configurations. Threshold displacement energies, Ed, are obtained for Mg and O along three low-index crystallographic directions, [100], [110], and [111]. The minimum values for Ed are found along the [110] direction consisting of the same element, either Mg or O atoms. Minimum threshold values of 29.5 eV for Mg and 25.5 eV for O, respectively, are suggested from the calculations. For other directions, the threshold energies are considerably higher, 65.5 and 150.0 eV for O along [111] and [100], and 122.5 eV for Mg along both [111] and [100] directions, respectively. These results show that the recoil events in MgO are partial-charge transfer assisted processes where the charge transfer plays an important role. There is a similar trend found in other oxide materials, where the threshold displacement energy correlates linearly with the peak partial-charge transfer, suggesting this behavior might be universal in ceramic oxides.
Saalfrank, Peter; Juaristi, J. I.
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.
Luo, Ye; Zen, Andrea; Sorella, Sandro
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.
Luo, Ye Sorella, Sandro; Zen, Andrea
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.
Calderín, L; González, L E; González, D J
2011-09-21
Fluid Hg undergoes a metal-nonmetal (M-NM) transition when expanded toward a density of around 9 g cm(-3). We have performed ab initio molecular dynamics simulations for several thermodynamic states around the M-NM transition range and the associated static, dynamic and electronic properties have been analyzed. The calculated static structure shows a good agreement with the available experimental data. It is found that the volume expansion decreases the number of nearest neighbors from 10 (near the triple point) to around 8 at the M-NM transition region. Moreover, these neighbors are arranged into two subshells and the decrease in the number of neighbors occurs in the inner subshell. The calculated dynamic structure factors agree fairly well with their experimental counterparts obtained by inelastic x-ray scattering experiments, which display inelastic side peaks. The derived dispersion relation exhibits some positive dispersion for all the states, although its value around the M-NM transition region is not as marked as suggested by the experiment. We have also calculated the electronic density of states, which shows the appearance of a gap at a density of around 8.3 g cm(-3).
Ab initio study of phosphaalkenes
Liu, M.
1992-01-01
This dissertation presents the application of computational chemistry to investigate a new class of organic compound-phosphaalkenes. The history of room temperature stable phosphaalkenes is a matter of the last 20 years. The existence of the C[double bond]P [pi] bond has challenged the concept that the 2p-3p [pi] bond is supposed to be very unstable and weak. Theoretical study of this type of compound can clear up the unknown properties, reactivities and reaction mechanisms of phosphaalkenes. The aim of this research is to theoretically determine the electronic and molecular properties, the chemical properties, and predict synthetic candidates for this family. Employing ab initio quantum chemistry, the authors have completed 7 related projects. First, the authors examined the reaction mechanism in the general synthesis of 1,3-diphosphallene and located the step that controls the stereo-outcome of the final product. Second, the authors predicted 4-phosphamethylenecylopropene to be a stable compound, which has been successfully synthesized after this research appeared. Third, the rotational energy surface of the rotation from s-trans to s-cis for mon- and di-phospha-1,3-butadienes were examined and concluded that the rotation does not have a high barrier. Fourth, fifth, and sixth, the authors continued their interest in phospha-1,3-butadienes and investigated [2+2] and Diels-Alder reactions. The energetics and stereo consequences of these reactions have been explored in this research. Finally, they also systematically studied the bonding properties of phosphacumulenes and provided some structural insight for this unsettled area.
NASA Astrophysics Data System (ADS)
Zabidi, Noriza Ahmad; Kassim, Hasan Abu; Shrivastava, Keshav N.
2008-05-01
Polonium is the only element with a simple cubic (sc) crystal structure. Atoms in solid polonium sit at the corners of a simple cubic unit cell and no where else. Polonium has a valence electron configuration 6s26p4 (Z = 84). The low temperature α-phase transforms into the rhombohedral (trigonal) β structure at ˜348 K. The sc α-Po unit cell constant is a = 3.345 Å. The beta form of polonium (β-Po) has the lattice parameters, aR = 3.359 Å and a rhombohedral angle 98°13'. We have performed an ab initio electronic structure calculation by using the density functional theory. We have performed the calculation with and without spin-orbit (SO) coupling by using both the LDA and the GGA for the exchange-correlations. The k-points in a simple cubic BZ are determined by R (0.5, 0.5, 0.5), Γ (0, 0, 0), X (0.5, 0, 0), M (0.5, 0.5, 0) and Γ (0, 0, 0). Other directions of k-points are Γ (0, 0, 0), X (0.5, 0, 0), R (0.5, 0.5, 0.5) and Γ (0, 0, 0). The SO splittings of p states at the Γ point in the GGA+SO scheme for α-Po are 0.04 eV and 0.02 eV while for the β-Po these are 0.03 eV and 0.97 eV. We have also calculated the vibrational spectra for the unit cells in both the structures. We find that exchanging of a Po atom by Pb atom produces several more bands and destabilizes the β phase.
Zabidi, Noriza Ahmad; Kassim, Hasan Abu; Shrivastava, Keshav N.
2008-05-20
Polonium is the only element with a simple cubic (sc) crystal structure. Atoms in solid polonium sit at the corners of a simple cubic unit cell and no where else. Polonium has a valence electron configuration 6s{sup 2}6p{sup 4} (Z = 84). The low temperature {alpha}-phase transforms into the rhombohedral (trigonal) {beta} structure at {approx}348 K. The sc {alpha}-Po unit cell constant is a = 3.345 A. The beta form of polonium ({beta}-Po) has the lattice parameters, a{sub R} = 3.359 A and a rhombohedral angle 98 deg. 13'. We have performed an ab initio electronic structure calculation by using the density functional theory. We have performed the calculation with and without spin-orbit (SO) coupling by using both the LDA and the GGA for the exchange-correlations. The k-points in a simple cubic BZ are determined by R (0.5, 0.5, 0.5), {gamma} (0, 0, 0), X (0.5, 0, 0), M (0.5, 0.5, 0) and {gamma} (0, 0, 0). Other directions of k-points are {gamma} (0, 0, 0), X (0.5, 0, 0), R (0.5, 0.5, 0.5) and {gamma} (0, 0, 0). The SO splittings of p states at the {gamma} point in the GGA+SO scheme for {alpha}-Po are 0.04 eV and 0.02 eV while for the {beta}-Po these are 0.03 eV and 0.97 eV. We have also calculated the vibrational spectra for the unit cells in both the structures. We find that exchanging of a Po atom by Pb atom produces several more bands and destabilizes the {beta} phase.
NASA Astrophysics Data System (ADS)
Bouzid, Assil; Pasquarello, Alfredo
2017-07-01
We show that constant-Fermi-level ab initio molecular dynamics can be used as a computer-based tool to reveal and control relevant defects in semiconductor materials. In this scheme, the Fermi level can be set at any position within the band gap during the defect generation process, in analogy to experimental growth conditions in the presence of extra electrons or holes. The scheme is illustrated in the case of GaAs, for which we generate melt-quenched amorphous structures through molecular dynamics at various Fermi levels. By a combined analysis which involves both the atomic structure and a Wannier-function decomposition of the electronic structure, we achieve a detailed description of the generated defects as a function of the Fermi level. This leads to the identification of As—As homopolar bonds and Ga dangling bonds for Fermi levels set in the vicinity of the valence band. These defects convert into As dangling bonds and Ga—Ga homopolar bonds, as the Fermi level moves toward the conduction band. This demonstrates a computer-aided procedure to identify semiconductor defects in an unbiased way.
Scherrer, Arne; Vuilleumier, Rodolphe; Sebastiani, Daniel
2016-08-28
We report the first fully ab initio calculation of dynamical vibrational circular dichroism spectra in the liquid phase using nuclear velocity perturbation theory (NVPT) derived electronic currents. Our approach is rigorous and general and thus capable of treating weak interactions of chiral molecules as, e.g., chirality transfer from a chiral molecule to an achiral solvent. We use an implementation of the NVPT that is projected along the dynamics to obtain the current and magnetic dipole moments required for accurate intensities. The gauge problem in the liquid phase is resolved in a twofold approach. The electronic expectation values are evaluated in a distributed origin gauge, employing maximally localized Wannier orbitals. In a second step, the gauge invariant spectrum is obtained in terms of a scaled molecular moments, which allows to systematically include solvent effects while keeping a significant signal-to-noise ratio. We give a thorough analysis and discussion of this choice of gauge for the liquid phase. At low temperatures, we recover the established double harmonic approximation. The methodology is applied to chiral molecules ((S)-d2-oxirane and (R)-propylene-oxide) in the gas phase and in solution. We find an excellent agreement with the theoretical and experimental references, including the emergence of signals due to chirality transfer from the solute to the (achiral) solvent.
NASA Astrophysics Data System (ADS)
Burresi, E.; Celino, M.
2012-05-01
A single wurtzite phase of cadmium sulfide cluster is investigated by ab-initio molecular dynamics simulations at different temperatures, ranging from 100 K to 600 K. In this study we propose a possible procedure to characterize the CdS quantum dots system by means of molecular dynamics calculations using a standard Car-Parrinello scheme. In order to ensure the accuracy of the numerical approach, preliminary calculations to test pseudopotentials, cutoff and box size on both single atoms systems and Cd-Cd, S-S, Cd-S dimers have been performed. Calculated binding energies and bond lengths are obtained in good agreement with experimental data. Subsequently, an uncapped CdS cluster with size below 2 nm, 48 atoms of cadmium and 48 atoms of sulfur, in a wurtzite geometry was structurally optimized to minimize internal stresses. The CdS cluster has been carefully characterized structurally at several temperatures up to T = 600 K. At the temperature of 340 K atomic diffusion on the surface allows the onset of a new stable atomic configuration.
NASA Astrophysics Data System (ADS)
Gambino, D.; Sangiovanni, D. G.; Alling, B.; Abrikosov, I. A.
2017-09-01
We use the color diffusion (CD) algorithm in nonequilibrium (accelerated) ab initio molecular dynamics simulations to determine Ti monovacancy jump frequencies in NaCl-structure titanium nitride (TiN), at temperatures ranging from 2200 to 3000 K. Our results show that the CD method extended beyond the linear-fitting rate-versus-force regime [Sangiovanni et al., Phys. Rev. B 93, 094305 (2016), 10.1103/PhysRevB.93.094305] can efficiently determine metal vacancy migration rates in TiN, despite the low mobilities of lattice defects in this type of ceramic compound. We propose a computational method based on gamma-distribution statistics, which provides unambiguous definition of nonequilibrium and equilibrium (extrapolated) vacancy jump rates with corresponding statistical uncertainties. The acceleration-factor achieved in our implementation of nonequilibrium molecular dynamics increases dramatically for decreasing temperatures from 500 for T close to the melting point Tm, up to 33 000 for T ≈0.7 Tm .
NASA Astrophysics Data System (ADS)
Weber, Hans; Schumacher, Mathias; Jóvári, Pál; Tsuchiya, Yoshimi; Skrotzki, Werner; Mazzarello, Riccardo; Kaban, Ivan
2017-08-01
GeTe is a prototypical phase-change material employed in data storage devices. In this work, the atomic structure of liquid GeTe is studied by x-ray and neutron diffraction in the temperature range from 1197 to 998 K. The dynamic viscosity is measured from 1273 to 953 K, which is 55 K below the solidification point, using an oscillating-cup viscometer. The density of liquid GeTe between 1293 and 973 K is determined by the high-energy γ -ray attenuation method. The experiments are complemented with ab initio molecular dynamics (AIMD) simulations based on density functional theory (DFT). Compatibility of the AIMD-DFT models with the diffraction data is proven by simultaneous fitting of all data sets in the frame of the reverse Monte Carlo simulation technique. It is shown that octahedral order dominates in liquid GeTe, although tetrahedral structures are also present. The viscosity of the equilibrium and weakly undercooled liquid GeTe obeys the Arrhenius law with a small activation energy of the order of 0.3 eV, which is indicative of a highly fragile liquid. The calculated density of states and electronic wave functions point to the existence of a pseudogap and localized electron states within the gap in the equilibrium liquid near the melting point as well as in the undercooled liquid.
Caro, Miguel A; Lopez-Acevedo, Olga; Laurila, Tomi
2017-08-08
We present a complete methodology to consistently estimate redox potentials strictly from first-principles, without any experimental input. The methodology is based on (i) ab initio molecular dynamics (MD) simulations, (ii) all-atom explicit solvation, (iii) the two-phase thermodynamic (2PT) model, and (iv) the use of electrostatic potentials as references for the absolute electrochemical scale. We apply the approach presented to compute reduction potentials of the following redox couples: Cr(2+/3+), V(2+/3+), Ru(NH3)6(2+/3+), Sn(2+/4+), Cu(1+/2+), FcMeOH(0/1+), and Fe(2+/3+) (in aqueous solution) and Fc(0/1+) (in acetonitrile). We argue that fully quantum-mechanical simulations are required to correctly model the intricate dynamical effects of the charged complexes on the surrounding solvent molecules within the solvation shell. Using the proposed methodology allows for a computationally efficient and statistically stable approach to compute free energy differences, yielding excellent agreement between our computed redox potentials and the experimental references. The root-mean-square deviation with respect to experiment for the aqueous test set and the two exchange-correlation density functionals used, PBE and PBE with van der Waals corrections, are 0.659 and 0.457 V, respectively. At this level of theory, depending on the functional employed, its ability to correctly describe each particular molecular complex seems to be the factor limiting the accuracy of the calculations.
NASA Astrophysics Data System (ADS)
Subotnik, Joseph
In this talk, I will give a broad overview of our work in nonadiabatic dynamics, i.e. the dynamics of strongly coupled nuclear-electronic motion whereby the relaxation of a photo-excited electron leads to the heating up of phonons. I will briefly discuss how to model such nuclear motion beyond mean field theory. Armed with the proper framework, I will then focus on how to calculate one flavor of electron-phonon couplings, known as derivative couplings in the chemical literature. Derivative couplings are the matrix elements that couple adiabatic electronic states within the Born-Oppenheimer treatment, and I will show that these matrix elements show spurious poles using formal (frequency-independent) time-dependent density functional theory. To correct this TD-DFT failure, a simple approximation will be proposed and evaluated. Finally, time permitting, I will show some ab initio calculations whereby one can use TD-DFT derivative couplings to study electronic relaxation through a conical intersection.
NASA Astrophysics Data System (ADS)
Walker, Brent; Michaelides, Angelos
2010-11-01
The impact of quantum nuclear effects on hydrogen (H-) bond strength has been inferred in earlier work from bond lengths obtained from path integral molecular dynamics (PIMD) simulations. To obtain a direct quantitative assessment of such effects, we use constrained-centroid PIMD simulations to calculate the free energy changes upon breaking the H-bonds in dimers of HF and water. Comparing ab initio simulations performed using PIMD and classical nucleus molecular dynamics (MD), we find smaller dissociation free energies with the PIMD method. Specifically, at 50 K, the H-bond in (HF)2 is about 30% weaker when quantum nuclear effects are included, while that in (H2O)2 is about 15% weaker. In a complementary set of simulations, we compare unconstrained PIMD and classical nucleus MD simulations to assess the influence of quantum nuclei on the structures of these systems. We find increased heavy atom distances, indicating weakening of the H-bond consistent with that observed by direct calculation of the free energies of dissociation.
NASA Astrophysics Data System (ADS)
Agosta, Lorenzo; Brandt, Erik G.; Lyubartsev, Alexander P.
2017-07-01
Ab initio molecular dynamics simulations are reported for water-embedded TiO2 surfaces to determine the diffusive and reactive behavior at full hydration. A three-domain model is developed for six surfaces [rutile (110), (100), and (001), and anatase (101), (100), and (001)] which describes waters as "hard" (irreversibly bound to the surface), "soft" (with reduced mobility but orientation freedom near the surface), or "bulk." The model explains previous experimental data and provides a detailed picture of water diffusion near TiO2 surfaces. Water reactivity is analyzed with a graph-theoretic approach that reveals a number of reaction pathways on TiO2 which occur at full hydration, in addition to direct water splitting. Hydronium (H3O+) is identified to be a key intermediate state, which facilitates water dissociation by proton hopping between intact and dissociated waters near the surfaces. These discoveries significantly improve the understanding of nanoscale water dynamics and reactivity at TiO2 interfaces under ambient conditions.
NASA Astrophysics Data System (ADS)
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
NASA Astrophysics Data System (ADS)
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.
Zhou, Zhaohui; Liu, Jin; Long, Run; Li, Linqiu; Guo, Liejin; Prezhdo, Oleg V
2017-05-17
Ultrafast charge recombination in hematite (α-Fe2O3) severely limits its applications in solar energy conversion and utilization, for instance, in photoelectrochemical water splitting. We report the first time-domain ab initio study of charge relaxation dynamics in α-Fe2O3 with and without the oxygen vacancy (Ov) defect, using non-adiabatic molecular dynamics implemented within time-dependent density functional theory. The simulations show that the hole trapping is the rate-limiting step in the electron-hole recombination process for both neutral and ionized Ov systems. The electron trapping is fast, and the trapped electron are relatively long-lived. A similar asymmetry is found for the relaxation of free charge carriers: relaxation of photoholes in the valence band is slower than relaxation of photoelectrons in the conduction band. The slower dynamics of holes offers an advantage to water oxidation at α-Fe2O3 photoanodes. Notably, the neutral Ov defect accelerates significantly the charge recombination rate, by about a factor of 30 compared to the ideal lattice, due to the stronger electron-vibrational coupling at the defect. However, the recombination rate in the ionized Ov defect is decreased by a factor of 10 with respect to the neutral defect, likely due to expansion of the local iron shell around the Ov site. The Ov defect ionization in α-Fe2O3 photoanodes is important for increasing both electrical conductivity and charge carrier lifetimes. The simulations reproduce well the time scales for the hot carrier cooling, trapping and recombination available from transient spectroscopy experiments, and suggest two alternative mechanisms for the Ov-assisted electron-hole recombination. The study provides a detailed atomistic understanding of carrier dynamics in hematite, and rationalizes the experimentally reported activation of α-Fe2O3 photoanodes by incorporation of Ov defects.
An ab initio potential energy surface and dynamics of the Ar+H2+ → ArH + + H reaction
NASA Astrophysics Data System (ADS)
Liu, Xinguo; Liu, Huirong; Zhang, Qinggang
2011-04-01
An ab initio potential energy surface (PES) for the ground state (1 2A') of the chemical reaction Ar+H2+ → ArH + + H has been constructed from a set of accurate ab initio data, which we have computed using the coupled-cluster theory including all single and double excitations plus perturbative corrections for the triples UCCSD(T) with a large orbital basis set of aug-cc-pV5Z. The new PES has a root-mean-square (rms) error of 0.5341 kcal/mol. The total integral reaction cross-sections have been calculated at three collision energies by means of the quasi-classical trajectory (QCT) calculation based on the new PES and compared with previous TSH results.
Ab initio molecular dynamics investigations of low-energy recoil events in Ni and NiCo
Liu, Bin; Yuan, Fenglin; Jin, Ke; ...
2015-10-06
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 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 atomsmore » 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.« less
Alber, F.; Carloni, P.
2000-01-01
Quantum-chemical methods are used to shed light on the functional role of residues involved in the resistance of HIV-1 reverse transcriptase against nucleoside-analog drugs. Ab initio molecular dynamics simulations are carried out for models representing the adduct between the triphosphate substrate and the nucleoside binding site. The triphosphate is considered either deprotonated or protonated at the gamma-position. Although the protonated form already experiences large rearrangements in the ps time scale, the fully deprotonated state exhibits a previously unrecognized low-barrier hydrogen bond between Lys65 and gamma-phosphate. Absence of this interaction in Lys65-->Arg HIV-1 RT might play a prominent role in the resistance of this mutant for nucleoside analogs (Gu Z et al., 1994b, Antimicrob Agents Chemother 38:275-281; Zhang D et al., 1994, Antimicrob Agents Chemother 38:282-287). Water molecules present in the active site, not detected in the X-ray structure, form a complex H-bond network. Among these waters, one may be crucial for substrate recognition as it bridges Gln151 and Arg72 with the beta-phosphate. Absence of this stabilizing interaction in Gln151-->Met HIV-1 RT mutant may be a key factor for the known drug resistance of this mutant toward dideoxy-type drugs and AZT (Shirasaka T et al., 1995, Proc Natl Acad Sci USA 92:2398-2402: Iversen AK et al., 1996, J Virol 70:1086-1090). PMID:11206075
Pepin, Robert; Petrone, Alessio; Laszlo, Kenneth J; Bush, Matthew F; Li, Xiaosong; Tureček, František
2016-07-21
Ab initio molecular dynamics (AIMD) with density functional theory (DFT) was applied to explore conformational motions and collision cross sections (Ω) of folded (2) and extended (7) conformers of doubly charged peptide ions, (Ala-Ala-Leu-Arg + 2H)(2+), in the gas phase at 300 and 473 K. The experimental Ω of (Ala-Ala-Leu-Arg +2H)(2+) was measured as 149 ± 1.2 Å(2) at 298 K. Thermally distributed mean values of Ω for 2 and 7 at 300 and 473 K were only 0.8-1.1% larger than for the equilibrium 0 K structures. Long (>10 ps) trajectory calculations indicated entropy-driven conformational change of 2 to 7 that occurred at random within a ∼ 4 ps time window. The experimental Ω was found to fit the calculated population averaged values for 2 and 7, indicating a rapid conformer interconversion. Overall, thermal breathing had only a minor effect on the peptide ion collision cross sections.
NASA Astrophysics Data System (ADS)
Ko, Hsin-Yu; Distasio, Robert A., Jr.; Santra, Biswajit; Car, Roberto
Molecular crystal structure prediction has posed a substantial challenge to first-principles methods and requires sophisticated electronic structure methods to determine the stabilities of nearly degenerate polymorphs. In this work, we demonstrate that the anharmonicity from van der Waals interactions is relevant to the finite-temperature structures of pyridine and pyridine-like molecular crystals. Using such an approach, we find that the equilibrium structures are well captured with classical ab initio molecular dynamics (AIMD), despite the presence of light atoms such as hydrogen. Employing path integral AIMD simulations, we demonstrate that the success of classical AIMD results from a separation of nuclear quantum effects between the intermolecular and intramolecular degrees of freedom. In this separation, the quasiclassical and anharmonic intermolecular degrees of freedom determine the equilibrium structure, while the quantum and harmonic intramolecular degrees of freedom are averaging to the correct intramolecular structure. This work has been supported by the Department of Energy under Grants No. DE-FG02-05ER46201 and DE-SC0008626.
NASA Astrophysics Data System (ADS)
Tsuchiya, T.; Ichikawa, H.; Satoshi, O.
2016-12-01
Although many light elements, such as C, N, O, H, S, and Si, have been proposed as possible constituents in the outer core, their concentrations have been strongly debated for years. In this study the equations of state (EoS) of Fe-light element alloy liquids with Ni are calculated by means of ab initio molecular dynamics (AIMD) simulations over the whole outer core P-Tcondition and P-wave velocities are evaluated based on the derived EoS within the internally consisitent manner. Then candicates for the plausible outer core compositions are searched for by analyzing joint misfits in terms of the seismological models (PREM) of both P-wave velocity and density as a function of ICB temperature. Results show that some compositions with different light elements can reproduce the seismological data within the similar degree and the influence of Ni with reasonable fraction is negligibe. Further constraints are placed combined with the geo/cosmochemical considerations and the melting phase relations. The outer core physical property are then evaluated from thermal conductivity calculations for the optimum compositions.
Ab initio molecular dynamics investigations of low-energy recoil events in Ni and NiCo
Liu, Bin; Yuan, Fenglin; Jin, Ke; Zhang, Yanwen; Weber, William J.
2015-10-06
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 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.
Hydration structures of U(III) and U(IV) ions from ab initio molecular dynamics simulations
Leung, Kevin; Nenoff, Tina M.
2012-08-21
We apply DFT+U-based ab initio molecular dynamics simulations to study the hydration structures of U(III) and U(IV) ions, pertinent to redox reactions associated with uranium salts in aqueous media. U(III) is predicted to be coordinated to 8 water molecules, while U(IV) has a hydration number between 7 and 8. At least one of the innershell water molecules of the hydrated U(IV) complex becomes spontaneously deprotonated. As a result, the U(IV)-O pair correlation function exhibits a satellite peak at 2.15 A associated with the shorter U(IV)-(OH{sup -}) bond. This feature is not accounted for in analysis of extended x-ray absorption fine structure and x-ray adsorption near edge structure measurements, which yield higher estimates of U(IV) hydration numbers. This suggests that it may be useful to include the effect of possible hydrolysis in future interpretation of experiments, especially when the experimental pH is close to the reported hydrolysis equilibrium constant value.
Canaval, Lorenz R; Hadisaputra, Saprizal; Hofer, Thomas S
2015-07-07
Ab initio QMCF-MD simulations of aqueous 18-crown-6 (18C6) and strontium(II)-18-crown-6 (18C6-Sr) were performed to gather insight into their hydration properties. Strongly different characteristics were found for the two solutes in terms of structure and dynamics such as H-bonding. They, however, have in common that their backbone shows high flexibility in aqueous medium, adopting structures significantly differing from idealized gas phase geometries. In particular, planar oxyethylene units stable in the picosecond range occurred in 18C6, while the strontium complex readily exhibits a bent structure. Detailed analysis of this high flexibility was done via two dimensional root mean square deviation plots as well as the evolution of dihedral angles and angles within the simulation trajectory. The vibrational spectra obtained from the QMCF-MD simulations are in excellent agreement with experimental data and show a pronounced blueshift upon complexation of the strontium(II) ion in 18C6.
NASA Astrophysics Data System (ADS)
Song, Bingyi; Jiang, Wenlong; Yang, Bin; Chen, Xiumin; Xu, Baoqiang; Kong, Lingxin; Liu, Dachun; Dai, Yongnian
2016-10-01
The possibility of the separation of Pb-Sb alloys by vacuum distillation was investigated theoretically. The results show that Pb and Sb can be separated by vacuum distillation. However, the experimental results show that vacuum distillation technique does not provide clear separation. According to the literature, Pb-Sb alloys belong to azeotropic compounds under some certain temperature; the experiment and computer simulation were carried out based on the exceptional condition so as to analyze the reason from the experiment and microstructure of Pb-Sb alloys perspective. The separation of Pb-Sb alloys by vacuum distillation was experimentally carried out to probe the azeotropic point. Also, the functions, such as partial radial distributions functions, the structure factor, mean square displacement, and the density of state, were calculated by ab-initio molecular dynamics for the representation of the structure and properties of Pb-Sb alloys with different composition of Sb. The experimental results indicate that there exists common volatilization for Pb-Sb alloys when Sb content is 16.5 wt pct. On the other hand, the calculation results show that there is an intense interaction between Pb and Sb when Sb content is 22 wt pct, which supports the experimental results although Sb content is slightly deviation.
NASA Astrophysics Data System (ADS)
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.
NASA Astrophysics Data System (ADS)
Plašienka, Dušan; Cifra, Peter; MartoÅák, Roman
2015-04-01
We present results of ab initio molecular dynamics study of the structural transformation occurring in hot liquid sulfur under high pressure, which corresponds to the recently observed chain-breakage phenomenon and to the electronic transition reported earlier. The transformation is temperature-induced and separates two distinct polymeric forms of liquid sulfur: high-temperature form composed of short chain-like fragments with open endings and low-temperature form with very long chains. We offer a structural description of the two liquid forms in terms of chain lengths, cross-linking, and chain geometry and investigate several physical properties. We conclude that the transformation is accompanied by changes in energy (but not density) as well as in diffusion coefficient and electronic properties—semiconductor-metal transition. We also describe the analogy of the investigated process to similar phenomena that take place in two other chalcogens selenium and tellurium. Finally, we remark that the behavior of heated liquid sulfur at ambient pressure might indicate a possible existence of a critical point in the low-pressure region of sulfur phase diagram.
NASA Astrophysics Data System (ADS)
Clelia Righi, Maria; Ferrario, Mauro
2008-03-01
Progress in the ability of understanding tribological properties in adsorbed film systems is of paramount importance to unravel fundamental issues in the emerging field of nanoscale science and technology. Many extensive studies have used a quartz-crystal microbalance (QCM) to measure the friction between adsorbed rare gas monolayers and metal substrates. In this work, we report a theoretical investigation of the tribological behavior of different rare gas-metal adsorbate systems, namely, Ar, Kr, Xe on Cu(111), and Xe on Ag(111), based on combined ab initio and classical molecular dynamics simulations. The frictional properties are analyzed in details as a function of system temperature, presence of interlayer defects, and load. The numerical simulations suggest that the simultaneous presence of thermal effects and of interlayer defects, lowering significantly the activation energy barrier, causes a considerable reduction of the static friction threshold. An unexpected dependence on load is also predicted. In particular, we show that friction of anticorrugating systems can be dramatically decreased by applying an external load [1]. The counterintuitive behavior that deviates from the macroscopic Amonton law is dictated by quantum mechanical effects that induce a transformation from anticorrugation to corrugation in the near-surface region. [1] M. C. Righi and M. Ferrario, Phys. Rev. Lett. 99, 176101 (2007).
NASA Astrophysics Data System (ADS)
Aoki, Masaru I.; Tsumuraya, Kazuo
1997-08-01
We study pressure-induced glass-to-crystal transitions in the sodium system. We apply an order-N ab initio molecular-dynamics (MD) method to study the transition. We use an isothermal-isobaric condition with an orbital-free density functional. The system contains 128 atoms in a supercell. We simulate the system at temperatures higher and lower than the glass-transition temperature Tg=120 K. At 50 K the pressure enhances the onset of crystallization from the glass. The system crystallizes at pressures greater than 2.75 GPa during which the crystalline atoms appear after the complete annihilation of the icosahedral clusters. At 290 K the system crystallizes at 10-3 GPa, during which the atoms appear before the annihilation of the clusters. The application of 1 GPa at this temperature retards the crystallization which is consistent with experiments on metallic glasses. Crystallization occurs after the clusters annihilate completely which is the same feature as the transitions at 50 K. The existence of the clusters disturbs the crystallization at high pressures irrespective of temperature. The icosahedral clusters are unstable and transform to other clusters at high pressures, although the clusters are elastically stable and the hardest within +/-0.07 GPa at 0 K [Masaru I. Aoki and Kazuo Tsumuraya, J. Chem. Phys. 104, 6719 (1996)]. The MD methods with the empirical pair potential is found to be insufficient to simulate the transition in this system.
Bučko, Tomáš; Šimko, František
2016-02-14
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 AlF6(3-), AlF5(2-), AlF4(-), as well as the bridged Al2Fm(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.
Plašienka, Dušan Martoňák, Roman; Cifra, Peter
2015-04-21
We present results of ab initio molecular dynamics study of the structural transformation occurring in hot liquid sulfur under high pressure, which corresponds to the recently observed chain-breakage phenomenon and to the electronic transition reported earlier. The transformation is temperature-induced and separates two distinct polymeric forms of liquid sulfur: high-temperature form composed of short chain-like fragments with open endings and low-temperature form with very long chains. We offer a structural description of the two liquid forms in terms of chain lengths, cross-linking, and chain geometry and investigate several physical properties. We conclude that the transformation is accompanied by changes in energy (but not density) as well as in diffusion coefficient and electronic properties—semiconductor-metal transition. We also describe the analogy of the investigated process to similar phenomena that take place in two other chalcogens selenium and tellurium. Finally, we remark that the behavior of heated liquid sulfur at ambient pressure might indicate a possible existence of a critical point in the low-pressure region of sulfur phase diagram.
NASA Astrophysics Data System (ADS)
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.
Konstantinou, Konstantinos; Sushko, Peter V; Duffy, Dorothy M
2016-09-21
The nature of chemical bonding of molybdenum in high level nuclear waste glasses has been elucidated by ab initio molecular dynamics simulations. Two compositions, (SiO2)57.5-(B2O3)10-(Na2O)15-(CaO)15-(MoO3)2.5 and (SiO2)57.3-(B2O3)20-(Na2O)6.8-(Li2O)13.4-(MoO3)2.5, were considered in order to investigate the effect of ionic and covalent components on the glass structure and the formation of the crystallisation precursors (Na2MoO4 and CaMoO4). The coordination environments of Mo cations and the corresponding bond lengths calculated from our model are in excellent agreement with experimental observations. The analysis of the first coordination shell reveals two different types of molybdenum host matrix bonds in the lithium sodium borosilicate glass. Based on the structural data and the bond valence model, we demonstrate that the Mo cation can be found in a redox state and the molybdate tetrahedron can be connected with the borosilicate network in a way that inhibits the formation of crystalline molybdates. These results significantly extend our understanding of bonding in Mo-containing nuclear waste glasses and demonstrate that tailoring the glass composition to specific heavy metal constituents can facilitate incorporation of heavy metals at high concentrations.
NASA Astrophysics Data System (ADS)
Distasio, Robert A., Jr.; Santra, Biswajit; Ko, Hsin-Yu; Car, Roberto
2014-03-01
In this work, we report highly accurate ab initio path-integral molecular dynamics (AI-PIMD) simulations on liquid water at ambient conditions utilizing the recently developed PBE0+vdW(SC) exchange-correlation functional, which accounts for exact exchange and a self-consistent pairwise treatment of van der Waals (vdW) or dispersion interactions, combined with nuclear quantum effects (via the colored-noise generalized Langevin equation). The importance of each of these effects in the theoretical prediction of the structure of liquid water will be demonstrated by a detailed comparative analysis of the predicted and experimental oxygen-oxygen (O-O), oxygen-hydrogen (O-H), and hydrogen-hydrogen (H-H) radial distribution functions as well as other structural properties. In addition, we will discuss the theoretically obtained proton momentum distribution, computed using the recently developed Feynman path formulation, in light of the experimental deep inelastic neutron scattering (DINS) measurements. DOE: DE-SC0008626, DOE: DE-SC0005180.
Castro-Palacios, Juan Carlos; Rubayo-Soneira, Jesús; Ishii, Keisaku; Yamashita, Koichi
2007-04-07
The intermolecular potentials for the NO(X 2Pi)-Kr and NO(A 2Sigma+)-Kr systems have been calculated using highly accurate ab initio calculations. The spin-restricted coupled cluster method for the ground 1 2A' state [NO(X 2Pi)-Kr] and the multireference singles and doubles configuration interaction method for the excited 2 2A' state [NO(A 2Sigma+)-Kr], respectively, were used. The potential energy surfaces (PESs) show two linear wells and one that is almost in the perpendicular position. An analytical representation of the PESs has been constructed for the triatomic systems and used to carry out molecular dynamics (MD) simulations of the NO-doped krypton matrix response after excitation of NO. MD results are shown comparatively for three sets of potentials: (1) anisotropic ab initio potentials [NO molecule direction fixed during the dynamics and considered as a point (its center of mass)], (2) isotropic ab initio potentials (isotropic part in a Legendre polynomial expansion of the PESs), and (3) fitted Kr-NO potentials to the spectroscopic data. An important finding of this work is that the anisotropic and isotropic ab initio potentials calculated for the Kr-NO triatomic system are not suitable for describing the dynamics of structural relaxation upon Rydberg excitation of a NO impurity in the crystal. However, the isotropic ab initio potential in the ground state almost overlaps the published experimental potential, being almost independent of the angle asymmetry. This fact is also manifested in the radial distribution function around NO. However, in the case of the excited state the isotropic ab initio potential differs from the fitted potentials, which indicates that the Kr-NO interaction in the matrix is quite different because of the presence of the surrounding Kr atoms acting on the NO molecule. MD simulations for isotropic potentials reasonably reproduce the experimental observables for the femtosecond response and the bubble size but do not match
Liu, Lihong; Liu, Jian; Martinez, Todd J.
2015-12-17
Here, we investigate the photoisomerization of a model retinal protonated Schiff base (trans-PSB3) using ab initio multiple spawning (AIMS) based on multi-state second order perturbation theory (MSPT2). Discrepancies between the photodynamical mechanism computed with three-root state-averaged complete active space self-consistent field (SA-3-CASSCF, which does not include dynamic electron correlation effects) and MSPT2 show that dynamic correlation is critical in this photoisomerization reaction. Furthermore, we show that the photodynamics of trans-PSB3 is not well described by predictions based on minimum energy conical intersections (MECIs) or minimum energy conical intersection (CI) seam paths. Instead, most of the CIs involved in the photoisomerization are far from MECIs and minimum energy CI seam paths. Thus, both dynamical nuclear effects and dynamic electron correlation are critical to understanding the photochemical mechanism.
Liu, Lihong; Liu, Jian; Martinez, Todd J.
2015-12-17
Here, we investigate the photoisomerization of a model retinal protonated Schiff base (trans-PSB3) using ab initio multiple spawning (AIMS) based on multi-state second order perturbation theory (MSPT2). Discrepancies between the photodynamical mechanism computed with three-root state-averaged complete active space self-consistent field (SA-3-CASSCF, which does not include dynamic electron correlation effects) and MSPT2 show that dynamic correlation is critical in this photoisomerization reaction. Furthermore, we show that the photodynamics of trans-PSB3 is not well described by predictions based on minimum energy conical intersections (MECIs) or minimum energy conical intersection (CI) seam paths. Instead, most of the CIs involved in the photoisomerizationmore » are far from MECIs and minimum energy CI seam paths. Thus, both dynamical nuclear effects and dynamic electron correlation are critical to understanding the photochemical mechanism.« less
Discovering chemistry with an ab initio nanoreactor
Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.
2014-11-02
Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. Ultimately, these results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings.
Ab Initio Reactive Computer Aided Molecular Design.
Martínez, Todd J
2017-03-21
Few would dispute that theoretical chemistry tools can now provide keen insights into chemical phenomena. Yet the holy grail of efficient and reliable prediction of complex reactivity has remained elusive. Fortunately, recent advances in electronic structure theory based on the concepts of both element- and rank-sparsity, coupled with the emergence of new highly parallel computer architectures, have led to a significant increase in the time and length scales which can be simulated using first principles molecular dynamics. This opens the possibility of new discovery-based approaches to chemical reactivity, such as the recently proposed ab initio nanoreactor. We argue that due to these and other recent advances, the holy grail of computational discovery for complex chemical reactivity is rapidly coming within our reach.
Discovering chemistry with an ab initio nanoreactor
Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; ...
2014-11-02
Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis frommore » primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. Ultimately, these results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings.« less
Discovering chemistry with an ab initio nanoreactor
NASA Astrophysics Data System (ADS)
Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.
2014-12-01
Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provide detailed physical insight. Although theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor—a highly accelerated first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor, we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, which provide new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery, in addition to its traditional role of interpreting experimental findings.
Discovering chemistry with an ab initio nanoreactor.
Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S; Martínez, Todd J
2014-12-01
Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provide detailed physical insight. Although theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor--a highly accelerated first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor, we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, which provide new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery, in addition to its traditional role of interpreting experimental findings.
Discovering chemistry with an ab initio nanoreactor
Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.
2014-01-01
Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings. PMID:25411881
Xie, Binbin; Liu, Lihong; Cui, Ganglong; Fang, Wei-Hai; Cao, Jun; Feng, Wei; Li, Xin-qi
2015-11-21
In this work, the recently introduced quantum trajectory mean-field (QTMF) approach is implemented and employed to explore photodissociation dynamics of diazirinone (N{sub 2}CO), which are based on the high-level ab initio calculation. For comparison, the photodissociation process has been simulated as well with the fewest-switches surface hopping (FSSH) and the ab initio multiple spawning (AIMS) methods. Overall, the dynamical behavior predicted by the three methods is consistent. The N{sub 2}CO photodissociation at λ > 335 nm is an ultrafast process and the two C—N bonds are broken in a stepwise way, giving birth to CO and N{sub 2} as the final products in the ground state. Meanwhile, some noticeable differences were found in the QTMF, FSSH, and AIMS simulated time constants for fission of the C—N bonds, excited-state lifetime, and nonadiabatic transition ratios in different intersection regions. These have been discussed in detail. The present study provides a clear evidence that direct ab initio QTMF approach is one of the reliable tools for simulating nonadiabatic dynamics processes.
Stein, Tamar; Bandyopadhyay, Biswajit; Troy, Tyler P.; ...
2017-05-08
The growth mechanism of hydrocarbons in ionizing environments, such as the interstellar medium (ISM), and some combustion conditions remains incompletely understood. Ab initio molecular dynamics (AIMD) simulations and molecular beam vacuum-UV (VUV) photoionization mass spectrometry experiments were performed to understand the ion-molecule growth mechanism of small acetylene clusters (up to hexamers). A dramatic dependence of product distribution on the ionization conditions is demonstrated experimentally and understood from simulations. The products change from reactive fragmentation products in a higher temperature, higher density gas regime toward a very cold collision-free cluster regime that is dominated by products whose empirical formula is (C2H2)n+,more » just like ionized acetylene clusters. The fragmentation products result from reactive ion- molecule collisions in a comparatively higher pressure and temperature regime followed by unimolecular decomposition. The isolated ionized clusters display rich dynamics that contain bonded C4H4+ and C6H6+ structures solvated with one or more neutral acetylene molecules. Such species contain large amounts ( > 2 eV) of excess internal energy. The role of the solvent acetylene molecules is to affect the barrier crossing dynamics in the potential energy surface (PES) between (C2H2)n+ isomers and provide evaporative cooling to dissipate the excess internal energy and stabilize products including the aromatic ring of the benzene cation. Formation of the benzene cation is demonstrated in AIMD simulations of acetylene clusters with n > 3, as well as other metastable C6H6+ isomers. Lastly, these results suggest a path for aromatic ring formation in cold acetylene-rich environments such as parts of the ISM.« less
Clark, Jeffrey K; Paddison, Stephen J
2014-09-07
Ab initio molecular dynamics simulations were performed to investigate the effects of nanoscale confinement on the structural and dynamical properties of water and slightly acidic water. Single-walled carbon nanotubes (CNTs) of two different diameters (11.0 and 13.3 Å) were used as confinement vessels, and the inner walls of the CNT were either left bare or fluorinated to explore the influence of the confined environment on the determined properties. The water molecules in the fluorinated nanotubes were found to preferentially localize near the CNT surface and exhibit highly ordered structures while those in the bare CNTs were more randomly distributed. Additionally, weak interactions that resembled hydrogen bonds between the water molecules and the fluorine atoms were observed which occurred at a greater frequency in the smaller diameter CNT indicating an influence of the confinement dimensions on these interactions. This was further pronounced when an excess proton was added where, on average, approximately half of the water molecules in the smaller tube were involved in these interactions. This also led to a structured hydrogen bond network with regular defect sites that hindered proton transfer along the channel axis. Addition of the proton in the larger fluorinated CNT, however, disrupted the structural ordering and proton transfer down the nanotube axis near the surface of the CNT wall readily occurred. Proton transfer through the channel was also observed in the smaller nonfluorinated system, however, the proton was located closer to the center of the CNT, while in the larger nonfluorinated CNT proton transfer exhibited less directional preference indicating an impact of the scale of confinement and nature of the surface on proton transfer.
Pacheco, Alexander B; Iyengar, Srinivasan S
2011-02-21
We recently proposed a multistage ab initio wavepacket dynamics (MS-AIWD) treatment for the study of delocalized electronic systems as well as electron transport through donor-bridge-acceptor systems such as those found in molecular-wire/electrode networks. In this method, the full donor-bridge-acceptor open system is treated through a rigorous partitioning scheme that utilizes judiciously placed offsetting absorbing and emitting boundary conditions. In this manner, the electronic coupling between the bridge molecule and surrounding electrodes is accounted. Here, we extend MS-AIWD to include the dynamics of open-electronic systems in conjunction with (a) simultaneous treatment of nuclear dynamics and (b) external electromagnetic fields. This generalization is benchmarked through an analysis of wavepackets propagated on a potential modeled on an Al(27) - C(7) - Al(27) nanowire. The wavepacket results are inspected in the momentum representation and the dependence of momentum of the wavepacket as well as its transmission probabilities on the magnitude of external bias are analyzed.
NASA Astrophysics Data System (ADS)
Pacheco, Alexander B.; Iyengar, Srinivasan S.
2011-02-01
We recently proposed a multistage ab initio wavepacket dynamics (MS-AIWD) treatment for the study of delocalized electronic systems as well as electron transport through donor-bridge-acceptor systems such as those found in molecular-wire/electrode networks. In this method, the full donor-bridge-acceptor open system is treated through a rigorous partitioning scheme that utilizes judiciously placed offsetting absorbing and emitting boundary conditions. In this manner, the electronic coupling between the bridge molecule and surrounding electrodes is accounted. Here, we extend MS-AIWD to include the dynamics of open-electronic systems in conjunction with (a) simultaneous treatment of nuclear dynamics and (b) external electromagnetic fields. This generalization is benchmarked through an analysis of wavepackets propagated on a potential modeled on an Al27 - C7 - Al27 nanowire. The wavepacket results are inspected in the momentum representation and the dependence of momentum of the wavepacket as well as its transmission probabilities on the magnitude of external bias are analyzed.
NASA Astrophysics Data System (ADS)
Gonzalez Del Rio, Beatriz; Gonzalez Tesedo, Luis Enrique
We report results of an orbital-free ab initio molecular dynamics (OF-AIMD) study of the free liquid surface of Sn at 1000 K. A key ingredient in the OF-AIMD method is the local ionic pseudopotential describing the ions-valence electrons interaction. We have developed a force-matching method to derive a local ionic pseudopotential suitable to account for a rapidly varying density system, such as in a free liquid surface. We obtain very good results for several structural properties. We have also studied the evolution of some dynamical properties when going from the central region (where the system behaves like the bulk liquid) towards the free liquid surface. We aknowledge the spanish MSI (Project FIS2012-33126) and the University of Valladolid for the provision of a PhD grant.
Towards SiC Surface Functionalization: An Ab Initio Study
Cicero, G; Catellani, A
2005-01-28
We present a microscopic model of the interaction and adsorption mechanism of simple organic molecules on SiC surfaces as obtained from ab initio molecular dynamics simulations. Our results open the way to functionalization of silicon carbide, a leading candidate material for bio-compatible devices.
Li, Xiaozhou; Tapmeyer, Lukas; Bolte, Michael
2016-01-01
Abstract The excellent results of dispersion‐corrected density functional theory (DFT‐D) calculations for static systems have been well established over the past decade. The introduction of dynamics into DFT‐D calculations is a target, especially for the field of molecular NMR crystallography. Four 13C ss‐NMR calibration compounds are investigated by single‐crystal X‐ray diffraction, molecular dynamics and DFT‐D calculations. The crystal structure of 3‐methylglutaric acid is reported. The rotator phases of adamantane and hexamethylbenzene at room temperature are successfully reproduced in the molecular dynamics simulations. The calculated 13C chemical shifts of these compounds are in excellent agreement with experiment, with a root‐mean‐square deviation of 2.0 ppm. It is confirmed that a combination of classical molecular dynamics and DFT‐D chemical shift calculation improves the accuracy of calculated chemical shifts. PMID:27276509
Simulation of a silica glass from combined classical and ab initio molecular-dynamics
NASA Astrophysics Data System (ADS)
Benoit, Magali; Ispas, Simona; Jund, Philippe; Jullien, Rémi
1999-11-01
We present structural and electronic characteristics of a vitreous silica glass obtained from combined classical and Car-Parrinello (CP) molecular-dynamics (MD) simulations. The equilibration of the liquid, quench and relaxation of the glass are performed classically using the van Beest et al. (BKS) potential and the resulting configuration is used as input for the CP simulation. A remarkable stability of the CP dynamics is observed justifying this procedure and validating the BKS potential.
Laporte, Sara; Finocchi, Fabio; Paulatto, Lorenzo; Blanchard, Marc; Balan, Etienne; Guyot, François; Saitta, Antonino Marco
2015-08-21
We report a density-functional theory (DFT)-based study of the interface of bulk water with a prototypical oxide surface, MgO(001), and focus our study on the often-overlooked surface electric field. In particular, we observe that the bare MgO(001) surface, although charge-neutral and defectless, has an intense electric field on the Å scale. The MgO(001) surface covered with 1 water monolayer (1 ML) is investigated via a supercell accounting for the experimentally-observed (2 × 3) reconstruction, stable at ambient temperature, and in which two out of six water molecules are dissociated. This 1 ML-hydrated surface is also found to have a high, albeit short-ranged, normal component of the field. Finally, the oxide/water interface is studied via room-temperature ab initio molecular dynamics (AIMD) using 34 H2O molecules between two MgO(001) surfaces. To our best knowledge this is the first AIMD study of the MgO(001)/liquid water interface in which all atoms are treated using DFT and including several layers above the first adsorbed layer. We observe that the surface electric field, averaged over the AIMD trajectories, is still very strong on the fully-wet surface, peaking at about 3 V Å(-1). Even in the presence of bulk-like water, the structure of the first layer in contact with the surface remains similar to the (2 × 3)-reconstructed ice ad-layer on MgO(001). Moreover, we observe proton exchange within the first layer, and between the first and second layers - indeed, the O-O distances close to the surface are found to be distributed towards shorter distances, a property which has been shown to directly promote proton transfer.
NASA Astrophysics Data System (ADS)
Xu, Dong
Accurate prediction of the vibrational spectra in polyatomic molecules and free radicals depends on obtaining high quality solutions to the vibrational Schrodinger equation. The quantum simple harmonic oscillator provides the traditional first approximation for modeling molecular vibrational states. Rarely does a vibrational analysis extend beyond this first approximation, and harmonic energy levels are routinely used to predict the infrared spectra and other dynamical properties of molecules. However, there are many large-amplitude molecular motions that are extremely anharmonic, including internal torsions about atom-atom single bonds, bending and stretching of weak bonds in van der Waals complexes, and isomerization along relocalization coordinates in free radicals. In these cases, the harmonic treatment provided by electronic structure quantum chemistry packages is completely inadequate. Furthermore, the anharmonicity often includes strong coupling among two or more distinct vibrational coordinates, necessitating a multi-dimensional analysis of the vibrational Schrodinger equation along the coupled coordinates. A novel ab initio solver package, FEMVib, is developed within the finite element method (FEM) framework. A mixed programming paradigm that combines C++, Fortran and Python is employed to take advantage of existing numerical libraries. FEMVib has been rigorously tested to resolve the eigenvalues and wavefunctions of hundreds of vibrational energy states to high accuracy and precision. It may be used to calculate the complete vibrational spectra of triatomic molecules or to approximate larger systems through a "relaxed" model that allows complete coupling of up to three selected vibrational coordinates. FEMVib provides physical chemists with a general, robust and accurate computational tool for molecular vibrational analysis.
NASA Astrophysics Data System (ADS)
Li, Xiaohu; Iyengar, Srinivasan S.
2010-11-01
We present a generalization to our previously developed quantum wavepacket ab initio molecular dynamics (QWAIMD) method by using multiple diabatic electronic reduced single particle density matrices, propagated within an extended Lagrangian paradigm. The Slater determinantal wavefunctions associated with the density matrices utilized may be orthogonal or nonorthogonal with respect to each other. This generalization directly results from an analysis of the variance in electronic structure with quantum nuclear degrees of freedom. The diabatic electronic states are treated here as classical parametric variables and propagated simultaneously along with the quantum wavepacket and classical nuclei. Each electronic density matrix is constrained to be N-representable. Consequently two sets of new methods are derived: extended Lagrangian-QWAIMD (xLag-QWAIMD) and diabatic extended Lagrangian-QWAIMD (DxLag-QWAIMD). In both cases, the instantaneous potential energy surface for the quantum nuclear degrees of freedom is constructed from the diabatic states using an on-the-fly nonorthogonal multireference formalism. By introducing generalized grid-based electronic basis functions, we eliminate the basis set dependence on the quantum nucleus. Subsequent reuse of the two-electron integrals during the on-the-fly potential energy surface computation stage yields a substantial reduction in computational costs. Specifically, both xLag-QWAIMD and DxLag-QWAIMD turn out to be about two orders of magnitude faster than our previously developed time-dependent deterministic sampling implementation of QWAIMD. Energy conservation properties, accuracy of the associated potential surfaces, and vibrational properties are analyzed for a family of hydrogen bonded systems.
NASA Astrophysics Data System (ADS)
Wang, C. C.; Tan, J. Y.; Liu, L. H.
2017-03-01
The temperature and pressure-dependent dielectric functions of liquids are of great importance to the thermal radiation transfer and the diagnosis and control of fuel combustion. In this work, we apply the state-of-the-art ab initio molecular dynamics (AIMD) method to calculate the infrared dielectric functions of liquid methanol at 183-573 K and 0.1-160 MPa in the spectral range 10-4000 cm-1, and study the temperature and pressure effects on the dielectric functions. The AIMD approach is validated by the Infrared Variable Angle Spectroscopic Ellipsometry (IR-VASE) experimental measurements at 298 K and 0.1 MPa, and the proposed IR-VASE method is verified by comparison with paper data of distilled water. The results of the AIMD approach agrees well with the experimental values of IR-VASE. The experimental and theoretical analyses indicate that the temperature and pressure exert a noticeable influence on the infrared dielectric functions of liquid methanol. As temperature increases, the average molecular dipole moment decreases. The amplitudes of dominant absorption peaks reduce to almost one half as temperature increases from 183 to 333 K at 0.1 MPa and from 273 to 573 K at 160 MPa. The absorption peaks below 1500 cm-1 show a redshift, while those centered around 3200 cm-1 show a blueshift. Moreover, larger average dipole moments are observed as pressure increases. The amplitudes of dominant absorption peaks increase to almost two times as pressure increases from 1 to 160 MPa at 373 K.
Comas-Vives, Aleix; Stirling, András; Lledós, Agustí; Ujaque, Gregori
2010-08-02
The Wacker process consists of the oxidation of ethylene catalyzed by a Pd(II) complex. The reaction mechanism has been largely debated in the literature; two modes for the nucleophilic addition of water to a Pd-coordinated alkene have been proposed: syn-inner- and anti-outer-sphere mechanisms. These reaction steps have been theoretically evaluated by means of ab initio molecular dynamics combined with metadynamics by placing the [Pd(C(2)H(4))Cl(2)(H(2)O)] complex in a box of water molecules, thereby resembling experimental conditions at low [Cl(-)]. The nucleophilic addition has also been evaluated for the [Pd(C(2)H(4))Cl(3)](-) complex, thus revealing that the water by chloride ligand substitution trans to ethene is kinetically favored over the generally assumed cis species in water. Hence, the resulting trans species can only directly undertake the outer-sphere nucleophilic addition, whereas the inner-sphere mechanism is hindered since the attacking water is located trans to ethene. In addition, all the simulations from the [Pd(C(2)H(4))Cl(2)(H(2)O)] species (either cis or trans) support an outer-sphere mechanism with a free-energy barrier compatible with that obtained experimentally, whereas that for the inner-sphere mechanism is significantly higher. Moreover, additional processes for a global understanding of the Wacker process in solution have also been identified, such as ligand substitutions, proton transfers that involve the aquo ligand, and the importance of the trans effect of the ethylene in the nucleophilic addition attack.
NASA Astrophysics Data System (ADS)
Janssen, W. B. J. M.; van der Avoird, A.
1990-07-01
Starting from an ab initio H2-H2 potential that contains anisotropic short-range and dispersion terms, in addition to the quadrupole-quadrupole interactions, we have performed lattice-dynamics calculations for the orientationally disordered hexagonal (hcp) and ordered cubic (Pa3) phases of solid (ortho and para) hydrogen and deuterium. The method used is the time-dependent Hartree (TDH) formalism, with the explicit inclusion of translation-rotation coupling. By an anharmonic expansion of the potential through sixth order in the molecular displacements and the use of wave functions for the translational vibrations that are sufficiently flexible to adapt to this strong anharmonicity, we could avoid the usual (effective) Jastrow correction to the potential. The calculated phonon and roton or libron frequencies are in fairly good agreement with infrared, Raman, and neutron-scattering data, significantly better in general than the results from earlier (separate) phonon calculations and roton or libron calculations that have used empirical potentials. The transition pressure for ordering para-H2 or ortho-D2 appears to be dominated by the classical quadrupole-quadrupole interactions. It is significantly affected by the increase of the rotational constant and, especially, by the reduction of the quadrupole moment, which follows from a shortening of the intramolecular bond. Translation-rotation coupling yields the observed mixing of phonons and rotons at high pressure, but its effect on the transition pressure is minute. The remaining discrepancy between the calculated and observed transition pressures must be caused by three-body interactions and by correlations between the molecular motions that are beyond the TDH approximation.
Liquid Aluminum: Atomic diffusion and viscosity from ab initio molecular dynamics
Jakse, Noel; Pasturel, Alain
2013-01-01
We present a study of dynamic properties of liquid aluminum using density-functional theory within the local-density (LDA) and generalized gradient (GGA) approximations. We determine the temperature dependence of the self-diffusion coefficient as well the viscosity using direct methods. Comparisons with experimental data favor the LDA approximation to compute dynamic properties of liquid aluminum. We show that the GGA approximation induce more important backscattering effects due to an enhancement of the icosahedral short range order (ISRO) that impact directly dynamic properties like the self-diffusion coefficient. All these results are then used to test the Stokes-Einstein relation and the universal scaling law relating the diffusion coefficient and the excess entropy of a liquid. PMID:24190311
Kafka, Graeme R; Masters, Sarah L; Rankin, David W H
2007-07-05
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).
NASA Astrophysics Data System (ADS)
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.
Miyamoto, Yoshiyuki; Zhang, Hong; Rubio, Angel
2012-06-05
Nanoscale molecular confinement substantially modifies the functionality and electronic properties of encapsulated molecules. Many works have approached this problem from the perspective of quantifying ground-state molecular changes, but little is known about the nonequilibrium dynamics of encapsulated molecular system. In this letter, we report an analysis of the nonequilibrium dynamics of acetylene (C(2)H(2)) inside a semiconducting carbon nanotube (CNT). An ultrashort high-intense laser pulse (2 fs width and 10(15) W/cm(2) intensity) brings the systems out of equilibrium. This process is modeled by comprehensive first-principles time-dependent density-functional simulations. When encapsulated, acetylene dimer, unlike a single acetylene molecule, exhibits correlated vibrational dynamics (C-C bond rotation and H-C-C bending) that is markedly different from the dynamics observed in the gas phase. This result highlights the role of CNT in modulating the optical electric field within the tube. At longer simulation timescales (> 20 fs) in the largest-diameter tube studied here [CNT(14,0)], we observe synchronized rotation about the C-C axes in the dimer and ultimately ejection of one of the four hydrogen atoms. Our results illustrate the richness of photochemical phenomena in confined geometries.
Reaction selectivity in an ionized water dimer: nonadiabatic ab initio dynamics simulations.
Svoboda, Ondřej; Hollas, Daniel; Ončák, Milan; Slavíček, Petr
2013-07-21
We study dynamical processes following water dimer ionization. The nonadiabatic dynamical simulations of the water dimer radical cation are performed using a surface hopping technique and a Complete Active Space-Self Consistent Field (CASSCF) method for the description of electronic structure. The main goal of this study is to find out whether a state-dependent reactivity is observed for the water dimer radical cation. We provide a detailed mapping of the potential energy surfaces (PESs) in the relevant coordinates for different electronic states. Dynamical patterns are discussed on the basis of static PES cuts and available experimental data. As a product of the reaction, we observed either proton transferred structure (H3O(+)···OH˙) or various dissociated structures (H3O(+) + OH˙, H2O˙(+) + H2O, H˙ + OH˙ + H2O˙(+)). The relative yields are controlled by the populated electronic state of the radical cation. The proton transfer upon the HOMO electron ionization is an ultrafast process, taking less than 100 fs, in cases of higher energy ionization the dynamical processes occur on longer timescales (200-300 fs). We also discuss the implications of our simulations for the efficiency of the recently identified intermolecular coulomb decay (ICD) process in the water dimer.
Ab-Initio Molecular Dynamics Simulations of Molten Ni-Based Superalloys (Preprint)
2008-07-01
Ni473W27 0 5 10 15 20 555 433 544 666 444 676 322 422 565 554 454 311 421 % Common Neighbour Analysis Signature ICOSAHEDRA...currently underway using an NPT ensemble with Parrinello-Rahman dynamics. These calculations use local density approximation PAW (Projector Augmented
Burisch, Christian; Markwick, Phineus R L; Doltsinis, Nikos L; Schlitter, Jürgen
2008-01-01
A versatile reaction coordinate, the "dynamic distance", is introduced for the study of reactions involving the rupture and formation of a series of chemical bonds or contacts. The dynamic distance is a mass-weighted mean of selected distances. When implemented as a generalized constraint, the dynamic distance is particularly suited for driving activated processes by controlled increase during a simulation. As a single constraint acting upon multiple degrees of freedom, the sequence of events along the resulting reaction pathway is determined unambiguously by the underlying energy landscape. Free energy profiles can be readily obtained from the mean constraint force. In this paper both theoretical aspects and numerical implementation are discussed, and the unique and diverse properties of this reaction coordinate are demonstrated using three examples: In the framework of Car-Parrinello molecular dynamics, we present results for the prototypical double proton-transfer reaction in formic acid dimer and the photocycle of the guanine-cytosine DNA base pair. As a classical mechanical example, the opening of the binding pocket of the enzyme rubisco is analyzed.
NASA Astrophysics Data System (ADS)
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.
Ab initio molecular-dynamics study of diffusion and defects in solid Li3N
NASA Astrophysics Data System (ADS)
Sarnthein, J.; Schwarz, K.; Blöchl, P. E.
1996-04-01
We investigate defects and diffusion in solid Li3N, a superionic conductor, using the projector-augmented-wave implementation of Car-Parrinello molecular dynamics. Static calculations are used to discuss the structure and formation of Li vacancies, where we also consider hydrogen interstitials. The barrier for lithium jumps to vacant adjacent sites in the Li2N plane (⊥c) was found to be extremely small, namely, 0.004 eV, whereas jumps perpendicular to the Li2N plane (∥c) have a barrier of 0.58 eV. Therefore diffusion in the plane (⊥c) is limited by the formation of vacancies, whereas the barrier dominates perpendicular (∥c) to the plane. A molecular-dynamics run at 800 K confirms the anisotropy of diffusion and leads to diffusion coefficients consistent with experiment. From the trajectories we deduce a microscopic diffusion mechanism and find that mainly isolated jumps take place.
Miller, J.; Miaskiewicz, K.; Osman, R.
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 simulations of the dynamic ion structure factor of warm dense lithium
Witte, B. B. L.; Shihab, M.; Glenzer, S. H.; ...
2017-04-06
Here, we present molecular dynamics simulations based on finite-temperature density functional theory that determine self-consistently the dynamic ion structure factor and the electronic form factor in lithium. Our comprehensive data set allows for the calculation of the dispersion relation for collective excitations, the calculation of the sound velocity, and the determination of the ion feature from the total electronic form factor and the ion structure factor. The results are compared with available experimental x-ray and neutron scattering data. Good agreement is found for both the liquid metal and warm dense matter domain. Finally, we study the impact of possible targetmore » inhomogeneities on x-ray scattering spectra.« less
Ab initio molecular dynamics study of topological defects in polyethylene strands
NASA Astrophysics Data System (ADS)
Saitta, Antonino Marco; Klein, Michael L.
2000-03-01
The mechanical resistance of polyethylene strands subject to tension and the way their properties are affected by the presence of knots(Nature 399), 46 (1999); JCP 111, 9434 (1999). and entanglements(JPCB, in press) (2000). are studied using first-principles molecular dynamics calculations. The presence of topological defects significantly weakens the chain strength, and the radicals generated at the rupture undergo a series of unexpected ``femto'' chemical reactions(JACS 121), 11827 (1999)..
Parsons, A J; Ahmed, I; Rudd, C D; Cuello, G J; Pellegrini, E; Richard, D; Johnson, M R
2010-12-08
Details of the microscopic structure of phosphate glasses destined for biomedical applications, which include sodium, magnesium and calcium cations, have been obtained from the static structure factor measured by means of neutron scattering. A complementary, molecular dynamics study has been performed on a range of phosphate glasses using density functional theory methods, which allow structural fluctuations, including bond breaking, in the liquid phase before quenching to the glass phase. Good agreement between experiment and simulation allows the molecular dynamics trajectories to be analysed in detail. In particular, attention is focused on the cross-linking of divalent cations in contrast with the structural aspects associated with monovalent cations. Magnesium cations are found equidistant and bridging between the phosphorus atoms of different phosphate chains, leading to a shorter phosphorus-phosphorus second neighbour distance (that is, a more compact packing of neighbouring phosphate chains) compared to the effect of sodium cations. Calcium cations show behaviour intermediate between those of magnesium and sodium. Molecular dynamics simulations give access to the cation mobility, which is lowest for magnesium, reflecting its structural, cross-linking role.
Phase behavior of metastable liquid silicon at negative pressure: Ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Zhao, G.; Yu, Y. J.; Yan, J. L.; Ding, M. C.; Zhao, X. G.; Wang, H. Y.
2016-04-01
Extensive first-principle molecular dynamics simulations are performed to study the phase behavior of metastable liquid Si at negative pressure. Our results show that the high-density liquid (HDL) and HDL-vapor spinodals indeed form a continuous reentrant curve and the liquid-liquid critical point seems to just coincide with its minimum. The line of density maxima also has a strong tendency to pass through this minimum. The phase behaviour of metastable liquid Si therefore tends to be a critical-point-free scenario rather than a second-critical-point one based on SW potential.
NASA Astrophysics Data System (ADS)
Bera, Anupam; Ghosh, Jayanta; Bhattacharya, Atanu
2017-07-01
Conical intersections are now firmly established to be the key features in the excited electronic state processes of polyatomic energetic molecules. In the present work, we have explored conical intersection-mediated nonadiabatic chemical dynamics of a simple analogue nitramine molecule, dimethylnitramine (DMNA, containing one N-NO2 energetic group), and its complex with an iron atom (DMNA-Fe). For this task, we have used the ab initio multiple spawning (AIMS) dynamics simulation at the state averaged-complete active space self-consistent field(8,5)/6-31G(d) level of theory. We have found that DMNA relaxes back to the ground (S0) state following electronic excitation to the S1 excited state [which is an (n,π*) excited state] with a time constant of approximately 40 fs. This AIMS result is in very good agreement with the previous surface hopping-result and femtosecond laser spectroscopy result. DMNA does not dissociate during this fast internal conversion from the S1 to the S0 state. DMNA-Fe also undergoes extremely fast relaxation from the upper S1 state to the S0 state; however, this relaxation pathway is dissociative in nature. DMNA-Fe undergoes initial Fe-O, N-O, and N-N bond dissociations during relaxation from the upper S1 state to the ground S0 state through the respective conical intersection. The AIMS simulation reveals the branching ratio of these three channels as N-N:Fe-O:N-O = 6:3:1 (based on 100 independent simulations). Furthermore, the AIMS simulation reveals that the Fe-O bond dissociation channel exhibits the fastest (time constant 24 fs) relaxation, while the N-N bond dissociation pathway features the slowest (time constant 128 fs) relaxation. An intermediate time constant (30 fs) is found for the N-O bond dissociation channel. This is the first nonadiabatic chemical dynamics study of metal-contained energetic molecules through conical intersections.
Huang, Baoling L.; Kaviany, Massoud
2010-05-25
The phonon conductivities of CoSb_{3} and its Ba-filled structure Ba_{x}(CoSb_{3})_{4} are investigated using first-principle calculations and molecular dynamics (MD) simulations, along with the Green–Kubo theory. The effects of fillers on the reduction of the phonon conductivity of filled skutterudites are then explored. It is found that the coupling between filler and host is strong, with minor anharmonicity. The phonon density of states and its dispersion are significantly influenced by filler-induced softening of the host bonds (especially the short Sb–Sb bonds). Lattice dynamics and MD simulations show that, without a change in the host interatomic potentials, the filler–host bonding alone cannot lead to significant alteration of acoustic phonons or lowering of phonon conductivity. The observed smaller phonon conductivity of partially filled skutterudites is explained by treating it as a solid solution of the empty and fully filled structures.
NASA Astrophysics Data System (ADS)
Gao, Ai-Hua; Wang, Mei-Shan
2017-03-01
The photoisomerization mechanisms of N-salicilydenemethylfurylamine upon excitation to the first singlet state are investigated by means of surface-hopping dynamics simulations based on the Zhu-Nakamura theory. Due to different orientations of the methyl-furyl part with respect to the salicylaldimine part and different orientations of hydroxy group with respect to the benzene ring, various stable structures are obtained in the optimization. The enol isomer, S0-ENOL-5a, is the most stable conformer. An ultrafast excited-state intramolecular proton transfer is observed after photoexcitation of the most stable enol conformer and then the molecule reaches the excited-state minimum. After the internal conversion around a conical intersection, the system relaxes to either the cis-keto or trans-keto region in the ground state. The potential energy profiles of the ground and the first excited singlet state are also calculated. According to full-dimensional nonadiabatic dynamics simulations and potential energy profiles, the trans-keto and cis-keto photoproducts can be responsible for the photochromic effect of N-salicilydenemethylfurylamine.
Ab-initio Charge and Spin Dynamics in Solids using TDDFT
NASA Astrophysics Data System (ADS)
Elliott, Peter; Krieger, K.; Sharma, S.; Dewhurst, J. K.; Gross, E. K. U.
2014-03-01
With the advent of ultrafast and high intensity laser pulses, we can probe many new and interesting phenomena. Due to the time-scale of such situations, fully quantum mechanical approaches for the electron dynamics are required. Time-dependent density functional theory (TDDFT) is the natural choice for this problem, as it balances accuracy and efficiency. Here we report on the implementation of real time TDDFT for periodic systems including non-collinear magnetization, in the ELK electronic structure code. This allows us to study situations beyond the usual linear-response, for example ultrafast demagnetization or laser-induced dielectric breakdown. Additionally, we are developing and testing new methods related to time-dependent problems, such as an exchange-correlation magnetic field which is locally non-collinear, a time-dependent polarization field, and coupling to Maxwell's equations. Support from European Communities FP7, through the CRONOS project Grant No. 280879.
Ab initio lattice dynamics and thermochemistry of layered bismuth telluride (Bi2Te3).
Zurhelle, Alexander F; Deringer, Volker L; Stoffel, Ralf P; Dronskowski, Richard
2016-03-23
We present density-functional theory calculations of the lattice dynamics of bismuth telluride, yielding force constants, mean-square displacements and partial densities of phonon states which corroborate and complement previous nuclear inelastic scattering experiments. From these data, we derive an element- and energy-resolved view of the vibrational anharmonicity, quantified by the macroscopic Grüneisen parameter γ which results in 1.56. Finally, we calculate thermochemical properties in the quasiharmonic approximation, especially the heat capacity at constant pressure and the enthalpy of formation for bismuth telluride; the latter arrives at ΔHf (Bi2Te3) = -102 kJ mol(-1) at 298 K.
Schiffmann, Florian; VandeVondele, Joost
2015-06-28
We present an improved preconditioning scheme for electronic structure calculations based on the orbital transformation method. First, a preconditioner is developed which includes information from the full Kohn-Sham matrix but avoids computationally demanding diagonalisation steps in its construction. This reduces the computational cost of its construction, eliminating a bottleneck in large scale simulations, while maintaining rapid convergence. In addition, a modified form of Hotelling’s iterative inversion is introduced to replace the exact inversion of the preconditioner matrix. This method is highly effective during molecular dynamics (MD), as the solution obtained in earlier MD steps is a suitable initial guess. Filtering small elements during sparse matrix multiplication leads to linear scaling inversion, while retaining robustness, already for relatively small systems. For system sizes ranging from a few hundred to a few thousand atoms, which are typical for many practical applications, the improvements to the algorithm lead to a 2-5 fold speedup per MD step.
Langevin spin dynamics based on ab initio calculations: numerical schemes and applications.
Rózsa, L; Udvardi, L; Szunyogh, L
2014-05-28
A method is proposed to study the finite-temperature behaviour of small magnetic clusters based on solving the stochastic Landau-Lifshitz-Gilbert equations, where the effective magnetic field is calculated directly during the solution of the dynamical equations from first principles instead of relying on an effective spin Hamiltonian. Different numerical solvers are discussed in the case of a one-dimensional Heisenberg chain with nearest-neighbour interactions. We performed detailed investigations for a monatomic chain of ten Co atoms on top of a Au(0 0 1) surface. We found a spiral-like ground state of the spins due to Dzyaloshinsky-Moriya interactions, while the finite-temperature magnetic behaviour of the system was well described by a nearest-neighbour Heisenberg model including easy-axis anisotropy.
NASA Astrophysics Data System (ADS)
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.
Strained rocksalt ScN: ab initio studies of electronic structure and lattice-dynamical properties
NASA Astrophysics Data System (ADS)
Ahmad, Sohail; Bouarissa, Nadir
2017-05-01
Generalized gradient approximation calculations are performed to determine electronic and lattice vibration properties of unstrained and strained rocksalt scandium nitride (ScN). In agreement with earlier studies, our results reveal that unstrained rocksalt ScN is an indirect gap semiconductor from the valence band at Γ point to the conduction band at the X point. The effect of strain is found to have a large variation of energy band gaps and optical phonon frequencies. A large longitudinal and transverse optical phonon frequencies splitting is noted for the material of interest suggesting thus a remarkable dynamic ionicity of rocksalt ScN which varies significantly when ScN is strained. This can lead to engineering novel behaviors and holds promise for new technological applications.
Ab Initio Path Integral Molecular Dynamics Simulation of Hydrogen in Silicon
NASA Astrophysics Data System (ADS)
Probert, M. I. J.; Glover, M. J.
2006-05-01
We report results of a first-principles theoretical study of an isolated neutral hydrogen atom in crystalline silicon. Spin-polarised density functional theory is used to treat the electrons, and the path-integral molecular dynamics method is used to describe the quantum properties of the nucleus at finite temperature. This is necessary as the hydrogen atom has sufficiently low mass that it exhibits significant nuclear quantum delocalisation and zero-point motion even at room temperature. Unlike post-hoc treatments, such as calculating a static potential energy surface, the path-integral treatment enables such effects to be included "on-the-fly". This is found to be significant, as a coupling is found between the structure of the host silicon lattice and the quantum delocalisation of the hydrogen defect.
NASA Astrophysics Data System (ADS)
Chagarov, Evgueni Anatolievich
Chemical-mechanical polishing (CMP) is a widely accepted process in the semiconductor industry. Despite intense theoretical and experimental research on CMP, there is a serious lack of fundamental understanding of the physical-chemical processes of polishing. The present work is intended to investigate these fundamental processes on an atomistic level. To model CMP on the atomic scale, a model of the amorphous silica is prepared by applying Design of Experiments (DOE) techniques to systematically investigate molecular dynamics preparation. These simulations yield high-quality models of amorphous silica, which are in excellent agreement with experimental results and are defect-free. Molecular dynamics simulations are performed to investigate the mechanical deformation during CMP of silica for different geometries and relative velocities. The simulations clarify asperity shape evolution during the process of shear and reveal temperature distributions as a function of time. It is found that the ratio of radii of a particle and asperity strongly affects the amount of the material removed whereas the relative velocity has a weaker affect on it. During shear, a significant local temperature increase occurs. This temperature increase lasts for a short time (picoseconds), but it can have a major impact on the amount of material removed. It is found that there could be significant deposition of the material from the particle to the slab, which can fill surface trenches and thereby make the surface smoother. An analytic model is developed for describing the amount of material removed as a function of asperity and particle radii and relative velocity. Density-functional calculations of different surfaces of two silica polymorphs, alpha-quartz and beta-cristobalite, are performed. The surface energies are calculated as a function of oxygen partial pressure for several different surface reconstructions and terminations. The case of hydrogen passivation is investigated to
Ab initio folding of proteins using all-atom discrete molecular dynamics
Ding, Feng; Tsao, Douglas; Nie, Huifen; Dokholyan, Nikolay V.
2008-01-01
Summary Discrete molecular dynamics (DMD) is a rapid sampling method used in protein folding and aggregation studies. Until now, DMD was used to perform simulations of simplified protein models in conjunction with structure-based force fields. Here, we develop an all-atom protein model and a transferable force field featuring packing, solvation, and environment-dependent hydrogen bond interactions. Using the replica exchange method, we perform folding simulations of six small proteins (20–60 residues) with distinct native structures. In all cases, native or near-native states are reached in simulations. For three small proteins, multiple folding transitions are observed and the computationally-characterized thermodynamics are in quantitative agreement with experiments. The predictive power of all-atom DMD highlights the importance of environment-dependent hydrogen bond interactions in modeling protein folding. The developed approach can be used for accurate and rapid sampling of conformational spaces of proteins and protein-protein complexes, and applied to protein engineering and design of protein-protein interactions. PMID:18611374
Ab initio molecular dynamics of H2O adsorbed on solid MgO
NASA Astrophysics Data System (ADS)
Langel, Walter; Parrinello, Michele
1995-08-01
The Car-Parrinello method has been applied to study the adsorption of water on solid magnesium oxide with surface defects. A step consisting of an (100) and an (010) surface on an (011) base plane allows us to model the experimentally observed microfaceting. In and on this step dissociation of water into a hydroxyl group and a H-atom took place following a complicated pathway only accessible by the simulation of thermal motion. Under comparable conditions physisorption only was observed on a regular (001) plane. This solves an experimental controversy and it is in agreement with the observation, that disordered surfaces are more active in initiating the dissociation of the water molecules. Our work allows us to identify an important active center. We can also account for the experimentally observed broadening and shifting to the red of the stretching mode of hydrogen bonded hydroxyl groups, and we provide a detailed explanation of the origin of this effect. This allows us to verify earlier theories of hydrogen bonding such as that of the adiabatic separation of the proton dynamics.
CO2 capture in amine solutions from ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Ma, Changru; Pietrucci, Fabio; Andreoni, Wanda
2014-03-01
The most mature technology for post-combustion CO2 capture exploits a cyclic process, in which CO2 is selectively and reversibly absorbed in an amine solution, typically monoethanolamine(MEA) at 30%wt concentration. Empirical efforts are ongoing worldwide to reduce the high energy penalty for amine regeneration and to increase the absorption rate. Computer simulations can help by providing new insights and the missing quantitative information. Using extensive large-scale Car-Parrinello molecular dynamics simulations, aided by accelerated sampling techniques, we have characterized the reactions leading to CO2 capture in MEA 30%wt solutions via the formation of the carbamate, and the subsequent CO2 release. Deprotonation and CO2 release turn out to be competitive for an intermediate zwitterion (free-energy barrier ~10kcal/mol), with sizable entropic contribution, whereas CO2 release from the carbamate has a much higher barrier (~50kcal/mol), mainly enthalpic and rather independent of temperature. An unprecedented characterization of structural and vibrational properties of the solution allows us to interpret recent experimental results. More results on other amines, allow us to rationalize their still unexplained better performance relative to MEA. We acknowledge PRACE for awarding us access to resource Juqueen based in Germany at Juelich.
Oxidation of ligand-protected aluminum clusters: An ab initio molecular dynamics study
Alnemrat, Sufian; Hooper, Joseph P.
2014-03-14
We report Car-Parrinello molecular dynamics simulations of the oxidation of ligand-protected aluminum clusters that form a prototypical cluster-assembled material. These clusters contain a small aluminum core surrounded by a monolayer of organic ligand. The aromatic cyclopentadienyl ligands form a strong bond with surface Al atoms, giving rise to an organometallic cluster that crystallizes into a low-symmetry solid and is briefly stable in air before oxidizing. Our calculations of isolated aluminum/cyclopentadienyl clusters reacting with oxygen show minimal reaction between the ligand and O{sub 2} molecules at simulation temperatures of 500 and 1000 K. In all cases, the reaction pathway involves O{sub 2} diffusing through the ligand barrier, splitting into atomic oxygen upon contact with the aluminum, and forming an oxide cluster with aluminum/ligand bonds still largely intact. Loss of individual aluminum-ligand units, as expected from unimolecular decomposition calculations, is not observed except following significant oxidation. These calculations highlight the role of the ligand in providing a steric barrier against oxidizers and in maintaining the large aluminum surface area of the solid-state cluster material.
Diffusion mechanism of hydrogen in amorphous silicon - Ab initio molecular dynamics simulation
NASA Astrophysics Data System (ADS)
Su, Y.-S.; Pantelides, S. T.
2001-03-01
Diffusion of hydrogen in hydrogenated amorphous silicon (a-Si:H) is an important process, but the mechanism is still not well understood and even controversial. The observed activation energy is only about 1.5 eV, whereas the energy to dissociate Si-H bonds is much larger ( 2.5 eV). H is generally believed to migrate as an interstitial, perhaps as in crystalline Si. We report first-principles density-functional molecular dynamics simulations and identify a wealth of processes that occur. The main mechanism for the release of H from Si-H bonds is the conversion of the Si atom to fivefold coordination by the arrival of a floating bond, as suggested by one of us (STP, Phys. Rev. Lett. 58, 1344 (1987)) but the H atom is not released in the interstitial regions. Migration occurs by a bond-interconversion process, with the H atom acting as the analog of a floating bond. Estimates of the diffusion constant are in agreement with observations. Work supported in part by NSF.
Sisto, Aaron; Glowacki, David R; Martinez, Todd J
2014-09-16
("fragmenting") a molecular system and then stitching it back together. In this Account, we address both of these problems, the first by using graphical processing units (GPUs) and electronic structure algorithms tuned for these architectures and the second by using an exciton model as a framework in which to stitch together the solutions of the smaller problems. The multitiered parallel framework outlined here is aimed at nonadiabatic dynamics simulations on large supramolecular multichromophoric complexes in full atomistic detail. In this framework, the lowest tier of parallelism involves GPU-accelerated electronic structure theory calculations, for which we summarize recent progress in parallelizing the computation and use of electron repulsion integrals (ERIs), which are the major computational bottleneck in both density functional theory (DFT) and time-dependent density functional theory (TDDFT). The topmost tier of parallelism relies on a distributed memory framework, in which we build an exciton model that couples chromophoric units. Combining these multiple levels of parallelism allows access to ground and excited state dynamics for large multichromophoric assemblies. The parallel excitonic framework is in good agreement with much more computationally demanding TDDFT calculations of the full assembly.
Ab initio dynamics of cellulose pyrolysis: nascent decomposition pathways at 327 and 600 °C.
Agarwal, Vishal; Dauenhauer, Paul J; Huber, George W; Auerbach, Scott M
2012-09-12
We modeled nascent decomposition processes in cellulose pyrolysis at 327 and 600 °C using Car-Parrinello molecular dynamics (CPMD) simulations with rare events accelerated with the metadynamics method. We used a simulation cell comprised of two unit cells of cellulose Iβ periodically repeated in three dimensions to mimic the solid cellulose. To obtain initial conditions at reasonable densities, we extracted coordinates from larger classical NPT simulations at the target temperatures. CPMD-metadynamics implemented with various sets of collective variables, such as coordination numbers of the glycosidic oxygen, yielded a variety of chemical reactions such as depolymerization, fragmentation, ring opening, and ring contraction. These reactions yielded precursors to levoglucosan (LGA)-the major product of pyrolysis-and also to minor products such as 5-hydroxy-methylfurfural (HMF) and formic acid. At 327 °C, we found that depolymerization via ring contraction of the glucopyranose ring to the glucofuranose ring occurs with the lowest free-energy barrier (20 kcal/mol). We suggest that this process is key for formation of liquid intermediate cellulose, observed experimentally above 260 °C. At 600 °C, we found that a precursor to LGA (pre-LGA) forms with a free-energy barrier of 36 kcal/mol via an intermediate/transition state stabilized by anchimeric assistance and hydrogen bonding. Conformational freedom provided by expansion of the cellulose matrix at 600 °C was found to be crucial for formation of pre-LGA. We performed several comparison calculations to gauge the accuracy of CPMD-metadynamics barriers with respect to basis set and level of theory. We found that free-energy barriers at 600 °C are in the order pre-LGA < pre-HMF < formic acid, explaining why LGA is the kinetically favored product of fast cellulose pyrolysis.
Ab initio and molecular dynamics predictions for electron and phonon transport in bismuth telluride
NASA Astrophysics Data System (ADS)
Huang, Bao-Ling; Kaviany, Massoud
2008-03-01
Phonon and electron transport in Bi2Te3 has been investigated using a multiscale approach, combining the first-principles calculations, molecular dynamics (MD) simulations, and Boltzmann transport equations (BTEs). Good agreements are found with the available experimental results. The MD simulations along with the Green-Kubo autocorrelation decay method are used to calculate the lattice thermal conductivity in both the in-plane and cross-plane directions, where the required classical interatomic potentials for Bi2Te3 are developed on the basis of first-principles calculations and experimental results. In the decomposition of the lattice thermal conductivity, the contributions from the short-range acoustic and optical phonons are found to be temperature independent and direction independent, while the long-range acoustic phonons dominate the phonon transport with a strong temperature and direction dependence (represented by a modified Slack relation). The sum of the short-range acoustic and optical phonon contribution is about 0.2W/mK and signifies the limit when the long-range transport is suppressed by nanostructure engineering. The electrical transport is calculated using the full-band structure from the linearized augmented plane-wave method, BTE, and the energy-dependent relaxation-time models with the nonparabolic Kane energy dispersion. Temperature dependence of the energy gap is found to be important for the prediction of electrical transport in the intrinsic regime. Appropriate modeling of relaxation times is also essential for the calculation of electric and thermal transport, especially in the intrinsic regime. The maximum of the Seebeck coefficient appears when the chemical potential approaches the band edge and can be estimated by a simple expression containing the band gap. The scatterings by the acoustic, optical, and polar-optical phonons dominate the electrical conductivity and electric thermal conductivity.
Furuhama, Ayako; Dupuis, Michel; Hirao, Kimihiko
2006-05-07
A quasi-classical ab initio dynamics calculation of the (H2O)17 cluster, which is the first water cluster that includes a four-fold coordinated water molecule, has been carried out to obtain a detailed picture of the elementary processes and energy redistribution induced by ionization in a model of aqueous water. Well within 100 fs after ionization, a proton is seen to have transferred from the “ionized molecule” to a neighboring molecule, forming a hydronium ion and a hydroxyl radical. Two neighboring water molecules to the ionized water molecule play an important role in the reaction, in what we term a “reactive trimer”. The reaction time is gated by the encounter of the “ionized” water molecule with these two neighboring molecules and this occurs at ~ 35 fs after ionization. We find that the distance of approach between the “ionized” molecule and the neighboring molecule reflects best the time characteristics of the transfer of a proton, and thus of the formation of a hydronium ion and an OH radical. These findings are consistent with those for smaller cyclic clusters, albeit the dynamics of the transferring proton is much damped in our simulation compared to the small cyclic cluster cases. We use a partitioning scheme for the kinetic energy of the << OLE Object: Microsoft Equation 3.0 >> system that distinguishes the “reactive trimer” and the surrounding medium. The analysis of the simulation indicates that the kinetic energy of the surrounding medium increases markedly right after the event of ionization. The increase in kinetic energy is consistent with a reorganization of the surrounding medium, in this case an orientation relaxation, from a configuration as a hydrogen bond donor to the “ionized” tetra-coordinated water molecule, into a configuration where the surrounding water molecule have turned their dipoles for a more favorable interaction with the “ionized” water cation. Battelle operates the Pacific Northwest National
NASA Astrophysics Data System (ADS)
Svoboda, Ondřej; Ončák, Milan; Slavíček, Petr
2011-10-01
We have performed large-scale simulations of UV absorption spectra of water clusters (monomer to octamer) using a combination of ab initio path-integral molecular dynamics with reflection principle. The aim of the present work is four-fold: (1) To explore the transition from isolated molecules to bulk water from the perspective of UV photoabsorption. (2) To investigate quantum nuclear and thermal effects on the shape of the water UV spectra. (3) To make an assessment of the density functional theory functionals to be used for water excited states. (4) To check the applicability of the QM/MM schemes for a description of the UV absorption. Within the path integral molecular dynamics (PIMD)/reflection principle approach both the thermal and quantum vibrational effects including anharmonicities are accounted for. We demonstrate that shape of the spectra is primarily controlled by the nuclear quantum effects. The excited states and transition characteristics of the water clusters were calculated with the time-dependent density functional theory and equation-of-motion coupled clusters singles and doubles methods. Based on our benchmark calculations considering the whole UV spectrum we argue that the BHandHLYP method performs best among the 6 functionals tested (B3LYP, BHandHLYP, BNL, CAM-B3LYP, LC-ωPBE, and M06HF). We observe a gradual blueshift of the maximum of the first absorption peak with the increasing cluster size. The UV absorption spectrum for the finite size clusters (i.e., the peak centers, peak widths, and photoabsorption cross section) essentially converges into the corresponding bulk water spectrum. The effect of distant molecules accounted for within the polarizable continuum model is shown to be almost negligible. Using the natural transition orbitals we demonstrate that the first absorption band is formed by localized excitations while the second band includes delocalized excited states. Consequently, the QM/MM electrostatic embedding scheme can only be
Kishi, Ryohei; Fujii, Hiroaki; Minami, Takuya; Shigeta, Yasuteru; Nakano, Masayoshi
2015-01-22
In this study, we apply the ab initio molecular orbital - configuration interaction based quantum master equation (MOQME) approach to the calculation and analysis of the dynamic first hyperpolarizabilities (β) of asymmetric π-conjugated molecules. In this approach, we construct the excited state models by the ab initio configuration interaction singles method. Then, time evolutions of system reduced density matrix ρ(t) and system polarization p(t) are calculated by the QME approach. Dynamic β in the second harmonic generation is calculated based on the nonperturbative definition of nonlinear optical susceptibility, using the frequency domain system polarization p(ω). Spatial contributions of electrons to β are analyzed based on the dynamic hyperpolarizability density map, which visualizes the second-order response of charge density oscillating with a frequency of 2ω. We apply the present method to the calculation of the dynamic β of a series of donor/acceptor substituted polyene oligomers, and then discuss the applicability of the MOQME method to the calculation and analysis of dynamic NLO properties of molecular systems.
Ab initio Theory of Semiconductor Nanocrystals
NASA Astrophysics Data System (ADS)
Wang, Lin-Wang
2007-03-01
With blooming experimental synthesis of various nanostructures out of many semiconductor materials, there is an urgent need to calculate the electronic structures and optical properties of these nanosystems based on reliable ab initio methods. Unfortunately, due to the O(N^3) scaling of the conventional ab initio calculation methods based on the density functional theory (DFT), and the >1000 atom sizes of the most experimental nanosystems, the direct applications of these conventional ab intio methods are often difficult. Here we will present the calculated results using our O(N) scaling charge patching method (CPM) [1,2] to nanosystems up to 10,000 atoms. The CPM yields the charge density of a nanosystem by patching the charge motifs generated from small prototype systems. The CPM electron/hole eigen energies differ from the directly calculated results by only ˜10-20 meV. We will present the optical band gaps of quantum dots and wires, quantum rods, quantum dot/quantum well, and quantum dots doped with impurities. Besides good agreements with experimental measurements, we will demonstrate why it is important to perform ab initio calculations, in contrast with the continuum model k.p calculations. We will show the effects of surface polarization potentials and the internal electric fields. Finally, a linear scaling 3 dimensional fragment (LS3DF) method will be discussed. The LS3DF method can be used to calculate the total energy and atomic forces of a large nanosystem, with the results practically the same as the direct DFT method. Our work demonstrates that, with the help of supercomputers, it is now feasible to calculate the electronic structures and optical properties of >10,000 atom nanocrystals with ab initio accuracy. [1] L.W. Wang, Phys. Rev. Lett. 88, 256402 (2002). [2] J. Li, L.W. Wang, Phys. Rev. B 72, 125325 (2005).
Kishi, Ryohei; Fujii, Hiroaki; Kishimoto, Shingo; Murata, Yusuke; Ito, Soichi; Okuno, Katsuki; Shigeta, Yasuteru; Nakano, Masayoshi
2012-05-03
We develop novel calculation and analysis methods for the dynamic first hyperpolarizabilities β [the second-order nonlinear optical (NLO) properties at the molecular level] in the second-harmonic generation based on the quantum master equation method combined with the ab initio molecular orbital (MO) configuration interaction method. As examples, we have evaluated off-resonant dynamic β values of donor (NH(2))- and/or acceptor (NO(2))-substituted benzenes using these methods, which are shown to reproduce those by the conventional summation-over-states method well. The spatial contributions of electrons to the dynamic β of these systems are also analyzed using the dynamic β density and its partition into the MO contributions. The present results demonstrate the advantage of these methods in unraveling the mechanism of dynamic NLO properties and in building the structure-dynamic NLO property relationships of real molecules.
Kroes, Geert-Jan Pavanello, Michele; Blanco-Rey, María; Alducin, Maite
2014-08-07
Energy loss from the translational motion of an atom or molecule impinging on a metal surface to the surface may determine whether the incident particle can trap on the surface, and whether it has enough energy left to react with another molecule present at the surface. Although this is relevant to heterogeneous catalysis, the relative extent to which energy loss of hot atoms takes place to phonons or electron-hole pair (ehp) excitation, and its dependence on the system's parameters, remain largely unknown. We address these questions for two systems that present an extreme case of the mass ratio of the incident atom to the surface atom, i.e., H + Cu(111) and H + Au(111), by presenting adiabatic ab initio molecular dynamics (AIMD) predictions of the energy loss and angular distributions for an incidence energy of 5 eV. The results are compared to the results of AIMDEFp calculations modeling energy loss to ehp excitation using an electronic friction (“EF”) model applied to the AIMD trajectories, so that the energy loss to the electrons is calculated “post” (“p”) the computation of the AIMD trajectory. The AIMD calculations predict average energy losses of 0.38 eV for Cu(111) and 0.13-0.14 eV for Au(111) for H-atoms that scatter from these surfaces without penetrating the surface. These energies closely correspond with energy losses predicted with Baule models, which is suggestive of structure scattering. The predicted adiabatic integral energy loss spectra (integrated over all final scattering angles) all display a lowest energy peak at an energy corresponding to approximately 80% of the average adiabatic energy loss for non-penetrative scattering. In the adiabatic limit, this suggests a way of determining the approximate average energy loss of non-penetratively scattered H-atoms from the integral energy loss spectrum of all scattered H-atoms. The AIMDEFp calculations predict that in each case the lowest energy loss peak should show additional energy loss
Kroes, Geert-Jan; Pavanello, Michele; Blanco-Rey, María; Alducin, Maite; Auerbach, Daniel J
2014-08-07
Energy loss from the translational motion of an atom or molecule impinging on a metal surface to the surface may determine whether the incident particle can trap on the surface, and whether it has enough energy left to react with another molecule present at the surface. Although this is relevant to heterogeneous catalysis, the relative extent to which energy loss of hot atoms takes place to phonons or electron-hole pair (ehp) excitation, and its dependence on the system's parameters, remain largely unknown. We address these questions for two systems that present an extreme case of the mass ratio of the incident atom to the surface atom, i.e., H + Cu(111) and H + Au(111), by presenting adiabatic ab initio molecular dynamics (AIMD) predictions of the energy loss and angular distributions for an incidence energy of 5 eV. The results are compared to the results of AIMDEFp calculations modeling energy loss to ehp excitation using an electronic friction ("EF") model applied to the AIMD trajectories, so that the energy loss to the electrons is calculated "post" ("p") the computation of the AIMD trajectory. The AIMD calculations predict average energy losses of 0.38 eV for Cu(111) and 0.13-0.14 eV for Au(111) for H-atoms that scatter from these surfaces without penetrating the surface. These energies closely correspond with energy losses predicted with Baule models, which is suggestive of structure scattering. The predicted adiabatic integral energy loss spectra (integrated over all final scattering angles) all display a lowest energy peak at an energy corresponding to approximately 80% of the average adiabatic energy loss for non-penetrative scattering. In the adiabatic limit, this suggests a way of determining the approximate average energy loss of non-penetratively scattered H-atoms from the integral energy loss spectrum of all scattered H-atoms. The AIMDEFp calculations predict that in each case the lowest energy loss peak should show additional energy loss in the
Vibrational properties of silica species in MgO-SiO2 glasses from ab initio molecular dynamics
NASA Astrophysics Data System (ADS)
Spiekermann, G.; Steele-MacInnis, M.; Kowalski, P. M.; Schmidt, C.; Jahn, S.
2012-04-01
Glasses and melts in the system MgO-SiO2 are analogs for magmas of the Earth's mantle. Therefore knowledge of the structure of these glasses and melts is important for understanding numerous geological processes. Raman spectroscopy is useful for probing the atomic-scale structure of glasses and melts. However, correct assignment of observed vibrational bands to specific structural and modal origins is challenging. We present the mode-projection technique to calculate vibrational subspectra for specific modal vibrations of several fundamental silica structures in silicate glasses. Structural subunits that we have studied include Q0 to Q4 tetrahedra, Si-O-Si bridging oxygen atoms for any degree of polymerization of the adjacent tetrahedra, the ethane-like symmetry of the dimer, and three- and four-fold rings. We apply this technique to ab initio molecular dynamics (MD) trajectories of MgO-SiO2 glasses at 1000 K. We found the tetrahedral symmetric stretch at 863 cm-1 for Q0, 885 cm-1 for Q1, a double peak of 960 cm-1 and 1037 cm-1 for Q2, 1032 cm-1 for Q3 and 1080 cm-1 for Q4. The bridging oxygen asymmetric stretch is at about 980 cm-1 for Q1-Q1, and it shifts to about 1100 cm-1 with increasing polymerization. This analysis has applications especially for understanding the structure of silica-poor glasses. For instance, two contradicting Raman spectroscopy studies of Mg2SiO4 glasses reported the most polymerized SiO4 tetrahedra in the glass structure to be either Q0 [1] or Q3 [2]. Our results indicate that the degree of polymerization is overestimated, if the Si-O-Si stretching modes are not considered in the interpretation of the measured Raman spectra. [1] Nasikas, N. K. and Chrissanthopoulos, A. and Bouropoulos, N. and Sen, S. and Papatheodorou, G. N., 2011, Chemistry of Materials 23, 3692-3697. [2] Kalampounias, A. G. and Nasikas, N. K. and Papatheodorou, G. N., 2009, Journal of Chemical Physics 131, 114513.
NASA Astrophysics Data System (ADS)
Shimamura, Kohei; Hakamata, Tomoya; Shimojo, Fuyuki; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya
2016-12-01
Rotation of methylammonium (CH3NH3 or MA) molecules is believed to govern the excellent transport properties of photocarriers in the MA lead iodide (MAPbI3) perovskite. Of particular interest is its cubic phase, which exists in industrially important films at room temperature. In order to investigate the rotational behaviors of the MA molecules, we have performed ab initio molecular dynamics simulations of cubic-MAPbI3 at room temperature. There are two types of rotational motions of MA molecules in a crystalline PbI3 cage: reorientation of a whole molecule and intramolecular rotation around the C-N bond within MA molecules. Using a cubic symmetry-assisted analysis (CSAA), we found that the prominent orientation of the C-N bond is the crystalline ⟨110 ⟩ directions, rather than the ⟨100 ⟩ and ⟨111 ⟩ directions. Rapid rotation around the C-N bond is also observed, which easily occurs when the rotational axis is parallel to the ⟨110 ⟩ directions according to the CSAA. To explain the atomistic mechanisms underlying these CSAA results, we have focused on the relation between H-I hydrogen bonds and the orientation of an MA molecule. Here, the hydrogen bonds were defined by population analysis, and it has been found that, while H atoms in the CH3 group (HC) hardly interacts with I atoms, those in the NH3 group (HN) form at least one hydrogen bond with I atoms and their interatomic distances are in a wide range, 2.2-3.7 Å. Based on these findings, we have given a possible explanation to why the ⟨110 ⟩ directions are preferred. Namely, the atomic arrangement and interatomic distance between MA and surrounding I atoms are most suitable for the formation of hydrogen bonds. In addition to films, these results are potentially applicable to the rotational behaviors in bulk MAPbI3 as well, considering that the atomistic structure and time constants regarding the rotation of MA molecules statistically agree with bulk experiments.
None, None
2016-01-01
The nature of chemical bonding of molybdenum in high level nuclear waste glasses has been elucidated by ab initio molecular dynamics simulations. Two compositions, (SiO2)57.5 – (B2O3)10 – (Na2O)15 – (CaO)15 – (MoO3)2.5 and (SiO2)57.3 – (B2O3)20 – (Na2O)6.8 – (Li2O)13.4 – (MoO3)2.5 , were considered in order to investigate the effect of ionic and covalent components on the glass structure and the formation of the crystallisation precursors (Na2MoO4 and CaMoO4). The coordination environments of Mo cations and the corresponding bond lengths calculated from our model are in excellent agreement with experimental observations. The analysis of the first coordination shell reveals two different types of molybdenum host matrix bonds in the lithium sodium borosilicate glass. Based on the structural data and the bond valence model, we demonstrate that the Mo cation can be found in a redox state and the molybdate tetrahedron can be connected with the borosilicate network in a way that inhibits the formation of crystalline molybdates. These results significantly extend our understanding of bonding in Mo-containing nuclear waste glasses and demonstrate that tailoring the glass composition to specific heavy metal constituents can facilitate incorporation of heavy metals at high concentrations. K.K. was supported through the Impact Studentship scheme at UCL co-funded by the IHI Corporation and UCL. P.V.S. thanks the Royal Society, which supported preliminary work on this project, and the Laboratory Directed Research and Development program at PNNL, a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy. Via our membership of the UK's HEC Materials Chemistry Consortium, which is funded by EPSRC (EP/L000202), this work used the ARCHER UK National Supercomputing Service (http://www.archer.ac.uk).
NASA Astrophysics Data System (ADS)
Campetella, M.; Bovi, D.; Caminiti, R.; Guidoni, L.; Bencivenni, L.; Gontrani, L.
2016-07-01
In this work we report an analysis of the bulk phase of 2-methoxyethylammonium nitrate based on ab initio molecular dynamics. The structural and dynamical features of the ionic liquid have been characterized and the computational findings have been compared with the experimental X-ray diffraction patterns, with infrared spectroscopy data, and with the results obtained from molecular dynamics simulations. The experimental infrared spectrum was interpreted with the support of calculated vibrational density of states as well as harmonic frequency calculations of selected gas phase clusters. Particular attention was addressed to the high frequency region of the cation (ω > 2000 cm-1), where the vibrational motions involve the NH3+ group responsible for hydrogen bond formation, and to the frequency range 1200-1400 cm-1 where the antisymmetric stretching mode (ν3) of nitrate is found. Its multiple absorption lines in the liquid arise from the removal of the degeneracy present in the D3h symmetry of the isolated ion. Our ab initio molecular dynamics leads to a rationalization of the frequency shifts and splittings, which are inextricably related to the structural modifications induced by a hydrogen bonding environment. The DFT calculations lead to an inhomogeneous environment.
NASA Astrophysics Data System (ADS)
Ramzan, M.; Hussain, T.; Ahuja, R.
2009-06-01
We present ab initio molecular dynamics calculations based on density functional theory to study the hydrogen-deuterium exchange in bulk and nanoclusters of MgH2. Our calculations reveal the important role of catalysts to diffuse the hydrogen at low temperatures and increase the diffusion rate. We determine the diffusion constants, ⟨D⟩ of deuterium, and show the single hydrogen-deuterium exchange in bulk and nanocluster of MgH2. Our calculated value of diffusion constant of deuterium in bulk MgH2 is in excellent agreement with the experimental value. Furthermore, we show the edge site importance of catalysts in the fast diffusion of hydrogen.
NASA Astrophysics Data System (ADS)
Okamoto, Akisumi; Yano, Atsushi; Nomura, Kazuya; Higai, Shin'ichi; Kurita, Noriyuki
2013-07-01
Aggregation of amyloid β-proteins (Aβ) plays a key role in the mechanism of molecular pathogenesis of Alzheimer’s disease (AD). It is known that full-length Aβ(1-42) is more prone to aggregation than Aβ(1-40). We here search stable conformations of solvated Aβ(1-42) monomer by replica exchange molecular dynamics simulations based on classical force fields, and the most stable conformation is determined from the total energies evaluated by the ab initio fragment molecular orbital (FMO) calculations. In addition, based on the FMO results, the amino acid residues of Aβ(1-42) contributing to the stabilization of the monomer are highlighted.
Ab initio infrared and Raman spectra
NASA Technical Reports Server (NTRS)
Fredkin, D. R.; White, S. R.; Wilson, K. R.; Komornicki, A.
1983-01-01
It is pointed out that with increased computer power and improved computational techniques, such as the gradients developed in recent years, it is becoming practical to compute spectra ab initio, from the fundamental constants of nature, for systems of increasing complexity. The present investigation has the objective to explore several possible ab initio approaches to spectra, giving particular attention to infrared and nonresonance Raman. Two approaches are discussed. The sequential approach, in which first the electronic part and then later the nuclear part of the Born-Oppenheimer approximation is solved, is appropriate for small systems. The simultaneous approach, in which the electronic and nuclear parts are solved at the same time, is more appropriate for many-atom systems. A review of the newer quantum gradient techniques is provided, and the infrared and Raman spectral band contours for the water molecule are computed.
Ab Initio Quantum Simulations of Liquid Water
NASA Astrophysics Data System (ADS)
Gergely, John; Ceperley, David; Gygi, Francois
2007-03-01
Some recent efforts at simulating liquid water have employed ``ab initio'' molecular dynamics (AIMD) methods with forces from a version of density functional theory (DFT) and, in some cases, imaginary-time path integrals (PI) to study quantum effects of the protons. Although AIMD methods have met with many successes, errors introduced by the approximations and choices of simulation parameters are not fully understood. We report on path integral Monte Carlo (PIMC) studies of liquid water using DFT energies that provide quantitative benchmarks for PI-AIMD work. Specifically, we present convergence studies of the path integrals and address whether the Trotter number can be reduced by improving the form of the (approximate) action. Also, we assess 1) whether typical AIMD simulations are sufficiently converged in simulation time, i.e., if there is reason to suspect that nonergodic behavior in PI-AIMD methods leads to poor convergence, and 2) the relative efficiency of the methods. E. Schwegler, J.C. Grossman, F. Gygi, G. Galli, J. Chem. Phys 121, 5400 (2004).
Phonocatalysis. An ab initio simulation experiment
Kim, Kwangnam; Kaviany, Massoud
2016-06-15
Using simulations, we postulate and show that heterocatalysis on large-bandgap semiconductors can be controlled by substrate phonons, i.e., phonocatalysis. With ab initio calculations, including molecular dynamic simulations, the chemisorbed dissociation of XeF{sub 6} on h-BN surface leads to formation of XeF{sub 4} and two surface F/h-BN bonds. The reaction pathway and energies are evaluated, and the sorption and reaction emitted/absorbed phonons are identified through spectral analysis of the surface atomic motion. Due to large bandgap, the atomic vibration (phonon) energy transfer channels dominate and among them is the match between the F/h-BN covalent bond stretching and the optical phonons. We show that the chemisorbed dissociation (the pathway activation ascent) requires absorption of large-energy optical phonons. Then using progressively heavier isotopes of B and N atoms, we show that limiting these high-energy optical phonons inhibits the chemisorbed dissociation, i.e., controllable phonocatalysis.
Jakowski, Jacek; Sumner, Isaiah; Iyengar, Srinivasan S
2006-09-01
In a recent publication, we introduced a computational approach to treat the simultaneous dynamics of electrons and nuclei. The method is based on a synergy between quantum wave packet dynamics and ab initio molecular dynamics. Atom-centered density-matrix propagation or Born-Oppenheimer dynamics can be used to perform ab initio dynamics. In this paper, wave packet dynamics is conducted using a three-dimensional direct product implementation of the distributed approximating functional free-propagator. A fundamental computational difficulty in this approach is that the interaction potential between the two components of the methodology needs to be calculated frequently. Here, we overcome this problem through the use of a time-dependent deterministic sampling measure that predicts, at every step of the dynamics, regions of the potential which are important. The algorithm, when combined with an on-the-fly interpolation scheme, allows us to determine the quantum dynamical interaction potential and gradients at every dynamics step in an extremely efficient manner. Numerical demonstrations of our sampling algorithm are provided through several examples arranged in a cascading level of complexity. Starting from a simple one-dimensional quantum dynamical treatment of the shared proton in [Cl-H-Cl](-) and [CH3-H-Cl](-) along with simultaneous dynamical treatment of the electrons and classical nuclei, through a complete three-dimensional treatment of the shared proton in [Cl-H-Cl](-) as well as treatment of a hydrogen atom undergoing donor-acceptor transitions in the biological enzyme, soybean lipoxygenase-1 (SLO-1), we benchmark the algorithm thoroughly. Apart from computing various error estimates, we also compare vibrational density of states, inclusive of full quantum effects from the shared proton, using a novel unified velocity-velocity, flux-flux autocorrelation function. In all cases, the potential-adapted, time-dependent sampling procedure is seen to improve the
Ab initio torsional potentials in silole dimers
Yamaguchi, Yoichi; Yamabe, Tokio
1996-01-05
The potential barriers for the internal rotation of silole dimers are studied theoretically using the ab initio molecular orbital method at the RHF/6-31G** level of calculations. In 2,2{prime}-bisilole, it is found that the anti-conformation is the most stable structure in the ground state and that the potential barrier height for rotation over the perpendicular conformation is 3.3 kcal/mol. 21 refs., 4 figs., 2 tabs.
AB initio infrared and Raman spectra
NASA Astrophysics Data System (ADS)
Fredkin, D. R.; Komornicki, A.; White, S. R.; Wilson, K. R.
1982-08-01
We discuss several ways in which molecular absorption and scattering spectra can be computed ab initio, from the fundamental constants of nature. These methods can be divided into two general categories. In the first, or sequential, type of approach, one first solves the electronic part of the Schroedinger equation in the Born-Oppenheimer approximation, mapping out the potential energy, dipole moment vector (for infrared absorption) and polarizability tensor (for Raman scattering) as functions of nuclear coordinates. Having completed the electronic part of the calculation, one then solves the nuclear part of the problem either classically or quantum mechanically. As an example of the sequential ab initio approach, the infrared and Raman rotational and vibrational-rotational spectral band contours for the water molecule are computed in the simplest rigid rotor, normal mode approximation. Quantum techniques, are used to calculate the necessary potential energy, dipole moment, and polarizability information at the equilibrium geometry. A new quick, accurate, and easy to program classical technique involving no reference to Euler angles or special functions is developed to compute the infrared and Raman angles or special functions is developed to compute the infrared and Raman band contours for any rigid rotor, including asymmetric tops. A second, or simultaneous, type of ab initio approach is suggested for large systems, particularly those for which normal mode analysis is inappropriate, such as liquids, clusters, or floppy molecules.
Gerber, R B; Shemesh, D; Varner, M E; Kalinowski, J; Hirshberg, B
2014-06-07
Recent progress in "on-the-fly" trajectory simulations of molecular reactions, using different electronic structure methods is discussed, with analysis of the insights that such calculations can provide and of the strengths and limitations of the algorithms available. New developments in the use of both ab initio and semi-empirical electronic structure algorithms are described. The emphasis is on: (i) calculations of electronic properties along the reactive trajectories and the unique insights this can contribute to the processes; (ii) electronic structure methods recently introduced to this topic to improve accuracy, extend applicability or enhance computational efficiency. The methods are presented with examples, including new results, of reactions of both isolated molecules and of molecules in media, mostly clusters. Possible future directions for this fast growing field are suggested.
Castillo-Chará, J; McIntosh, A L; Wang, Z; Lucchese, R R; Bevan, J W
2004-06-08
Supersonic jet investigations of the (HBr)(2) dimer have been carried out using a tunable diode laser spectrometer to provide accurate data for comparison with results from a four-dimensional (4-D) ab initio potential energy surface (PES). The near-infrared nu(1) (+/-), nu(2) (+/-), and (nu(1)+nu(4))(-) bands of (H (79)Br)(2), (H (79)Br-H (81)Br), and (H (81)Br)(2) isotopomers have been recorded in the range 2500-2600 cm(-1) using a CW slit jet expansion with an upgraded near-infrared diode laser spectrometer. The 4-D PES has been calculated for (HBr)(2) using second-order Møller-Plesset perturbation theory with an augmented and polarized 6-311G basis set. The potential is characterized by a global minimum occurring at the H bond structure with the distance between the center of masses (CM) of the monomer being R(CM)=4.10 A with angles theta(A)=10 degrees, theta(B)=100 degrees and a well depth of 692.2 cm(-1), theta(A) is the angle the HBr bond of monomer A makes with the vector from the CM of A to the CM of B, and theta(B) is the corresponding angle monomer B makes with the same CM-CM vector. The barrier for the H interchange occurs at the closed C(2h) structure for which R(CM)=4.07 A, theta(A)=45 degrees, theta(B)=135 degrees, and the barrier height is 73.9 cm(-1). The PES was fitted using a linear-least squares method and the rovibrational energy levels of the complex were calculated by a split pseudospectral method. The spectroscopic data provide accurate molecular parameters for the dimer that are then compared with the results predicted on the basis of the 4-D ab initio PES.
NASA Astrophysics Data System (ADS)
Novko, Dino; Lončarić, Ivor; Blanco-Rey, María; Juaristi, J. Iñaki; Alducin, Maite
2017-08-01
We study surface temperature effects on the adsorption and relaxation of N atoms on Ag(111). To this aim, we perform ab initio molecular dynamics simulations with electronic friction, in which the surface is coupled to a thermostat that fixes the desired surface temperature. Simulations performed at 80 and 700 K show that the surface temperature has minor effects on magnitudes such as the initial adsorption probability, the relaxation rate of the adsorbing N, and the energy lost in electronic excitations. Slight differences are identified in the adsorption paths with the appearance of subsurface absorption events at 700 K that are not observed at 80 K. Furthermore, we perform additional simulations without a thermostat in order to examine the validity of commonly used ab initio molecular dynamics simulations in which no heat dissipation from the simulation cell is allowed. Our results show that such a methodology may not suffice to simulate the low-temperature regime since the surface becomes unphysically heated within a few picoseconds upon adsorption of the N atom. However, neither in this unfavorable case are the magnitudes defining the dynamics of the adsorbates at the same time scale significantly modified from those obtained at constant surface temperature.
Willow, Soohaeng Yoo; Salim, Michael A.; Kim, Kwang S.; Hirata, So
2015-01-01
A direct, simultaneous calculation of properties of a liquid using an ab initio electron-correlated theory has long been unthinkable. Here we present structural, dynamical, and response properties of liquid water calculated by ab initio molecular dynamics using the embedded-fragment spin-component-scaled second-order many-body perturbation method with the aug-cc-pVDZ basis set. This level of theory is chosen as it accurately and inexpensively reproduces the water dimer potential energy surface from the coupled-cluster singles, doubles, and noniterative triples with the aug-cc-pVQZ basis set, which is nearly exact. The calculated radial distribution function, self-diffusion coefficient, coordinate number, and dipole moment, as well as the infrared and Raman spectra are in excellent agreement with experimental results. The shapes and widths of the OH stretching bands in the infrared and Raman spectra and their isotropic-anisotropic Raman noncoincidence, which reflect the diverse local hydrogen-bond environment, are also reproduced computationally. The simulation also reveals intriguing dynamic features of the environment, which are difficult to probe experimentally, such as a surprisingly large fluctuation in the coordination number and the detailed mechanism by which the hydrogen donating water molecules move across the first and second shells, thereby causing this fluctuation. PMID:26400690
Willow, Soohaeng Yoo; Salim, Michael A; Kim, Kwang S; Hirata, So
2015-09-24
A direct, simultaneous calculation of properties of a liquid using an ab initio electron-correlated theory has long been unthinkable. Here we present structural, dynamical, and response properties of liquid water calculated by ab initio molecular dynamics using the embedded-fragment spin-component-scaled second-order many-body perturbation method with the aug-cc-pVDZ basis set. This level of theory is chosen as it accurately and inexpensively reproduces the water dimer potential energy surface from the coupled-cluster singles, doubles, and noniterative triples with the aug-cc-pVQZ basis set, which is nearly exact. The calculated radial distribution function, self-diffusion coefficient, coordinate number, and dipole moment, as well as the infrared and Raman spectra are in excellent agreement with experimental results. The shapes and widths of the OH stretching bands in the infrared and Raman spectra and their isotropic-anisotropic Raman noncoincidence, which reflect the diverse local hydrogen-bond environment, are also reproduced computationally. The simulation also reveals intriguing dynamic features of the environment, which are difficult to probe experimentally, such as a surprisingly large fluctuation in the coordination number and the detailed mechanism by which the hydrogen donating water molecules move across the first and second shells, thereby causing this fluctuation.
Singh, Baltej; Gupta, Mayanak Kumar; Mishra, Sanjay Kumar; Mittal, Ranjan; Sastry, P U; Rols, Stephane; Chaplot, Samrath Lal
2017-07-21
We present structural and dynamical studies of layered vanadium pentaoxide (V2O5). The temperature dependent X-ray diffraction measurements reveal highly anisotropic and anomalous thermal expansion from 12 K to 853 K. The results do not show any evidence of structural phase transition or decomposition of α-V2O5, contrary to the previous transmission electron microscopy (TEM) and electron energy loss spectroscopy (EELS) experiments. The inelastic neutron scattering measurements performed up to 673 K corroborate the result of our X-ray diffraction measurements. The analysis of the experimental data is carried out using ab initio lattice dynamics calculations. The important role of van der Waals dispersion and Hubbard interactions in the structure and dynamics is revealed through ab initio calculations. The calculated anisotropic thermal expansion behavior agrees well with temperature dependent X-ray diffraction. The mechanism of anisotropic thermal expansion and anisotropic linear compressibility is discussed in terms of calculated anisotropy in the Grüneisen parameters and elastic coefficients. The calculated Gibbs free energy in various phases of V2O5 is used to understand the high pressure and temperature phase diagram of the compound.
Agrawal, Paras M; Raff, Lionel M; Hagan, Martin T; Komanduri, Ranga
2006-04-07
The neural network (NN) procedure to interpolate ab initio data for the purpose of molecular dynamics (MD) simulations has been tested on the SiO(2) system. Unlike other similar NN studies, here, we studied the dissociation of SiO(2) without the initial use of any empirical potential. During the dissociation of SiO(2) into Si+O or Si+O(2), the spin multiplicity of the system changes from singlet to triplet in the first reaction and from singlet to pentet in the second. This paper employs four potential surfaces. The first is a NN fit [NN(STP)] to a database comprising the lowest of the singlet, triplet, and pentet energies obtained from density functional calculations in 6673 nuclear configurations. The other three potential surfaces are obtained from NN fits to the singlet, triplet, and pentet-state energies. The dissociation dynamics on the singlet-state and NN(STP) surfaces are reported. The results obtained using the singlet surface correspond to those expected if the reaction were to occur adiabatically. The dynamics on the NN(STP) surface represent those expected if the reaction follows a minimum-energy pathway. This study on a small system demonstrates the application of NNs for MD studies using ab initio data when the spin multiplicity of the system changes during the dissociation process.
NASA Astrophysics Data System (ADS)
Agrawal, Paras M.; Raff, Lionel M.; Hagan, Martin T.; Komanduri, Ranga
2006-04-01
The neural network (NN) procedure to interpolate ab initio data for the purpose of molecular dynamics (MD) simulations has been tested on the SiO2 system. Unlike other similar NN studies, here, we studied the dissociation of SiO2 without the initial use of any empirical potential. During the dissociation of SiO2 into Si +O or Si +O2, the spin multiplicity of the system changes from singlet to triplet in the first reaction and from singlet to pentet in the second. This paper employs four potential surfaces. The first is a NN fit [NN(STP)] to a database comprising the lowest of the singlet, triplet, and pentet energies obtained from density functional calculations in 6673 nuclear configurations. The other three potential surfaces are obtained from NN fits to the singlet, triplet, and pentet-state energies. The dissociation dynamics on the singlet-state and NN(STP) surfaces are reported. The results obtained using the singlet surface correspond to those expected if the reaction were to occur adiabatically. The dynamics on the NN(STP) surface represent those expected if the reaction follows a minimum-energy pathway. This study on a small system demonstrates the application of NNs for MD studies using ab initio data when the spin multiplicity of the system changes during the dissociation process.
Ab Initio and Ab Exitu No-Core Shell Model
Vary, J P; Navratil, P; Gueorguiev, V G; Ormand, W E; Nogga, A; Maris, P; Shirokov, A
2007-10-02
We outline two complementary approaches based on the no core shell model (NCSM) and present recent results. In the ab initio approach, nuclear properties are evaluated with two-nucleon (NN) and three-nucleon interactions (TNI) derived within effective field theory (EFT) based on chiral perturbation theory (ChPT). Fitting two available parameters of the TNI generates good descriptions of light nuclei. In a second effort, an ab exitu approach, results are obtained with a realistic NN interaction derived by inverse scattering theory with off-shell properties tuned to fit light nuclei. Both approaches produce good results for observables sensitive to spin-orbit properties.
NASA Astrophysics Data System (ADS)
Futera, Zdenek; English, Niall J.
2017-07-01
The response of water to externally applied electric fields is of central relevance in the modern world, where many extraneous electric fields are ubiquitous. Historically, the application of external fields in non-equilibrium molecular dynamics has been restricted, by and large, to relatively inexpensive, more or less sophisticated, empirical models. Here, we report long-time non-equilibrium ab initio molecular dynamics in both static and oscillating (time-dependent) external electric fields, therefore opening up a new vista in rigorous studies of electric-field effects on dynamical systems with the full arsenal of electronic-structure methods. In so doing, we apply this to liquid water with state-of-the-art non-local treatment of dispersion, and we compute a range of field effects on structural and dynamical properties, such as diffusivities and hydrogen-bond kinetics.
Vchirawongkwin, Viwat; Kritayakornupong, Chinapong; Tongraar, Anan; Rode, Bernd M
2012-10-14
Hydration structure and dynamics of an aqueous Sc(III) solution were characterized by means of an extended ab initio quantum mechanical/molecular dynamical (QM/MM) molecular dynamics simulation at Hartree-Fock level. A monocapped trigonal prismatic structure composed of seven water molecules surrounding scandium(III) ion was proposed by the QM/MM simulation including the quantum mechanical effects for the first and second hydration shells. The mean Sc(III)-O bond length of 2.14 Å was identified for six prism water molecules with one capping water located at around 2.26 Å, reproducing well the X-ray diffraction data. The Sc(III)-O stretching frequency of 432 cm(-1) corresponding to a force constant of 130 N m(-1), evaluated from the enlarged QM/MM simulation, is in good agreement with the experimentally determined value of 430 cm(-1) (128 N m(-1)). Various water exchange processes in the second hydration shell of the hydrated Sc(III) ion predict a mean ligand residence time of 7.3 ps.
Lim, Len Herald V; Bhattacharjee, Anirban; Asam, S Sikander; Hofer, Thomas S; Randolf, Bernhard R; Rode, Bernd M
2010-03-01
An ab initio quantum mechanical charge field molecular dynamics (QMCF MD) simulation was performed to investigate the behavior of the Sb(3+) ion in aqueous solution. The simulation reveals a significant influence of the residual valence shell electron density on the solvation structure and dynamics of Sb(3+). A strong hemidirectional behavior of the ligand binding pattern is observed for the first hydration shell extending up to the second hydration layer. The apparent domain partitioned structural behavior was probed by solvent reorientational kinetics and three-body distribution functions. The three-dimensional hydration space was conveniently segmented such that domains having different properties were properly resolved. The approach afforded a fair isolation of localized solvent structural and dynamical motifs that Sb(3+) seems to induce to a remarkable degree. Most intriguing is the apparent impact of the lone pair electrons on the second hydration shell, which offers insight into the mechanistic aspects of hydrogen bonding networks in water. Such electronic effects observed in the hydration of Sb(3+) can only be studied by applying a suitable quantum mechanical treatment including first and second hydration shell as provided by the QMCF ansatz.
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
Study of Nuclear Clustering from an Ab Initio Perspective
NASA Astrophysics Data System (ADS)
Kravvaris, Konstantinos; Volya, Alexander
2017-08-01
We put forward a new ab initio approach that seamlessly bridges the structure, clustering, and reactions aspects of the nuclear quantum many-body problem. The configuration interaction technique combined with the resonating group method based on a harmonic oscillator basis allows us to treat the reaction and multiclustering dynamics in a translationally invariant way and preserve the Pauli principle. Our presentation includes studies of Be,108 and an exploration of 3 α clustering in 12C.
NASA Astrophysics Data System (ADS)
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
NASA Astrophysics Data System (ADS)
Mei, Yuan; Sherman, David M.; Liu, Weihua; Etschmann, Barbara; Testemale, Denis; Brugger, Joël
2015-02-01
The solubility of zinc minerals in hydrothermal fluids is enhanced by chloride complexation of Zn2+. Thermodynamic models of these complexation reactions are central to models of Zn transport and ore formation. However, existing thermodynamic models, derived from solubility measurements, are inconsistent with spectroscopic measurements of Zn speciation. Here, we used ab initio molecular dynamics simulations (with the PBE exchange-correlation functional) to predict the speciation of Zn-Cl complexes from 25 to 600 °C. We also obtained in situ XAS measurements of Zn-Cl solutions at 30-600 °C. Qualitatively, the simulations reproduced the main features derived from in situ XANES and EXAFS measurements: octahedral to tetrahedral transition with increasing temperature and salinity, stability of ZnCl42- at high chloride concentration up to ⩾500 °C, and increasing stability of the trigonal planar [ZnCl3]- complex at high temperature. Having confirmed the dominant species, we directly determined the stability constants for the Zn-Cl complexes using thermodynamic integration along constrained Zn-Cl distances in a series of MD simulations. We corrected our stability constants to infinite dilution using the b-dot model for the activity coefficients of the solute species. In order to compare the ab initio results with experiments, we need to re-model the existing solubility data using the species we identified in our MD simulations. The stability constants derived from refitting published experimental data are in reasonable agreement with those we obtained using ab initio MD simulations. Our new thermodynamic model accurately predicts the experimentally observed changes in ZnO(s) and ZnCO3(s) solubility as a function of chloride concentration from 200 (Psat) to 600 °C (2000 bar). This study demonstrates that metal speciation and geologically useful stability constants can be derived for species in hydrothermal fluids from ab initio MD simulations even at the generalized
Ab Initio Molecular Dynamics Simulations of Low-Energy Recoil Events in ThO2, CeO2, and ZrO2
Xiao, Haiyan Y.; Zhang, Yanwen; Weber, William J.
2012-08-13
Ab initio molecular dynamics simulations of low-energy recoil events in ThO2, CeO2, and ZrO2 have been carried out to determine the threshold displacement energies, resulting defect configurations, dynamics of defect generation, and role of charge transfer during the process. The results reveal that, in most cases, these fluorite structure oxides exhibit a similar response to low-energy recoils. A variety of different defect configurations are created, consisting mainly of vacancies and interstitials. Charge transfer occurs during the dynamic displacement process. Local charge redistribution leads to cation and O vacancies being negatively and positively charged, respectively. Likewise, due to charge redistribution, the cation and O interstitials are less positively and negatively charged, respectively, than the ions on lattice sites in perfect MO2.
Ab initio molecular dynamics simulations of low energy recoil events in ThO2, CeO2 and ZrO2
Xiao, Haiyan; Zhang, Yanwen; Weber, William J
2012-01-01
Ab initio molecular dynamics simulations of low energy recoil events in ThO2, CeO2 and ZrO2 have been carried out to determine the threshold displacement energies, resulting defect configurations, dynamics of defect generation, and role of charge transfer during the process. The results reveal that, in most cases, these fluorite structure oxides exhibit a similar response to low-energy recoils. A variety of different defect configurations are created, consisting mainly of vacancies and interstitials. Charge transfer occurs during the dynamic displacement process. Local charge redistribution leads to cation and O vacancies being negatively and positively charged, respectively. Likewise, due to charge redistribution, the cation and O interstitials are less positively and negatively charged, respectively, than the ions on lattice sites in perfect MO2.
Nattino, Francesco; Ueta, Hirokazu; Chadwick, Helen; van Reijzen, Maarten E; Beck, Rainer D; Jackson, Bret; van Hemert, Marc C; Kroes, Geert-Jan
2014-04-17
The dissociative chemisorption of methane on metal surfaces is of fundamental and practical interest, being a rate-limiting step in the steam reforming process. The reaction is best modeled with quantum dynamics calculations, but these are currently not guaranteed to produce accurate results because they rely on potential energy surfaces based on untested density functionals and on untested dynamical approximations. To help overcome these limitations, here we present for the first time statistically accurate reaction probabilities obtained with ab initio molecular dynamics (AIMD) for a polyatomic gas-phase molecule reacting with a metal surface. Using a general purpose density functional, the AIMD reaction probabilities are in semiquantitative agreement with new quantum-state-resolved experiments on CHD3 + Pt(111). The comparison suggests the use of the sudden approximation for treating the rotations even though CHD3 has large rotational constants and yields an estimated reaction barrier of 0.9 eV for CH4 + Pt(111).
Wu, S.; Kramer, M.J.; Fang, X.W.; Wang, S.Y.; Wang, C.Z.; Ho, K.M.; Ding, Z.J.; Chen, L.Y.
2012-02-06
The local structures and dynamical properties of the liquid Cu{sub 80}Si{sub 20} alloy have been studied by x-ray diffraction and ab initio molecular dynamics (MD) simulations. The pair-correlation functions and the structure factors derived from the three-dimensional coordinates of the MD configurations agree well with the experimental results. The local structure of the liquids is analyzed using Honeycutt-Andersen (HA) indices, Voronoi tessellation (VT), and an atomic cluster-alignment method. The HA indices analysis shows that the pentagonal bipyramid, a fragment of an icosahedron (ICO), plays a dominant role in the short-range order (SRO) of the Cu{sub 80}Si{sub 20} liquid. The HA indices corresponding to the pentagonal bipyramid increase dramatically with decreasing temperature. VT analysis indicates that, while the liquid does exhibit a strong icosahedral SRO, fcc-like SRO is also measurable. The results from VT analysis are further confirmed using the recently developed atomic cluster-alignment method. Finally, self-diffusion constants, as a function of temperature for both Cu and Si species, are calculated.
Choudhary, Ashu; Chandra, Amalendu
2016-02-17
The anisotropic structure and dynamics of the hydration shell of a benzene solute in liquid water have been investigated by means of ab initio molecular dynamics simulations using the BLYP (Becke-Lee-Yang-Parr) and dispersion corrected BLYP-D functionals. The main focus has been to look at the influence of π-hydrogen-bonding and hydrophobic interactions on the distance and angle resolved various structural and dynamic properties of solvation shell. The structure of hydration shell water molecules around benzene is found to be highly anisotropic as revealed by the radial distribution functions of different conical regions and joint radial/angular distribution functions. The benzene-water dimer potential energy curves are calculated for a variety of orientations of water along the axial and equatorial directions for both BLYP and BLYP-D functionals. The simulation results of the hydration shell structure of benzene, particularly the axial and equatorial benzene-water RDFs are discussed based on the differences in the benzene-water potential energies for different orientations and functionals. The inter-particle distance/angle correlations show an enhanced water structure in the solvation shell of benzene compared to that between the solvation shell and bulk and also between the bulk molecules. On average, a single πH-bond is found to be formed between water and benzene in the 45° axial conical region of the solvation shell. The πH-bonded water molecules are found to have faster translational dynamics and also found to follow a fast jump mechanism of reorientation to change their hydrogen bonded partners. The presence of π-hydrogen-bonded water makes the overall dynamics of the axial region faster than that of the equatorial region where the water molecules are hydrophobically solvated and hydrogen bonded to other water molecules.
Li, Y. Q.; Zhang, P. Y.; Han, K. L.
2015-03-28
A global many-body expansion potential energy surface is reported for the electronic ground state of CH{sub 2}{sup +} by fitting high level ab initio energies calculated at the multireference configuration interaction level with the aug-cc-pV6Z basis set. The topographical features of the new global potential energy surface are examined in detail and found to be in good agreement with those calculated directly from the raw ab initio energies, as well as previous calculations available in the literature. In turn, in order to validate the potential energy surface, a test theoretical study of the reaction CH{sup +}(X{sup 1}Σ{sup +})+H({sup 2}S)→C{sup +}({sup 2}P)+H{sub 2}(X{sup 1}Σ{sub g}{sup +}) has been carried out with the method of time dependent wavepacket on the title potential energy surface. The total integral cross sections and the rate coefficients have been calculated; the results determined that the new potential energy surface can both be recommended for dynamics studies of any type and as building blocks for constructing the potential energy surfaces of larger C{sup +}/H containing systems.
E. Bohm A. Bhatele L. V. Kale M. E. Tuckerman S. Kumar J. A. Gunnels G. J. Martyna; Bohm, E.; Bhatele, A.; Kale, L. V.; Tuckerman, M. E.; Kumar, S.; Gunnels, J. A.; Martyna, G. J.
2008-01-01
Important scientific problems can be treated via ab initio-based molecular modeling approaches, wherein atomic forces are derived from an energy Junction that explicitly considers the electrons. The Car-Parrinello ab initio molecular dynamics (CPAIMD) method is widely used to study small systems containing on the order of 10 to 103 atoms. However, the impact of CPAIMD has been limited until recently because of difficulties inherent to scaling the technique beyond processor numbers about equal to the number of electronic states. CPAIMD computations involve a large number of interdependent phases with high interprocessor communication overhead. These phases require the evaluation of various transforms and non-square matrix multiplications that require large interprocessor data movement when efficiently parallelized. Using the Charm++ parallel programming language and runtime system, the phases are discretized into a large number of virtual processors, which are, in turn, mapped flexibly onto physical processors, thereby allowing interleaving of work. Algorithmic and IBM Blue Gene/L(tm) system-specific optimizations are employed to scale the CPAIMD method to at least 30 times the number of electronic states in small systems consisting of 24 to 768 atoms (32 to 1,024 electronic states) in order to demonstrate fine-grained parallelism. The largest systems studied scaled well across the entire machine (20,480 nodes).
NASA Astrophysics Data System (ADS)
Rao, Mala N.; Lamago, D.; Ivanov, A.; d'Astuto, M.; Postnikov, A. V.; Hussein, R. Hajj; Basak, Tista; Chaplot, S. L.; Firszt, F.; Paszkowicz, W.; Deb, S. K.; Pagès, O.
2014-04-01
The random Zn1-xBexSe zincblende alloy is known to exhibit a peculiar three-mode [1×(Zn-Se),2×(Be-Se)] vibration pattern near the Brillouin zone (BZ) center, of the so-called percolation type, apparent in its Raman spectra. This is due to an unusually large contrast between the physical properties (length, ionicity) of the constituting bonds. In the present work, the inelastic neutron scattering is applied to study the dispersion of modes away from the BZ center, with special attention to the q⃗ dependence of the BeSe-like transverse optic doublet. The discussion is supported by calculations of lattice dynamics done both ab initio (using the siesta code) and within the shell model. The BeSe-like doublet is found to survive nearly unchanged throughout the BZ up to the zone edge, indicating that its origin is at the ultimate bond scale. The microscopic mechanism of splitting is clarified by ab initio calculations. Namely, the local lattice relaxation needed to accommodate the contrast in physical properties of the Zn-Se and Be-Se bonds splits the stretching and bending modes of connected, i.e., percolativelike, (Be-Se) bonds.
NASA Astrophysics Data System (ADS)
Attaccalite, C.; Grüning, M.
2013-12-01
We present an ab initio real-time-based computational approach to study nonlinear optical properties in condensed matter systems that is especially suitable for crystalline solids and periodic nanostructures. The equations of motion and the coupling of the electrons with the external electric field are derived from the Berry-phase formulation of the dynamical polarization [Souza , Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.69.085106 69, 085106 (2004)]. Many-body effects are introduced by adding single-particle operators to the independent-particle Hamiltonian. We add a Hartree operator to account for crystal local effects and a scissor operator to correct the independent particle band structure for quasiparticle effects. We also discuss the possibility of accurately treating excitonic effects by adding a screened Hartree-Fock self-energy operator. The approach is validated by calculating the second-harmonic generation of SiC and AlAs bulk semiconductors: an excellent agreement is obtained with existing ab initio calculations from response theory in frequency domain [Luppi , Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.82.235201 82, 235201 (2010)]. We finally show applications to the second-harmonic generation of CdTe and the third-harmonic generation of Si.
Wu, Ruibo; Hu, Po; Wang, Shenglong; Cao, Zexing; Zhang, Yingkai
2009-01-01
Abstracs The different coordination modes and fast ligand exchange of zinc coordination has been suggested to be one key catalytic feature of the zinc ion which makes it an invaluable metal in biological catalysis. However, partly due to the well known difficulties for zinc to be characterized by spectroscopy methods, evidence for dynamic nature of the catalytic zinc coordination has so far mainly been indirect. In this work, Born-Oppenheimer ab initio QM/MM molecular dynamics simulation has been employed, which allows for a first-principle description of the dynamics of the metal active site while properly including effects of the heterogeneous and fluctuating protein environment. Our simulations have provided direct evidence regarding inherent flexibility of the catalytic zinc coordination shell in Thermolysin (TLN) and Histone Deacetylase 8 (HDAC8). We have observed different coordination modes and fast ligand exchange during the picosecond's time-scale. For TLN, the coordination of the carboxylate group of Glu166 to Zinc is found to continuously change between monodentate and bidentate manner dynamically; while for HDAC8, the flexibility mainly comes from the coordination to a non-amino-acid ligand. Such distinct dynamics in the zinc coordination shell between two enzymes suggests that the catalytic role of Zinc in TLN and HDAC8 is likely to be different in spite of the fact that both catalyze the hydrolysis of amide bond. Meanwhile, considering that such Born-Oppenheimer ab initio QM/MM MD simulations are very much desired but are widely considered to be too computationally expensive to be feasible, our current study demonstrates the viability and powerfulness of this state-of-the-art approach in simulating metalloenzymes. PMID:20161624
Ab initio quantum chemistry: Methodology and applications
Friesner, Richard A.
2005-01-01
This Perspective provides an overview of state-of-the-art ab initio quantum chemical methodology and applications. The methods that are discussed include coupled cluster theory, localized second-order Moller–Plesset perturbation theory, multireference perturbation approaches, and density functional theory. The accuracy of each approach for key chemical properties is summarized, and the computational performance is analyzed, emphasizing significant advances in algorithms and implementation over the past decade. Incorporation of a condensed-phase environment by means of mixed quantum mechanical/molecular mechanics or self-consistent reaction field techniques, is presented. A wide range of illustrative applications, focusing on materials science and biology, are discussed briefly. PMID:15870212
Ab-initio phasing in protein crystallography
NASA Astrophysics Data System (ADS)
van der Plas, J. L.; Millane, Rick P.
2000-11-01
The central problem in the determination of protein structures form x-ray diffraction dada (x-ray crystallography) corresponds to a phase retrieval problem with undersampled amplitude data. Algorithms for this problem that have an increased radius of convergence have the potential for reducing the amount of experimental work, and cost, involved in determining protein structures. We describe such an algorithm. Application of the algorithm to a simulated crystallographic problem shows that it converges to the correct solution, with no initial phase information, where currently used algorithms fail. The results lend support to the possibility of ab initio phasing in protein crystallography.
Germacrene D Cyclization: An Ab Initio Investigation
Setzer, William N.
2008-01-01
Essential oils that contain large concentrations of germacrene D are typically accompanied by cadinane sesquiterpenoids. The acid-catalyzed cyclization of germacrene D to give cadinane and selinane sesquiterpenes has been computationally investigated using both density functional (B3LYP/6-31G*) and post Hartree-Fock (MP2/6-31G* *) ab initio methods. The calculated energies are in general agreement with experimentally observed product distributions, both from acid-catalyzed cyclizations as well as distribution of the compounds in essential oils. PMID:19325722
Molecular associations from ab initio pair potentials
NASA Astrophysics Data System (ADS)
Iglesias, E.; Sordo, T. L.; Sordo, J. A.
1991-12-01
A method of building up stable molecular associations by using pair potentials from ab initio calculations is presented. The Matsuoka-Clementi-Yoshimine potential has been chosen to emulate the water-water interactions while 1-6-12 potentials are used to compute both solute-solvent and solute-solute interactions. Parameters for neutral-amino-acid-water and neutral- amino-acid-neutral-amino-acid interactions are provided by the program. Supermolecules are constructed by minimization of the interaction energy of the molecules involved. Both steepest-decent and Fletcher-Powell algorithms are available to carry out such a minimization.
Ab-initio calculations on melting of thorium
Mukherjee, D. Sahoo, B. D.; Joshi, K. D.; Kaushik, T. C.; Gupta, Satish C.
2016-05-23
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 (a{sub 0}){sup 3} and (1.02a{sub 0}){sup 3} and (1.04a{sub 0}){sup 3} increases gradually with temperature and undergoes a sharp jump at ~2200 K, ~2100 K and ~1800 K, respectively. Here, a{sub 0} = 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 2023 K. Further, the same has been verified by plotting the atomic arrangement evolved at various temperatures and corresponding pair correlation functions.
Ab initio calculations of the melting temperatures of refractory bcc metals.
Wang, L G; van de Walle, A
2012-01-28
We present ab initio calculations of the melting temperatures for bcc metals Nb, Ta and W. The calculations combine phase coexistence molecular dynamics (MD) simulations using classical embedded-atom method potentials and ab initio density functional theory free energy corrections. The calculated melting temperatures for Nb, Ta and W are, respectively, within 3%, 4%, and 7% of the experimental values. We compare the melting temperatures to those obtained from direct ab initio molecular dynamics simulations and see if they are in excellent agreement with each other. The small remaining discrepancies with experiment are thus likely due to inherent limitations associated with exchange-correlation energy approximations within density-functional theory.
Dynamics of the O(3P) + CHD3(vCH = 0,1) reactions on an accurate ab initio potential energy surface
Czakó, Gábor; Bowman, Joel M.
2012-01-01
Recent experimental and theoretical studies on the dynamics of the reactions of methane with F and Cl atoms have modified our understanding of mode-selective chemical reactivity. The O + methane reaction is also an important candidate to extend our knowledge on the rules of reactivity. Here, we report a unique full-dimensional ab initio potential energy surface for the O(3P) + methane reaction, which opens the door for accurate dynamics calculations using this surface. Quasiclassical trajectory calculations of the angular and vibrational distributions for the ground state and CH stretching excited O + CHD3(v1 = 0,1) → OH + CD3 reactions are in excellent agreement with the experiment. Our theory confirms what was proposed experimentally: The mechanistic origin of the vibrational enhancement is that the CH-stretching excitation enlarges the reactive cone of acceptance. PMID:22566657
NASA Astrophysics Data System (ADS)
Ray, Keith; Wang, Zhenxing; Daniels, Isaak; Olmsted, David; Laird, Brian; Asta, Mark
2015-03-01
Pseudocapacitors are devices that store electrical energy faradaically, but feature fast reactions/intercalations enabling high power applications. Power density may be improved by utilizing electrolytes with fast Li ion diffusion. In this study we utilize ab-initio molecular dynamics to elucidate the solvation structure as well as the vibrational and diffusion dynamics of Li ions in the acetonitrile electrolyte. Acetonitrile is a promising electrolyte for energy storage applications due to its lower viscosity and higher ionic conductivity when compared to other battery electrolytes such as ethylene carbonate and propylene carbonate. Interestingly, the trends in the Li ion concentration dependent diffusivity are calculated to be qualitatively different depending on whether the PBE or vdW-DF density functional is used. This work was supported as part of the Molecularly Engineered Energy Materials (MEEM), an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Award DE-SC0001342.
AIDA: ab initio domain assembly server.
Xu, Dong; Jaroszewski, Lukasz; Li, Zhanwen; Godzik, Adam
2014-07-01
AIDA: ab initio domain assembly server, available at http://ffas.burnham.org/AIDA/ is a tool that can identify domains in multi-domain proteins and then predict their 3D structures and relative spatial arrangements. The server is free and open to all users, and there is an option for a user to provide an e-mail to get the link to result page. Domains are evolutionary conserved and often functionally independent units in proteins. Most proteins, especially eukaryotic ones, consist of multiple domains while at the same time, most experimentally determined protein structures contain only one or two domains. As a result, often structures of individual domains in multi-domain proteins can be accurately predicted, but the mutual arrangement of different domains remains unknown. To address this issue we have developed AIDA program, which combines steps of identifying individual domains, predicting (separately) their structures and assembling them into multiple domain complexes using an ab initio folding potential to describe domain-domain interactions. AIDA server not only supports the assembly of a large number of continuous domains, but also allows the assembly of domains inserted into other domains. Users can also provide distance restraints to guide the AIDA energy minimization. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.
Kołaski, Maciej; Lee, Han Myoung; Pak, Chaeho; Kim, Kwang S
2008-01-09
In contrast to the extensive theoretical investigation of the solvation phenomena, the dissolution phenomena have hardly been investigated theoretically. Upon the excitation of hydrated halides, which are important substances in atmospheric chemistry, an excess electron transfers from the anionic precursor (halide anion) to the solvent and is stabilized by the water cluster. This results in the dissociation of hydrated halides into halide radicals and electron-water clusters. Here we demonstrate the charge-transfer-to-solvent (CTTS)-driven femtosecond-scale dissolution dynamics for I-(H2O)n=2-5 clusters using excited state (ES) ab initio molecular dynamics (AIMD) simulations employing the complete-active-space self-consistent-field (CASSCF) method. This study shows that after the iodine radical is released from I-(H2O)n=2-5, a simple population decay is observed for small clusters (2 dynamics could be useful in designing the receptors which are able to bind and release ions in host-guest chemistry.
NASA Astrophysics Data System (ADS)
MacDonell, Ryan J.; Schalk, Oliver; Geng, Ting; Thomas, Richard D.; Feifel, Raimund; Hansson, Tony; Schuurman, Michael S.
2016-09-01
We report a joint experimental and theoretical study on the photoinitiated ultrafast dynamics of acrylonitrile (AN) and two methylated analogs: crotonitrile (CrN) and methacrylonitrile (MeAN). Time-resolved photoelectron spectroscopy (TRPES) and ab initio simulation are employed to discern the conical intersection mediated vibronic dynamics leading to relaxation to the ground electronic state. Each molecule is pumped with a femtosecond pulse at 200 nm and the ensuing wavepackets are probed by means of one and two photon ionization at 267 nm. The predominant vibrational motions involved in the de-excitation process, determined by ab initio trajectory simulations, are an initial twisting about the C=C axis followed by pyramidalization at a carbon atom. The decay of the time-resolved photoelectron signal for each molecule is characterized by exponential decay lifetimes for the passage back to the ground state of 60 ± 10, 86 ± 11, and 97 ± 9 fs for AN, CrN, and MeAN, respectively. As these results show, the excited state dynamics are sensitive to the choice of methylation site and the explanation for the observed trend may be found in the trajectory simulations. Specifically, since the pyramidalization motion leading to the conical intersection with the ground state is accompanied by the development of a partial negative charge at the central atom of the pyramidal group, the electron donation of the cyano group ensures that this occurs exclusively at the medial carbon atom. In this way, the donated electron density from the cyano group "directs" the wavepacket to a particular region of the intersection seam. The excellent agreement between the experimental and simulated TRPES spectra, the latter determined by employing trajectory simulations, demonstrates that this mechanistic picture is consistent with the spectroscopic results.
NASA Astrophysics Data System (ADS)
Evans, M. W.; Refson, K.; Swamy, K. N.; Lie, G. C.; Clementi, E.
1987-10-01
A computer simulation of liquid water using the ab initio Matsuoka-Clementi-Yoshimine-Lie (MCYL) potential has been analyzed in comprehensive detail with use of pertinent auto-correlation and cross-correlation functions of the water molecule's vibrational, rotational, and translational dynamics. The autocorrelation functions (ACF's) of dynamical quantities such as atom velocity, center-of-mass velocity, molecular angular momentum, molecular angular velocity, molecular dipole moment, and molecular rotational velocity vectors have been computed with 3400 configurations generated in a simulation with 343 molecules in the laboratory frame and in the frame of the principal molecular moments of inertia. Furthermore, cross-correlation functions (CCF's) of many different kinds have been computed in both frames in order to study in detail the mutual effects of vibration, rotation, and translation at the single-molecule level. In some respects the inclusion of vibrational effects in the MCYL potential does not significantly change the pattern of dynamical information summarized in these time correlation functions. The rotation-translation CCF's which were obtained recently by Evans et al. from a rigid empirical model for the intermolecular pair potential energy in liquid water appear once more from the ab initio MCYL potential with the same symmetry and time dependence. This is a strong corroborative evidence for the correctness of the methods used in both cases. However, the inclusion of vibrational effects by Lie and Clementi in their MCYL potential leads in this work to considerable further insight obtained by a detailed study of cross-correlation functions between vibration and rotation and between vibration and center-of-mass translation.
NASA Astrophysics Data System (ADS)
Malbon, Christopher L.; Zhu, Xiaolei; Guo, Hua; Yarkony, David R.
2016-12-01
For two electronic states coupled by conical intersections, the line integral of the derivative coupling can be used to construct a complex-valued multiplicative phase factor that makes the real-valued adiabatic electronic wave function single-valued, provided that the curl of the derivative coupling is zero. Unfortunately for ab initio determined wave functions, the curl is never rigorously zero. However, when the wave functions are determined from a coupled two diabatic state Hamiltonian Hd (fit to ab initio data), the resulting derivative couplings are by construction curl free, except at points of conical intersection. In this work we focus on a recently introduced diabatization scheme that produces the Hd by fitting ab initio determined energies, energy gradients, and derivative couplings to the corresponding Hd determined quantities in a least squares sense, producing a removable approximation to the ab initio determined derivative coupling. This approach and related numerical issues associated with the nonremovable ab initio derivative couplings are illustrated using a full 33-dimensional representation of phenol photodissociation. The use of this approach to provide a general framework for treating the molecular Aharonov Bohm effect is demonstrated.
Malbon, Christopher L; Zhu, Xiaolei; Guo, Hua; Yarkony, David R
2016-12-21
For two electronic states coupled by conical intersections, the line integral of the derivative coupling can be used to construct a complex-valued multiplicative phase factor that makes the real-valued adiabatic electronic wave function single-valued, provided that the curl of the derivative coupling is zero. Unfortunately for ab initio determined wave functions, the curl is never rigorously zero. However, when the wave functions are determined from a coupled two diabatic state Hamiltonian H(d) (fit to ab initio data), the resulting derivative couplings are by construction curl free, except at points of conical intersection. In this work we focus on a recently introduced diabatization scheme that produces the H(d) by fitting ab initio determined energies, energy gradients, and derivative couplings to the corresponding H(d) determined quantities in a least squares sense, producing a removable approximation to the ab initio determined derivative coupling. This approach and related numerical issues associated with the nonremovable ab initio derivative couplings are illustrated using a full 33-dimensional representation of phenol photodissociation. The use of this approach to provide a general framework for treating the molecular Aharonov Bohm effect is demonstrated.
Towards Accurate Ab Initio Predictions of the Spectrum of Methane
NASA Technical Reports Server (NTRS)
Schwenke, David W.; Kwak, Dochan (Technical Monitor)
2001-01-01
We have carried out extensive ab initio calculations of the electronic structure of methane, and these results are used to compute vibrational energy levels. We include basis set extrapolations, core-valence correlation, relativistic effects, and Born- Oppenheimer breakdown terms in our calculations. Our ab initio predictions of the lowest lying levels are superb.
Matsubara, Toshiaki; Dupuis, Michel; Aida, Misako
2008-02-01
We applied the ONIOM-molecular dynamics (MD) method to cytosine deaminase to examine the environmental effects of the amino acid residues in the pocket of the active site on the substrate taking account of their thermal motion. The ab initio ONIOM-MD simulations show that the substrate uracil is strongly perturbed by the amino acid residue Ile33, which sandwiches the uracil with His62, through the steric contact due to the thermal motion. As a result, the magnitude of the thermal oscillation of the potential energy and structure of the substrate uracil significantly increases. TM and MA were partly supported by grants from the Ministry of Education, Culture, Sports, Science and Technology of Japan.MD was supported by the Division of Chemical Sciences, Office of Basic Energy Sciences, and by the Office of Biological and Environmental Research of the U.S. Department of Energy DOE. Battelle operates Pacific Northwest National Laboratory for DOE.
Gerber, Iann C; Jolibois, Franck
2015-05-14
Chemical shift requires the knowledge of both the sample and a reference magnetic shielding. In few cases as nitrogen (15N), the standard experimental reference corresponds to its liquid phase. Theoretical estimate of NMR magnetic shielding parameters of compounds in their liquid phase is then mandatory but usually replaced by an easily-get gas phase value, forbidding direct comparisons with experiments. We propose here to combine ab initio molecular dynamic simulations with the calculations of magnetic shielding using GIAO approach on extracted cluster's structures from MD. Using several computational strategies, we manage to accurately calculate 15N magnetic shielding of nitromethane in its liquid phase. Theoretical comparison between liquid and gas phase allows us to extrapolate an experimental value for the 15N magnetic shielding of nitromethane in gas phase between -121.8 and -120.8 ppm.
Parkes, Marie V.; Greathouse, Jeffery A.; Hart, David B.; ...
2016-04-04
The separation of oxygen from nitrogen using metal–organic frameworks (MOFs) is of great interest for potential pressure-swing adsorption processes for the generation of purified O2 on industrial scales. This study uses ab initio molecular dynamics (AIMD) simulations to examine for the first time the pure-gas and competitive gas adsorption of O2 and N2 in the M2(dobdc) (M = Cr, Mn, Fe) MOF series with coordinatively unsaturated metal centers. Effects of metal, temperature, and gas composition are explored. Lastly, this unique application of AIMD allows us to study in detail the adsorption/desorption processes and to visualize the process of multiple guestsmore » competitively binding to coordinatively unsaturated metal sites of a MOF.« less
NASA Astrophysics Data System (ADS)
Wang, Yaocen; Takeuchi, Akira; Makino, Akihiro; Liang, Yunye; Kawazoe, Yoshiyuki
2015-05-01
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.
NASA Astrophysics Data System (ADS)
Hermansson, Kersti; Baudin, Micael; Ensing, Bernd; Alfredsson, Maria; Wojcik, Mark
1998-11-01
2D periodic ab initio calculations have been performed for H2 interacting with a temperature-reconstructed MgO(111) surface, created from a molecular dynamics (MD) simulation at 300 K. The temperature effects involve both a long-time reconstruction of the surface and instantaneous vibrational displacements. Chemisorption energies of ˜60 μJ/mol were found. Comparisons with adsorption on ideal and relaxed MgO(111) slabs show that the physi- and chemisorption properties for the H2/MgO(111) system are very sensitive to small topological details in the surface structure. The large surface reconstruction at 300 K involves drastic changes of the surface's adsorption properties. We also find that a low coordination number of the surface ions is not sufficient to make the site attractive for chemisorption.
Dixon, J. A.; Elliott, S. R.
2014-04-07
A large number of phase-change materials (PCMs) have been developed experimentally; however, only Ge{sub 2}Sb{sub 2}Te{sub 5}-based PCMs have been significantly explored using ab initio molecular-dynamics (AIMD) simulations. We present an AIMD study of the full melt/quench/anneal PC cycle for Ga-Sb materials, namely, the stoichiometric composition, GaSb, and the near-eutectic alloy, Ga{sub 16}Sb{sub 84}. The calculated electronic densities of states and optical reflectivities are compared between the amorphous and crystalline phases for both compositions, and it is shown that the contrasting opto-electronic properties of each crystalline material can be attributed to different structural transformations of Ga and Sb on crystallization from the amorphous state.
NASA Astrophysics Data System (ADS)
Hayashi, Aiko; Shiga, Motoyuki; Tachikawa, Masanori
2006-11-01
In order to investigate the H /D isotope effect on a dihydrogen bonded cation system, we have studied NH4+⋯BeH2 and its isotopomers by ab initio path integral molecular dynamics. It is found that the dihydrogen bond can be exchanged by NH4+ rotation. The deuterated isotopomer (ND4+⋯BeD2; DD) can exchange the dihydrogen bond more easily than other isotopomers such as (NH4+⋯BeH2; HH). This unusual isotope effect is ascribed to the "quantum localization" which occurs when the effective energy barrier for the rotational mode becomes higher by the zero point energy of other modes. We also found that the binding energy of dihydrogen bonds for DD species is the smallest among the isotopomers.
Ab Initio Infrared and Raman Spectra.
1982-08-01
tions. For parameters not depending on momenta, a parallel ab fhti Monte Carlo approach would use electronic energies and other parameters of... Monte Carlo approach. Specifically, as one of us has suggested,t I classical molecular dynamics may be integrated with ab iniHo quan- tum force...alternative approach, for phenomena which are not explicitly time dependent, is a Monte Carlo procedure in which at each trial nuclear configuration
Borah, Sangkha; Padma Kumar, P
2016-06-07
Microscopic investigation of solvation of selenic acid (H2SeO4) in the aqueous environment has been carried out using the Car-Parrinello molecular dynamics simulation technique. The species deprotonates to HSeO4(-) in a few picoseconds owing to its low pKa1 value of -3.0. A dynamic equilibrium between HSeO4(-) and SeO4(2-), is observed in qualitative agreement with the reported pKa2 value of 1.70. The governing deprotonation mechanism and the structural and dynamic evolutions of the system, particularly the nature of hydrogen bonding, their strengths and lifetimes are investigated comprehensively. A comparison of the vibrational spectra of the species recorded in the gas phase and in the aqueous environment provides further insights on the nature of the interaction between the solute species and water. The results are in good agreement with the available experimental data and other recent computational studies.
Rezac, Jan; Hobza, Pavel
2008-10-15
The dynamic nature of the benzene dimer was explored by on-the-fly molecular dynamics simulations based on the DFT-D method covering the dispersion energy. An all-electron DFT was performed at the BLYP/TZVP level. The parameters in the dispersion correction term were fitted to mimic the benchmark CCSD(T)/complete basis set limit potential energy curves for both the parallel-displaced (PD) and T-shaped (TS) structures of the dimer exactly. A dynamic description is important at temperatures above 10 K, where interconversion between the TS and PD structures is possible and a mixture of these two species exists. The higher the temperature, the more dominant the TS structure because of a favorable entropic contribution to the free energy. An analysis of the TS structures revealed that the symmetric c₂v structure, a low-lying transition state, is practically not populated and that the tilted cs TS structure is prevalent. This finding is in perfect agreement with infrared spectroscopy.
Lee, Mal -Soon; Peter McGrail, B.; Rousseau, Roger; ...
2015-10-12
Here, the interface between a solid and a complex multi-component liquid forms a unique reaction environment whose structure and composition can significantly deviate from either bulk or liquid phase and is poorly understood due the innate difficulty to obtain molecular level information. Feldspar minerals, as typified by the Ca-end member Anorthite, serve as prototypical model systems to assess the reactivity and ion mobility at solid/water-bearing supercritical fluid (WBSF) interfaces due to recent X-ray based measurements that provide information on water-film formation, and cation vacancies at these surfaces. Using density functional theory based molecular dynamics, which allows the evaluation of reactivitymore » and condensed phase dynamics on equal footing, we report on the structure and dynamics of water nucleation and surface aggregation, carbonation and Ca mobilization under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar). We find that water has a strong enthalpic preference for aggregation on a Ca-rich, O-terminated anorthite (001) surface, but entropy strongly hinders the film formation at very low water concentrations. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies, when in contact with supercritical CO2. Cation vacancies of this type can form readily in the presence of a water layer that allows for facile and enthalpicly favorable Ca2+ extraction and solvation. Apart from providing unprecedented molecular level detail of a complex three component (mineral, water and scCO2) system), this work highlights the ability of modern capabilities of AIMD methods to begin to qualitatively and quantitatively address structure and reactivity at solid-liquid interfaces of high chemical complexity. This work was supported by the US Department of Energy, Office of Fossil Energy (M.-S. L., B. P. M. and V.-A. G.) and the Office of Basic Energy Science, Division of Chemical Sciences
Ab Initio Calculation of the Hoyle State
Epelbaum, Evgeny; Krebs, Hermann; Lee, Dean; Meissner, Ulf-G.
2011-05-13
The Hoyle state plays a crucial role in the helium 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 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 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 the properties of the Hoyle state and in agreement with the experimentally observed energy.
An ab initio study of hydroxylated graphane.
Buonocore, Francesco; Capasso, Andrea; Lisi, Nicola
2017-09-14
Graphene-based derivatives with covalent functionalization and well-defined stoichiometry are highly desirable in view of their application as functional surfaces. Here, we have evaluated by ab initio calculations the energy of formation and the phase diagram of hydroxylated graphane structures, i.e., fully functionalized graphene derivatives coordinated with -H and -OH groups. We compared these structures to different hydrogenated and non-hydrogenated graphene oxide derivatives, with high level of epoxide and hydroxyl groups functionalization. Based on our calculations, stable phases of hydroxylated graphane with low and high contents of hydrogen are demonstrated for high oxygen and hydrogen partial pressure, respectively. Stable phases of graphene oxide with a mixed carbon hybridization are also found. Notably, the synthesis of hydroxylated graphane has been recently reported in the literature.
An ab initio study of hydroxylated graphane
NASA Astrophysics Data System (ADS)
Buonocore, Francesco; Capasso, Andrea; Lisi, Nicola
2017-09-01
Graphene-based derivatives with covalent functionalization and well-defined stoichiometry are highly desirable in view of their application as functional surfaces. Here, we have evaluated by ab initio calculations the energy of formation and the phase diagram of hydroxylated graphane structures, i.e., fully functionalized graphene derivatives coordinated with -H and -OH groups. We compared these structures to different hydrogenated and non-hydrogenated graphene oxide derivatives, with high level of epoxide and hydroxyl groups functionalization. Based on our calculations, stable phases of hydroxylated graphane with low and high contents of hydrogen are demonstrated for high oxygen and hydrogen partial pressure, respectively. Stable phases of graphene oxide with a mixed carbon hybridization are also found. Notably, the synthesis of hydroxylated graphane has been recently reported in the literature.
Guiding ab initio calculations by alchemical derivatives
NASA Astrophysics Data System (ADS)
to Baben, M.; Achenbach, J. O.; von Lilienfeld, O. A.
2016-03-01
We assess the concept of alchemical transformations for predicting how a further and not-tested change in composition would change materials properties. This might help to guide ab initio calculations through multidimensional property-composition spaces. Equilibrium volumes, bulk moduli, and relative lattice stability of fcc and bcc 4d transition metals Zr, Nb, Mo, Tc, Ru, Rh, Pd, and Ag are calculated using density functional theory. Alchemical derivatives predict qualitative trends in lattice stability while equilibrium volumes and bulk moduli are predicted with less than 9% and 28% deviation, respectively. Predicted changes in equilibrium volume and bulk moduli for binary and ternary mixtures of Rh-Pd-Ag are in qualitative agreement even for predicted bulk modulus changes as large as +100% or -50%. Based on these results, it is suggested that alchemical transformations could be meaningful for enhanced sampling in the context of virtual high-throughput materials screening projects.
Ab Initio Modeling of Molecular Radiation
NASA Technical Reports Server (NTRS)
Jaffe, Richard; Schwenke, David
2014-01-01
Radiative emission from excited states of atoms and molecules can comprise a significant fraction of the total heat flux experienced by spacecraft during atmospheric entry at hypersonic speeds. For spacecraft with ablating heat shields, some of this radiative flux can be absorbed by molecular constituents in the boundary layer that are formed by the ablation process. Ab initio quantum mechanical calculations are carried out to predict the strengths of these emission and absorption processes. This talk will describe the methods used in these calculations using, as examples, the 4th positive emission bands of CO and the 1g+ 1u+ absorption in C3. The results of these calculations are being used as input to NASA radiation modeling codes like NeqAir, HARA and HyperRad.
Discovering chemistry with an ab initio nanoreactor
NASA Astrophysics Data System (ADS)
Martinez, Todd
Traditional approaches for modeling chemical reaction networks such as those involved in combustion have focused on identifying individual reactions and using theoretical approaches to explore the underlying mechanisms. Recent advances involving graphical processing units (GPUs), commodity products developed for the videogaming industry, have made it possible to consider a distinct approach wherein one attempts to discover chemical reactions and mechanisms. We provide a brief summary of these developments and then discuss the concept behind the ``ab initio nanoreactor'' which explores the space of possible chemical reactions and molecular species for a given stoichiometry. The nanoreactor concept is exemplified with an example to the Urey-Miller reaction network which has been previously advanced as a potential model for prebiotic chemistry. We briefly discuss some of the future directions envisioned for the development of this nanoreactor concept.
Ab initio alpha-alpha scattering
NASA Astrophysics Data System (ADS)
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
2015-12-03
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
Yu, Feng
2012-02-05
The bimolecular nucleophilic substitution (S(N)2) reaction of F(a)(-) with NH(2)F(b) has been investigated with the ab initio direct classical trajectory method. According to our trajectory calculations, a dynamic behavior of nonstatistical central barrier recrossing is revealed. Among the 64 trajectories calculated in this work, 45 trajectories follow the dynamic reaction pathways as assumed by statistical theory and other 19 trajectories with central barrier recrossings are nonstatistical. For the nonstatistical trajectories, the central barrier recrossings may originate from the inefficient kinetic energy transfer from the intramolecular modes of the NH(2)F(a) moiety in the dynamic F(b)(-)…H-NH-F(a) complex to the intermolecular modes of the dynamic F(b)(-)…H-NH-F(a) complex on the exit-channel potential energy surface. With respect to the dynamic behavior of the nonstatistical central barrier recrossing, the statistical theories such as the Rice-Ramsperger-Kassel-Marcus and transition state theories without further corrections cannot be used to model the reaction kinetics for this S(N)2 reaction.
Liu, Ping; Zhao, Jing; Liu, Jinxiang; Zhang, Meng; Bu, Yuxiang
2014-01-28
In view of the important implications of excess electrons (EEs) interacting with CO2-H2O clusters in many fields, using ab initio molecular dynamics simulation technique, we reveal the structures and dynamics of an EE associated with its localization and subsequent time evolution in heterogeneous CO2-H2O mixed media. Our results indicate that although hydration can increase the electron-binding ability of a CO2 molecule, it only plays an assisting role. Instead, it is the bending vibrations that play the major role in localizing the EE. Due to enhanced attraction of CO2, an EE can stably reside in the empty, low-lying π(*) orbital of a CO2 molecule via a localization process arising from its initial binding state. The localization is completed within a few tens of femtoseconds. After EE trapping, the ∠OCO angle of the core CO2 (-) oscillates in the range of 127°∼142°, with an oscillation period of about 48 fs. The corresponding vertical detachment energy of the EE is about 4.0 eV, which indicates extreme stability of such a CO2-bound solvated EE in [CO2(H2O)n](-) systems. Interestingly, hydration occurs not only on the O atoms of the core CO2 (-) through formation of O⋯H-O H-bond(s), but also on the C atom, through formation of a C⋯H-O H-bond. In the latter binding mode, the EE cloud exhibits considerable penetration to the solvent water molecules, and its IR characteristic peak is relatively red-shifted compared with the former. Hydration on the C site can increase the EE distribution at the C atom and thus reduce the C⋯H distance in the C⋯H-O H-bonds, and vice versa. The number of water molecules associated with the CO2 (-) anion in the first hydration shell is about 4∼7. No dimer-core (C2O4 (-)) and core-switching were observed in the double CO2 aqueous media. This work provides molecular dynamics insights into the localization and time evolution dynamics of an EE in heterogeneous CO2-H2O media.
Evans, R James; Rustad, James R; Casey, William H
2008-05-01
We have simulated exchange of inner-sphere and bulk water molecules for different sizes of Al3+(aq) clusters, Al(H2O)63+ + nH2O for n = 0, 1, 6, or 12, with ab initio and molecular dynamics simulations, in order to understand how robust the ab initio method is for identifying hydrolytic reaction pathways of particular importance to geochemistry. In contrast to many interfacial reactions, this particular elementary reaction is particularly simple and well-constrained by experiment. Nevertheless, we find that a rich array of parallel reaction pathways depend sensitively on the details of the solvation sphere and structure and that larger clusters are not necessarily better. Inner-sphere water exchange in Al3+(aq) may occur through two Langford-Gray dissociative pathways, one in which the incoming and outgoing waters are cis, the other in which they are trans to one another. A large majority of exchanges in the molecular dynamics simulations occurred via the trans mechanism, in contrast to the predictions of the ab initio method. In Al(H2O)63+ + H2O, the cis mechanism has a transition state of 84.3 kJ/mol, which is in good agreement with previous experimental and ab initio results, while the trans mechanism has only a saddle point with two negative frequencies, not a transition state, at 89.7 kJ/mol. In addition to the exchange mechanisms, dissociation pathways could be identified that were considerably lower in energy than experiment and varied considerably between 60 and 100 kJ/mol, depending on the particular geometry and cluster size, with no clear relation between the two. Ab initio calculations using large clusters with full second coordination spheres (n = 12) were unable to find dissociation or exchange transition states because the network of hydrogen bonds in the second coordination sphere was too rigid to accommodate the outgoing inner-sphere water. Our results indicate that caution should surround ab initio simulation of complicated dynamic processes such
Xin, H.; LaRue, J.; Oberg, H.; Beye, M.; Dell'Angela, M.; Turner, J. J.; Gladh, J.; Ng, M. L.; Sellberg, J. A.; Kaya, S.; Mercurio, G.; Hieke, F.; Nordlund, D.; Schlotter, W. F.; Dakovski, G. L.; Minitti, M. P.; Fohlisch, A.; Wolf, M.; Wurth, W.; Ogasawara, H.; Norskov, J. K.; Ostrom, H.; Pettersson, L. G. M.; Nilsson, A.; Ablid-Pedersen, F.
2015-04-16
We show that coadsorbed oxygen atoms have a dramatic influence on the CO desorption dynamics from Ru(0001). In contrast to the precursor-mediated desorption mechanism on Ru(0001), the presence of surface oxygen modifies the electronic structure of Ru atoms such that CO desorption occurs predominantly via the direct pathway. This phenomenon is directly observed in an ultrafast pump-probe experiment using a soft x-ray free-electron laser to monitor the dynamic evolution of the valence electronic structure of the surface species. This is supported with the potential of mean force along the CO desorption path obtained from density-functional theory calculations. Charge density distribution and frozen-orbital analysis suggest that the oxygen-induced reduction of the Pauli repulsion, and consequent increase of the dative interaction between the CO 5σ and the charged Ru atom, is the electronic origin of the distinct desorption dynamics. Ab initio molecular dynamics simulations of CO desorption from Ru(0001) and oxygen-coadsorbed Ru(0001) provide further insights into the surface bond-breaking process.
Xin, H; LaRue, J; Öberg, H; Beye, M; Dell'Angela, M; Turner, J J; Gladh, J; Ng, M L; Sellberg, J A; Kaya, S; Mercurio, G; Hieke, F; Nordlund, D; Schlotter, W F; Dakovski, G L; Minitti, M P; Föhlisch, A; Wolf, M; Wurth, W; Ogasawara, H; Nørskov, J K; Öström, H; Pettersson, L G M; Nilsson, A; Abild-Pedersen, F
2015-04-17
We show that coadsorbed oxygen atoms have a dramatic influence on the CO desorption dynamics from Ru(0001). In contrast to the precursor-mediated desorption mechanism on Ru(0001), the presence of surface oxygen modifies the electronic structure of Ru atoms such that CO desorption occurs predominantly via the direct pathway. This phenomenon is directly observed in an ultrafast pump-probe experiment using a soft x-ray free-electron laser to monitor the dynamic evolution of the valence electronic structure of the surface species. This is supported with the potential of mean force along the CO desorption path obtained from density-functional theory calculations. Charge density distribution and frozen-orbital analysis suggest that the oxygen-induced reduction of the Pauli repulsion, and consequent increase of the dative interaction between the CO 5σ and the charged Ru atom, is the electronic origin of the distinct desorption dynamics. Ab initio molecular dynamics simulations of CO desorption from Ru(0001) and oxygen-coadsorbed Ru(0001) provide further insights into the surface bond-breaking process.
NASA Astrophysics Data System (ADS)
Müller, Jens; Hartmann, Benedikt; Rommel, Robert; Brandenburg, Jens; Winter, Stephen M.; Schlueter, John A.
2015-08-01
We have studied the low-frequency dynamics of the charge carriers in different organic charge-transfer salts κ-(BEDT-TTF)2X with polymeric anions X by using resistance noise spectroscopy. Our aim is to investigate the structural, glass-like transition caused by the conformational degrees of freedom of the BEDT-TTF molecules’ terminal ethylene groups. Although of fundamental importance for studies of the electronic ground-state properties, the phenomenology of the glassy dynamics has been minimally investigated and its origin is not understood. Our systematic studies of fluctuation spectroscopy of various different compounds reveal a universal, pronounced maximum in the resistance noise power spectral density related to the glass transition. The energy scale of this process can be identified with the activation energy of the glass-like ethylene endgroup structural dynamics as determined from thermodynamic and NMR measurements. For the first time for this class of ‘plastic crystals’, we report a typical glassy property of the relaxation time, namely a Vogel-Fulcher-Tammann law, and are able to determine the degree of fragility of the glassy system. Supporting ab initio calculations provide an explanation for the origin and phenomenology of the glassy dynamics in different systems in terms of a simple two-level model, where the relevant energy scales are determined by the coupling of the ethylene endgroups to the anions.
Fedorov, Dmitry A; Pruitt, Spencer R; Keipert, Kristopher; Gordon, Mark S; Varganov, Sergey A
2016-05-12
Dynamics at intersystem crossings are fundamental to many processes in chemistry, physics, and biology. The ab initio multiple spawning (AIMS) method was originally developed to describe internal conversion dynamics at conical intersections where derivative coupling is responsible for nonadiabatic transitions between electronic states with the same spin multiplicity. Here, the applicability of the AIMS method is extended to intersystem crossing dynamics in which transitions between electronic states with different spin multiplicities are mediated by relativistic spin-orbit coupling. In the direct AIMS dynamics, the nuclear wave function is expanded in the basis of frozen multidimensional Gaussians propagating on the coupled electronic potential energy surfaces calculated on the fly. The AIMS method for intersystem crossing is used to describe the nonadiabatic transitions between the (3)B1 and (1)A1 states of GeH2. The potential energies and gradients were obtained at the CASSCF(6,6)/6-31G(d) level of theory. The spin-orbit coupling matrix elements were calculated with the configuration interaction method using the two-electron Breit-Pauli Hamiltonian. The excited (3)B1 state lifetime and intersystem crossing rate constants were estimated by fitting the AIMS state population with the first-order kinetics equation for a reversible unimolecular reaction. The obtained rate constants are compared with the values predicted by the statistical nonadiabatic transition state theory with transition probabilities calculated using the Landau-Zener and weak coupling formulas.
Cooperative effects in spherical spasers: Ab initio analytical model
NASA Astrophysics Data System (ADS)
Bordo, V. G.
2017-06-01
A fully analytical semiclassical theory of cooperative optical processes which occur in an ensemble of molecules embedded in a spherical core-shell nanoparticle is developed from first principles. Both the plasmonic Dicke effect and spaser generation are investigated for the designs in which a shell/core contains an arbitrarily large number of active molecules in the vicinity of a metallic core/shell. An essential aspect of the theory is an ab initio account of the feedback from the core/shell boundaries which significantly modifies the molecular dynamics. The theory provides rigorous, albeit simple and physically transparent, criteria for both plasmonic superradiance and surface plasmon generation.
NASA Astrophysics Data System (ADS)
Singh, Baltej; Gupta, Mayanak Kumar; Mittal, Ranjan; Zbiri, Mohamed; Rols, Stephane; Patwe, Sadequa Jahedkhan; Achary, Srungarpu Nagabhusan; Schober, Helmut; Tyagi, Avesh Kumar; Chaplot, Samrath Lal
2017-02-01
β-Eucryptite (LiAlSiO4) shows anisotropic thermal expansion as well as one-dimensional super-ionic conductivity. We have performed the lattice dynamical calculations using ab-initio density functional theory along with inelastic neutron scattering measurements. The anisotropic stress dependence of the phonon spectrum is calculated to obtain the thermal expansion behavior along various axes. The calculations show that the Grüneisen parameters of the low-energy phonon modes around 10 meV have large negative values and govern the negative thermal expansion behavior at low temperatures along both the "a"- and "c"-axes. On the other hand, anisotropic elasticity along with anisotropic positive values of the Grüneisen parameters of the high-energy modes in the range 30-70 meV are responsible for the thermal expansion at high temperatures, which is positive in the a-b plane and negative along the c-axis. The analysis of the polarization vectors of the phonon modes sheds light on the mechanism of the anomalous thermal expansion behavior. The softening of a Γ-point mode at about 2 GPa may be related to the high-pressure phase transition.
Comparison of SAMO and ab initio model calculations for pyrazine
NASA Astrophysics Data System (ADS)
Duke, B. J.; Collins, M. P. S.
1981-04-01
The simulated ab initio molecular orbital (SAMO) technique and the ab initio model calculation of Butkus and Fink are compared for the pyrazine molecule. Both methods construct the wave function of pyrazine from wave functions of smaller pattern molecules. The methods are complimentary in that the strengths of one are often the weakness of the other. The SAMO method gives good orbital energies which are not given by the ab initio model method, while the latter is more readily extended to the ionic protonated molecules.
Ab initio derivation of model energy density functionals
NASA Astrophysics Data System (ADS)
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.
Herbert, John M; Head-Gordon, Martin
2004-12-15
A dynamical extension of the "curvy-steps" approach to linear-scaling self-consistent field calculations is presented, which yields an extended-Lagrangian formulation of ab initio molecular dynamics. An exponential parametrization of the one-electron density matrix, expressed in terms of atom-centered Gaussian basis functions, facilitates propagation along the manifold of density matrices in a geometrically correct fashion that automatically enforces idempotency constraints. The extended Lagrangian itself is constraint free, thus neither density matrix purification nor expensive, iterative solution for Lagrange multipliers is required. Propagation is highly efficient, and time steps compare favorably to those used in Car-Parrinello molecular dynamics simulations. The behavior of the method, especially with regard to the maintenance of adiabatic decoupling of nuclei and electrons, is examined for a sequence of diatomic molecules, and comparison is made to trajectories propagated on the converged Born-Oppenheimer surface. Certain claims to the contrary notwithstanding, our results demonstrate that vibrational frequencies may depend on the value of the fictitious mass parameter, even in an atom-centered basis. Light-atom stretching frequencies can be significantly redshifted, even when the nuclear and electronic energy scales are well separated. With a sufficiently small fictitious mass and a short time step, accurate frequencies can be obtained; we characterize appropriate values of these parameters for a wide range of vibrational frequencies.
NASA Astrophysics Data System (ADS)
Marqués, Miriam; González, Luis E.; González, David J.
2016-02-01
The static and dynamic properties of liquid Fe at high pressure and temperature have been studied using an ab initio molecular dynamics method. We have focused on four thermodynamic states at pressures of 27, 42, 50 and 58 GPa for which x-ray scattering data are available. The calculated static structure shows very good agreement with the available experimental data, including an asymmetric second peak which becomes more marked with increasing pressure. The dynamical structure reveals the existence of propagating density fluctuations and the associated dispersion relation has also been determined. The relaxation mechanisms for the density fluctuations have been analyzed in terms of a model with two decay channels (fast and slow, respectively). We found that the thermal relaxation proceeds along the slow decaying channel whereas the fast one is that of the viscoelastic relaxation. The possible coupling between longitudinal and transverse excitation modes has been investigated by looking at specific signatures in two wavevector regions: the first one is located around the position of the main peak of the structure factor, q p , as suggested by the recently reported appearance of high frequency transverse waves in liquid Li under high pressures; the second region is around q p /2, as suggested by the recent finding of transverse acoustic modes in inelastic x-ray scattering intensities of liquid Fe at ambient pressure. Finally, results are also reported for several transport coefficients.
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.
NASA Astrophysics Data System (ADS)
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.
Li, Junjie; Iyengar, Srinivasan S
2015-09-08
Here, we demonstrate the application of fragment-based electronic structure calculations in (a) ab initio molecular dynamics (AIMD) and (b) reduced dimensional potential calculations, for medium- and large-sized protonated water clusters. The specific fragmentation algorithm used here is derived from ONIOM, but includes multiple, overlapping “model” systems. The interaction between the various overlapping model systems is (a) approximated by invoking the principle of inclusion-exclusion at the chosen higher level of theory and (b) within a real calculation performed at the chosen lower level of theory. The fragmentation algorithm itself is written using bit-manipulation arithmetic, which will prove to be advantageous, since the number of fragments in such methods has the propensity to grow exponentially with system size. Benchmark calculations are performed for three different protonated water clusters: H₉O₄⁺, H₁₃O₆⁺ and H(H₂O)₂₁⁺. For potential energy surface benchmarks, we sample the normal coordinates and compare our surface energies with full MP2 and CCSD(T) calculations. The mean absolute error for the fragment-based algorithm is <0.05 kcal/mol, when compared with MP2 calculations, and <0.07 kcal/mol, when compared with CCSD(T) calculations over 693 different geometries for the H₉O₄⁺ system. For the larger H(H₂O)₂₁⁺ water cluster, the mean absolute error is on the order of a 0.1 kcal/mol, when compared with full MP2 calculations for 84 different geometries, at a fraction of the computational cost. Ab initio dynamics calculations were performed for H₉O₄⁺ and H₁₃O₆⁺, and the energy conservation was found to be of the order of 0.01 kcal/mol for short trajectories (on the order of a picosecond). The trajectories were kept short because our algorithm does not currently include dynamical fragmentation, which will be considered in future publications. Nevertheless, the velocity autocorrelation functions and their
Ab initio molecular simulations with numeric atom-centered orbitals
NASA Astrophysics Data System (ADS)
Blum, Volker; Gehrke, Ralf; Hanke, Felix; Havu, Paula; Havu, Ville; Ren, Xinguo; Reuter, Karsten; Scheffler, Matthias
2009-11-01
We describe a complete set of algorithms for ab initio molecular simulations based on numerically tabulated atom-centered orbitals (NAOs) to capture a wide range of molecular and materials properties from quantum-mechanical first principles. The full algorithmic framework described here is embodied in the Fritz Haber Institute "ab initio molecular simulations" (FHI-aims) computer program package. Its comprehensive description should be relevant to any other first-principles implementation based on NAOs. The focus here is on density-functional theory (DFT) in the local and semilocal (generalized gradient) approximations, but an extension to hybrid functionals, Hartree-Fock theory, and MP2/GW electron self-energies for total energies and excited states is possible within the same underlying algorithms. An all-electron/full-potential treatment that is both computationally efficient and accurate is achieved for periodic and cluster geometries on equal footing, including relaxation and ab initio molecular dynamics. We demonstrate the construction of transferable, hierarchical basis sets, allowing the calculation to range from qualitative tight-binding like accuracy to meV-level total energy convergence with the basis set. Since all basis functions are strictly localized, the otherwise computationally dominant grid-based operations scale as O(N) with system size N. Together with a scalar-relativistic treatment, the basis sets provide access to all elements from light to heavy. Both low-communication parallelization of all real-space grid based algorithms and a ScaLapack-based, customized handling of the linear algebra for all matrix operations are possible, guaranteeing efficient scaling (CPU time and memory) up to massively parallel computer systems with thousands of CPUs.
Ab Initio: And a New Era of Airline Pilot Training.
ERIC Educational Resources Information Center
Gesell, Laurence E.
1995-01-01
Expansion of air transportation and decreasing numbers seeking pilot training point to a shortage of qualified pilots. Ab initio training, in which candidates with no flight time are trained to air transport proficiency, could resolve the problem. (SK)
Direct ab initio molecular dynamics study on a microsolvated SN2 reaction of OH-(H2O) with CH3Cl.
Tachikawa, Hiroto
2006-10-07
Reaction dynamics for a microsolvated SN2 reaction OH-(H2O)+CH3Cl have been investigated by means of the direct ab initio molecular dynamics method. The relative center-of-mass collision energies were chosen as 10, 15, and 25 kcal/mol. Three reaction channels were found as products. These are (1) a channel leading to complete dissociation (the products are CH3OH+Cl- +H2O: denoted by channel I), (2) a solvation channel (the products are Cl-(H2O)+CH3OH: channel II), and (3) a complex formation channel (the products are CH3OH...H2O+Cl-: channel III). The branching ratios for the three channels were drastically changed as a function of center-of-mass collision energy. The ratio of complete dissociation channel (channel I) increased with increasing collision energy, whereas that of channel III decreased. The solvation channel (channel II) was minor at all collision energies. The selectivity of the reaction channels and the mechanism are discussed on the basis of the theoretical results.
Direct ab initio molecular dynamics study on a microsolvated SN2 reaction of OH-(H2O) with CH3Cl
NASA Astrophysics Data System (ADS)
Tachikawa, Hiroto
2006-10-01
Reaction dynamics for a microsolvated SN2 reaction OH-(H2O)+CH3Cl have been investigated by means of the direct ab initio molecular dynamics method. The relative center-of-mass collision energies were chosen as 10, 15, and 25kcal/mol. Three reaction channels were found as products. These are (1) a channel leading to complete dissociation (the products are CH3OH+Cl-+H2O: denoted by channel I), (2) a solvation channel (the products are Cl-(H2O)+CH3OH: channel II), and (3) a complex formation channel (the products are CH3OH ⋯H2O+Cl-: channel III). The branching ratios for the three channels were drastically changed as a function of center-of-mass collision energy. The ratio of complete dissociation channel (channel I) increased with increasing collision energy, whereas that of channel III decreased. The solvation channel (channel II) was minor at all collision energies. The selectivity of the reaction channels and the mechanism are discussed on the basis of the theoretical results.