Reductive half-reaction of aldehyde oxidoreductase toward acetaldehyde: Ab initio and free energy quantum mechanical/molecular mechanical calculations.

PubMed

Dieterich, Johannes M; Werner, Hans-Joachim; Mata, Ricardo A; Metz, Sebastian; Thiel, Walter

2010-01-21

Energy and free energy barriers for acetaldehyde conversion in aldehyde oxidoreductase are determined for three reaction pathways using quantum mechanical/molecular mechanical (QM/MM) calculations on the solvated enzyme. Ab initio single-point QM/MM energies are obtained at the stationary points optimized at the DFT(B3LYP)/MM level. These ab initio calculations employ local correlation treatments [LMP2 and LCCSD(T0)] in combination with augmented triple- and quadruple-zeta basis sets, and the final coupled cluster results include MP2-based corrections for basis set incompleteness and for the domain approximation. Free energy perturbation (FEP) theory is used to generate free energy profiles at the DFT(B3LYP)/MM level for the most important reaction steps by sampling along the corresponding reaction paths using molecular dynamics. The ab initio and FEP QM/MM results are combined to derive improved estimates of the free energy barriers, which differ from the corresponding DFT(B3LYP)/MM energy barriers by about 3 kcal mol(-1). The present results confirm the qualitative mechanistic conclusions from a previous DFT(B3LYP)/MM study. Most favorable is a three-step Lewis base catalyzed mechanism with an initial proton transfer from the cofactor to the Glu869 residue, a subsequent nucleophilic attack that yields a tetrahedral intermediate (IM2), and a final rate-limiting hydride transfer. The competing metal center activated pathway has the same final step but needs to overcome a higher barrier in the initial step on the route to IM2. The concerted mechanism has the highest free energy barrier and can be ruled out. While confirming the qualitative mechanistic scenario proposed previously on the basis of DFT(B3LYP)/MM energy profiles, the present ab initio and FEP QM/MM calculations provide corrections to the barriers that are important when aiming at high accuracy.

Dynamics and Novel Mechanisms of SN2 Reactions on ab Initio Analytical Potential Energy Surfaces.

PubMed

Szabó, István; Czakó, Gábor

2017-11-30

We describe a novel theoretical approach to the bimolecular nucleophilic substitution (S N 2) reactions that is based on analytical potential energy surfaces (PESs) obtained by fitting a few tens of thousands high-level ab initio energy points. These PESs allow computing millions of quasi-classical trajectories thereby providing unprecedented statistical accuracy for S N 2 reactions, as well as performing high-dimensional quantum dynamics computations. We developed full-dimensional ab initio PESs for the F - + CH 3 Y [Y = F, Cl, I] systems, which describe the direct and indirect, complex-forming Walden-inversion, the frontside attack, and the new double-inversion pathways as well as the proton-transfer channels. Reaction dynamics simulations on the new PESs revealed (a) a novel double-inversion S N 2 mechanism, (b) frontside complex formation, (c) the dynamics of proton transfer, (d) vibrational and rotational mode specificity, (e) mode-specific product vibrational distributions, (f) agreement between classical and quantum dynamics, (g) good agreement with measured scattering angle and product internal energy distributions, and (h) significant leaving group effect in accord with experiments.

Ab Initio-Based Predictions of Hydrocarbon Combustion Chemistry

DTIC Science & Technology

2015-07-15

There are two prime objectives of the research. One is to develop and apply efficient methods for using ab initio potential energy surfaces (PESs...31-Mar-2015 Approved for Public Release; Distribution Unlimited Final Report: Ab Initio -Based Predictions of Hydrocarbon Combustion Chemistry The...Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 hydrocarbon combustion, ab initio quantum chemistry, potential energy surfaces, chemical

Quantum calculations of the IR spectrum of liquid water using ab initio and model potential and dipole moment surfaces and comparison with experiment.

PubMed

Liu, Hanchao; Wang, Yimin; Bowman, Joel M

2015-05-21

The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H2O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previous spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0-4000 cm(-1) is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.

Quantum calculations of the IR spectrum of liquid water using ab initio and model potential and dipole moment surfaces and comparison with experiment

NASA Astrophysics Data System (ADS)

Liu, Hanchao; Wang, Yimin; Bowman, Joel M.

2015-05-01

The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H2O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previous spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0-4000 cm-1 is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.

Ab Initio Potential Energy Surfaces and Quantum Dynamics for Polyatomic Bimolecular Reactions.

PubMed

Fu, Bina; Zhang, Dong H

2018-05-08

There has been great progress in the development of potential energy surfaces (PESs) and quantum dynamics calculations in the gas phase. The establishment of a fitting procedure for highly accurate PESs and new developments in quantum reactive scattering on reliable PESs allow accurate characterization of reaction dynamics beyond triatomic systems. This review will give the recent development in our group in constructing ab initio PESs based on neural networks and the time-dependent wave packet calculations for bimolecular reactions beyond three atoms. Bimolecular reactions of current interest to the community, namely, OH + H 2 , H + H 2 O, OH + CO, H + CH 4 , and Cl + CH 4 , are focused on. Quantum mechanical characterization of these reactions uncovers interesting dynamical phenomena with an unprecedented level of sophistication and has greatly advanced our understanding of polyatomic reaction dynamics.

Internal force corrections with machine learning for quantum mechanics/molecular mechanics simulations.

PubMed

Wu, Jingheng; Shen, Lin; Yang, Weitao

2017-10-28

Ab initio quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation is a useful tool to calculate thermodynamic properties such as potential of mean force for chemical reactions but intensely time consuming. In this paper, we developed a new method using the internal force correction for low-level semiempirical QM/MM molecular dynamics samplings with a predefined reaction coordinate. As a correction term, the internal force was predicted with a machine learning scheme, which provides a sophisticated force field, and added to the atomic forces on the reaction coordinate related atoms at each integration step. We applied this method to two reactions in aqueous solution and reproduced potentials of mean force at the ab initio QM/MM level. The saving in computational cost is about 2 orders of magnitude. The present work reveals great potentials for machine learning in QM/MM simulations to study complex chemical processes.

Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions

PubMed Central

2015-01-01

We parametrize a linear-scaling quantum mechanical force field called mDC for the accurate reproduction of nonbonded interactions. We provide a new benchmark database of accurate ab initio interactions between sulfur-containing molecules. A variety of nonbond databases are used to compare the new mDC method with other semiempirical, molecular mechanical, ab initio, and combined semiempirical quantum mechanical/molecular mechanical methods. It is shown that the molecular mechanical force field significantly and consistently reproduces the benchmark results with greater accuracy than the semiempirical models and our mDC model produces errors twice as small as the molecular mechanical force field. The comparisons between the methods are extended to the docking of drug candidates to the Cyclin-Dependent Kinase 2 protein receptor. We correlate the protein–ligand binding energies to their experimental inhibition constants and find that the mDC produces the best correlation. Condensed phase simulation of mDC water is performed and shown to produce O–O radial distribution functions similar to TIP4P-EW. PMID:24803856

Ab Initio Studies of Stratospheric Ozone Depletion Chemistry

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Head-Gordon, Martin; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

An overview of the current understanding of ozone depletion chemistry, particularly with regards the formation of the so-called Antarctic ozone hole, will be presented together with an outline as to how ab initio quantum chemistry can be used to further our understanding of stratospheric chemistry. The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of fluorine, chlorine, bromine and nitrogen oxide species will be demonstrated by presentation of some example studies. The ab initio results will be shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the theoretical results are shown to fill in the gaps and to resolve experimental controversies. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of halogen oxide species will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of experimental studies.

Quantum Fragment Based ab Initio Molecular Dynamics for Proteins.

PubMed

Liu, Jinfeng; Zhu, Tong; Wang, Xianwei; He, Xiao; Zhang, John Z H

2015-12-08

Developing ab initio molecular dynamics (AIMD) methods for practical application in protein dynamics is of significant interest. Due to the large size of biomolecules, applying standard quantum chemical methods to compute energies for dynamic simulation is computationally prohibitive. In this work, a fragment based ab initio molecular dynamics approach is presented for practical application in protein dynamics study. In this approach, the energy and forces of the protein are calculated by a recently developed electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method. For simulation in explicit solvent, mechanical embedding is introduced to treat protein interaction with explicit water molecules. This AIMD approach has been applied to MD simulations of a small benchmark protein Trpcage (with 20 residues and 304 atoms) in both the gas phase and in solution. Comparison to the simulation result using the AMBER force field shows that the AIMD gives a more stable protein structure in the simulation, indicating that quantum chemical energy is more reliable. Importantly, the present fragment-based AIMD simulation captures quantum effects including electrostatic polarization and charge transfer that are missing in standard classical MD simulations. The current approach is linear-scaling, trivially parallel, and applicable to performing the AIMD simulation of proteins with a large size.

Quantum calculations of the IR spectrum of liquid water using ab initio and model potential and dipole moment surfaces and comparison with experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Hanchao; Wang, Yimin; Bowman, Joel M.

2015-05-21

The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H{sub 2}O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previousmore » spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0–4000 cm{sup −1} is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.« less

Instructional Approach to Molecular Electronic Structure Theory

ERIC Educational Resources Information Center

Dykstra, Clifford E.; Schaefer, Henry F.

1977-01-01

Describes a graduate quantum mechanics projects in which students write a computer program that performs ab initio calculations on the electronic structure of a simple molecule. Theoretical potential energy curves are produced. (MLH)

A QUANTUM MECHANICAL STUDY OF THE PROTONATION AND COVALENT HYDRATION OF QUINAZOLINE IN THE PRESENCE OF METAL CATIONS

EPA Science Inventory

We have investigated the protonation and reversible covalent hydration of quinazoline in the presence of Li+, Na+, and Ca2+ ions using ab initio quantum mechanical calculations at the MP2/6-31G**//HF/6-31G*level of theory. Proton affinities, enthalpies of hydration at 298.15K (DH...

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

NASA Astrophysics Data System (ADS)

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

2008-02-01

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

Ab-initio study of the energetics and thermodynamics of the reaction CH3H + O( 3P) → CF3H … O → CF3 + OH

NASA Astrophysics Data System (ADS)

Kreye, W. C.

1996-07-01

Ab-initio computations at 298.15 K were made of the activation quantities ΔH ‡, ΔS ‡, and ΔG ‡ and of the reaction quantities ΔHr and ΔSr for CF3H + O( 3P) → CF3H … O → .CF3.OH. CF 3H … O is the transition state (TS). GAUSSIAN92 was used and energies computed at a slightly modified Gaussian-2 level. Two potential surfaces for the TS had symmetries 3A' and 3A″. The two rate constants included a semi-classical, quantum-mechanical-tunneling transmission coefficient. The ab-initio ΔH ‡and ΔH r values were in excellent agreement (± 1 kcal/mol) with experiment; but the ΔS ‡, ΔG ‡, and ΔS r values yielded somewhat poorer agreement. Experimental and ab-initio structures were in excellent agreement.

S/G-1: an ab initio force-field blending frozen Hermite Gaussian densities and distributed multipoles. Proof of concept and first applications to metal cations.

PubMed

Chaudret, Robin; Gresh, Nohad; Narth, Christophe; Lagardère, Louis; Darden, Thomas A; Cisneros, G Andrés; Piquemal, Jean-Philip

2014-09-04

We demonstrate as a proof of principle the capabilities of a novel hybrid MM'/MM polarizable force field to integrate short-range quantum effects in molecular mechanics (MM) through the use of Gaussian electrostatics. This lead to a further gain in accuracy in the representation of the first coordination shell of metal ions. It uses advanced electrostatics and couples two point dipole polarizable force fields, namely, the Gaussian electrostatic model (GEM), a model based on density fitting, which uses fitted electronic densities to evaluate nonbonded interactions, and SIBFA (sum of interactions between fragments ab initio computed), which resorts to distributed multipoles. To understand the benefits of the use of Gaussian electrostatics, we evaluate first the accuracy of GEM, which is a pure density-based Gaussian electrostatics model on a test Ca(II)-H2O complex. GEM is shown to further improve the agreement of MM polarization with ab initio reference results. Indeed, GEM introduces nonclassical effects by modeling the short-range quantum behavior of electric fields and therefore enables a straightforward (and selective) inclusion of the sole overlap-dependent exchange-polarization repulsive contribution by means of a Gaussian damping function acting on the GEM fields. The S/G-1 scheme is then introduced. Upon limiting the use of Gaussian electrostatics to metal centers only, it is shown to be able to capture the dominant quantum effects at play on the metal coordination sphere. S/G-1 is able to accurately reproduce ab initio total interaction energies within closed-shell metal complexes regarding each individual contribution including the separate contributions of induction, polarization, and charge-transfer. Applications of the method are provided for various systems including the HIV-1 NCp7-Zn(II) metalloprotein. S/G-1 is then extended to heavy metal complexes. Tested on Hg(II) water complexes, S/G-1 is shown to accurately model polarization up to quadrupolar response level. This opens up the possibility of embodying explicit scalar relativistic effects in molecular mechanics thanks to the direct transferability of ab initio pseudopotentials. Therefore, incorporating GEM-like electron density for a metal cation enable the introduction of nonambiguous short-range quantum effects within any point-dipole based polarizable force field without the need of an extensive parametrization.

Cost-Effective Method for Free-Energy Minimization in Complex Systems with Elaborated Ab Initio Potentials.

PubMed

Bistafa, Carlos; Kitamura, Yukichi; Martins-Costa, Marilia T C; Nagaoka, Masataka; Ruiz-López, Manuel F

2018-06-12

We describe a method to locate stationary points in the free-energy hypersurface of complex molecular systems using high-level correlated ab initio potentials. In this work, we assume a combined QM/MM description of the system although generalization to full ab initio potentials or other theoretical schemes is straightforward. The free-energy gradient (FEG) is obtained as the mean force acting on relevant nuclei using a dual level strategy. First, a statistical simulation is carried out using an appropriate, low-level quantum mechanical force-field. Free-energy perturbation (FEP) theory is then used to obtain the free-energy derivatives for the target, high-level quantum mechanical force-field. We show that this composite FEG-FEP approach is able to reproduce the results of a standard free-energy minimization procedure with high accuracy, while simultaneously allowing for a drastic reduction of both computational and wall-clock time. The method has been applied to study the structure of the water molecule in liquid water at the QCISD/aug-cc-pVTZ level of theory, using the sampling from QM/MM molecular dynamics simulations at the B3LYP/6-311+G(d,p) level. The obtained values for the geometrical parameters and for the dipole moment of the water molecule are within the experimental error, and they also display an excellent agreement when compared to other theoretical estimations. The developed methodology represents therefore an important step toward the accurate determination of the mechanism, kinetics, and thermodynamic properties of processes in solution, in enzymes, and in other disordered chemical systems using state-of-the-art ab initio potentials.

Molecular modeling studies of interactions between sodium polyacrylate polymer and calcite surface

NASA Astrophysics Data System (ADS)

Ylikantola, A.; Linnanto, J.; Knuutinen, J.; Oravilahti, A.; Toivakka, M.

2013-07-01

The interactions between calcite pigment and sodium polyacrylate dispersing agent, widely used in papermaking as paper coating components, were investigated using classical force field and quantum chemical approaches. The objective was to understand interactions between the calcite surface and sodium polyacrylate polymer at 300 K using molecular dynamics simulations. A quantum mechanical ab initio Hartree-Fock method was also used to obtain detailed information about the sodium polyacrylate polymer structure. The effect of water molecules (moisture) on the interactions was also examined. Calculations showed that molecular weight, branching and the orientation of sodium polyacrylate polymers influence the interactions between the calcite surface and the polymer. The force field applied, and also water molecules, were found to have an impact on all systems studied. Ab initio Hartree-Fock calculations indicated that there are two types of coordination between sodium atoms and carboxylate groups of the sodium polyacrylate polymer, inter- and intra-carboxylate group coordination. In addition, ab initio Hartree-Fock calculations of the structure of the sodium polyacrylate polymer produced important information regarding interactions between the polymers and carboxylated styrene-butadiene latex particles.

Ab initio vel ex eventu

NASA Astrophysics Data System (ADS)

Thiessen, P. A.; Treder, H.-J.

Der gegenwärtige Stand der physikalischen Erkenntnis, in Sonderheit die Atomistik und die Quantentheorie, ermöglicht (in wohldefinierten Energie-Bereichen) eine ab initio-Berechnung aller physikalischen und chemischen Prozesse und Strukturen. Die Schrödinger-Gleichung erlaubt zusammen mit den Prinzipien der Quantenstatistik (Pauli-Prinzip) aus dem Planckschen Wirkungsquantum h und den atomischen Konstanten die Berechnung aller Energieumsätze, Zeitabläufe etc., die insbesondere die chemische Physik bestimmen. Die Rechenresultate gelten auch quantitativ bis auf die unvermeidliche Stochastik.Die ab initio-Berechnungen korrespondieren einerseits und sind andererseits komplementär zu den auf den Methoden der theoretischen Chemie und der klassischen Thermodynamik beruhenden Ergebnissen ex eventu. Die theoretische Behandlung ab initio führt zu mathematischen Experimenten, die die Laboratoriums-Experimente ergänzen oder auch substituieren.Translated AbstractAb initio vel ex eventuThe present state of physical knowledge, in peculiar atomistic and quantum theory, makes an ab initio calculation of all physical and chemical processes and structures possible (in well defined reaches of energy). The Schrödinger equation together with the principles of quantum statistics (Pauli principle) permits from the Planck and atomistic constants to calculate all exchanges of energy, courses of time, etc. which govern chemical physics. The calculated results are valid even quantitatively apart from the unavoidable stochastics.These ab initio calculations on the one hand correspond and are on the other complimentary to results ex eventu based on the methods of theoretical chemistry and classical thermodynamics. Theoretical treatment ab initio leads to mathematical experiments which add to or even substitute experiments in the laboratory.

The many-body Wigner Monte Carlo method for time-dependent ab-initio quantum simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sellier, J.M., E-mail: jeanmichel.sellier@parallel.bas.bg; Dimov, I.

2014-09-15

The aim of ab-initio approaches is the simulation of many-body quantum systems from the first principles of quantum mechanics. These methods are traditionally based on the many-body Schrödinger equation which represents an incredible mathematical challenge. In this paper, we introduce the many-body Wigner Monte Carlo method in the context of distinguishable particles and in the absence of spin-dependent effects. Despite these restrictions, the method has several advantages. First of all, the Wigner formalism is intuitive, as it is based on the concept of a quasi-distribution function. Secondly, the Monte Carlo numerical approach allows scalability on parallel machines that is practicallymore » unachievable by means of other techniques based on finite difference or finite element methods. Finally, this method allows time-dependent ab-initio simulations of strongly correlated quantum systems. In order to validate our many-body Wigner Monte Carlo method, as a case study we simulate a relatively simple system consisting of two particles in several different situations. We first start from two non-interacting free Gaussian wave packets. We, then, proceed with the inclusion of an external potential barrier, and we conclude by simulating two entangled (i.e. correlated) particles. The results show how, in the case of negligible spin-dependent effects, the many-body Wigner Monte Carlo method provides an efficient and reliable tool to study the time-dependent evolution of quantum systems composed of distinguishable particles.« less

Ab initio Computations of the Electronic, Mechanical, and Thermal Properties of Ultra High Temperature Ceramics (UHTC) ZrB2 and HfB2

NASA Technical Reports Server (NTRS)

Lawson, John W.; Bauschlicher, Charles W.; Daw, Murray

2011-01-01

Refractory materials such as metallic borides, often considered as ultra high temperature ceramics (UHTC), are characterized by high melting point, high hardness, and good chemical inertness. These materials have many applications which require high temperature materials that can operate with no or limited oxidation. Ab initio, first principles methods are the most accurate modeling approaches available and represent a parameter free description of the material based on the quantum mechanical equations. Using these methods, many of the intrinsic properties of these material can be obtained. We performed ab initio calculations based on density functional theory for the UHTC materials ZrB2 and HfB2. Computational results are presented for structural information (lattice constants, bond lengths, etc), electronic structure (bonding motifs, densities of states, band structure, etc), thermal quantities (phonon spectra, phonon densities of states, specific heat), as well as information about point defects such as vacancy and antisite formation energies.

Development of a Polarizable Force Field For Proteins via Ab Initio Quantum Chemistry: First Generation Model and Gas Phase Tests

PubMed Central

KAMINSKI, GEORGE A.; STERN, HARRY A.; BERNE, B. J.; FRIESNER, RICHARD A.; CAO, YIXIANG X.; MURPHY, ROBERT B.; ZHOU, RUHONG; HALGREN, THOMAS A.

2014-01-01

We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic-size systems. Employing high-level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using the fast and reliable quantum mechanical methods supplies robust fitting data for the resulting parameter sets. As a result, gas-phase many-body effects for dipeptides are captured within the average RMSD of 0.22 kcal/mol from their ab initio values, and conformational energies for the di- and tetrapeptides are reproduced within the average RMSD of 0.43 kcal/mol from their quantum mechanical counterparts. The latter is achieved in part because of application of a novel torsional fitting technique recently developed in our group, which has already been used to greatly improve accuracy of the peptide conformational equilibrium prediction with the OPLS-AA force field.1 Finally, we have employed the newly developed first-generation model in computing gas-phase conformations of real proteins, as well as in molecular dynamics studies of the systems. The results show that, although the overall accuracy is no better than what can be achieved with a fixed-charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields. It can be considered as a solid basis for building a more accurate and complete second-generation model. PMID:12395421

An efficient and accurate molecular alignment and docking technique using ab initio quality scoring

PubMed Central

Füsti-Molnár, László; Merz, Kenneth M.

2008-01-01

An accurate and efficient molecular alignment technique is presented based on first principle electronic structure calculations. This new scheme maximizes quantum similarity matrices in the relative orientation of the molecules and uses Fourier transform techniques for two purposes. First, building up the numerical representation of true ab initio electronic densities and their Coulomb potentials is accelerated by the previously described Fourier transform Coulomb method. Second, the Fourier convolution technique is applied for accelerating optimizations in the translational coordinates. In order to avoid any interpolation error, the necessary analytical formulas are derived for the transformation of the ab initio wavefunctions in rotational coordinates. The results of our first implementation for a small test set are analyzed in detail and compared with published results of the literature. A new way of refinement of existing shape based alignments is also proposed by using Fourier convolutions of ab initio or other approximate electron densities. This new alignment technique is generally applicable for overlap, Coulomb, kinetic energy, etc., quantum similarity measures and can be extended to a genuine docking solution with ab initio scoring. PMID:18624561

Increasing the efficiency and accuracy of time-resolved electronic spectra calculations with on-the-fly ab initio quantum dynamics methods

NASA Astrophysics Data System (ADS)

Vanicek, Jiri

2014-03-01

Rigorous quantum-mechanical calculations of coherent ultrafast electronic spectra remain difficult. I will present several approaches developed in our group that increase the efficiency and accuracy of such calculations: First, we justified the feasibility of evaluating time-resolved spectra of large systems by proving that the number of trajectories needed for convergence of the semiclassical dephasing representation/phase averaging is independent of dimensionality. Recently, we further accelerated this approximation with a cellular scheme employing inverse Weierstrass transform and optimal scaling of the cell size. The accuracy of potential energy surfaces was increased by combining the dephasing representation with accurate on-the-fly ab initio electronic structure calculations, including nonadiabatic and spin-orbit couplings. Finally, the inherent semiclassical approximation was removed in the exact quantum Gaussian dephasing representation, in which semiclassical trajectories are replaced by communicating frozen Gaussian basis functions evolving classically with an average Hamiltonian. Among other examples I will present an on-the-fly ab initio semiclassical dynamics calculation of the dispersed time-resolved stimulated emission spectrum of the 54-dimensional azulene. This research was supported by EPFL and by the Swiss National Science Foundation NCCR MUST (Molecular Ultrafast Science and Technology) and Grant No. 200021124936/1.

Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations.

PubMed

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.

On Predicting the Crystal Structure of Energetic Materials From Quantum Mechanics

DTIC Science & Technology

2008-12-01

DE ABSTRACT A quantum-mechanically-based potential energy function that describes interactions of dimers of the explosive ...method is capable of producing force fields for interactions of the molecular crystalline explosive RDX, and appears to be suitable to enable reliable...Ridge, TN. Byrd, E.F.C., Scuseria, G.E., Chabalowski, C.F., 2004: “An ab initio study of solid nitromethane , HMX, RDX and CL20: Successes and

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ivanov, Sergei D., E-mail: sergei.ivanov@unirostock.de; Grant, Ian M.; Marx, Dominik

With the goal of computing quantum free energy landscapes of reactive (bio)chemical systems in multi-dimensional space, we combine the metadynamics technique for sampling potential energy surfaces with the ab initio path integral approach to treating nuclear quantum motion. This unified method is applied to the double proton transfer process in the formic acid dimer (FAD), in order to study the nuclear quantum effects at finite temperatures without imposing a one-dimensional reaction coordinate or reducing the dimensionality. Importantly, the ab initio path integral metadynamics technique allows one to treat the hydrogen bonds and concomitant proton transfers in FAD strictly independently andmore » thus provides direct access to the much discussed issue of whether the double proton transfer proceeds via a stepwise or concerted mechanism. The quantum free energy landscape we compute for this H-bonded molecular complex reveals that the two protons move in a concerted fashion from initial to product state, yet world-line analysis of the quantum correlations demonstrates that the protons are as quantum-uncorrelated at the transition state as they are when close to the equilibrium structure.« less

Ab Initio Analysis of Auger-Assisted Electron Transfer.

PubMed

Hyeon-Deuk, Kim; Kim, Joonghan; Prezhdo, Oleg V

2015-01-15

Quantum confinement in nanoscale materials allows Auger-type electron-hole energy exchange. We show by direct time-domain atomistic simulation and analytic theory that Auger processes give rise to a new mechanism of charge transfer (CT) on the nanoscale. Auger-assisted CT eliminates the renown Marcus inverted regime, rationalizing recent experiments on CT from quantum dots to molecular adsorbates. The ab initio simulation reveals a complex interplay of the electron-hole and charge-phonon channels of energy exchange, demonstrating a variety of CT scenarios. The developed Marcus rate theory for Auger-assisted CT describes, without adjustable parameters, the experimental plateau of the CT rate in the region of large donor-acceptor energy gap. The analytic theory and atomistic insights apply broadly to charge and energy transfer in nanoscale systems.

Quantum chemical calculation of the equilibrium structures of small metal atom clusters

NASA Technical Reports Server (NTRS)

Kahn, L. R.

1982-01-01

Metal atom clusters are studied based on the application of ab initio quantum mechanical approaches. Because these large 'molecular' systems pose special practical computational problems in the application of the quantum mechanical methods, there is a special need to find simplifying techniques that do not compromise the reliability of the calculations. Research is therefore directed towards various aspects of the implementation of the effective core potential technique for the removal of the metal atom core electrons from the calculations.

Steel — ab Initio: Quantum Mechanics Guided Design of New Fe-Based Materials

NASA Astrophysics Data System (ADS)

Prahl, Ulrich; Bleck, Wolfgang; Saeed-Akbari, Alireza

This contribution reports the results of the collaborative research unit SFB 761 "Steel — ab initio", a cooperative project between RWTH Aachen University and the Max-Planck-Institute for Iron Research in Düsseldorf (MPIE) financed by the German Research Foundation (DFG). For the first time, it is exploited how ab initio approaches may lead to a detailed understanding and thus to a specific improvement of material development. The challenge lies in the combination of abstract natural science theories with rather engineering-like established concepts. Aiming at the technological target of the development of a new type of structural materials based on Fe-Mn-C alloys, the combination of ab initio and engineering methods is new, but could be followed quite successfully. Three major topics are treated in this research unit: a) development of a new method for material- and process-development based on ab initio calculations; b) design of a new class of structural materials with extraordinary property combinations; c) acceleration of development time and reduction of experimental efforts and complexity for material- and process-development. In the present work, an overview of the results of the first five years as well as an outlook for the upcoming three-year period is given.

ENVIRONMENTAL ANALYSIS BY AB INITIO QUANTUM MECHANICAL COMPUTATION AND GAS CHROMATOGRAPHY/FOURIER TRANSFORM INFRARED SPECTROMETRY.

EPA Science Inventory

Computational chemistry, in conjunction with gas chromatography/mass spectrometry/Fourier transform infrared spectrometry (GC/MS/FT-IR), was used to tentatively identify seven tetrachlorobutadiene (TCBD) isomers detected in an environmental sample. Computation of the TCBD infrare...

The accuracy of ab initio calculations without ab initio calculations for charged systems: Kriging predictions of atomistic properties for ions in aqueous solutions

NASA Astrophysics Data System (ADS)

Di Pasquale, Nicodemo; Davie, Stuart J.; Popelier, Paul L. A.

2018-06-01

Using the machine learning method kriging, we predict the energies of atoms in ion-water clusters, consisting of either Cl- or Na+ surrounded by a number of water molecules (i.e., without Na+Cl- interaction). These atomic energies are calculated following the topological energy partitioning method called Interacting Quantum Atoms (IQAs). Kriging predicts atomic properties (in this case IQA energies) by a model that has been trained over a small set of geometries with known property values. The results presented here are part of the development of an advanced type of force field, called FFLUX, which offers quantum mechanical information to molecular dynamics simulations without the limiting computational cost of ab initio calculations. The results reported for the prediction of the IQA components of the energy in the test set exhibit an accuracy of a few kJ/mol, corresponding to an average error of less than 5%, even when a large cluster of water molecules surrounding an ion is considered. Ions represent an important chemical system and this work shows that they can be correctly taken into account in the framework of the FFLUX force field.

Ab initio study of the chlorine nitrate protonation reaction - Implications for loss of ClONO2 in the stratosphere

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Rice, Julia E.

1993-01-01

Ab initio quantum mechanical methods, including coupled-cluster theory, are used to determine the equilibrium geometries, dipole moments, and harmonic vibrational frequencies of ClONO2, NO2(+), and four isomers of protonated ClONO2. It was found that, for the equilibrium structures and harmonic frequencies of ClONO2, HOCl, and NO2(+), the highest-level theoretical predictions are consistent with the available experimental information concerning the reactions of ClONO2 and HOCl with HCl on the surface of polar stratospheric clouds (PSCs). The study supports a recent hypothesis that the reaction of ClONO2 on the surface of PSCs is proton catalyzed, although the mechanism is different.

Ab initio quantum chemical study of electron transfer in carboranes

NASA Astrophysics Data System (ADS)

Pati, Ranjit; Pineda, Andrew C.; Pandey, Ravindra; Karna, Shashi P.

2005-05-01

The electron transfer (ET) properties of 10- and 12-vertex carboranes are investigated by the ab initio Hartree-Fock method within the Marcus-Hush (MH) two-state model and the Koopman theorem (KT) approach. The calculated value of the ET coupling matrix element, VAB, is consistently higher in the KT approach than in the MH two-state model. For the carborane molecules functionalized by -CH 2 groups at C-vertices, VAB strongly depends on the relative orientation of the planes containing the terminal -CH 2 groups. The predicted conformation dependence of VAB offers a molecular mechanism to control ET between two active centers in molecular systems.

Computer Series, 86. Bits and Pieces, 35.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1987-01-01

Describes eight applications of the use of computers in teaching chemistry. Includes discussions of audio frequency measurements of heat capacity ratios, quantum mechanics, ab initio calculations, problem solving using spreadsheets, simplex optimization, faradaic impedance diagrams, and the recording and tabulation of student laboratory data. (TW)

Ab Initio Studies of Halogen and Nitrogen Oxide Species of Interest in Stratospheric Chemistry

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of fluorine, chlorine, bromine and nitrogen oxide species will be demonstrated by presentation of some example studies. The ab initio results are shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the theoretical results are shown to fill in the gaps and to resolve experimental controversies. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of halogen oxide species will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of experimental studies.

Quantum transition state dynamics of the cyclooctatetraene unimolecular reaction on ab initio potential energy surfaces

NASA Astrophysics Data System (ADS)

Tokizaki, Chihiro; Yoshida, Takahiko; Takayanagi, Toshiyuki

2016-05-01

The cyclooctatetraene (COT) anion has a stable D4h structure that is similar to the transition state configurations of the neutral C-C bond-alternation (D4h ↔ D8h ↔ D4h) and ring-inversion (D2d ↔ D4h ↔ D2d) unimolecular reactions. The previously measured photodetachment spectrum of COT- revealed the reaction dynamics in the vicinity of the two transition states on the neutral potential energy surface. In this work, the photodetachment spectrum is calculated quantum mechanically on ab initio-level potential energy surfaces within a three degree-of-freedom reduced-dimensionality model. Very good agreement has been obtained between theory and experiment, providing reliable interpretations for the experimental spectrum. A detailed picture of the reactive molecular dynamics of the COT unimolecular reaction in the transition state region is also discussed.

Direct Simulation Monte Carlo Application of the Three Dimensional Forced Harmonic Oscillator Model

DTIC Science & Technology

2017-12-07

quasi -classical scattering theory [3,4] or trajectory [5] calculations, semiclassical, as well as close-coupled [6,7] or full [8] quantum mechanical...the quasi -classical trajectory (QCT) calculations approach for ab initio modeling of collision processes. The DMS method builds on an earlier work...nu ar y 30 , 2 01 8 | h ttp :// ar c. ai aa .o rg | D O I: 1 0. 25 14 /1 .T 52 28 to directly use quasi -classical or quantum mechanic

DOE Office of Scientific and Technical Information (OSTI.GOV)

Strubbe, David

Octopus is a scientific program aimed at the ab initio virtual experimentation on a hopefully ever-increasing range of system types. Electrons are described quantum-mechanically within density-functional theory (DFT), in its time-dependent form (TDDFT) when doing simulations in time. Nuclei are described classically as point particles. Electron-nucleus interaction is described within the pseudopotential approximation.

Ab initio theory of the N2V defect in diamond for quantum memory implementation

NASA Astrophysics Data System (ADS)

Udvarhelyi, Péter; Thiering, Gergő; Londero, Elisa; Gali, Adam

2017-10-01

The N2V defect in diamond is characterized by means of ab initio methods relying on density functional theory calculated parameters of a Hubbard model Hamiltonian. It is shown that this approach appropriately describes the energy levels of correlated excited states induced by this defect. By determining its critical magneto-optical parameters, we propose to realize a long-living quantum memory by N2V defect, i.e., H 3 color center in diamond.

Continuum-atomistic simulation of picosecond laser heating of copper with electron heat capacity from ab initio calculation

NASA Astrophysics Data System (ADS)

Ji, Pengfei; Zhang, Yuwen

2016-03-01

On the basis of ab initio quantum mechanics (QM) calculation, the obtained electron heat capacity is implemented into energy equation of electron subsystem in two temperature model (TTM). Upon laser irradiation on the copper film, energy transfer from the electron subsystem to the lattice subsystem is modeled by including the electron-phonon coupling factor in molecular dynamics (MD) and TTM coupled simulation. The results show temperature and thermal melting difference between the QM-MD-TTM integrated simulation and pure MD-TTM coupled simulation. The successful construction of the QM-MD-TTM integrated simulation provides a general way that is accessible to other metals in laser heating.

Ab initio quantum direct dynamics simulations of ultrafast photochemistry with Multiconfigurational Ehrenfest approach

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.

Quantal Study of the Exchange Reaction for N + N2 using an ab initio Potential Energy Surface

NASA Technical Reports Server (NTRS)

Wang, Dunyou; Stallcop, James R.; Huo, Winifred M.; Dateo, Christopher E.; Schwenke, David W.; Partridge, Harry; Kwak, Dochan (Technical Monitor)

2002-01-01

The N + N2 exchange rate is calculated using a time-dependent quantum dynamics method on a newly determined ab initio potential energy surface (PES) for the ground A" state. This ab initio PES shows a double barrier feature in the interaction region with the barrier height at 47.2 kcal/mol, and a shallow well between these two barriers, with the minimum at 43.7 kcal/mol. A quantum dynamics wave packet calculation has been carried out using the fitted PES to compute the cumulative reaction probability for the exchange reaction of N + N2(J=O). The J - K shift method is then employed to obtain the rate constant for this reaction. The calculated rate constant is compared with experimental data and a recent quasi-classical calculation using a LEPS PES. Significant differences are found between the present and quasiclassical results. The present rate calculation is the first accurate 3D quantal dynamics study for N + N2 reaction system and the ab initio PES reported here is the first such surface for N3.

Perspective: Ab initio force field methods derived from quantum mechanics

NASA Astrophysics Data System (ADS)

Xu, Peng; Guidez, Emilie B.; Bertoni, Colleen; Gordon, Mark S.

2018-03-01

It is often desirable to accurately and efficiently model the behavior of large molecular systems in the condensed phase (thousands to tens of thousands of atoms) over long time scales (from nanoseconds to milliseconds). In these cases, ab initio methods are difficult due to the increasing computational cost with the number of electrons. A more computationally attractive alternative is to perform the simulations at the atomic level using a parameterized function to model the electronic energy. Many empirical force fields have been developed for this purpose. However, the functions that are used to model interatomic and intermolecular interactions contain many fitted parameters obtained from selected model systems, and such classical force fields cannot properly simulate important electronic effects. Furthermore, while such force fields are computationally affordable, they are not reliable when applied to systems that differ significantly from those used in their parameterization. They also cannot provide the information necessary to analyze the interactions that occur in the system, making the systematic improvement of the functional forms that are used difficult. Ab initio force field methods aim to combine the merits of both types of methods. The ideal ab initio force fields are built on first principles and require no fitted parameters. Ab initio force field methods surveyed in this perspective are based on fragmentation approaches and intermolecular perturbation theory. This perspective summarizes their theoretical foundation, key components in their formulation, and discusses key aspects of these methods such as accuracy and formal computational cost. The ab initio force fields considered here were developed for different targets, and this perspective also aims to provide a balanced presentation of their strengths and shortcomings. Finally, this perspective suggests some future directions for this actively developing area.

Towards ab initio Calculations with the Dynamical Vertex Approximation

NASA Astrophysics Data System (ADS)

Galler, Anna; Kaufmann, Josef; Gunacker, Patrik; Pickem, Matthias; Thunström, Patrik; Tomczak, Jan M.; Held, Karsten

2018-04-01

While key effects of the many-body problem — such as Kondo and Mott physics — can be understood in terms of on-site correlations, non-local fluctuations of charge, spin, and pairing amplitudes are at the heart of the most fascinating and unresolved phenomena in condensed matter physics. Here, we review recent progress in diagrammatic extensions to dynamical mean-field theory for ab initio materials calculations. We first recapitulate the quantum field theoretical background behind the two-particle vertex. Next we discuss latest algorithmic advances in quantum Monte Carlo simulations for calculating such two-particle quantities using worm sampling and vertex asymptotics, before giving an introduction to the ab initio dynamical vertex approximation (AbinitioDΓA). Finally, we highlight the potential of AbinitioDΓA by detailing results for the prototypical correlated metal SrVO3.

Development of reactive force fields using ab initio molecular dynamics simulation minimally biased to experimental data

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.

Hybrid classical/quantum simulation for infrared spectroscopy of water

NASA Astrophysics Data System (ADS)

Maekawa, Yuki; Sasaoka, Kenji; Ube, Takuji; Ishiguro, Takashi; Yamamoto, Takahiro

2018-05-01

We have developed a hybrid classical/quantum simulation method to calculate the infrared (IR) spectrum of water. The proposed method achieves much higher accuracy than conventional classical molecular dynamics (MD) simulations at a much lower computational cost than ab initio MD simulations. The IR spectrum of water is obtained as an ensemble average of the eigenvalues of the dynamical matrix constructed by ab initio calculations, using the positions of oxygen atoms that constitute water molecules obtained from the classical MD simulation. The calculated IR spectrum is in excellent agreement with the experimental IR spectrum.

Spectroscopic fingerprints of toroidal nuclear quantum delocalization via ab initio path integral simulations.

PubMed

Schütt, Ole; Sebastiani, Daniel

2013-04-05

We investigate the quantum-mechanical delocalization of hydrogen in rotational symmetric molecular systems. To this purpose, we perform ab initio path integral molecular dynamics simulations of a methanol molecule to characterize the quantum properties of hydrogen atoms in a representative system by means of their real-space and momentum-space densities. In particular, we compute the spherically averaged momentum distribution n(k) and the pseudoangular momentum distribution n(kθ). We interpret our results by comparing them to path integral samplings of a bare proton in an ideal torus potential. We find that the hydroxyl hydrogen exhibits a toroidal delocalization, which leads to characteristic fingerprints in the line shapes of the momentum distributions. We can describe these specific spectroscopic patterns quantitatively and compute their onset as a function of temperature and potential energy landscape. The delocalization patterns in the projected momentum distribution provide a promising computational tool to address the intriguing phenomenon of quantum delocalization in condensed matter and its spectroscopic characterization. As the momentum distribution n(k) is also accessible through Nuclear Compton Scattering experiments, our results will help to interpret and understand future measurements more thoroughly. Copyright © 2012 Wiley Periodicals, Inc.

Ab Initio Studies of Chlorine Oxide and Nitrogen Oxide Species of Interest in Stratospheric Chemistry

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of chlorine oxide and nitrogen oxide species will be demonstrated by presentation of some example studies. In particular the geometrical structures, vibrational spectra, and heats of formation Of ClNO2, CisClONO, and trans-ClONO are shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the ab initio results are shown to fill in the gaps and to resolve the experimental controversy. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of ClONO2, HONO2, ClOOC17 ClOOH, and HOOH will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of the experimental studies.

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.

UTChem - A Program for Ab Initio Quantum Chemistry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yanai, Takeshi; Nakano, Haruyuki; Nakajima, Takahito

2003-06-18

UTChem is a quantum chemistry software developed by Hirao's group at the University of Tokyo. UTChem is a research product of our work to develop new and better theoretical methods in quantum chemistry.

Ab initio implementation of quantum trajectory mean-field approach and dynamical simulation of the N{sub 2}CO photodissociation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xie, Binbin; Liu, Lihong; Cui, Ganglong

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 themore » 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.« less

Approximate Quantum Dynamics using Ab Initio Classical Separable Potentials: Spectroscopic Applications.

PubMed

Hirshberg, Barak; Sagiv, Lior; Gerber, R Benny

2017-03-14

Algorithms for quantum molecular dynamics simulations that directly use ab initio methods have many potential applications. In this article, the ab initio classical separable potentials (AICSP) method is proposed as the basis for approximate algorithms of this type. The AICSP method assumes separability of the total time-dependent wave function of the nuclei and employs mean-field potentials that govern the dynamics of each degree of freedom. In the proposed approach, the mean-field potentials are determined by classical ab initio molecular dynamics simulations. The nuclear wave function can thus be propagated in time using the effective potentials generated "on the fly". As a test of the method for realistic systems, calculations of the stationary anharmonic frequencies of hydrogen stretching modes were carried out for several polyatomic systems, including three amino acids and the guanine-cytosine pair of nucleobases. Good agreement with experiments was found. The method scales very favorably with the number of vibrational modes and should be applicable for very large molecules, e.g., peptides. The method should also be applicable for properties such as vibrational line widths and line shapes. Work in these directions is underway.

Ab initio quantum mechanical calculation of the reaction probability for the Cl-+PH2Cl→ClPH2+Cl- reaction

NASA Astrophysics Data System (ADS)

Farahani, Pooria; Lundberg, Marcus; Karlsson, Hans O.

2013-11-01

The SN2 substitution reactions at phosphorus play a key role in organic and biological processes. Quantum molecular dynamics simulations have been performed to study the prototype reaction Cl-+PH2Cl→ClPH2+Cl-, using one and two-dimensional models. A potential energy surface, showing an energy well for a transition complex, was generated using ab initio electronic structure calculations. The one-dimensional model is essentially reflection free, whereas the more realistic two-dimensional model displays involved resonance structures in the reaction probability. The reaction rate is almost two orders of magnitude smaller for the two-dimensional compared to the one-dimensional model. Energetic errors in the potential energy surface is estimated to affect the rate by only a factor of two. This shows that for these types of reactions it is more important to increase the dimensionality of the modeling than to increase the accuracy of the electronic structure calculation.

Structural and Thermodynamic Properties of the Argon Dimer: A Computational Chemistry Exercise in Quantum and Statistical Mechanics

ERIC Educational Resources Information Center

Halpern, Arthur M.

2010-01-01

Using readily available computational applications and resources, students can construct a high-level ab initio potential energy surface (PES) for the argon dimer. From this information, they can obtain detailed molecular constants of the dimer, including its dissociation energy, which compare well with experimental determinations. Using both…

New insights into mechanistic photoisomerization of ethylene-bridged azobenzene from ab initio multiple spawning simulation.

PubMed

Liu, Lihong; Wang, Yating; Fang, Qiu

2017-02-14

Ethylene-bridged azobenzene (br-AB) has aroused broad interests due to its unique photoswitching properties. Numerous dynamical simulations have been performed for the br-AB photoisomerization, which focused mainly on the conformational effect and the funnel role of minimum-energy conical intersection (MECI) on the mechanism. In the present work, we use the "full quantum" ab initio multiple spawning method to simulate the br-AB photoisomerization, which provides new insights into the mechanism. Upon irradiation of br-AB to the first excited singlet state (S 1 ), most of the excess energies are trapped in the azo-moiety. Since the intramolecular vibrational energy redistribution is slower than the S 1 relaxation processes, the nonadiabatic transition from S 1 to the ground state (S 0 ) occurs in the vicinity of high-energy crossing seam and even the largest probabilities of the S 1 → S 0 transition are not distributed in the MECI regions. Once decaying to the S 0 state through the high-energy region, the subsequent isomerization and re-formation of the initial isomer are ultrafast processes in the S 0 state. It is the nonergodic behavior of the S 1 and S 0 dynamics that is mainly responsible for the unique photoswitching properties of the ethylene-bridged azobenzene, which will be discussed in detail.

IR Spectra of (HCOOH)2 and (DCOOH)2: Experiment, VSCF/VCI, and Ab Initio Molecular Dynamics Calculations Using Full-Dimensional Potential and Dipole Moment Surfaces.

PubMed

Qu, Chen; Bowman, Joel M

2018-05-17

We report quantum VSCF/VCI and ab initio molecular dynamics (AIMD) calculations of the IR spectra of (HCOOH) 2 and (DCOOH) 2 , using full-dimensional, ab initio potential energy and dipole moment surfaces (PES and DMS). These surfaces are fits, using permutationally invariant polynomials, to 13 475 ab initio CCSD(T)-F12a electronic energies and MP2 dipole moments. Here "AIMD" means using these ab initio potential and dipole moment surfaces in the MD calculations. The VSCF/VCI calculations use all (24) normal modes for coupling, with a four-mode representation of the potential. The quantum spectra align well with jet-cooled and room-temperature experimental spectra over the spectral range 600-3600 cm -1 . Analyses of the complex O-H and C-H stretch bands are made based on the mixing of the VSCF/VCI basis functions. The comparisons of the AIMD IR spectra with both experimental and VSCF/VCI ones provide tests of the accuracy of the AIMD approach. These indicate good accuracy for simple bands but not for the complex O-H stretch band, which is upshifted from experimental and VSCF/VCI bands by roughly 300 cm -1 . In addition to testing the AIMD approach, the PES, DMS, and VSCF/VCI calculations for formic acid dimer provide opportunities for testing other methods to represent high-dimensional data and other methods that perform postharmonic vibrational calculations.

Ab Initio Modeling of Structure and Properties of Single and Mixed Alkali Silicate Glasses.

PubMed

Baral, Khagendra; Li, Aize; Ching, Wai-Yim

2017-10-12

A density functional theory (DFT)-based ab initio molecular dynamics (AIMD) has been applied to simulate models of single and mixed alkali silicate glasses with two different molar concentrations of alkali oxides. The structural environments and spatial distributions of alkali ions in the 10 simulated models with 20% and 30% of Li, Na, K and equal proportions of Li-Na and Na-K are studied in detail for subtle variations among the models. Quantum mechanical calculations of electronic structures, interatomic bonding, and mechanical and optical properties are carried out for each of the models, and the results are compared with available experimental observation and other simulations. The calculated results are in good agreement with the experimental data. We have used the novel concept of using the total bond order density (TBOD), a quantum mechanical metric, to characterize internal cohesion in these glass models. The mixed alkali effect (MAE) is visible in the bulk mechanical properties but not obvious in other physical properties studied in this paper. We show that Li doping deviates from expected trend due to the much stronger Li-O bonding than those of Na and K doping. The approach used in this study is in contrast with current studies in alkali-doped silicate glasses based only on geometric characterizations.

A walk through the approximations of ab initio multiple spawning

NASA Astrophysics Data System (ADS)

Mignolet, Benoit; Curchod, Basile F. E.

2018-04-01

Full multiple spawning offers an in principle exact framework for excited-state dynamics, where nuclear wavefunctions in different electronic states are represented by a set of coupled trajectory basis functions that follow classical trajectories. The couplings between trajectory basis functions can be approximated to treat molecular systems, leading to the ab initio multiple spawning method which has been successfully employed to study the photochemistry and photophysics of several molecules. However, a detailed investigation of its approximations and their consequences is currently missing in the literature. In this work, we simulate the explicit photoexcitation and subsequent excited-state dynamics of a simple system, LiH, and we analyze (i) the effect of the ab initio multiple spawning approximations on different observables and (ii) the convergence of the ab initio multiple spawning results towards numerically exact quantum dynamics upon a progressive relaxation of these approximations. We show that, despite the crude character of the approximations underlying ab initio multiple spawning for this low-dimensional system, the qualitative excited-state dynamics is adequately captured, and affordable corrections can further be applied to ameliorate the coupling between trajectory basis functions.

Predicting vapor-liquid phase equilibria with augmented ab initio interatomic potentials

NASA Astrophysics Data System (ADS)

Vlasiuk, Maryna; Sadus, Richard J.

2017-06-01

The ability of ab initio interatomic potentials to accurately predict vapor-liquid phase equilibria is investigated. Monte Carlo simulations are reported for the vapor-liquid equilibria of argon and krypton using recently developed accurate ab initio interatomic potentials. Seventeen interatomic potentials are studied, formulated from different combinations of two-body plus three-body terms. The simulation results are compared to either experimental or reference data for conditions ranging from the triple point to the critical point. It is demonstrated that the use of ab initio potentials enables systematic improvements to the accuracy of predictions via the addition of theoretically based terms. The contribution of three-body interactions is accounted for using the Axilrod-Teller-Muto plus other multipole contributions and the effective Marcelli-Wang-Sadus potentials. The results indicate that the predictive ability of recent interatomic potentials, obtained from quantum chemical calculations, is comparable to that of accurate empirical models. It is demonstrated that the Marcelli-Wang-Sadus potential can be used in combination with accurate two-body ab initio models for the computationally inexpensive and accurate estimation of vapor-liquid phase equilibria.

A walk through the approximations of ab initio multiple spawning.

PubMed

Mignolet, Benoit; Curchod, Basile F E

2018-04-07

Full multiple spawning offers an in principle exact framework for excited-state dynamics, where nuclear wavefunctions in different electronic states are represented by a set of coupled trajectory basis functions that follow classical trajectories. The couplings between trajectory basis functions can be approximated to treat molecular systems, leading to the ab initio multiple spawning method which has been successfully employed to study the photochemistry and photophysics of several molecules. However, a detailed investigation of its approximations and their consequences is currently missing in the literature. In this work, we simulate the explicit photoexcitation and subsequent excited-state dynamics of a simple system, LiH, and we analyze (i) the effect of the ab initio multiple spawning approximations on different observables and (ii) the convergence of the ab initio multiple spawning results towards numerically exact quantum dynamics upon a progressive relaxation of these approximations. We show that, despite the crude character of the approximations underlying ab initio multiple spawning for this low-dimensional system, the qualitative excited-state dynamics is adequately captured, and affordable corrections can further be applied to ameliorate the coupling between trajectory basis functions.

Predicting vapor-liquid phase equilibria with augmented ab initio interatomic potentials.

PubMed

Vlasiuk, Maryna; Sadus, Richard J

2017-06-28

The ability of ab initio interatomic potentials to accurately predict vapor-liquid phase equilibria is investigated. Monte Carlo simulations are reported for the vapor-liquid equilibria of argon and krypton using recently developed accurate ab initio interatomic potentials. Seventeen interatomic potentials are studied, formulated from different combinations of two-body plus three-body terms. The simulation results are compared to either experimental or reference data for conditions ranging from the triple point to the critical point. It is demonstrated that the use of ab initio potentials enables systematic improvements to the accuracy of predictions via the addition of theoretically based terms. The contribution of three-body interactions is accounted for using the Axilrod-Teller-Muto plus other multipole contributions and the effective Marcelli-Wang-Sadus potentials. The results indicate that the predictive ability of recent interatomic potentials, obtained from quantum chemical calculations, is comparable to that of accurate empirical models. It is demonstrated that the Marcelli-Wang-Sadus potential can be used in combination with accurate two-body ab initio models for the computationally inexpensive and accurate estimation of vapor-liquid phase equilibria.

Many-body optimization using an ab initio monte carlo method.

PubMed

Haubein, Ned C; McMillan, Scott A; Broadbelt, Linda J

2003-01-01

Advances in computing power have made it possible to study solvated molecules using ab initio quantum chemistry. Inclusion of discrete solvent molecules is required to determine geometric information about solute/solvent clusters. Monte Carlo methods are well suited to finding minima in many-body systems, and ab initio methods are applicable to the widest range of systems. A first principles Monte Carlo (FPMC) method was developed to find minima in many-body systems, and emphasis was placed on implementing moves that increase the likelihood of finding minimum energy structures. Partial optimization and molecular interchange moves aid in finding minima and overcome the incomplete sampling that is unavoidable when using ab initio methods. FPMC was validated by studying the boron trifluoride-water system, and then the method was used to examine the methyl carbenium ion in water to demonstrate its application to solvation problems.

Ab initio atomic recombination reaction energetics on model heat shield surfaces

NASA Technical Reports Server (NTRS)

Senese, Fredrick; Ake, Robert

1992-01-01

Ab initio quantum mechanical calculations on small hydration complexes involving the nitrate anion are reported. The self-consistent field method with accurate basis sets has been applied to compute completely optimized equilibrium geometries, vibrational frequencies, thermochemical parameters, and stable site labilities of complexes involving 1, 2, and 3 waters. The most stable geometries in the first hydration shell involve in-plane waters bridging pairs of nitrate oxygens with two equal and bent hydrogen bonds. A second extremely labile local minimum involves out-of-plane waters with a single hydrogen bond and lies about 2 kcal/mol higher. The potential in the region of the second minimum is extremely flat and qualitatively sensitive to changes in the basis set; it does not correspond to a true equilibrium structure.

[Structural and Dipole Structure Peculiarities of Hoogsteen Base Pairs Formed in Complementary Nucleobases according to ab initio Quantum Mechanics Studies].

PubMed

Petrenko, Y M

2015-01-01

Ab initio quantum mechanics studies for the detection of structure and dipole structure peculiarities of Hoogsteen base pairs relative to Watson-Crick base pairs, were performed during our work. These base pairs are formed as a result of complementary interactions. It was revealed, that adenine-thymine Hoogsteen base pair and adenine-thymine Watson-Crick base pairs can be formed depending on initial configuration. Cytosine-guanine Hoogsteen pairs are formed only when cytosine was originally protonated. Both types of Hoogsteen pairs have noticeable difference in the bond distances and angles. These differences appeared in purine as well as in pyrimidine parts of the pairs. Hoogsteen pairs have mostly shorter hydrogen bond lengths and significantly larger angles of hydrogen bonds and larger angles between the hydrogen bonds than Watson-Crick base pairs. Notable differences are also observed with respect to charge distribution and dipole moment. Quantitative data on these differences are shown in our work. It is also reported that the values of local parameters (according to Cambridge classification of the parameters which determine DNA properties) in Hoogsteen base pairs, are greatly different from Watson-Crick ones.

Exploring the Nature of the H[subscript 2] Bond. 2. Using Ab Initio Molecular Orbital Calculations to Obtain the Molecular Constants

ERIC Educational Resources Information Center

Halpern, Arthur M.; Glendening, Eric D.

2013-01-01

A project for students in an upper-level course in quantum or computational chemistry is described in which they are introduced to the concepts and applications of a high quality, ab initio treatment of the ground-state potential energy curve (PEC) for H[subscript 2] and D[subscript 2]. Using a commercial computational chemistry application and a…

Amorphous Ge quantum dots embedded in crystalline Si: ab initio results.

PubMed

Laubscher, M; Küfner, S; Kroll, P; Bechstedt, F

2015-10-14

We study amorphous Ge quantum dots embedded in a crystalline Si matrix through structure modeling and simulation using ab initio density functional theory including spin-orbit interaction and quasiparticle effects. Three models are generated by replacing a spherical region within diamond Si by Ge atoms and creating a disordered bond network with appropriate density inside the Ge quantum dot. After total-energy optimisations of the atomic geometry we compute the electronic and optical properties. We find three major effects: (i) the resulting nanostructures adopt a type-I heterostructure character; (ii) the lowest optical transitions occur only within the Ge quantum dots, and do not involve or cross the Ge-Si interface. (iii) for larger amorphous Ge quantum dots, with diameters of about 2.0 and 2.7 nm, absorption peaks appear in the mid-infrared spectral region. These are promising candidates for intense luminescence at photon energies below the gap energy of bulk Ge.

Ab initio theories for light nuclei and neutron stars

NASA Astrophysics Data System (ADS)

Gezerlis, Alexandros

2016-09-01

In this talk I will touch upon several features of modern ab initio low-energy nuclear theory. I will start by discussing what ``ab initio'' means in this context. Specifically, I will spend some time going over nucleon-nucleon and three-nucleon interactions and their connections with the underlying theory of Quantum Chromodynamics. I will then show how these interactions are used to describe light nuclei using essentially exact few-body methods. I will then discuss heavier systems, especially those of astrophysical relevance, as well as the methods used to tackle them. This work was supported by the Natural Sciences and Engineering Research Council (NSERC) of Canada and the Canada Foundation for Innovation (CFI).

Mechanistic Insights into Radical-Mediated Oxidation of Tryptophan from ab Initio Quantum Chemistry Calculations and QM/MM Molecular Dynamics Simulations.

PubMed

Wood, Geoffrey P F; Sreedhara, Alavattam; Moore, Jamie M; Wang, John; Trout, Bernhardt L

2016-05-12

An assessment of the mechanisms of (•)OH and (•)OOH radical-mediated oxidation of tryptophan was performed using density functional theory calculations and ab initio plane-wave Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics simulations. For the (•)OH reactions, addition to the pyrrole ring at position 2 is the most favored site with a barrierless reaction in the gas phase. The subsequent degradation of this adduct through a H atom transfer to water was intermittently observed in aqueous-phase molecular dynamics simulations. For the (•)OOH reactions, addition to the pyrrole ring at position 2 is the most favored pathway, in contrast to the situation in the model system ethylene, where concerted addition to the double bond is preferred. From the (•)OOH position 2 adduct QM/MM simulations show that formation of oxy-3-indolanaline occurs readily in an aqueous environment. The observed transformation starts from an initial rupture of the O-O bond followed by a H atom transfer with the accompanying loss of an (•)OH radical to solution. Finally, classical molecular dynamics simulations were performed to equate observed differential oxidation rates of various tryptophan residues in monoclonal antibody fragments. It was found that simple parameters derived from simulation correlate well with the experimental data.

Multiple emissions of benzil at room temperature and 77 K and their assignments from ab initio quantum chemical calculations

NASA Astrophysics Data System (ADS)

Bhattacharya, Bhaswati; Jana, Barnali; Bose, Debosreeta; Chattopadhyay, Nitin

2011-01-01

Multiple emissions have been observed from benzil under different conditions in solutions at room temperature as well as in low temperature glass matrices at 77 K. Low temperature emission has been monitored in rigid matrices frozen under different conditions of illumination. Steady state and time-resolved results together with the ab initio quantum chemical calculations provide, for the first time, the assignments of the different fluorescence bands to the different geometries and/or electronic states of the fluorophore molecule. It is revealed that the skew form of benzil emits from the first (S1) as well as the second excited singlet (S2) states depending on the excitation wavelength, while the relaxed transplanar conformer fluoresces only from the S1 state. The yet unexplored emission band peaking at around 360 nm has been assigned to originate from the S2 state. Ab initio calculations using the density functional theory at B3LYP/6-31G** level corroborate well with the experimental observations.

Multiple emissions of benzil at room temperature and 77 K and their assignments from ab initio quantum chemical calculations.

PubMed

Bhattacharya, Bhaswati; Jana, Barnali; Bose, Debosreeta; Chattopadhyay, Nitin

2011-01-28

Multiple emissions have been observed from benzil under different conditions in solutions at room temperature as well as in low temperature glass matrices at 77 K. Low temperature emission has been monitored in rigid matrices frozen under different conditions of illumination. Steady state and time-resolved results together with the ab initio quantum chemical calculations provide, for the first time, the assignments of the different fluorescence bands to the different geometries and∕or electronic states of the fluorophore molecule. It is revealed that the skew form of benzil emits from the first (S(1)) as well as the second excited singlet (S(2)) states depending on the excitation wavelength, while the relaxed transplanar conformer fluoresces only from the S(1) state. The yet unexplored emission band peaking at around 360 nm has been assigned to originate from the S(2) state. Ab initio calculations using the density functional theory at B3LYP∕6-31G∗∗ level corroborate well with the experimental observations.

A permutationally invariant full-dimensional ab initio potential energy surface for the abstraction and exchange channels of the H + CH{sub 4} system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Jun, E-mail: jli15@cqu.edu.cn, E-mail: zhangdh@dicp.ac.cn; Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131; Chen, Jun

2015-05-28

We report a permutationally invariant global potential energy surface (PES) for the H + CH{sub 4} system based on ∼63 000 data points calculated at a high ab initio level (UCCSD(T)-F12a/AVTZ) using the recently proposed permutation invariant polynomial-neural network method. The small fitting error (5.1 meV) indicates a faithful representation of the ab initio points over a large configuration space. The rate coefficients calculated on the PES using tunneling corrected transition-state theory and quasi-classical trajectory are found to agree well with the available experimental and previous quantum dynamical results. The calculated total reaction probabilities (J{sub tot} = 0) including themore » abstraction and exchange channels using the new potential by a reduced dimensional quantum dynamic method are essentially the same as those on the Xu-Chen-Zhang PES [Chin. J. Chem. Phys. 27, 373 (2014)].« less

A Multidimensional B-Spline Correction for Accurate Modeling Sugar Puckering in QM/MM Simulations.

PubMed

Huang, Ming; Dissanayake, Thakshila; Kuechler, Erich; Radak, Brian K; Lee, Tai-Sung; Giese, Timothy J; York, Darrin M

2017-09-12

The computational efficiency of approximate quantum mechanical methods allows their use for the construction of multidimensional reaction free energy profiles. It has recently been demonstrated that quantum models based on the neglect of diatomic differential overlap (NNDO) approximation have difficulty modeling deoxyribose and ribose sugar ring puckers and thus limit their predictive value in the study of RNA and DNA systems. A method has been introduced in our previous work to improve the description of the sugar puckering conformational landscape that uses a multidimensional B-spline correction map (BMAP correction) for systems involving intrinsically coupled torsion angles. This method greatly improved the adiabatic potential energy surface profiles of DNA and RNA sugar rings relative to high-level ab initio methods even for highly problematic NDDO-based models. In the present work, a BMAP correction is developed, implemented, and tested in molecular dynamics simulations using the AM1/d-PhoT semiempirical Hamiltonian for biological phosphoryl transfer reactions. Results are presented for gas-phase adiabatic potential energy surfaces of RNA transesterification model reactions and condensed-phase QM/MM free energy surfaces for nonenzymatic and RNase A-catalyzed transesterification reactions. The results show that the BMAP correction is stable, efficient, and leads to improvement in both the potential energy and free energy profiles for the reactions studied, as compared with ab initio and experimental reference data. Exploration of the effect of the size of the quantum mechanical region indicates the best agreement with experimental reaction barriers occurs when the full CpA dinucleotide substrate is treated quantum mechanically with the sugar pucker correction.

Artificial Bee Colony Optimization of Capping Potentials for Hybrid Quantum Mechanical/Molecular Mechanical Calculations.

PubMed

Schiffmann, Christoph; Sebastiani, Daniel

2011-05-10

We present an algorithmic extension of a numerical optimization scheme for analytic capping potentials for use in mixed quantum-classical (quantum mechanical/molecular mechanical, QM/MM) ab initio calculations. Our goal is to minimize bond-cleavage-induced perturbations in the electronic structure, measured by means of a suitable penalty functional. The optimization algorithm-a variant of the artificial bee colony (ABC) algorithm, which relies on swarm intelligence-couples deterministic (downhill gradient) and stochastic elements to avoid local minimum trapping. The ABC algorithm outperforms the conventional downhill gradient approach, if the penalty hypersurface exhibits wiggles that prevent a straight minimization pathway. We characterize the optimized capping potentials by computing NMR chemical shifts. This approach will increase the accuracy of QM/MM calculations of complex biomolecules.

New ab initio potential surfaces and three-dimensional quantum dynamics for transition state spectroscopy in ozone photodissociation

NASA Astrophysics Data System (ADS)

Yamashita, Koichi; Morokuma, Keiji; Le Quéré, Frederic; Leforestier, Claude

1992-04-01

New ab initio potential energy surfaces (PESs) of the ground and B ( 1B 2) states of ozone have been calculated with the CASSCF-SECI/DZP method to describe the three-dimensional photodissociation process. The dissociation energy of the ground state and the vertical barrier height of the B PES are obtained to be 0.88 and 1.34 eV, respectively, in better agreement with the experimental values than the previous calculation. The photodissociation autocorrelation function, calculated on the new B PES, based on exact three-dimensional quantum dynamics, reproduces well the main recurrence feature extracted from the experimental spectra.

Ab initio simulation of particle momentum distributions in high-pressure water

NASA Astrophysics Data System (ADS)

Ceriotti, M.

2014-12-01

Applying pressure to water reduces the average oxygen-oxygen distance, and facilitates the delocalisation of protons along the hydrogen bond. This pressure-induced delocalisation is further enhanced by the quantum nature of hydrogen nuclei, which is very significant even well above room temperature. Here we will evaluate the quantum kinetic energy and the particle momentum distribution of hydrogen and oxygen nuclei in water at extreme pressure, using ab initio path integral molecular dynamics. We will show that (transient) dissociation of water molecules induce measurable changes in the kinetic energy hydrogen atoms, although current deep inelastic scattering experiments are probably unable to capture the heterogeneity of the sample.

Scattering study of the Ne + NeH+(v0 = 0, j0 = 0) → NeH+ + Ne reaction on an ab initio based analytical potential energy surface

NASA Astrophysics Data System (ADS)

Koner, Debasish; Barrios, Lizandra; González-Lezana, Tomás; Panda, Aditya N.

2016-01-01

Initial state selected dynamics of the Ne + NeH+(v0 = 0, j0 = 0) → NeH+ + Ne reaction is investigated by quantum and statistical quantum mechanical (SQM) methods on the ground electronic state. The three-body ab initio energies on a set of suitably chosen grid points have been computed at CCSD(T)/aug-cc-PVQZ level and analytically fitted. The fitting of the diatomic potentials, computed at the same level of theory, is performed by spline interpolation. A collinear [NeHNe]+ structure lying 0.72 eV below the Ne + NeH+ asymptote is found to be the most stable geometry for this system. Energies of low lying vibrational states have been computed for this stable complex. Reaction probabilities obtained from quantum calculations exhibit dense oscillatory structures, particularly in the low energy region and these get partially washed out in the integral cross section results. SQM predictions are devoid of oscillatory structures and remain close to 0.5 after the rise at the threshold thus giving a crude average description of the quantum probabilities. Statistical cross sections and rate constants are nevertheless in sufficiently good agreement with the quantum results to suggest an important role of a complex-forming dynamics for the title reaction.

Cis-trans photoisomerization of azobenzene upon excitation to the S1 state: an ab initio molecular dynamics and QM/MM study

NASA Astrophysics Data System (ADS)

Pederzoli, Marek; Pittner, Jiří; Barbatti, Mario; Lischka, Hans

2012-10-01

The cis-trans isomerization of azobenzene upon S1(n,π*) excitation is studied both in gas phase and in solution. Our study is based on ab initio non-adiabatic dynamics simulations with the non-adiabatic effects included via the fewest-switches surface hopping method with potential-energy surfaces and couplings determined on the fly. The non-adiabatic couplings have been computed based on overlaps of CASSCF wave functions. The solvent is described using classical molecular dynamics employing the quantum mechanics/molecular mechanics (QM/MM) approach. Azobenzene photoisomerization upon S1(n,π*) excitation occurs purely as a rotational motion of the central CNNC moiety. Two non-equivalent rotational pathways, corresponding to clockwise or counterclockwise rotation, are available. The course of the rotational motion is strongly dependent on the initial conditions. The internal conversion occurs via a S0/S1 crossing seam located near the midpoint of both of these rotational pathways. Based on statistical analysis it is shown that the occurrence of one or other pathways can be completely controlled by selecting adequate initial conditions. The effect of the solvent on the reaction mechanism is small. The lifetime of the S1 state is marginally lowered; the effect does not depend on the polarity, but rather on the viscosity of the solvent. The quantum yield is solvent dependent; the simulations in water give smaller quantum yield than those obtained in n-hexane and in gas phase.

Rate Constants for Fine-Structure Excitations in O - H Collisions with Error Bars Obtained by Machine Learning

NASA Astrophysics Data System (ADS)

Vieira, Daniel; Krems, Roman

2017-04-01

Fine-structure transitions in collisions of O(3Pj) with atomic hydrogen are an important cooling mechanism in the interstellar medium; knowledge of the rate coefficients for these transitions has a wide range of astrophysical applications. The accuracy of the theoretical calculation is limited by inaccuracy in the ab initio interaction potentials used in the coupled-channel quantum scattering calculations from which the rate coefficients can be obtained. In this work we use the latest ab initio results for the O(3Pj) + H interaction potentials to improve on previous calculations of the rate coefficients. We further present a machine-learning technique based on Gaussian Process regression to determine the sensitivity of the rate coefficients to variations of the underlying adiabatic interaction potentials. To account for the inaccuracy inherent in the ab initio calculations we compute error bars for the rate coefficients corresponding to 20% variation in each of the interaction potentials. We obtain these error bars by fitting a Gaussian Process model to a data set of potential curves and rate constants. We use the fitted model to do sensitivity analysis, determining the relative importance of individual adiabatic potential curves to a given fine-structure transition. NSERC.

Ab Initio Values of the Thermophysical Properties of Helium as Standards

PubMed Central

Hurly, John J.; Moldover, Michael R.

2000-01-01

Recent quantum mechanical calculations of the interaction energy of pairs of helium atoms are accurate and some include reliable estimates of their uncertainty. We combined these ab initio results with earlier published results to obtain a helium-helium interatomic potential that includes relativistic retardation effects over all ranges of interaction. From this potential, we calculated the thermophysical properties of helium, i.e., the second virial coefficients, the dilute-gas viscosities, and the dilute-gas thermal conductivities of 3He, 4He, and their equimolar mixture from 1 K to 104 K. We also calculated the diffusion and thermal diffusion coefficients of mixtures of 3He and 4He. For the pure fluids, the uncertainties of the calculated values are dominated by the uncertainties of the potential; for the mixtures, the uncertainties of the transport properties also include contributions from approximations in the transport theory. In all cases, the uncertainties are smaller than the corresponding experimental uncertainties; therefore, we recommend the ab initio results be used as standards for calibrating instruments relying on these thermophysical properties. We present the calculated thermophysical properties in easy-to-use tabular form. PMID:27551630

Ab Initio Potential Energy Surfaces and the Calculation of Accurate Vibrational Frequencies

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Dateo, Christopher E.; Martin, Jan M. L.; Taylor, Peter R.; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

Due to advances in quantum mechanical methods over the last few years, it is now possible to determine ab initio potential energy surfaces in which fundamental vibrational frequencies are accurate to within plus or minus 8 cm(exp -1) on average, and molecular bond distances are accurate to within plus or minus 0.001-0.003 Angstroms, depending on the nature of the bond. That is, the potential energy surfaces have not been scaled or empirically adjusted in any way, showing that theoretical methods have progressed to the point of being useful in analyzing spectra that are not from a tightly controlled laboratory environment, such as vibrational spectra from the interstellar medium. Some recent examples demonstrating this accuracy will be presented and discussed. These include the HNO, CH4, C2H4, and ClCN molecules. The HNO molecule is interesting due to the very large H-N anharmonicity, while ClCN has a very large Fermi resonance. The ab initio studies for the CH4 and C2H4 molecules present the first accurate full quartic force fields of any kind (i.e., whether theoretical or empirical) for a five-atom and six-atom system, respectively.

Ab Initio Calculation of Accurate Vibrational Frequencies for Molecules of Interest in Atmospheric Chemistry

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

1996-01-01

Due to advances in quantum mechanical methods over the last few years, it is now possible to determine ab initio potential energy surfaces in which fundamental vibrational frequencies are accurate to within +/- 8 cm(sup -1) on average, and molecular bond distances are accurate to within +/- 0.001-0.003 A, depending on the nature of the bond. That is, the potential energy surfaces have not been scaled or empirically adjusted in any way, showing that theoretical methods have progressed to the point of being useful in analyzing spectra that are not from a tightly controlled laboratory environment, such as rovibrational spectra from the interstellar medium. Some recent examples demonstrating this accuracy win be presented and discussed. These include the HNO, CH4, C2H4, and ClCN molecules. The HNO molecule is interesting due to the very large H-N anharmonicity, while ClCN has a very large Fermi resonance. The ab initio studies for the CH4 and C2H4 molecules present the first accurate full quartic force fields of any kind (i.e., whether theoretical or empirical) for a five-atom and six-atom system, respectively.

Ab initio thermal rate calculations of HO + HO = O(3P) + H2O reaction and isotopologues.

PubMed

Nguyen, Thanh Lam; Stanton, John F

2013-04-04

The forward and reverse reactions, HO + HO ⇌ O((3)P) + H2O, which play roles in both combustion and laboratory studies, were theoretically characterized with a master equation approach to compute thermal reaction rate constants at both the low and high pressure limits. Our ab initio k(T) results for the title reaction and two isotopic variants agree very well with experiments (within 15%) over a wide temperature range. The calculated reaction rate shows a distinctly non-Arrhenius behavior and a strong curvature consistent with the experiment. This characteristic behavior is due to effects of positive barrier height and quantum mechanical tunneling. Tunneling is very important and contributes more than 70% of total reaction rate at room temperature. A prereactive complex is also important in the overall reaction scheme.

Proton affinity of methyl nitrate - Less than proton affinity of nitric acid

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Rice, Julia E.

1992-01-01

Several state-of-the-art ab initio quantum mechanical methods were used to investigate the equilibrium structure, dipole moments, harmonic vibrational frequencies, and IR intensities of methyl nitrate, methanol, and several structures of protonated methyl nitrate, using the same theoretical methods as in an earlier study (Lee and Rice, 1992) of nitric acid. The ab initio results for methyl nitrate and methanol were found to be in good agreement with available experimental data. The proton affinity (PA) of methyl nitrate was calculated to be 176.9 +/-5 kcal/mol, in excellent agreement with the experimental value 176 kcal/mol obtained by Attina et al. (1987) and less than the PA value of nitric acid. An explanation of the discrepancy of the present results with those of an earlier study on protonated nitric acid is proposed.

An extensive ab initio study of the structures, vibrational spectra, quadratic force fields, and relative energetics of three isomers of Cl2O2

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Rohlfing, Celeste MCM.; Rice, Julia E.

1992-01-01

Quantum mechanical computational methods are employed for an ab initio investigation of: (1) the molecular properties of the lowest isomers of the ClO dimer; and (2) predicted molecular and thermochemical properties. Techniques employed include electron correlation and particularly singles and doubles coupled-cluster (CCSD) theory with or without perturbational estimates of the effects of connected triple excitations. The isomers ClOClO and ClClO2 are found to have higher energies than the ClOOCl isomer, and the theoretical vibrational frequencies of the isomers are well correlated with experimental data. Experimental values of the heat of formation for the isomers are also compared with calculations based on an isodesmic reaction with Cl2O, H2O, and HOOH.

Ab initio non-adiabatic study of the 4pσ B'' 1Σ+u state of H2

NASA Astrophysics Data System (ADS)

Glass-Maujean, M.; Schmoranzer, H.

2018-05-01

Fully ab initio non-adiabatic multichannel quantum defect calculations of the 4pσ B'' 1∑u+ energy levels, line intensities and widths, based on the latest quantum-chemical clamped-nuclei calculations of Wolniewicz and collaborators are presented for H2. The B″ state corresponds to the inner well of the ? state. The B'' v ≥ 1 levels are rapidly predissociated through vibrational coupling with the 3pσ B' 1Σ+u continuum so that coupled-equation calculations become unstable. Multichannel quantum defect theory, on the other hand, is demonstrated to be particularly suited to this situation. Experimental data as level energies, line intensities and dissociation widths were revisited and corrected. Reinvestigating previously published spectra, several new lines were assigned.

Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications

PubMed Central

2016-01-01

Semiempirical (SE) methods can be derived from either Hartree–Fock or density functional theory by applying systematic approximations, leading to efficient computational schemes that are several orders of magnitude faster than ab initio calculations. Such numerical efficiency, in combination with modern computational facilities and linear scaling algorithms, allows application of SE methods to very large molecular systems with extensive conformational sampling. To reliably model the structure, dynamics, and reactivity of biological and other soft matter systems, however, good accuracy for the description of noncovalent interactions is required. In this review, we analyze popular SE approaches in terms of their ability to model noncovalent interactions, especially in the context of describing biomolecules, water solution, and organic materials. We discuss the most significant errors and proposed correction schemes, and we review their performance using standard test sets of molecular systems for quantum chemical methods and several recent applications. The general goal is to highlight both the value and limitations of SE methods and stimulate further developments that allow them to effectively complement ab initio methods in the analysis of complex molecular systems. PMID:27074247

Density-matrix based determination of low-energy model Hamiltonians from ab initio wavefunctions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Changlani, Hitesh J.; Zheng, Huihuo; Wagner, Lucas K.

2015-09-14

We propose a way of obtaining effective low energy Hubbard-like model Hamiltonians from ab initio quantum Monte Carlo calculations for molecular and extended systems. The Hamiltonian parameters are fit to best match the ab initio two-body density matrices and energies of the ground and excited states, and thus we refer to the method as ab initio density matrix based downfolding. For benzene (a finite system), we find good agreement with experimentally available energy gaps without using any experimental inputs. For graphene, a two dimensional solid (extended system) with periodic boundary conditions, we find the effective on-site Hubbard U{sup ∗}/t tomore » be 1.3 ± 0.2, comparable to a recent estimate based on the constrained random phase approximation. For molecules, such parameterizations enable calculation of excited states that are usually not accessible within ground state approaches. For solids, the effective Hamiltonian enables large-scale calculations using techniques designed for lattice models.« less

QMCPACK: an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids

NASA Astrophysics Data System (ADS)

Kim, Jeongnim; Baczewski, Andrew D.; Beaudet, Todd D.; Benali, Anouar; Chandler Bennett, M.; Berrill, Mark A.; Blunt, Nick S.; Josué Landinez Borda, Edgar; Casula, Michele; Ceperley, David M.; Chiesa, Simone; Clark, Bryan K.; Clay, Raymond C., III; Delaney, Kris T.; Dewing, Mark; Esler, Kenneth P.; Hao, Hongxia; Heinonen, Olle; Kent, Paul R. C.; Krogel, Jaron T.; Kylänpää, Ilkka; Li, Ying Wai; Lopez, M. Graham; Luo, Ye; Malone, Fionn D.; Martin, Richard M.; Mathuriya, Amrita; McMinis, Jeremy; Melton, Cody A.; Mitas, Lubos; Morales, Miguel A.; Neuscamman, Eric; Parker, William D.; Pineda Flores, Sergio D.; Romero, Nichols A.; Rubenstein, Brenda M.; Shea, Jacqueline A. R.; Shin, Hyeondeok; Shulenburger, Luke; Tillack, Andreas F.; Townsend, Joshua P.; Tubman, Norm M.; Van Der Goetz, Brett; Vincent, Jordan E.; ChangMo Yang, D.; Yang, Yubo; Zhang, Shuai; Zhao, Luning

2018-05-01

QMCPACK is an open source quantum Monte Carlo package for ab initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater–Jastrow type trial wavefunctions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary-field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performance computing architectures, including multicore central processing unit and graphical processing unit systems. We detail the program’s capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://qmcpack.org.

QMCPACK: an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids.

PubMed

Kim, Jeongnim; Baczewski, Andrew T; Beaudet, Todd D; Benali, Anouar; Bennett, M Chandler; Berrill, Mark A; Blunt, Nick S; Borda, Edgar Josué Landinez; Casula, Michele; Ceperley, David M; Chiesa, Simone; Clark, Bryan K; Clay, Raymond C; Delaney, Kris T; Dewing, Mark; Esler, Kenneth P; Hao, Hongxia; Heinonen, Olle; Kent, Paul R C; Krogel, Jaron T; Kylänpää, Ilkka; Li, Ying Wai; Lopez, M Graham; Luo, Ye; Malone, Fionn D; Martin, Richard M; Mathuriya, Amrita; McMinis, Jeremy; Melton, Cody A; Mitas, Lubos; Morales, Miguel A; Neuscamman, Eric; Parker, William D; Pineda Flores, Sergio D; Romero, Nichols A; Rubenstein, Brenda M; Shea, Jacqueline A R; Shin, Hyeondeok; Shulenburger, Luke; Tillack, Andreas F; Townsend, Joshua P; Tubman, Norm M; Van Der Goetz, Brett; Vincent, Jordan E; Yang, D ChangMo; Yang, Yubo; Zhang, Shuai; Zhao, Luning

2018-05-16

QMCPACK is an open source quantum Monte Carlo package for ab initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater-Jastrow type trial wavefunctions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary-field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performance computing architectures, including multicore central processing unit and graphical processing unit systems. We detail the program's capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://qmcpack.org.

Prediction of folding preference of 10 kDa silk-like proteins using a Lego approach and ab initio calculations.

PubMed

Pohl, Gábor; Beke, Tamás; Borbély, János; Perczel, András

2006-11-15

Because of their great flexibility and strength resistance, both spider silks and silkworm silks are of increasing scientific and commercial interest. Despite numerous spectroscopic and theoretical studies, several structural properties at the atomic level have yet to be identified. The present theoretical investigation focuses on these issues by studying three silk-like model peptides: (AG)(64), [(AG)(4)EG](16), and [(AG)(4)PEG](16), using a Lego-type approach to construct these polypeptides. On the basis of these examples it is shown that thermoneutral isodesmic reactions and ab initio calculations provide a capable method to investigate structural properties of repetitive polypeptides. The most probable overall fold schema of these molecules with respect to the type of embedded hairpin structures were determined at the ab initio level of theory (RHF/6-311++G(d,p)//RHF/3-21G). Further on, analysis is carried out on the possible hairpin and turn regions and on their effect on the global fold. In the case of the (AG)(64) model peptide, the optimal beta-sheet/turn ratio was also determined, which provided good support for experimental observations. In addition, lateral shearing of a hairpin "folding unit" was investigated at the quantum chemical level to explain the mechanical properties of spider silk. The unique mechanical characteristics of silk bio-compounds are now investigated at the atomic level.

Challenges in modelling homogeneous catalysis: new answers from ab initio molecular dynamics to the controversy over the Wacker process.

PubMed

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.

Structure and dynamics of the CrIII ion in aqueous solution: Ab initio QM/MM molecular dynamics simulation.

PubMed

Kritayakornupong, Chinapong; Plankensteiner, Kristof; Rode, Bernd M

2004-10-01

Structural and dynamical properties of the Cr(III) ion in aqueous solution have been investigated using a combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation. The hydration structure of Cr(III) was determined in terms of radial distribution functions, coordination numbers, and angular distributions. The QM/MM simulation gives coordination numbers of 6 and 15.4 for the first and second hydration shell, respectively. The first hydration shell is kinetically very inert but by no means rigid and variations of the first hydration shell geometry lead to distinct splitting in the vibrational spectra of Cr(H(2)O)(6) (3+). A mean residence time of 22 ps was obtained for water ligands residing in the second hydration shell, which is remarkably shorter than the experimentally estimated value. The hydration energy of -1108 +/- 7 kcal/mol, obtained from the QM/MM simulation, corresponds well to the experimental hydration enthalpy value. Copyright 2004 Wiley Periodicals, Inc.

Ab initio calculation of the G peak intensity of graphene: Laser-energy and Fermi-energy dependence and importance of quantum interference effects

NASA Astrophysics Data System (ADS)

Reichardt, Sven; Wirtz, Ludger

2017-05-01

We present the results of a diagrammatic, fully ab initio calculation of the G peak intensity of graphene. The flexibility and generality of our approach enables us to go beyond the previous analytical calculations in the low-energy regime. We study the laser and Fermi energy dependence of the G peak intensity and analyze the contributions from resonant and nonresonant electronic transitions. In particular, we explicitly demonstrate the importance of quantum interference and nonresonant states for the G peak process. Our method of analysis and computational concept is completely general and can easily be applied to study other materials as well.

Full-Dimensional Quantum Calculations of Vibrational Levels of NH4(+) and Isotopomers on An Accurate Ab Initio Potential Energy Surface.

PubMed

Yu, Hua-Gen; Han, Huixian; Guo, Hua

2016-04-14

Vibrational energy levels of the ammonium cation (NH4(+)) and its deuterated isotopomers are calculated using a numerically exact kinetic energy operator on a recently developed nine-dimensional permutation invariant semiglobal potential energy surface fitted to a large number of high-level ab initio points. Like CH4, the vibrational levels of NH4(+) and ND4(+) exhibit a polyad structure, characterized by a collective quantum number P = 2(v1 + v3) + v2 + v4. The low-lying vibrational levels of all isotopomers are assigned and the agreement with available experimental data is better than 1 cm(-1).

The shear instability energy: a new parameter for materials design?

NASA Astrophysics Data System (ADS)

Kanani, M.; Hartmaier, A.; Janisch, R.

2017-10-01

Reliable and predictive relationships between fundamental microstructural material properties and observable macroscopic mechanical behaviour are needed for the successful design of new materials. In this study we establish a link between physical properties that are defined on the atomic level and the deformation mechanisms of slip planes and interfaces that govern the mechanical behaviour of a metallic material. To accomplish this, the shear instability energy Γ is introduced, which can be determined via quantum mechanical ab initio calculations or other atomistic methods. The concept is based on a multilayer generalised stacking fault energy calculation and can be applied to distinguish the different shear deformation mechanisms occurring at TiAl interfaces during finite-temperature molecular dynamics simulations. We use the new parameter Γ to construct a deformation mechanism map for different interfaces occurring in this intermetallic. Furthermore, Γ can be used to convert the results of ab initio density functional theory calculations into those obtained with an embedded atom method type potential for TiAl. We propose to include this new physical parameter into material databases to apply it for the design of materials and microstructures, which so far mainly relies on single-crystal values for the unstable and stable stacking fault energy.

Protein's electronic polarization contributes significantly to its catalytic function

NASA Astrophysics Data System (ADS)

Xiang, Yun; Duan, Lili; Zhang, John Z. H.

2011-05-01

Ab initio quantum mechanical/molecular mechanical method is combined with the polarized protein-specific charge to study the chemical reactions catalyzed by protein enzymes. Significant improvement in the accuracy and efficiency of free-energy simulation is demonstrated by calculating the free-energy profile of the primary proton transfer reaction in triosephosphate isomerase. Quantitative agreement with experimental results is achieved. Our simulation results indicate that electronic polarization makes important contribution to enzyme catalysis by lowering the energy barrier by as much as 3 kcal/mol.

From ab Initio Potential Energy Surfaces to State-Resolved Reactivities: X + H 2O ↔ HX + OH [X = F, Cl, and O( 3P)] Reactions

DOE PAGES

Li, Jun; Jiang, Bin; Song, Hongwei; ...

2015-04-17

Here, we survey the recent advances in theoretical understanding of quantum state resolved dynamics, using the title reactions as examples. It is shown that the progress was made possible by major developments in two areas. First, an accurate analytical representation of many high-level ab initio points over a large configuration space can now be made with high fidelity and the necessary permutation symmetry. The resulting full-dimensional global potential energy surfaces enable dynamical calculations using either quasi-classical trajectory or more importantly quantum mechanical methods. The second advance is the development of accurate and efficient quantum dynamical methods, which are necessary formore » providing a reliable treatment of quantum effects in reaction dynamics such as tunneling, resonances, and zero-point energy. The powerful combination of the two advances has allowed us to achieve a quantitatively accurate characterization of the reaction dynamics, which unveiled rich dynamical features such as steric steering, strong mode specificity, and bond selectivity. The dependence of reactivity on reactant modes can be rationalized by the recently proposed sudden vector projection model, which attributes the mode specificity and bond selectivity to the coupling of reactant modes with the reaction coordinate at the relevant transition state. The deeper insights provided by these theoretical studies have advanced our understanding of reaction dynamics to a new level.« less

A new ab initio potential energy surface of LiClH (1A') system and quantum dynamics calculation for Li + HCl (v = 0, j = 0-2) → LiCl + H reaction

NASA Astrophysics Data System (ADS)

Tan, Rui Shan; Zhai, Huan Chen; Yan, Wei; Gao, Feng; Lin, Shi Ying

2017-04-01

A new ab initio potential energy surface (PES) for the ground state of Li + HCl reactive system has been constructed by three-dimensional cubic spline interpolation of 36 654 ab initio points computed at the MRCI+Q/aug-cc-pV5Z level of theory. The title reaction is found to be exothermic by 5.63 kcal/mol (9 kcal/mol with zero point energy corrections), which is very close to the experimental data. The barrier height, which is 2.99 kcal/mol (0.93 kcal/mol for the vibrationally adiabatic barrier height), and the depth of van der Waals minimum located near the entrance channel are also in excellent agreement with the experimental findings. This study also identified two more van der Waals minima. The integral cross sections, rate constants, and their dependence on initial rotational states are calculated using an exact quantum wave packet method on the new PES. They are also in excellent agreement with the experimental measurements.

Origins of the different metal preferences of Escherichia coli peptide deformylase and Bacillus thermoproteolyticus thermolysin: a comparative quantum mechanical/molecular mechanical study.

PubMed

Dong, Minghui; Liu, Haiyan

2008-08-21

The Escherichia coli peptide deformylase (PDF) and Bacillus thermoproteolyticus thermolysin (TLN) are two representative metal-requiring peptidases having remarkably similar active centers but distinctively different metal preferences. Zinc is a competent catalytic cofactor for TLN but not for PDF. Reaction pathways and the associated energetics for both enzymes were determined using combined semiempirical and ab initio quantum mechanical/molecular mechanical modeling, without presuming reaction coordinates. The results confirmed that both enzymes catalyze via the same chemical steps, and reproduced their different preferences for zinc or iron as competent cofactors. Further analyses indicated that different feasibility of the nucleophilic attack step leads to different metal preferences of the two enzymes. In TLN, the substrate is strongly activated and can serve as the fifth coordination ligand of zinc prior to the chemical steps. In PDF, the substrate carbonyl is activated by the chemical step itself, and becomes the fifth coordination partner of zinc only in a later stage of the nucleophilic attack. These leads to a much more difficult nucleophilic attack in PDF than in TLN. Different from some earlier suggestions, zinc has no difficulty in accepting an activated substrate as the fifth ligand to switch from tetra- to penta-coordination in either PDF or TLN. When iron replaces zinc, its stronger interaction with the hydroxide ligand may lead to higher activation barrier in TLN. In PDF, the stronger interactions of iron with ligands allow iron-substrate coordination to take place either before or at a very early stage of the chemical step, leading to effective catalysis. Our calculations also show combined semiempirical and ab initio quantum mechanical modeling can be efficient approaches to explore complicated reaction pathways in enzyme systems.

Determination of the electronic energy levels of colloidal nanocrystals using field-effect transistors and Ab-initio calculations.

PubMed

Bisri, Satria Zulkarnaen; Degoli, Elena; Spallanzani, Nicola; Krishnan, Gopi; Kooi, Bart Jan; Ghica, Corneliu; Yarema, Maksym; Heiss, Wolfgang; Pulci, Olivia; Ossicini, Stefano; Loi, Maria Antonietta

2014-08-27

Colloidal nanocrystals electronic energy levels are determined by strong size-dependent quantum confinement. Understanding the configuration of the energy levels of nanocrystal superlattices is vital in order to use them in heterostructures with other materials. A powerful method is reported to determine the energy levels of PbS nanocrystal assemblies by combining the utilization of electric-double-layer-gated transistors and advanced ab-initio theory. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Thermalization and its mechanism for generic quantum isolated systems

NASA Astrophysics Data System (ADS)

Olshanii, Maxim; Dunjko, Vanja; Rigol, Marcos

2008-05-01

Time dynamics of isolated many-body quantum systems has long been an elusive subject, perhaps most urgently needed in the foundations of quantum statistical mechanics. In generic systems, one expects the nonequilibrium dynamics to lead to thermalization: a relaxation to states where the values of macroscopic quantities are stationary, universal with respect to widely differing initial conditions, and predictable through the time-tested recipe of statistical mechanics. The relaxation mechanism is not obvious, however; dynamical chaos cannot play the key role as it does in classical systems since quantum evolution is linear. Here we demonstrateootnotetextM. Rigol, V. Dunjko, and M. Olshanii, to appear in Nature (2008), using the results of an ab initio numerical experiment with 5 hard-core bosons moving in a 5x5 lattice, that in quantum systems thermalization happens not in course of time evolution but instead at the level of individual eigenstates, as first proposed by DeutschootnotetextJ. M. Deutsch, Phys.Rev. A 43, 2046 (1991) and SrednickiootnotetextM. Srednicki, Phys. Rev. E 50, 888 (1994).

Scattering study of the Ne + NeH{sup +}(v{sub 0} = 0, j{sub 0} = 0) → NeH{sup +} + Ne reaction on an ab initio based analytical potential energy surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koner, Debasish; Panda, Aditya N., E-mail: adi07@iitg.ernet.in; Barrios, Lizandra

2016-01-21

Initial state selected dynamics of the Ne + NeH{sup +}(v{sub 0} = 0, j{sub 0} = 0) → NeH{sup +} + Ne reaction is investigated by quantum and statistical quantum mechanical (SQM) methods on the ground electronic state. The three-body ab initio energies on a set of suitably chosen grid points have been computed at CCSD(T)/aug-cc-PVQZ level and analytically fitted. The fitting of the diatomic potentials, computed at the same level of theory, is performed by spline interpolation. A collinear [NeHNe]{sup +} structure lying 0.72 eV below the Ne + NeH{sup +} asymptote is found to be the most stablemore » geometry for this system. Energies of low lying vibrational states have been computed for this stable complex. Reaction probabilities obtained from quantum calculations exhibit dense oscillatory structures, particularly in the low energy region and these get partially washed out in the integral cross section results. SQM predictions are devoid of oscillatory structures and remain close to 0.5 after the rise at the threshold thus giving a crude average description of the quantum probabilities. Statistical cross sections and rate constants are nevertheless in sufficiently good agreement with the quantum results to suggest an important role of a complex-forming dynamics for the title reaction.« less

A Group Increment Scheme for Infrared Absorption Intensities of Greenhouse Gases

NASA Technical Reports Server (NTRS)

Kokkila, Sara I.; Bera, Partha P.; Francisco, Joseph S.; Lee, Timothy J.

2012-01-01

A molecule's absorption in the atmospheric infrared (IR) window (IRW) is an indicator of its efficiency as a greenhouse gas. A model for estimating the absorption of a fluorinated molecule within the IRW was developed to assess its radiative impact. This model will be useful in comparing different hydrofluorocarbons and hydrofluoroethers contribution to global warming. The absorption of radiation by greenhouse gases, in particular hydrofluoroethers and hydrofluorocarbons, was investigated using ab initio quantum mechanical methods. Least squares regression techniques were used to create a model based on this data. The placement and number of fluorines in the molecule were found to affect the absorption in the IR window and were incorporated into the model. Several group increment models are discussed. An additive model based on one-carbon groups is found to work satisfactorily in predicting the ab initio calculated vibrational intensities.

Ab initio treatment of ion-induced charge transfer dynamics of isolated 2-deoxy-D-ribose.

PubMed

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.

Local atomic and electronic structures in ferromagnetic topological insulator Cr-doped (BixSb1-x) 2Te3 studied by XAFS and ab initio calculations

NASA Astrophysics Data System (ADS)

Liu, Zhen; Wei, Xinyuan; Wang, Jiajia; Pan, Hong; Ji, Fuhao; Ye, Mao; Yang, Zhongqin; Qiao, Shan

2015-09-01

The local atomic and electronic structures around the dopants in Cr-doped (BixSb1 -x )2Te3 are studied by x-ray absorption fine structure (XAFS) measurements and first-principles calculations. Both Cr and Bi are confirmed substituting Sb sites (CrSb and BiSb). The six nearest Te atoms around Cr move towards Cr and shorten the Cr-Te bond lengths to 2.76 Å and 2.77 Å for x =0.1 and x =0.2 , respectively. Importantly, we reveal the hybridization between the Sb/Te p states and Cr d states by the presence of a pre-edge peak at Cr K -absorption edge, which is also supported by our ab initio calculations. These findings provide important clues to understand the mechanism of ferromagnetic order in this system with quantum anomalous Hall effect.

An ab initio molecular dynamics and density functional theory study of the formation of phosphate chains from metathiophosphates.

PubMed

Mosey, Nicholas J; Woo, Tom K

2006-09-04

The reactions that occur between metathiophosphate (MTP) molecules are identified and examined through ab initio molecular dynamics simulations and static quantum chemical calculations at the density functional level of theory. The simulations show that certain types of MTPs can react to yield phosphate chains, while others only dimerize. These differences are rationalized in terms of reaction energies and the electronic structures of these molecules. In the reaction leading to the formation of phosphate chains, the reactive center, a tri-coordinate phosphorus atom, is continually regenerated. A polymerization mechanism linking MTPs to phosphate chains is developed on the basis of these results. This information sheds light on the underlying processes that may be responsible for the formation of phosphates under high-temperature conditions and may prove useful in the development of protocols for the rational synthesis of complex phosphate structures.

The electromigration force in metallic bulk

NASA Astrophysics Data System (ADS)

Lodder, A.; Dekker, J. P.

1998-01-01

The voltage induced driving force on a migrating atom in a metallic system is discussed in the perspective of the Hellmann-Feynman force concept, local screening concepts and the linear-response approach. Since the force operator is well defined in quantum mechanics it appears to be only confusing to refer to the Hellmann-Feynman theorem in the context of electromigration. Local screening concepts are shown to be mainly of historical value. The physics involved is completely represented in ab initio local density treatments of dilute alloys and the implementation does not require additional precautions about screening, being typical for jellium treatments. The linear-response approach is shown to be a reliable guide in deciding about the two contributions to the driving force, the direct force and the wind force. Results are given for the wind valence for electromigration in a number of FCC and BCC metals, calculated using an ab initio KKR-Green's function description of a dilute alloy.

On the room-temperature phase diagram of high pressure hydrogen: an ab initio molecular dynamics perspective and a diffusion Monte Carlo study.

PubMed

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.

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.

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 coordinates from the Python interface, and to return the forces and energy that are used to integrate the equations of motion. Restrictions: This code only deals with distinguishable particles. It does not include fermonic or bosonic exchanges between equivalent nuclei, which can become important at very low temperatures. Running time: Depends dramatically on the nature of the simulation being performed. A few minutes for short tests with empirical force fields, up to several weeks for production calculations with ab initio forces. The examples provided with the code run in less than an hour.

Full-dimensional quantum calculations of vibrational levels of NH 4 + and isotopomers on an accurate ab initio potential energy surface

DOE PAGES

Hua -Gen Yu; Han, Huixian; Guo, Hua

2016-03-29

Vibrational energy levels of the ammonium cation (NH 4 +) and its deuterated isotopomers are calculated using a numerically exact kinetic energy operator on a recently developed nine-dimensional permutation invariant semiglobal potential energy surface fitted to a large number of high-level ab initio points. Like CH4, the vibrational levels of NH 4 + and ND 4 + exhibit a polyad structure, characterized by a collective quantum number P = 2(v 1 + v 3) + v 2 + v 4. As a result, the low-lying vibrational levels of all isotopomers are assigned and the agreement with available experimental data ismore » better than 1 cm –1.« less

Energetics of Single Substitutional Impurities in NiTi

NASA Technical Reports Server (NTRS)

Good, Brian S.; Noebe, Ronald

2003-01-01

Shape-memory alloys are of considerable current interest, with applications ranging from stents to Mars rover components. In this work, we present results on the energetics of single substitutional impurities in B2 NiTi. Specifically, energies of Pd, Pt, Zr and Hf impurities at both Ni and Ti sites are computed. All energies are computed using the CASTEP ab initio code, and, for comparison, using the quantum approximate energy method of Bozzolo, Ferrante and Smith. Atomistic relaxation in the vicinity of the impurities is investigated via quantum approximate Monte Carlo simulation, and in cases where the relaxation is found to be important, the resulting relaxations are applied to the ab initio calculations. We compare our results with available experimental work.

Quantum Monte Carlo Methods for First Principles Simulation of Liquid Water

ERIC Educational Resources Information Center

Gergely, John Robert

2009-01-01

Obtaining an accurate microscopic description of water structure and dynamics is of great interest to molecular biology researchers and in the physics and quantum chemistry simulation communities. This dissertation describes efforts to apply quantum Monte Carlo methods to this problem with the goal of making progress toward a fully "ab initio"…

A Model for Predicting Thermoelectric Properties of Bi2Te3

NASA Technical Reports Server (NTRS)

Lee, Seungwon; VonAllmen, Paul

2009-01-01

A parameterized orthogonal tight-binding mathematical model of the quantum electronic structure of the bismuth telluride molecule has been devised for use in conjunction with a semiclassical transport model in predicting the thermoelectric properties of doped bismuth telluride. This model is expected to be useful in designing and analyzing Bi2Te3 thermoelectric devices, including ones that contain such nano - structures as quantum wells and wires. In addition, the understanding gained in the use of this model can be expected to lead to the development of better models that could be useful for developing other thermoelectric materials and devices having enhanced thermoelectric properties. Bi2Te3 is one of the best bulk thermoelectric materials and is widely used in commercial thermoelectric devices. Most prior theoretical studies of the thermoelectric properties of Bi2Te3 have involved either continuum models or ab-initio models. Continuum models are computationally very efficient, but do not account for atomic-level effects. Ab-initio models are atomistic by definition, but do not scale well in that computation times increase excessively with increasing numbers of atoms. The present tight-binding model bridges the gap between the well-scalable but non-atomistic continuum models and the atomistic but poorly scalable ab-initio models: The present tight-binding model is atomistic, yet also computationally efficient because of the reduced (relative to an ab-initio model) number of basis orbitals and flexible parameterization of the Hamiltonian.

Unified ab initio approaches to nuclear structure and reactions

DOE PAGES

Navratil, Petr; Quaglioni, Sofia; Hupin, Guillaume; ...

2016-04-13

The description of nuclei starting from the constituent nucleons and the realistic interactions among them has been a long-standing goal in nuclear physics. In addition to the complex nature of the nuclear forces, with two-, three- and possibly higher many-nucleon components, one faces the quantum-mechanical many-nucleon problem governed by an interplay between bound and continuum states. In recent years, significant progress has been made in ab initio nuclear structure and reaction calculations based on input from QCD-employing Hamiltonians constructed within chiral effective field theory. After a brief overview of the field, we focus on ab initio many-body approaches—built upon the no-core shell model—that are capable of simultaneously describing both bound and scattering nuclear states, and present results for resonances in light nuclei, reactions important for astrophysics and fusion research. In particular, we review recent calculations of resonances in the 6He halo nucleus, of five- and six-nucleon scattering, and an investigation of the role of chiral three-nucleon interactions in the structure of 9Be. Further, we discuss applications to the 7Bemore » $${({\\rm{p}},\\gamma )}^{8}{\\rm{B}}$$ radiative capture. Lastly, we highlight our efforts to describe transfer reactions including the 3H$${({\\rm{d}},{\\rm{n}})}^{4}$$He fusion.« less

Thiol Versus Hydroxamate as Zinc Binding Group In HDAC Inhibition: An Ab Initio QM/MM Molecular Dynamics Study

PubMed Central

Gong, Wenjing; Wu, Ruibo; Zhang, Yingkai

2015-01-01

Zinc-dependent histone deacetylases (HDACs) play a critical role in transcriptional repression and gene silencing, and are among the most attractive targets for the development of new therapeutics against cancer and various other diseases. Two HDAC inhibitors have been approved by FDA as anti-cancer drugs: one is SAHA whose hydroxamate is directly bound to zinc, the other is FK228 whose active form may use thiol as the zinc binding group. In spite of extensive studies, it remains to be ambiguous regarding how thiol and hydroxamate are bound to the zinc active site of HDACs. In this work, our computational approaches center on Born-Oppenheimer ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics with umbrella sampling, which allow for modeling of the zinc active site with reasonable accuracy while properly including dynamics and effects of protein environment. Meanwhile, an improved short-long effective function (SLEF2) to describe non-bonded interactions between zinc and other atoms has been employed in initial MM equilibrations. Our ab initio QM/MM MD simulations have confirmed that hydroxamate is neutral when it is bound to HDAC8, and found that thiol is deprotonated when directly bound to zinc in the HDAC active site. By comparing thiol and hydroxamate, our results elucidated the differences in their binding environment in the HDAC active sites, and emphasized the importance of the linker design to achieve more specific binding towards class IIa HDACs. PMID:26452222

Thiol versus hydroxamate as zinc binding group in HDAC inhibition: An ab initio QM/MM molecular dynamics study.

PubMed

Gong, Wenjing; Wu, Ruibo; Zhang, Yingkai

2015-11-15

Zinc-dependent histone deacetylases (HDACs) play a critical role in transcriptional repression and gene silencing, and are among the most attractive targets for the development of new therapeutics against cancer and various other diseases. Two HDAC inhibitors have been approved by FDA as anti-cancer drugs: one is SAHA whose hydroxamate is directly bound to zinc, the other is FK228 whose active form may use thiol as the zinc binding group. In spite of extensive studies, it remains to be ambiguous regarding how thiol and hydroxamate are bound to the zinc active site of HDACs. In this work, our computational approaches center on Born-Oppenheimer ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics with umbrella sampling, which allow for modeling of the zinc active site with reasonable accuracy while properly including dynamics and effects of protein environment. Meanwhile, an improved short-long effective function (SLEF2) to describe non-bonded interactions between zinc and other atoms has been employed in initial MM equilibrations. Our ab initio QM/MM MD simulations have confirmed that hydroxamate is neutral when it is bound to HDAC8, and found that thiol is deprotonated when directly bound to zinc in the HDAC active site. By comparing thiol and hydroxamate, our results elucidated the differences in their binding environment in the HDAC active sites, and emphasized the importance of the linker design to achieve more specific binding toward class IIa HDACs. © 2015 Wiley Periodicals, Inc.

QMCPACK : an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids

DOE PAGES

Kim, Jeongnim; Baczewski, Andrew T.; Beaudet, Todd D.; ...

2018-04-19

QMCPACK is an open source quantum Monte Carlo package for ab-initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater-Jastrow type trial wave functions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performancemore » computing architectures, including multicore central processing unit (CPU) and graphical processing unit (GPU) systems. We detail the program’s capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://www.qmcpack.org.« less

QMCPACK : an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Jeongnim; Baczewski, Andrew T.; Beaudet, Todd D.

QMCPACK is an open source quantum Monte Carlo package for ab-initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater-Jastrow type trial wave functions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performancemore » computing architectures, including multicore central processing unit (CPU) and graphical processing unit (GPU) systems. We detail the program’s capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://www.qmcpack.org.« less

Determination of NMR chemical shifts for cholesterol crystals from first-principles

NASA Astrophysics Data System (ADS)

Kucukbenli, Emine; de Gironcoli, Stefano

2011-03-01

Solid State Nuclear Magnetic Resonance (NMR) is a powerful tool in crystallography when combined with theoretical predictions. So far, empirical calculations of spectra have been employed for an unambiguous identification. However, many complex systems are outside the scope of these methods. Our implementation of ultrasoft and projector augmented wave pseudopotentials within ab initio gauge including projector augmented plane wave (GIPAW) method in Quantum Espresso simulation package allows affordable calculations of NMR spectra for systems of thousands of electrons. We report here the first ab initio determination of NMR spectra for several crystal structures of cholesterol. Cholesterol crystals, the main component of human gallstones, are of interest to medical research as their structural properties can shed light on the pathologies of gallbladder. With our application we show that ab initio calculations can be employed to aid NMR crystallography.

Ab Initio Optimized Effective Potentials for Real Molecules in Optical Cavities: Photon Contributions to the Molecular Ground State

PubMed Central

2018-01-01

We introduce a simple scheme to efficiently compute photon exchange-correlation contributions due to the coupling to transversal photons as formulated in the newly developed quantum-electrodynamical density-functional theory (QEDFT).1−5 Our construction employs the optimized-effective potential (OEP) approach by means of the Sternheimer equation to avoid the explicit calculation of unoccupied states. We demonstrate the efficiency of the scheme by applying it to an exactly solvable GaAs quantum ring model system, a single azulene molecule, and chains of sodium dimers, all located in optical cavities and described in full real space. While the first example is a two-dimensional system and allows to benchmark the employed approximations, the latter two examples demonstrate that the correlated electron-photon interaction appreciably distorts the ground-state electronic structure of a real molecule. By using this scheme, we not only construct typical electronic observables, such as the electronic ground-state density, but also illustrate how photon observables, such as the photon number, and mixed electron-photon observables, for example, electron–photon correlation functions, become accessible in a density-functional theory (DFT) framework. This work constitutes the first three-dimensional ab initio calculation within the new QEDFT formalism and thus opens up a new computational route for the ab initio study of correlated electron–photon systems in quantum cavities. PMID:29594185

Endo-Fullerene and Doped Diamond Nanocrystallite Based Models of Qubits for Solid-State Quantum Computers

NASA Technical Reports Server (NTRS)

Park, Seongjun; Srivastava, Deepak; Cho, Kyeongjae; Biegel, Bryan (Technical Monitor)

2001-01-01

Models of encapsulated 1/2 nuclear spin H-1 and P-31 atoms in fullerene and diamond nanocrystallite, respectively, are proposed and examined with ab-initio local density functional method for possible applications as single quantum bits (qubits) in solid-state quantum computers. A H-1 atom encapsulated in a fully deuterated fullerene, C(sub 20)D(sub 20), forms the first model system and ab-initio calculation shows that H-1 atom is stable in atomic state at the center of the fullerene with a barrier of about 1 eV to escape. A P-31 atom positioned at the center of a diamond nanocrystallite is the second model system, and 3 1P atom is found to be stable at the substitutional site relative to interstitial sites by 15 eV, Vacancy formation energy is 6 eV in diamond so that substitutional P-31 atom will be stable against diffusion during the formation mechanisms within the nanocrystallite. The coupling between the nuclear spin and weakly bound (valance) donor electron coupling in both systems is found to be suitable for single qubit applications, where as the spatial distributions of (valance) donor electron wave functions are found to be preferentially spread along certain lattice directions facilitating two or more qubit applications. The feasibility of the fabrication pathways for both model solid-state qubit systems within practical quantum computers is discussed with in the context of our proposed solid-state qubits.

Ab Initio Simulation of Charge Transfer at the Semiconductor Quantum Dot/TiO 2 Interface in Quantum Dot-Sensitized Solar Cells

DOE PAGES

Xin, Xukai; Li, Bo; Jung, Jaehan; ...

2014-07-24

Quantum dot-sensitized solar cells (QDSSCs) have emerged as a promising solar architecture for next-generation solar cells. The QDSSCs exhibit a remarkably fast electron transfer from the quantum dot (QD) donor to the TiO 2 acceptor with size quantization properties of QDs that allows for the modulation of band energies to control photoresponse and photoconversion efficiency of solar cells. In order to understand the mechanisms that underpin this rapid charge transfer, the electronic properties of CdSe and PbSe QDs with different sizes on the TiO 2 substrate are simulated using a rigorous ab initio density functional method. Our method capitalizes onmore » localized orbital basis set, which is computationally less intensive. Quite intriguingly, a remarkable set of electron bridging states between QDs and TiO 2 occurring via the strong bonding between the conduction bands of QDs and TiO 2 is revealed. Such bridging states account for the fast adiabatic charge transfer from the QD donor to the TiO 2 acceptor, and may be a general feature for strongly coupled donor/acceptor systems. All the QDs/TiO 2 systems exhibit type II band alignments, with conduction band offsets that increase with the decrease in QD size. This facilitates the charge transfer from QDs donors to TiO 2 acceptors and explains the dependence of the increased charge transfer rate with the decreased QD size.« less

Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations.

PubMed

Zhu, Tong; Zhang, John Z H; He, Xiao

2014-09-14

In this work, protein side chain (1)H chemical shifts are used as probes to detect and correct side-chain packing errors in protein's NMR structures through structural refinement. By applying the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method for ab initio calculation of chemical shifts, incorrect side chain packing was detected in the NMR structures of the Pin1 WW domain. The NMR structure is then refined by using molecular dynamics simulation and the polarized protein-specific charge (PPC) model. The computationally refined structure of the Pin1 WW domain is in excellent agreement with the corresponding X-ray structure. In particular, the use of the PPC model yields a more accurate structure than that using the standard (nonpolarizable) force field. For comparison, some of the widely used empirical models for chemical shift calculations are unable to correctly describe the relationship between the particular proton chemical shift and protein structures. The AF-QM/MM method can be used as a powerful tool for protein NMR structure validation and structural flaw detection.

Transitioning NWChem to the Next Generation of Manycore Machines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bylaska, Eric J.; Apra, E; Kowalski, Karol

The NorthWest chemistry (NWChem) modeling software is a popular molecular chemistry simulation software that was designed from the start to work on massively parallel processing supercomputers [1-3]. It contains an umbrella of modules that today includes self-consistent eld (SCF), second order Møller-Plesset perturbation theory (MP2), coupled cluster (CC), multiconguration self-consistent eld (MCSCF), selected conguration interaction (CI), tensor contraction engine (TCE) many body methods, density functional theory (DFT), time-dependent density functional theory (TDDFT), real-time time-dependent density functional theory, pseudopotential plane-wave density functional theory (PSPW), band structure (BAND), ab initio molecular dynamics (AIMD), Car-Parrinello molecular dynamics (MD), classical MD, hybrid quantum mechanicsmore » molecular mechanics (QM/MM), hybrid ab initio molecular dynamics molecular mechanics (AIMD/MM), gauge independent atomic orbital nuclear magnetic resonance (GIAO NMR), conductor like screening solvation model (COSMO), conductor-like screening solvation model based on density (COSMO-SMD), and reference interaction site model (RISM) solvation models, free energy simulations, reaction path optimization, parallel in time, among other capabilities [4]. Moreover, new capabilities continue to be added with each new release.« less

Ab Initio Molecular Dynamics and Lattice Dynamics-Based Force Field for Modeling Hexagonal Boron Nitride in Mechanical and Interfacial Applications.

PubMed

Govind Rajan, Ananth; Strano, Michael S; Blankschtein, Daniel

2018-04-05

Hexagonal boron nitride (hBN) is an up-and-coming two-dimensional material, with applications in electronic devices, tribology, and separation membranes. Herein, we utilize density-functional-theory-based ab initio molecular dynamics (MD) simulations and lattice dynamics calculations to develop a classical force field (FF) for modeling hBN. The FF predicts the crystal structure, elastic constants, and phonon dispersion relation of hBN with good accuracy and exhibits remarkable agreement with the interlayer binding energy predicted by random phase approximation calculations. We demonstrate the importance of including Coulombic interactions but excluding 1-4 intrasheet interactions to obtain the correct phonon dispersion relation. We find that improper dihedrals do not modify the bulk mechanical properties and the extent of thermal vibrations in hBN, although they impact its flexural rigidity. Combining the FF with the accurate TIP4P/Ice water model yields excellent agreement with interaction energies predicted by quantum Monte Carlo calculations. Our FF should enable an accurate description of hBN interfaces in classical MD simulations.

N-H stretching modes of adenosine monomer in solution studied by ultrafast nonlinear infrared spectroscopy and ab initio calculations.

PubMed

Greve, Christian; Preketes, Nicholas K; Costard, Rene; Koeppe, Benjamin; Fidder, Henk; Nibbering, Erik T J; Temps, Friedrich; Mukamel, Shaul; Elsaesser, Thomas

2012-07-26

The N-H stretching vibrations of adenine, one of the building blocks of DNA, are studied by combining infrared absorption and nonlinear two-dimensional infrared spectroscopy with ab initio calculations. We determine diagonal and off-diagonal anharmonicities of N-H stretching vibrations in chemically modified adenosine monomer dissolved in chloroform. For the single-quantum excitation manifold, the normal mode picture with symmetric and asymmetric NH(2) stretching vibrations is fully appropriate. For the two-quantum excitation manifold, however, the interplay between intermode coupling and frequency shifts due to a large diagonal anharmonicity leads to a situation where strong mixing does not occur. We compare our findings with previously reported values obtained on overtone spectroscopy of coupled hydrogen stretching oscillators.

The Momentum Distribution of Liquid ⁴He

DOE PAGES

Prisk, T. R.; Bryan, M. S.; Sokol, P. E.; ...

2017-07-24

We report a high-resolution neutron Compton scattering study of liquid ⁴He under milli-Kelvin temperature control. To interpret the scattering data, we performed Quantum Monte Carlo calculations of the atomic momentum distribution and final state effects for the conditions of temperature and density considered in the experiment. There is excellent agreement between the observed scattering and ab initio calculations of its lineshape at all temperatures. We also used model fit functions to obtain from the scattering data empirical estimates of the average atomic kinetic energy and Bose condensate fraction. These quantities are also in excellent agreement with ab initio calculations. Wemore » conclude that contemporary Quantum Monte Carlo methods can furnish accurate predictions for the properties of Bose liquids, including the condensate fraction, close to the superfluid transition temperature.« less

The ab-initio density matrix renormalization group in practice.

PubMed

Olivares-Amaya, Roberto; Hu, Weifeng; Nakatani, Naoki; Sharma, Sandeep; Yang, Jun; Chan, Garnet Kin-Lic

2015-01-21

The ab-initio density matrix renormalization group (DMRG) is a tool that can be applied to a wide variety of interesting problems in quantum chemistry. Here, we examine the density matrix renormalization group from the vantage point of the quantum chemistry user. What kinds of problems is the DMRG well-suited to? What are the largest systems that can be treated at practical cost? What sort of accuracies can be obtained, and how do we reason about the computational difficulty in different molecules? By examining a diverse benchmark set of molecules: π-electron systems, benchmark main-group and transition metal dimers, and the Mn-oxo-salen and Fe-porphine organometallic compounds, we provide some answers to these questions, and show how the density matrix renormalization group is used in practice.

Giant photocurrent enhancement by transition metal doping in quantum dot sensitized solar cells

NASA Astrophysics Data System (ADS)

Rimal, Gaurab; Pimachev, Artem K.; Yost, Andrew J.; Poudyal, Uma; Maloney, Scott; Wang, Wenyong; Chien, TeYu; Dahnovsky, Yuri; Tang, Jinke

2016-09-01

A huge enhancement in the incident photon-to-current efficiency of PbS quantum dot (QD) sensitized solar cells by manganese doping is observed. In the presence of Mn dopants with relatively small concentration (4 at. %), the photoelectric current increases by an average of 300% (up to 700%). This effect cannot be explained by the light absorption mechanism because both the experimental and theoretical absorption spectra demonstrate several times decreases in the absorption coefficient. To explain such dramatic increase in the photocurrent we propose the electron tunneling mechanism from the LUMO of the QD excited state to the Zn2SnO4 (ZTO) semiconductor photoanode. This change is due to the presence of the Mn instead of Pb atom at the QD/ZTO interface. The ab initio calculations confirm this mechanism. This work proposes an alternative route for a significant improvement of the efficiency for quantum dot sensitized solar cells.

Exploring the High-Pressure Behavior of PETN: A Combined Quantum Mechanical and Experimental Study

DTIC Science & Technology

2006-11-01

calculations to explore the hypothesized compression-induced polymorphic phase transition [Gruzdkov 2004]. The initial crystal in these Figure 4...Scuseria, G.E., and Chabalowski, C.F. 2004: An ab Initio Study of Solid Nitromethane, HMX , RDX , and CL20: Successes and Failures of DFT. J. Phys. Chem... RDX , HMX , HNIW, and PETN Crystals. J. Phys. Chem. B, 103, 6783. Trotter, J., 1963: Bond lengths and angles in Pentaerythritol Tetranitrate. Acta

Exploring the Temperature Dependent Solid-State ALC Spectrum of the C6H6Mu• Radical with Ab-Initio Simulation Techniques

NASA Astrophysics Data System (ADS)

Sturniolo, S.; Liborio, L.; Pratt, F. L.; Cottrell, S. P.; Jochym, D. B.; Montanari, B.

The longitudinal field Avoided Level Crossing (ALC) muon spectrum of crystalline benzene is found to exhibit multiple complex features that strongly depend on temperature. In this work, a number of different computational techniques were used in conjunction to explain this behavior. An overall picture emerges in which the spectrum appears to be the result of an interplay of multiple dynamical effects, both classical and quantum mechanical.

Towards A Predictive First Principles Understanding Of Molecular Adsorption On Graphene

DTIC Science & Technology

2016-10-05

used and developed state-of-the-art quantum mechanical methods to make accurate predictions about the interaction strength and adsorption structure...density functional theory, ab initio methods 16.  SECURITY CLASSIFICATION OF: 17.  LIMITATION OF ABSTRACT SAR 18.  NUMBER OF PAGES   11   19a.  NAME OF...important physical properties for a whole class of systems with weak non-covalent interactions, for example those involving the binding between water

Structure of Low-Lying Excited States of Guanine in DNA and Solution: Combined Molecular Mechanics and High-Level Coupled Cluster Studies

DOE PAGES

Kowalski, Karol; Valiev, Marat

2007-01-01

High-level ab-initio equation-of-motion coupled-cluster methods with singles, doubles, and noniterative triples are used, in conjunction with the combined quantum mechanical molecular mechanics approach, to investigate the structure of low-lying excited states of the guanine base in DNA and solvated environments. Our results indicate that while the excitation energy of the first excited state is barely changed compared to its gas-phase counterpart, the excitation energy of the second excited state is blue-shifted by 0.24 eV.

Ab initio determination of mode coupling in HSSH - The torsional splitting in the first excited S-S stretching state

NASA Technical Reports Server (NTRS)

Herbst, Eric; Winnewisser, G.; Yamada, K. M. T.; Defrees, D. J.; Mclean, A. D.

1989-01-01

A mechanism for the enhanced splitting detected in the millimeter-wave rotational spectra of the first excited S-S stretching state of HSSH (disulfane) has been studied. The mechanism, which involves a potential coupling between the first excited S-S stretching state and excited torsional states, has been investigated in part by the use of ab initio theory. Based on an ab initio potential surface, coupling matrix elements have been calculated, and the amount of splitting has then been estimated by second-order perturbation theory. The result, while not in quantitative agreement with the measured splitting, lends plausibility to the assumed mechanism.

Atomic defects in monolayer WSe2 tunneling FETs studied by systematic ab initio calculations

NASA Astrophysics Data System (ADS)

Wu, Jixuan; Fan, Zhiqiang; Chen, Jiezhi; Jiang, Xiangwei

2018-05-01

Atomic defects in monolayer WSe2 tunneling FETs (TFETs) are studied through systematic ab initio calculations aiming at performance predictions and enhancements. The effects of various defect positions and different passivation atoms are characterized in WSe2 TFETs by rigorous ab initio quantum transport simulations. It is suggested that the Se vacancy (VSe) defect located in the gate-controlled channel region tends to increase the OFF current (I off), whereas it can be well suppressed by oxygen passivation. It is demonstrated that chlorine (Cl) passivation at the source-side tunneling region can largely suppress I off, leading to an impressively improved on–off ratio (I on/I off) compared with that without any defect. However, it is also observed that randomly positioned atomic defects tend to induce significant fluctuation of the TFET output. Further discussions are made with focus on the performance-variability trade-off for robust circuit design.

Poster 2:Ab initio calculations of low temperature hydrocarbon spectra for astrophysics: application to the modeling of methane absorption in the Titan atmosphere in a wide IR range

NASA Astrophysics Data System (ADS)

Rey, Michael; Nikitin, Andrei; Bezard, Bruno; Rannou, Pascal; Coustenis, Athena; Tyuterev, Vladimir

2016-06-01

Knowledge of intensities of spectral transitions in various temperature ranges including very low-T conditions is essential for the modeling of optical properties of planetary atmospheres and for other astrophysical applications. The temperature dependence of spectral features is crucial, but quantified experimental information in a wide spectral range is generally missing. A significant progress has been recently achieved in first principles quantum mechanical predictions (ab initio electronic structure + variational nuclear motion calculations) of rotationally resolved spectra for hydrocarbon molecules such as methane , ethylene and their isotopic species [1,2] . We have recently reported the TheoReTS information system (theorets.univ-reims.fr, theorets.tsu.ru) for theoretical spectra based on variational predictions from molecular potential energy and dipole moment surfaces [3] that permits online simulation of radiative properties including low-T conditions of cold planets. In this work, we apply ab initio predictions of the spectra of methane isotopologues down to T=80 K for the modeling of the transmittance in the atmosphere of Titan, Saturn's largest satellite explored by the Cassini-Huygens space mission. A very good agreement over the whole infrared range from 6,000 to 11,000 cm-1 compared with observations obtained by the Descent Imager / Spectral Radiometer (DISR) on the Huygens probe [4,5] at various altitudes will be reported.

Machine learning of accurate energy-conserving molecular force fields.

PubMed

Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel E; Poltavsky, Igor; Schütt, Kristof T; Müller, Klaus-Robert

2017-05-01

Using conservation of energy-a fundamental property of closed classical and quantum mechanical systems-we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio molecular dynamics (AIMD) trajectories. The GDML implementation is able to reproduce global potential energy surfaces of intermediate-sized molecules with an accuracy of 0.3 kcal mol -1 for energies and 1 kcal mol -1 Å̊ -1 for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative molecular dynamics simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods.

Electronic structure, dielectric response, and surface charge distribution of RGD (1FUV) peptide.

PubMed

Adhikari, Puja; Wen, Amy M; French, Roger H; Parsegian, V Adrian; Steinmetz, Nicole F; Podgornik, Rudolf; Ching, Wai-Yim

2014-07-08

Long and short range molecular interactions govern molecular recognition and self-assembly of biological macromolecules. Microscopic parameters in the theories of these molecular interactions are either phenomenological or need to be calculated within a microscopic theory. We report a unified methodology for the ab initio quantum mechanical (QM) calculation that yields all the microscopic parameters, namely the partial charges as well as the frequency-dependent dielectric response function, that can then be taken as input for macroscopic theories of electrostatic, polar, and van der Waals-London dispersion intermolecular forces. We apply this methodology to obtain the electronic structure of the cyclic tripeptide RGD-4C (1FUV). This ab initio unified methodology yields the relevant parameters entering the long range interactions of biological macromolecules, providing accurate data for the partial charge distribution and the frequency-dependent dielectric response function of this peptide. These microscopic parameters determine the range and strength of the intricate intermolecular interactions between potential docking sites of the RGD-4C ligand and its integrin receptor.

Ab initio modeling of CW-ESR spectra of the double spin labeled peptide Fmoc-(Aib-Aib-TOAC)2-Aib-OMe in acetonitrile.

PubMed

Zerbetto, Mirco; Carlotto, Silvia; Polimeno, Antonino; Corvaja, Carlo; Franco, Lorenzo; Toniolo, Claudio; Formaggio, Fernando; Barone, Vincenzo; Cimino, Paola

2007-03-15

In this work we address the interpretation, via an ab initio integrated computational approach, of the CW-ESR spectra of the double spin labeled, 310-helical, peptide Fmoc-(Aib-Aib-TOAC)2-Aib-OMe dissolved in acetonitrile. Our approach is based on the determination of geometric and local magnetic parameters of the heptapeptide by quantum mechanical density functional calculations taking into account solvent and, when needed, vibrational averaging contributions. The system is then described by a stochastic Liouville equation for the two electron spins interacting with each other and with two 14N nuclear spins, in the presence of diffusive rotational dynamics. Parametrization of the diffusion rotational tensor is provided by a hydrodynamic model. CW-ESR spectra are simulated with minimal resorting to fitting procedures, proving that the combination of sensitive ESR spectroscopy and sophisticated modeling can be highly helpful in providing 3D structural and dynamic information on molecular systems.

Machine learning of accurate energy-conserving molecular force fields

PubMed Central

Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel E.; Poltavsky, Igor; Schütt, Kristof T.; Müller, Klaus-Robert

2017-01-01

Using conservation of energy—a fundamental property of closed classical and quantum mechanical systems—we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio molecular dynamics (AIMD) trajectories. The GDML implementation is able to reproduce global potential energy surfaces of intermediate-sized molecules with an accuracy of 0.3 kcal mol−1 for energies and 1 kcal mol−1 Å̊−1 for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative molecular dynamics simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods. PMID:28508076

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ma, Xiaoyao; Hall, Randall W.; Löffler, Frank

The Sign Learning Kink (SiLK) based Quantum Monte Carlo (QMC) method is used to calculate the ab initio ground state energies for multiple geometries of the H2O, N2, and F2 molecules. The method is based on Feynman’s path integral formulation of quantum mechanics and has two stages. The first stage is called the learning stage and reduces the well-known QMC minus sign problem by optimizing the linear combinations of Slater determinants which are used in the second stage, a conventional QMC simulation. The method is tested using different vector spaces and compared to the results of other quantum chemical methodsmore » and to exact diagonalization. Our findings demonstrate that the SiLK method is accurate and reduces or eliminates the minus sign problem.« less

The HCO+-H2 van der Waals interaction: Potential energy and scattering

NASA Astrophysics Data System (ADS)

Massó, H.; Wiesenfeld, L.

2014-11-01

We compute the rigid-body, four-dimensional interaction potential between HCO+ and H2. The ab initio energies are obtained at the coupled-cluster single double triple level of theory, corrected for Basis Set Superposition Errors. The ab initio points are fit onto the spherical basis relevant for quantum scattering. We present elastic and rotationally inelastic coupled channels scattering between low lying rotational levels of HCO+ and para-/ortho-H2. Results are compared with similar earlier computations with He or isotropic para-H2 as the projectile. Computations agree with earlier pressure broadening measurements.

The HCO⁺-H₂ van der Waals interaction: potential energy and scattering.

PubMed

Massó, H; Wiesenfeld, L

2014-11-14

We compute the rigid-body, four-dimensional interaction potential between HCO(+) and H2. The ab initio energies are obtained at the coupled-cluster single double triple level of theory, corrected for Basis Set Superposition Errors. The ab initio points are fit onto the spherical basis relevant for quantum scattering. We present elastic and rotationally inelastic coupled channels scattering between low lying rotational levels of HCO(+) and para-/ortho-H2. Results are compared with similar earlier computations with He or isotropic para-H2 as the projectile. Computations agree with earlier pressure broadening measurements.

Electron capture in collisions of N^+ with H and H^+ with N

NASA Astrophysics Data System (ADS)

Lin, C. Y.; Stancil, P. C.; Gu, J. P.; Buenker, R. J.; Kimura, M.

2004-05-01

Charge transfer processes due to collisions of N^+ with atomic hydrogen and H^+ with atomic nitrogen are investigated using the quantum-mechanical molecular-orbital close-coupling (MOCC) method. The MOCC calculations utilize ab initio adiabatic potential curves and nonadiabatic radial and rotational coupling matrix elements obtained with the multireference single- and double-excitation configuration interaction approach. Total and state-selective cross sections for the energy range 0.1-500 eV/u will be presented and compared with existing experimental and theoretical data.

Finding Effective Models in Transition Metals using Quantum Monte Carlo

NASA Astrophysics Data System (ADS)

Williams, Kiel; Wagner, Lucas K.

There is a gap between high-accuracy ab-initio calculations, like those produced from Quantum Monte Carlo (QMC), and effective lattice models such as the Hubbard model. We have developed a method that combines data produced from QMC with fitting techniques taken from data science, allowing us to determine which degrees of freedom are required to connect ab-initio and model calculations. We test this approach for transition metal atoms, where spectroscopic reference data exists. We report on the accuracy of several derived effective models that include different degrees of freedom, and comment on the quality of the parameter values we obtain from our fitting procedure. We gratefully acknowledge funding from the National Science Foundation Graduate Research Fellowship Program under Grant Number DGE-1144245 (K.T.W.) and from SciDAC Grant DE-FG02-12ER46875 (L.K.W.).

Ab initio quantum chemical calculation of electron transfer matrix elements for large molecules

NASA Astrophysics Data System (ADS)

Zhang, Linda Yu; Friesner, Richard A.; Murphy, Robert B.

1997-07-01

Using a diabatic state formalism and pseudospectral numerical methods, we have developed an efficient ab initio quantum chemical approach to the calculation of electron transfer matrix elements for large molecules. The theory is developed at the Hartree-Fock level and validated by comparison with results in the literature for small systems. As an example of the power of the method, we calculate the electronic coupling between two bacteriochlorophyll molecules in various intermolecular geometries. Only a single self-consistent field (SCF) calculation on each of the monomers is needed to generate coupling matrix elements for all of the molecular pairs. The largest calculations performed, utilizing 1778 basis functions, required ˜14 h on an IBM 390 workstation. This is considerably less cpu time than would be necessitated with a supermolecule adiabatic state calculation and a conventional electronic structure code.

Quantum calculations of the rate constant for the O(3P)+HCl reaction on new ab initio 3A″ and 3A' surfaces

NASA Astrophysics Data System (ADS)

Xie, Tiao; Bowman, Joel M.; Peterson, K. A.; Ramachandran, B.

2003-11-01

We report the thermal rate constant of the O(3P)+HCl→OH+Cl reaction calculated from 200 to 3200 K, using new fits to extensive ab initio calculations [B. Ramachandran and K. A. Peterson, J. Chem. Phys. 119, 9590 (2003), preceding paper]. The rate constants are obtained for both the 3A″ and 3A' surfaces using exact quantum reactive scattering calculations for selected values of the total angular momentum and the J-shifting approximation for both the 3A″ and 3A' surfaces. The results are compared with the ICVT/μOMT rate constants calculated by the POLYRATE program and all available experimental data. Other related high-energy reaction channels are also studied qualitatively for their contribution to the total thermal rate constant at high temperature.

Compactness Aromaticity of Atoms in Molecules

PubMed Central

Putz, Mihai V.

2010-01-01

A new aromaticity definition is advanced as the compactness formulation through the ratio between atoms-in-molecule and orbital molecular facets of the same chemical reactivity property around the pre- and post-bonding stabilization limit, respectively. Geometrical reactivity index of polarizability was assumed as providing the benchmark aromaticity scale, since due to its observable character; with this occasion new Hydrogenic polarizability quantum formula that recovers the exact value of 4.5 a03 for Hydrogen is provided, where a0 is the Bohr radius; a polarizability based–aromaticity scale enables the introduction of five referential aromatic rules (Aroma 1 to 5 Rules). With the help of these aromatic rules, the aromaticity scales based on energetic reactivity indices of electronegativity and chemical hardness were computed and analyzed within the major semi-empirical and ab initio quantum chemical methods. Results show that chemical hardness based-aromaticity is in better agreement with polarizability based-aromaticity than the electronegativity-based aromaticity scale, while the most favorable computational environment appears to be the quantum semi-empirical for the first and quantum ab initio for the last of them, respectively. PMID:20480020

Energetics and solvation structure of a dihalogen dopant (I2) in (4)He clusters.

PubMed

Pérez de Tudela, Ricardo; Barragán, Patricia; Valdés, Álvaro; Prosmiti, Rita

2014-08-21

The energetics and structure of small HeNI2 clusters are analyzed as the size of the system changes, with N up to 38. The full interaction between the I2 molecule and the He atoms is based on analytical ab initio He-I2 potentials plus the He-He interaction, obtained from first-principle calculations. The most stable structures, as a function of the number of solvent He atoms, are obtained by employing an evolutionary algorithm and compared with CCSD(T) and MP2 ab initio computations. Further, the classical description is completed by explicitly including thermal corrections and quantum features, such as zero-point-energy values and spatial delocalization. From quantum PIMC calculations, the binding energies and radial/angular probability density distributions of the thermal equilibrium state for selected-size clusters are computed at a low temperature. The sequential formation of regular shell structures is analyzed and discussed for both classical and quantum treatments.

Vibrational Properties of Hydrogen-Bonded Systems Using the Multireference Generalization to the "On-the-Fly" Electronic Structure within Quantum Wavepacket ab Initio Molecular Dynamics (QWAIMD).

PubMed

Li, Junjie; Li, Xiaohu; Iyengar, Srinivasan S

2014-06-10

We discuss a multiconfigurational treatment of the "on-the-fly" electronic structure within the quantum wavepacket ab initio molecular dynamics (QWAIMD) method for coupled treatment of quantum nuclear effects with electronic structural effects. Here, multiple single-particle electronic density matrices are simultaneously propagated with a quantum nuclear wavepacket and other classical nuclear degrees of freedom. The multiple density matrices are coupled through a nonorthogonal configuration interaction (NOCI) procedure to construct the instantaneous potential surface. An adaptive-mesh-guided set of basis functions composed of Gaussian primitives are used to simplify the electronic structure calculations. Specifically, with the replacement of the atom-centered basis functions positioned on the centers of the quantum-mechanically treated nuclei by a mesh-guided band of basis functions, the two-electron integrals used to compute the electronic structure potential surface become independent of the quantum nuclear variable and hence reusable along the entire Cartesian grid representing the quantum nuclear coordinates. This reduces the computational complexity involved in obtaining a potential surface and facilitates the interpretation of the individual density matrices as representative diabatic states. The parametric nuclear position dependence of the diabatic states is evaluated at the initial time-step using a Shannon-entropy-based sampling function that depends on an approximation to the quantum nuclear wavepacket and the potential surface. This development is meant as a precursor to an on-the-fly fully multireference electronic structure procedure embedded, on-the-fly, within a quantum nuclear dynamics formalism. We benchmark the current development by computing structural, dynamic, and spectroscopic features for a series of bihalide hydrogen-bonded systems: FHF(-), ClHCl(-), BrHBr(-), and BrHCl(-). We find that the donor-acceptor structural features are in good agreement with experiments. Spectroscopic features are computed using a unified velocity/flux autocorrelation function and include vibrational fundamentals and combination bands. These agree well with experiments and other theories.

Ab initio relaxation times and time-dependent Hamiltonians within the steepest-entropy-ascent quantum thermodynamic framework

NASA Astrophysics Data System (ADS)

Kim, Ilki; von Spakovsky, Michael R.

2017-08-01

Quantum systems driven by time-dependent Hamiltonians are considered here within the framework of steepest-entropy-ascent quantum thermodynamics (SEAQT) and used to study the thermodynamic characteristics of such systems. In doing so, a generalization of the SEAQT framework valid for all such systems is provided, leading to the development of an ab initio physically relevant expression for the intrarelaxation time, an important element of this framework and one that had as of yet not been uniquely determined as an integral part of the theory. The resulting expression for the relaxation time is valid as well for time-independent Hamiltonians as a special case and makes the description provided by the SEAQT framework more robust at the fundamental level. In addition, the SEAQT framework is used to help resolve a fundamental issue of thermodynamics in the quantum domain, namely, that concerning the unique definition of process-dependent work and heat functions. The developments presented lead to the conclusion that this framework is not just an alternative approach to thermodynamics in the quantum domain but instead one that uniquely sheds new light on various fundamental but as of yet not completely resolved questions of thermodynamics.

An ab-initio study of mechanical, dynamical and electronic properties of MgEu intermetallic

NASA Astrophysics Data System (ADS)

Kumar, S. Ramesh; Jaiganesh, G.; Jayalakshmi, V.

2018-04-01

The theoretical investigation on the mechanical, dynamical and electronic properties of MgEu in CsCl-type structure has been carried out through the ab-initio calculations within the framework of the density functional theory and the density functional perturbation theory. For the purpose, Vienna Ab initio Simulation Package and Phonopy packages were used. Our calculated ground-state properties of MgEu are in good agreement with other available results. Our computed elastic constants and phonon spectrum results suggest that MgEu is mechanically and dynamically stable up to 5 GPa. The thermodynamic quantities as a function of temperatures are also reported and discussed. The band structure, density of states and charge density also calculated to understand the electronic properties of MgEu.

An ab initio molecular orbital study of the mechanism for the gas-phase water-mediated decomposition and the formation of hydrates of peroxyacetyl nitrate (PAN).

PubMed

Li, Yumin; Francisco, Joseph S

2005-08-31

There is uncertainty in the mechanism for the hydrolysis of peroxyacetyl nitrate (PAN), and experimental attempts to detect products of the direct reaction have been unsuccessful. Ab initio calculations are used to examine the energetics of water-mediated decomposition of gas-phase PAN into acetic acid and peroxynitric acid. On the basis of ab initio calculations, an alternative reaction mechanism for the decomposition of PAN is proposed. The calculations indicate that the barrier for one water addition to PAN is large. However, including additional water molecules reveals a substantially lower energy route. The calculations suggest that the formation of PAN hydrate complexes are energetically favorable and stable. Additional waters are increasingly efficient at stabilizing hydrated PAN.

WatAA: Atlas of Protein Hydration. Exploring synergies between data mining and ab initio calculations.

PubMed

Černý, Jiří; Schneider, Bohdan; Biedermannová, Lada

2017-07-14

Water molecules represent an integral part of proteins and a key determinant of protein structure, dynamics and function. WatAA is a newly developed, web-based atlas of amino-acid hydration in proteins. The atlas provides information about the ordered first hydration shell of the most populated amino-acid conformers in proteins. The data presented in the atlas are drawn from two sources: experimental data and ab initio quantum-mechanics calculations. The experimental part is based on a data-mining study of a large set of high-resolution protein crystal structures. The crystal-derived data include 3D maps of water distribution around amino-acids and probability of occurrence of each of the identified hydration sites. The quantum mechanics calculations validate and extend this primary description by optimizing the water position for each hydration site, by providing hydrogen atom positions and by quantifying the interaction energy that stabilizes the water molecule at the particular hydration site position. The calculations show that the majority of experimentally derived hydration sites are positioned near local energy minima for water, and the calculated interaction energies help to assess the preference of water for the individual hydration sites. We propose that the atlas can be used to validate water placement in electron density maps in crystallographic refinement, to locate water molecules mediating protein-ligand interactions in drug design, and to prepare and evaluate molecular dynamics simulations. WatAA: Atlas of Protein Hydration is freely available without login at .

On the use of symmetry in the ab initio quantum mechanical simulation of nanotubes and related materials.

PubMed

Noel, Yves; D'arco, Philippe; Demichelis, Raffaella; Zicovich-Wilson, Claudio M; Dovesi, Roberto

2010-03-01

Nanotubes can be characterized by a very high point symmetry, comparable or even larger than the one of the most symmetric crystalline systems (cubic, 48 point symmetry operators). For example, N = 2n rototranslation symmetry operators connect the atoms of the (n,0) nanotubes. This symmetry is fully exploited in the CRYSTAL code. As a result, ab initio quantum mechanical large basis set calculations of carbon nanotubes containing more than 150 atoms in the unit cell become very cheap, because the irreducible part of the unit cell reduces to two atoms only. The nanotube symmetry is exploited at three levels in the present implementation. First, for the automatic generation of the nanotube structure (and then of the input file for the SCF calculation) starting from a two-dimensional structure (in the specific case, graphene). Second, the nanotube symmetry is used for the calculation of the mono- and bi-electronic integrals that enter into the Fock (Kohn-Sham) matrix definition. Only the irreducible wedge of the Fock matrix is computed, with a saving factor close to N. Finally, the symmetry is exploited for the diagonalization, where each irreducible representation is separately treated. When M atomic orbitals per carbon atom are used, the diagonalization computing time is close to Nt, where t is the time required for the diagonalization of each 2M x 2M matrix. The efficiency and accuracy of the computational scheme is documented. (c) 2009 Wiley Periodicals, Inc.

Introduction to dissociative recombination

NASA Technical Reports Server (NTRS)

Guberman, Steven L.; Mitchell, J. Brian A.

1989-01-01

Dissociative recombination (DR) of molecular ions with electrons has important consequences in many areas of physical science. Ab-initio calculations coupled with resonant scattering theory and multichannel quantum defect studies have produced detailed results illuminating the role of ion vibrational excitation, the quantum yields of the DR products, and the role of Rydberg states. The theoretical and experimental results are discussed.

Structure reconstruction of TiO2-based multi-wall nanotubes: first-principles calculations.

PubMed

Bandura, A V; Evarestov, R A; Lukyanov, S I

2014-07-28

A new method of theoretical modelling of polyhedral single-walled nanotubes based on the consolidation of walls in the rolled-up multi-walled nanotubes is proposed. Molecular mechanics and ab initio quantum mechanics methods are applied to investigate the merging of walls in nanotubes constructed from the different phases of titania. The combination of two methods allows us to simulate the structures which are difficult to find only by ab initio calculations. For nanotube folding we have used (1) the 3-plane fluorite TiO2 layer; (2) the anatase (101) 6-plane layer; (3) the rutile (110) 6-plane layer; and (4) the 6-plane layer with lepidocrocite morphology. The symmetry of the resulting single-walled nanotubes is significantly lower than the symmetry of initial coaxial cylindrical double- or triple-walled nanotubes. These merged nanotubes acquire higher stability in comparison with the initial multi-walled nanotubes. The wall thickness of the merged nanotubes exceeds 1 nm and approaches the corresponding parameter of the experimental patterns. The present investigation demonstrates that the merged nanotubes can integrate the two different crystalline phases in one and the same wall structure.

Photodissociation of phenol via nonadiabatic tunneling: Comparison of two ab initio based potential energy surfaces

NASA Astrophysics Data System (ADS)

Xie, Changjian; Guo, Hua

2017-09-01

The nonadiabatic tunneling-facilitated photodissociation of phenol is investigated using a reduced-dimensional quantum model on two ab initio-based coupled potential energy surfaces (PESs). Although dynamics occurs largely on the lower adiabat, the proximity to a conical intersection between the S1 and S2 states requires the inclusion of both the geometric phase (GP) and diagonal Born-Oppenheimer correction (DBOC). The lifetime of the lowest-lying vibronic state is computed using the diabatic and various adiabatic models. The GP and DBOC terms are found to be essential on one set of PESs, but have a small impact on the other.

Wigner-Eisenbud-Smith photoionization time delay due to autoioinization resonances

NASA Astrophysics Data System (ADS)

Deshmukh, P. C.; Kumar, A.; Varma, H. R.; Banerjee, S.; Manson, Steven T.; Dolmatov, V. K.; Kheifets, A. S.

2018-03-01

An empirical ansatz for the complex photoionization amplitude and Wigner-Eisenbud-Smith time delay in the vicinity of a Fano autoionization resonance are proposed to evaluate and interpret the time delay in the resonant region. The utility of this expression is evaluated in comparison with accurate numerical calculations employing the ab initio relativistic random phase approximation and relativistic multichannel quantum defect theory. The indisputably good qualitative agreement (and semiquantitative agreement) between corresponding results of the proposed model and results produced by the ab initio theories proves the usability of the model. In addition, the phenomenology of the time delay in the vicinity of multichannel autoionizing resonances is detailed.

Towards an ab-initio treatment of nonlocal electronic correlations with dynamical vertex approximation

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.

Vibrational inelastic and charge transfer processes in H++H2 system: An ab initio study

NASA Astrophysics Data System (ADS)

Amaran, Saieswari; Kumar, Sanjay

2007-12-01

State-resolved differential cross sections, total and integral cross sections, average vibrational energy transfer, and the relative probabilities are computed for the H++H2 system using the newly obtained ab initio potential energy surfaces at the full CI/cc-pVQZ level of accuracy which allow for both the direct vibrational inelastic and the charge transfer processes. The quantum dynamics is treated within the vibrational close-coupling infinite-order-sudden approximation approach using the two ab initio quasidiabatic potential energy surfaces. The computed collision attributes for both the processes are compared with the available state-to-state scattering experiments at Ec.m.=20eV. The results are in overall good agreement with most of the observed scattering features such as rainbow positions, integral cross sections, and relative vibrational energy transfers. A comparison with the earlier theoretical study carried out on the semiempirical surfaces (diatomics in molecules) is also made to illustrate the reliability of the potential energy surfaces used in the present work.

Quantum mechanical force field for hydrogen fluoride with explicit electronic polarization.

PubMed

Mazack, Michael J M; Gao, Jiali

2014-05-28

The explicit polarization (X-Pol) theory is a fragment-based quantum chemical method that explicitly models the internal electronic polarization and intermolecular interactions of a chemical system. X-Pol theory provides a framework to construct a quantum mechanical force field, which we have extended to liquid hydrogen fluoride (HF) in this work. The parameterization, called XPHF, is built upon the same formalism introduced for the XP3P model of liquid water, which is based on the polarized molecular orbital (PMO) semiempirical quantum chemistry method and the dipole-preserving polarization consistent point charge model. We introduce a fluorine parameter set for PMO, and find good agreement for various gas-phase results of small HF clusters compared to experiments and ab initio calculations at the M06-2X/MG3S level of theory. In addition, the XPHF model shows reasonable agreement with experiments for a variety of structural and thermodynamic properties in the liquid state, including radial distribution functions, interaction energies, diffusion coefficients, and densities at various state points.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ma, Xiaoyao; Hall, Randall W.; Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803

The Sign Learning Kink (SiLK) based Quantum Monte Carlo (QMC) method is used to calculate the ab initio ground state energies for multiple geometries of the H{sub 2}O, N{sub 2}, and F{sub 2} molecules. The method is based on Feynman’s path integral formulation of quantum mechanics and has two stages. The first stage is called the learning stage and reduces the well-known QMC minus sign problem by optimizing the linear combinations of Slater determinants which are used in the second stage, a conventional QMC simulation. The method is tested using different vector spaces and compared to the results of othermore » quantum chemical methods and to exact diagonalization. Our findings demonstrate that the SiLK method is accurate and reduces or eliminates the minus sign problem.« less

Atomic-scale investigation of nuclear quantum effects of surface water: Experiments and theory

NASA Astrophysics Data System (ADS)

Guo, Jing; Li, Xin-Zheng; Peng, Jinbo; Wang, En-Ge; Jiang, Ying

2017-12-01

Quantum behaviors of protons in terms of tunneling and zero-point motion have significant effects on the macroscopic properties, structure, and dynamics of water even at room temperature or higher. In spite of tremendous theoretical and experimental efforts, accurate and quantitative description of the nuclear quantum effects (NQEs) is still challenging. The main difficulty lies in that the NQEs are extremely susceptible to the structural inhomogeneity and local environments, especially when interfacial systems are concerned. In this review article, we will highlight the recent advances of scanning tunneling microscopy and spectroscopy (STM/S), which allows the access to the quantum degree of freedom of protons both in real and energy space. In addition, we will also introduce recent development of ab initio path-integral molecular dynamics (PIMD) simulations at surfaces/interfaces, in which both the electrons and nuclei are treated as quantum particles in contrast to traditional ab initio molecular dynamics (MD). Then we will discuss how the combination of STM/S and PIMD are used to directly visualize the concerted quantum tunneling of protons within the water clusters and quantify the impact of zero-point motion on the strength of a single hydrogen bond (H bond) at a water/solid interface. Those results may open up the new possibility of exploring the exotic quantum states of light nuclei at surfaces, as well as the quantum coupling between the electrons and nuclei.

Car and Parrinello meet Green and Kubo: simulating atomic heat transport from equilibrium ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Baroni, Stefano

Modern simulation methods based on electronic-structure theory have long been deemed unfit to compute heat transport coefficients within the Green-Kubo formalism. This is so because the quantum-mechanical energy density from which the heat flux is derived is inherently ill defined, thus allegedly hampering the use of the Green-Kubo formula. While this objection would actually apply to classical systems as well, I will demonstrate that the thermal conductivity is indeed independent of the specific microscopic expression for the energy density and current from which it is derived. This fact results from a kind of gauge invariance stemming from energy conservation and extensivity, which I will illustrate numerically for a classical Lennard-Jones fluid. I will then introduce an expression for the adiabatic energy flux, derived within density-functional theory, that allows simulating atomic heat transport using equilibrium ab initio molecular dynamics. The resulting methodology is demonstrated by comparing results from ab-initio and classical molecular-dynamics simulations of a model liquid-Argon system, for which accurate inter-atomic potentials are derived by the force-matching method, and applied to compute the thermal conductivity of heavy water at ambient conditions. The problem of evaluating transport coefficients along with their accuracy from relatively short trajectories is finally addressed and discussed with a few representative examples. Partially funded by the European Union through the MaX Centre of Excellence (Grant No. 676598).

A high level Ab initio study of the anionic hydrogen-bonded complexes FH-CN-, FH-NC-, H2O-CN- and H2O-NC-

NASA Technical Reports Server (NTRS)

Lee, Timothy J.

1989-01-01

HF, H2O, CN- and their hydrogen-bonded complexes were studied using state-of-the-art ab initio quantum mechanical methods. A large Gaussian one particle basis set consisting of triple zeta plus double polarization plus diffuse s and p functions (TZ2P + diffuse) was used. The theoretical methods employed include self consistent field, second order Moller-Plesset perturbation theory, singles and doubles configuration interaction theory and the singles and doubles coupled cluster approach. The FH-CN- and FH-NC- and H2O-CN-, H2O-NC- pairs of complexes are found to be essentially isoenergetic. The first pair of complexes are predicted to be bound by approx. 24 kcal/mole and the latter pair bound by approximately 15 kcal/mole. The ab initio binding energies are in good agreement with the experimental values. The two being shorter than the analogous C-N hydrogen bond. The infrared (IR) spectra of the two pairs of complexes are also very similar, though a severe perturbation of the potential energy surface by proton exchange means that the accurate prediction of the band center of the most intense IR mode requires a high level of electronic structure theory as well as a complete treatment of anharmonic effects. The bonding of anionic hydrogen-bonded complexes is discussed and contrasted with that of neutral hydrogen-bonded complexes.

Second Harmonic Generation Mediated by Aligned Water in Starch Granules.

PubMed

Cisek, Richard; Tokarz, Danielle; Krouglov, Serguei; Steup, Martin; Emes, Michael J; Tetlow, Ian J; Barzda, Virginijus

2014-12-26

The origin of second harmonic generation (SHG) in starch granules was investigated using ab initio quantum mechanical modeling and experimentally examined using polarization-in, polarization-out (PIPO) second harmonic generation microscopy. Ab initio calculations revealed that the largest contribution to the SHG signal from A- and B-type allomorphs of starch originates from the anisotropic organization of hydroxide and hydrogen bonds mediated by aligned water found in the polymers. The hypothesis was experimentally tested by imaging maize starch granules under various hydration and heat treatment conditions that alter the hydrogen bond network. The highest SHG intensity was found in fully hydrated starch granules, and heat treatment diminished the SHG intensity. The PIPO SHG imaging showed that dried starch granules have a much higher nonlinear optical susceptibility component ratio than fully hydrated granules. In contrast, deuterated starch granules showed a smaller susceptibility component ratio demonstrating that SHG is highly sensitive to the organization of the hydroxyl and hydrogen bond network. The polarization SHG imaging results of potato starch granules, representing starch allomorph B, were compared to those of maize starch granules representing allomorph A. The results showed that the amount of aligned water was higher in the maize granules. Nonlinear microscopy of starch granules provides evidence that varying hydration conditions leads to significant changes in the nonlinear susceptibility ratio as well as the SHG intensity, supporting the hypothesis from ab initio calculations that the dominant contribution to SHG is due to the ordered hydroxide and hydrogen bond network.

An ab initio mechanism for efficient population of triplet states in cytotoxic sulfur substituted DNA bases: the case of 6-thioguanine.

PubMed

Martínez-Fernández, Lara; González, Leticia; Corral, Inés

2012-02-18

The deactivation mechanism of the cytotoxic 6-thioguanine, the 6-sulfur-substituted analogue of the canonical DNA base, is unveiled by ab initio calculations. Oxygen-by-sulfur substitution leads to efficient population of triplet states-the first step for generating singlet oxygen-which is responsible for its cytotoxicity. This journal is © The Royal Society of Chemistry 2012

Development of a Scaled Quantum Mechanical Force Field for Peptides in Aqueous Solution

DTIC Science & Technology

1996-03-01

differ. Raman and IR techniques are complimentary which helps in assignment of observed vibrational modes. As described in beginning organic ...1588 I NH, .i.sor(98) 2076 2100 24 CH3 55(95) 2125 2207 82 CH3 as’ (56), CH3 as’ (43) 2235 2253 18 CH3 as’(55), CH3 as’(41) 2888 COff .(100) 3155 NH...Application of self- consistent-field ab initio calculations to organic molecules I. Equilibrium struc- ture and force constants of hydrocarbons

Quantum state preparation of homonuclear molecular ions enabled via a cold buffer gas: An ab initio study for the H2+ and the D2+ case

NASA Astrophysics Data System (ADS)

Schiller, S.; Kortunov, I.; Hernández Vera, M.; Gianturco, F.; da Silva, H.

2017-04-01

Precision vibrational spectroscopy of the molecular hydrogen ions is of significant interest for determining fundamental constants, for searching for new forces, and for testing quantum electrodynamics calculations. Future experiments can profit from the ability of preparing molecular hydrogen ions at ultralow kinetic energy and in preselected internal states, with respect to vibration, rotation, and spin degrees of freedom. For the homonuclear ions (H2+ , D2+ ), direct laser cooling of the rotational degree of freedom is not feasible. We show by quantum calculations that rotational cooling by cold He buffer gas is an effective approach. For this purpose we have computed the energy-dependent cross sections for rotationally elastic and inelastic collisions, h2+ (v =0 ,N ) +He → h2+ (v =0 ,N') +He (where h =H ,D ) , using ab initio coupled-channel calculations. We find that rotational cooling to the lowest rotational state is possible within tens of seconds under experimentally realistic conditions. We furthermore describe possible protocols for the preparation of a single quantum state, where also the spin state is well defined.

Controlling the thermoelectric effect by mechanical manipulation of the electron's quantum phase in atomic junctions.

PubMed

Aiba, Akira; Demir, Firuz; Kaneko, Satoshi; Fujii, Shintaro; Nishino, Tomoaki; Tsukagoshi, Kazuhito; Saffarzadeh, Alireza; Kirczenow, George; Kiguchi, Manabu

2017-08-11

The thermoelectric voltage developed across an atomic metal junction (i.e., a nanostructure in which one or a few atoms connect two metal electrodes) in response to a temperature difference between the electrodes, results from the quantum interference of electrons that pass through the junction multiple times after being scattered by the surrounding defects. Here we report successfully tuning this quantum interference and thus controlling the magnitude and sign of the thermoelectric voltage by applying a mechanical force that deforms the junction. The observed switching of the thermoelectric voltage is reversible and can be cycled many times. Our ab initio and semi-empirical calculations elucidate the detailed mechanism by which the quantum interference is tuned. We show that the applied strain alters the quantum phases of electrons passing through the narrowest part of the junction and hence modifies the electronic quantum interference in the device. Tuning the quantum interference causes the energies of electronic transport resonances to shift, which affects the thermoelectric voltage. These experimental and theoretical studies reveal that Au atomic junctions can be made to exhibit both positive and negative thermoelectric voltages on demand, and demonstrate the importance and tunability of the quantum interference effect in the atomic-scale metal nanostructures.

Quantum dynamics of hydrogen atoms on graphene. I. System-bath modeling.

PubMed

Bonfanti, Matteo; Jackson, Bret; Hughes, Keith H; Burghardt, Irene; Martinazzo, Rocco

2015-09-28

An accurate system-bath model to investigate the quantum dynamics of hydrogen atoms chemisorbed on graphene is presented. The system comprises a hydrogen atom and the carbon atom from graphene that forms the covalent bond, and it is described by a previously developed 4D potential energy surface based on density functional theory ab initio data. The bath describes the rest of the carbon lattice and is obtained from an empirical force field through inversion of a classical equilibrium correlation function describing the hydrogen motion. By construction, model building easily accommodates improvements coming from the use of higher level electronic structure theory for the system. Further, it is well suited to a determination of the system-environment coupling by means of ab initio molecular dynamics. This paper details the system-bath modeling and shows its application to the quantum dynamics of vibrational relaxation of a chemisorbed hydrogen atom, which is here investigated at T = 0 K with the help of the multi-configuration time-dependent Hartree method. Paper II deals with the sticking dynamics.

Quantum dynamics of hydrogen atoms on graphene. I. System-bath modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bonfanti, Matteo, E-mail: matteo.bonfanti@unimi.it; Jackson, Bret; Hughes, Keith H.

2015-09-28

An accurate system-bath model to investigate the quantum dynamics of hydrogen atoms chemisorbed on graphene is presented. The system comprises a hydrogen atom and the carbon atom from graphene that forms the covalent bond, and it is described by a previously developed 4D potential energy surface based on density functional theory ab initio data. The bath describes the rest of the carbon lattice and is obtained from an empirical force field through inversion of a classical equilibrium correlation function describing the hydrogen motion. By construction, model building easily accommodates improvements coming from the use of higher level electronic structure theorymore » for the system. Further, it is well suited to a determination of the system-environment coupling by means of ab initio molecular dynamics. This paper details the system-bath modeling and shows its application to the quantum dynamics of vibrational relaxation of a chemisorbed hydrogen atom, which is here investigated at T = 0 K with the help of the multi-configuration time-dependent Hartree method. Paper II deals with the sticking dynamics.« less

Ab initio Kinetics and Thermal Decomposition Mechanism of Mononitrobiuret and 1,5-Dinitrobiuret

DTIC Science & Technology

2016-03-14

Journal Article 3. DATES COVERED (From - To) Feb 2015-May 2015 4. TITLE AND SUBTITLE Ab initio Kinetics and Thermal Decomposition Mechanism of 5a...tetrazole-free, nitrogen-rich, energetic compounds. For the first time, the thermal decomposition mechanisms of MNB and DNB have been investigated...potential energy surfaces for thermal decomposition of MNB and DNB were characterized at the RCCSD(T)/cc-pV∞Z//M06-2X/aug- cc-pVTZ level of theory

Vibrational energy transport in acetylbenzonitrile described by an ab initio-based quantum tier model

NASA Astrophysics Data System (ADS)

Fujisaki, Hiroshi; Yagi, Kiyoshi; Kikuchi, Hiroto; Takami, Toshiya; Stock, Gerhard

2017-01-01

Performing comprehensive quantum-chemical calculations, a vibrational Hamiltonian of acetylbenzonitrile is constructed, on the basis of which a quantum-mechanical "tier model" is developed that describes the vibrational dynamics following excitation of the CN stretch mode. Taking into account 36 vibrational modes and cubic and quartic anharmonic couplings between up to three different modes, the tier model calculations are shown to qualitatively reproduce the main findings of the experiments of Rubtsov and coworkers (2011), including the energy relaxation of the initially excited CN mode and the structure-dependent vibrational transport. Moreover, the calculations suggest that the experimentally measured cross-peak among the CN and CO modes does not correspond to direct excitation of the CO normal mode but rather reflects excited low-frequency vibrations that anharmonically couple to the CO mode. Complementary quasiclassical trajectory calculations are found to be in good overall agreement with the quantum calculations.

Ab initio rate constants from hyperspherical quantum scattering: Application to H+C2H6 and H+CH3OH

NASA Astrophysics Data System (ADS)

Kerkeni, Boutheïna; Clary, David C.

2004-10-01

The dynamics and kinetics of the abstraction reactions of H atoms with ethane and methanol have been studied using a quantum mechanical procedure. Bonds being broken and formed are treated with explicit hyperspherical quantum dynamics. The ab initio potential energy surfaces for these reactions have been developed from a minimal number of grid points (average of 48 points) and are given by analytical functionals. All the degrees of freedom except the breaking and forming bonds are optimized using the second order perturbation theory method with a correlation consistent polarized valence triple zeta basis set. Single point energies are calculated on the optimized geometries with the coupled cluster theory and the same basis set. The reaction of H with C2H6 is endothermic by 1.5 kcal/mol and has a vibrationally adiabatic barrier of 12 kcal/mol. The reaction of H with CH3OH presents two reactive channels: the methoxy and the hydroxymethyl channels. The former is endothermic by 0.24 kcal/mol and has a vibrationally adiabatic barrier of 13.29 kcal/mol, the latter reaction is exothermic by 7.87 kcal/mol and has a vibrationally adiabatic barrier of 8.56 kcal/mol. We report state-to-state and state-selected cross sections together with state-to-state rate constants for the title reactions. Thermal rate constants for these reactions exhibit large quantum tunneling effects when compared to conventional transition state theory results. For H+CH3OH, it is found that the CH2OH product is the dominant channel, and that the CH3O channel contributes just 2% at 500 K. For both reactions, rate constants are in good agreement with some measurements.

Development of glue type potentials for the Al-Pb system: computer simulation of Pb/Al interfaces and phase diagram calculation

NASA Astrophysics Data System (ADS)

Landa, Alex; Wynblatt, Paul; Siegel, Donald; Adams, Jim; Johnson, Erik; Dahmen, Uli

2000-03-01

Empirical many-body potentials have been constructed for the Al-Pb system using the ``force matching" method. The potentials have been fitted to a set of the ground state physical quantities calculated within ab initio approach and a massive quantum mechanical forces database for samples of bulk Al-Pb liquid alloys generated using ab initio molecular dynamics program VASP. Monte Carlo simulations using these potentials have been employed to compute an Al-Pb phase diagram, which is in fair agreement with experimental data, and to model the structure of (111) and (100) Pb/Al interfaces. The calculated free energy ratios for the Pb/Al 100 and 111 interfaces are in good agreement with recent high-resolution transmission electron microscopy measurements. The constructed glue potentials correctly reflects the large change in anisotropy which is observed experimentally between isolated Pb crystals and Pb crystals embedded in Al. Support by the DOE under grants DE-FG02-99ER45773 and DE-AC03-76SF00098, the NSF under grant DMR9619353 and the Danish Natural Sciences Research Council.

Ab initio study of charge transfer in B2+ low-energy collisions with atomic hydrogen

NASA Astrophysics Data System (ADS)

Turner, A. R.; Cooper, D. L.; Wang, J. G.; Stancil, P. C.

2003-07-01

Charge transfer processes due to collisions of ground state B2+(2s 2S) ions with atomic hydrogen are investigated using the quantum-mechanical molecular-orbital close-coupling (MOCC) method. The MOCC calculations utilize ab initio adiabatic potentials and nonadiabatic radial and rotational coupling matrix elements obtained with the spin-coupled valence-bond approach. Total and state-selective cross sections and rate coefficients are presented. Comparison with the existing experiments shows our results to be in good agreement. When E<80 eV/u, the differences between the current total MOCC cross sections with and without rotational coupling are small (<3%). Rotational coupling becomes more important with increasing energy: for collision energies E>400 eV/u, inclusion of rotational coupling increases the total cross section by 50% 80%, improving the agreement between the current calculations and experiments. For state-selective cross sections, rotational coupling induces mixing between different symmetries; however, its effect, especially at low collision energies, is not as important as had been suggested in previous work.

Mutual influence between triel bond and cation-π interactions: an ab initio study

NASA Astrophysics Data System (ADS)

Esrafili, Mehdi D.; Mousavian, Parisasadat

2017-12-01

Using ab initio calculations, the cooperative and solvent effects on cation-π and B...N interactions are studied in some model ternary complexes, where these interactions coexist. The nature of the interactions and the mechanism of cooperativity are investigated by means of quantum theory of atoms in molecules (QTAIM), noncovalent interaction (NCI) index and natural bond orbital analysis. The results indicate that all cation-π and B...N binding distances in the ternary complexes are shorter than those of corresponding binary systems. The QTAIM analysis reveals that ternary complexes have higher electron density at their bond critical points relative to the corresponding binary complexes. In addition, according to the QTAIM analysis, the formation of cation-π interaction increases covalency of B...N bonds. The NCI analysis indicates that the cooperative effects in the ternary complexes make a shift in the location of the spike associated with each interaction, which can be regarded as an evidence for the reinforcement of both cation-π and B...N interactions in these systems. Solvent effects on the cooperativity of cation-π and B...N interactions are also investigated.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Starrett, C. E.; Saumon, D.

Here, we present an approximation for calculating the equation of state (EOS) of warm and hot dense matter that is built on the previously published pseudoatom molecular dynamics (PAMD) model of dense plasmas [Starrett et al., Phys. Rev. E 91, 013104 (2015)]. And while the EOS calculation with PAMD was previously limited to orbital-free density functional theory (DFT), the new approximation presented here allows a Kohn-Sham DFT treatment of the electrons. The resulting EOS thus includes a quantum mechanical treatment of the electrons with a self-consistent model of the ionic structure, while remaining tractable at high temperatures. The method ismore » validated by comparisons with pressures from ab initio simulations of Be, Al, Si, and Fe. The EOS in the Thomas-Fermi approximation shows remarkable thermodynamic consistency over a wide range of temperatures for aluminum. We also calculate the principal Hugoniots of aluminum and silicon up to 500 eV. We find that the ionic structure of the plasma has a modest effect that peaks at temperatures of a few eV and that the features arising from the electronic structure agree well with ab initio simulations.« less

Ab initio calculation of infrared intensities for hydrogen peroxide

NASA Technical Reports Server (NTRS)

Rogers, J. D.; Hillman, J. J.

1982-01-01

Results of an ab initio SCF quantum mechanical study are used to derive estimates for the infrared intensities of the fundamental vibrations of hydrogen peroxide. Atomic polar tensors (APTs) were calculated on the basis of a 4-31G basis set, and used to derive absolute intensities for the vibrational transitions. Comparison of the APTs calculated for H2O2 with those previously obtained for H2O and CH3OH, and of the absolute intensities derived from the H2O2 APTs with those derived from APTs transferred from H2O and CH3OH, reveals the sets of values to differ by no more than a factor of two, supporting the validity of the theoretical calculation. Values of the infrared intensities obtained correspond to A1 = 14.5 km/mol, A2 = 0.91 km/mol, A3 = 0.058 km/mol, A4 = 123 km/mol, A5 = 46.2 km/mol, and A6 = 101 km/mol. Charge, charge flux and overlap contributions to the dipole moment derivatives are also computed.

Ab initio calculation of infrared intensities for hydrogen peroxide

NASA Astrophysics Data System (ADS)

Rogers, J. D.; Hillman, J. J.

1982-04-01

Results of an ab initio SCF quantum mechanical study are used to derive estimates for the infrared intensities of the fundamental vibrations of hydrogen peroxide. Atomic polar tensors (APTs) were calculated on the basis of a 4-31G basis set, and used to derive absolute intensities for the vibrational transitions. Comparison of the APTs calculated for H2O2 with those previously obtained for H2O and CH3OH, and of the absolute intensities derived from the H2O2 APTs with those derived from APTs transferred from H2O and CH3OH, reveals the sets of values to differ by no more than a factor of two, supporting the validity of the theoretical calculation. Values of the infrared intensities obtained correspond to A1 = 14.5 km/mol, A2 = 0.91 km/mol, A3 = 0.058 km/mol, A4 = 123 km/mol, A5 = 46.2 km/mol, and A6 = 101 km/mol. Charge, charge flux and overlap contributions to the dipole moment derivatives are also computed.

Electronic Structure, Dielectric Response, and Surface Charge Distribution of RGD (1FUV) Peptide

PubMed Central

Adhikari, Puja; Wen, Amy M.; French, Roger H.; Parsegian, V. Adrian; Steinmetz, Nicole F.; Podgornik, Rudolf; Ching, Wai-Yim

2014-01-01

Long and short range molecular interactions govern molecular recognition and self-assembly of biological macromolecules. Microscopic parameters in the theories of these molecular interactions are either phenomenological or need to be calculated within a microscopic theory. We report a unified methodology for the ab initio quantum mechanical (QM) calculation that yields all the microscopic parameters, namely the partial charges as well as the frequency-dependent dielectric response function, that can then be taken as input for macroscopic theories of electrostatic, polar, and van der Waals-London dispersion intermolecular forces. We apply this methodology to obtain the electronic structure of the cyclic tripeptide RGD-4C (1FUV). This ab initio unified methodology yields the relevant parameters entering the long range interactions of biological macromolecules, providing accurate data for the partial charge distribution and the frequency-dependent dielectric response function of this peptide. These microscopic parameters determine the range and strength of the intricate intermolecular interactions between potential docking sites of the RGD-4C ligand and its integrin receptor. PMID:25001596

Machine Learning of Accurate Energy-Conserving Molecular Force Fields

NASA Astrophysics Data System (ADS)

Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel; Poltavsky, Igor; Schütt, Kristof; Müller, Klaus-Robert; GDML Collaboration

Efficient and accurate access to the Born-Oppenheimer potential energy surface (PES) is essential for long time scale molecular dynamics (MD) simulations. Using conservation of energy - a fundamental property of closed classical and quantum mechanical systems - we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio MD trajectories (AIMD). The GDML implementation is able to reproduce global potential-energy surfaces of intermediate-size molecules with an accuracy of 0.3 kcal/mol for energies and 1 kcal/mol/Å for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, malonaldehyde, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative MD simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods.

Nuclear quantum effect with pure anharmonicity and the anomalous thermal expansion of silicon.

PubMed

Kim, D S; Hellman, O; Herriman, J; Smith, H L; Lin, J Y Y; Shulumba, N; Niedziela, J L; Li, C W; Abernathy, D L; Fultz, B

2018-02-27

Despite the widespread use of silicon in modern technology, its peculiar thermal expansion is not well understood. Adapting harmonic phonons to the specific volume at temperature, the quasiharmonic approximation, has become accepted for simulating the thermal expansion, but has given ambiguous interpretations for microscopic mechanisms. To test atomistic mechanisms, we performed inelastic neutron scattering experiments from 100 K to 1,500 K on a single crystal of silicon to measure the changes in phonon frequencies. Our state-of-the-art ab initio calculations, which fully account for phonon anharmonicity and nuclear quantum effects, reproduced the measured shifts of individual phonons with temperature, whereas quasiharmonic shifts were mostly of the wrong sign. Surprisingly, the accepted quasiharmonic model was found to predict the thermal expansion owing to a large cancellation of contributions from individual phonons.

Vibrational spectra and ab initio analysis of tert-butyl, trimethylsilyl, and trimethylgermyl derivatives of 3,3-dimethylcyclopropene III. 3,3-Dimethyl-1-(trimethylsilyl)cyclopropene

NASA Astrophysics Data System (ADS)

De Maré, G. R.; Panchenko, Yu. N.; Abramenkov, A. V.; Baird, M. S.; Tverezovsky, V. V.; Nizovtsev, A. V.; Bolesov, I. G.

2003-07-01

The experimental Raman and IR vibrational spectra of 3,3-dimethyl-1-(trimethylsilyl)cyclopropene in the liquid phase were recorded. Total geometry optimisation was carried out at the HF/6-31G* level and the HF/6-31G*//HF/6-31G* force field was computed. This force field was corrected by scale factors determined previously (using Pulay's method) for correction of the HF/6-31G*//HF/6-31G* force fields of 3,3-dimethylbutene-1, 1-methyl-, 1,2-dimethyl-, and 3,3-dimethylcyclopropene. The theoretical vibrational frequencies calculated from the scaled quantum mechanical force field and the theoretical intensities obtained from the quantum mechanical calculation were used to construct predicted spectra and to perform the vibrational analysis of the experimental spectra.

Comparison between Gaussian-type orbitals and plane wave ab initio density functional theory modeling of layer silicates: Talc [Mg{sub 3}Si{sub 4}O{sub 10}(OH){sub 2}] as model system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ulian, Gianfranco; Valdrè, Giovanni, E-mail: giovanni.valdre@unibo.it; Tosoni, Sergio

2013-11-28

The quantum chemical characterization of solid state systems is conducted with many different approaches, among which the adoption of periodic boundary conditions to deal with three-dimensional infinite condensed systems. This method, coupled to the Density Functional Theory (DFT), has been proved successful in simulating a huge variety of solids. Only in relatively recent years this ab initio quantum-mechanic approach has been used for the investigation of layer silicate structures and minerals. In the present work, a systematic comparison of different DFT functionals (GGA-PBEsol and hybrid B3LYP) and basis sets (plane waves and all-electron Gaussian-type orbitals) on the geometry, energy, andmore » phonon properties of a model layer silicate, talc [Mg{sub 3}Si{sub 4}O{sub 10}(OH){sub 2}], is presented. Long range dispersion is taken into account by DFT+D method. Results are in agreement with experimental data reported in literature, with minimal deviation given by the GTO/B3LYP-D* method regarding both axial lattice parameters and interaction energy and by PW/PBE-D for the unit-cell volume and angular values. All the considered methods adequately describe the experimental talc infrared spectrum.« less

Ab initio density-functional calculations in materials science: from quasicrystals over microporous catalysts to spintronics.

PubMed

Hafner, Jürgen

2010-09-29

During the last 20 years computer simulations based on a quantum-mechanical description of the interactions between electrons and atomic nuclei have developed an increasingly important impact on materials science, not only in promoting a deeper understanding of the fundamental physical phenomena, but also enabling the computer-assisted design of materials for future technologies. The backbone of atomic-scale computational materials science is density-functional theory (DFT) which allows us to cast the intractable complexity of electron-electron interactions into the form of an effective single-particle equation determined by the exchange-correlation functional. Progress in DFT-based calculations of the properties of materials and of simulations of processes in materials depends on: (1) the development of improved exchange-correlation functionals and advanced post-DFT methods and their implementation in highly efficient computer codes, (2) the development of methods allowing us to bridge the gaps in the temperature, pressure, time and length scales between the ab initio calculations and real-world experiments and (3) the extension of the functionality of these codes, permitting us to treat additional properties and new processes. In this paper we discuss the current status of techniques for performing quantum-based simulations on materials and present some illustrative examples of applications to complex quasiperiodic alloys, cluster-support interactions in microporous acid catalysts and magnetic nanostructures.

An ab initio study of ion induced charge transfer dynamics in collision of carbon ions with thymine.

PubMed

Bacchus-Montabonel, Marie-Christine; Tergiman, Yvette Suzanne

2011-05-28

Charge transfer in collisions of carbon ions on a thymine target has been studied theoretically in a wide collision range by means of ab initio quantum chemistry molecular methods. The process appears markedly anisotropic in the whole energy domain, significantly favoured in the perpendicular orientation. A specific decrease of the charge transfer cross sections at low collision energies may be pointed out and could induce an enhancement of the complementary fragmentation processes for collision energies down to about 10 eV, as observed for the low-electron fragmentation process. Such feature may be of important interest in ion-induced biomolecular radiation damage. This journal is © the Owner Societies 2011

Dynamical spin structure factors of α-RuCl3

NASA Astrophysics Data System (ADS)

Suzuki, Takafumi; Suga, Sei-ichiro

2018-03-01

Honeycomb-lattice magnet α-RuCl3 is considered to be a potential candidate of realizing Kitaev spin liquid, although this material undergoes a phase transition to the zigzag magnetically ordered state at T N ∼ 7 K. Quite recently, inelastic neutron-scattering experiments using single crystal α-RuCl3 have unveiled characteristic dynamical properties. We calculate dynamical spin structure factors of three ab-initio models for α-RuCl3 with an exact numerical diagonalization method. We also calculate temperature dependences of the specific heat by employing thermal pure quantum states. We compare our numerical results with the experiments and discuss characteristics obtained by using three ab-initio models.

Ionic liquids. Combination of combustion calorimetry with high-level quantum chemical calculations for deriving vaporization enthalpies.

PubMed

Emel'yanenko, Vladimir N; Verevkin, Sergey P; Heintz, Andreas; Schick, Christoph

2008-07-10

In this work, the molar enthalpies of formation of the ionic liquids [C2MIM][NO3] and [C4MIM][NO3] were measured by means of combustion calorimetry. The molar enthalpy of fusion of [C2MIM][NO3] was measured using differential scanning calorimetry. Ab initio calculations of the enthalpy of formation in the gaseous phase have been performed for the ionic species using the G3MP2 theory. We have used a combination of traditional combustion calorimetry with modern high-level ab initio calculations in order to obtain the molar enthalpies of vaporization of a series of the ionic liquids under study.

Structure of alcohol cluster ions in the gas phase, according to spectrometry and ab initio calculations

NASA Astrophysics Data System (ADS)

Krisilov, A. V.; Lantsuzskaya, E. V.; Levina, A. M.

2017-01-01

Reduced ion mobility and scattering cross sections are calculated from experimentally obtained spectra of the ion mobility of linear aliphatic alcohols with carbon atom numbers from 2 to 9. A linear increase in the scattering cross sections as the molecular weight grows is found. According to the results from experiments and quantum chemical calculations, alcohol cluster ions do not form a compact structure. Neither are dipole moments compensated for during dimerization, in contrast to the aldehydes and ketones described earlier. It was concluded from ab initio calculations that charge delocalization in monomeric and dimeric ions of alcohols increases the dipole moment many times over.

Discovering charge density functionals and structure-property relationships with PROPhet: A general framework for coupling machine learning and first-principles methods

DOE PAGES

Kolb, Brian; Lentz, Levi C.; Kolpak, Alexie M.

2017-04-26

Modern ab initio methods have rapidly increased our understanding of solid state materials properties, chemical reactions, and the quantum interactions between atoms. However, poor scaling often renders direct ab initio calculations intractable for large or complex systems. There are two obvious avenues through which to remedy this problem: (i) develop new, less expensive methods to calculate system properties, or (ii) make existing methods faster. This paper describes an open source framework designed to pursue both of these avenues. PROPhet (short for PROPerty Prophet) utilizes machine learning techniques to find complex, non-linear mappings between sets of material or system properties. Themore » result is a single code capable of learning analytical potentials, non-linear density functionals, and other structure-property or property-property relationships. These capabilities enable highly accurate mesoscopic simulations, facilitate computation of expensive properties, and enable the development of predictive models for systematic materials design and optimization. Here, this work explores the coupling of machine learning to ab initio methods through means both familiar (e.g., the creation of various potentials and energy functionals) and less familiar (e.g., the creation of density functionals for arbitrary properties), serving both to demonstrate PROPhet’s ability to create exciting post-processing analysis tools and to open the door to improving ab initio methods themselves with these powerful machine learning techniques.« less

Discovering charge density functionals and structure-property relationships with PROPhet: A general framework for coupling machine learning and first-principles methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kolb, Brian; Lentz, Levi C.; Kolpak, Alexie M.

Modern ab initio methods have rapidly increased our understanding of solid state materials properties, chemical reactions, and the quantum interactions between atoms. However, poor scaling often renders direct ab initio calculations intractable for large or complex systems. There are two obvious avenues through which to remedy this problem: (i) develop new, less expensive methods to calculate system properties, or (ii) make existing methods faster. This paper describes an open source framework designed to pursue both of these avenues. PROPhet (short for PROPerty Prophet) utilizes machine learning techniques to find complex, non-linear mappings between sets of material or system properties. Themore » result is a single code capable of learning analytical potentials, non-linear density functionals, and other structure-property or property-property relationships. These capabilities enable highly accurate mesoscopic simulations, facilitate computation of expensive properties, and enable the development of predictive models for systematic materials design and optimization. Here, this work explores the coupling of machine learning to ab initio methods through means both familiar (e.g., the creation of various potentials and energy functionals) and less familiar (e.g., the creation of density functionals for arbitrary properties), serving both to demonstrate PROPhet’s ability to create exciting post-processing analysis tools and to open the door to improving ab initio methods themselves with these powerful machine learning techniques.« less

Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.

PubMed

Shen, Lin; Yang, Weitao

2016-04-12

We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multiresolution model, in which an atomic-level layer of water molecules around redox center is solvated in supramolecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multilayer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer.

Charge Transfer in Collisions of S^4+ with H.

NASA Astrophysics Data System (ADS)

Stancil, P. C.; Turner, A. R.; Cooper, D. L.; Schultz, D. R.; Rakovic, M. J.; Fritsch, W.; Zygelman, B.

2001-05-01

Charge transfer processes due to collisions of ground state S^4+ ions with atomic hydrogen were investigated for energies between 1 meV/u and 10 MeV/u using the quantum-mechanical molecular-orbital close-coupling (MOCC), atomic-orbital close-coupling, classical trajectory Monte Carlo (CTMC), and continuum distorted wave methods. The MOCC calculations utilized ab initio adiabatic potentials and nonadiabatic radial coupling matrix elements obtained with the spin-coupled valence-bond approach. A number of variants of the CTMC approach were explored, including different momentum and radial distributions for the initial state, as well as effective charge and quantum-defect models to determine the corresponding quantum state after capture into final partially-stripped S^3+ excited classical states. Hydrogen target isotope effects were explored and rate coefficients for temperatures between 100 and 10^6 K will be presented

Optical properties of Si and Ge nanocrystals: Parameter-free calculations

NASA Astrophysics Data System (ADS)

Ramos, L. E.; Weissker, H.-Ch.; Furthmüller, J.; Bechstedt, F.

2005-12-01

The cover picture of the current issue refers to the Edi-tor's Choice article of Ramos et al. [1]. The paper gives an overview of the electronic and optical properties of silicon and germanium nanocrystals determined by state-of-the-art ab initio methods. Nanocrystals have promising applications in opto-electronic devices, since they can be used to confine electrons and holes and facilitate radiative recombination. Since meas-urements for single nanoparticles are difficult to make, ab initio theoretical investigations become important to understand the mechanisms of luminescence.The cover picture shows nanocrystals of four sizes with tetrahedral coordination whose dangling bonds at the surface are passivated with hydrogen. As often observed in experiments, the nanocrystals are not perfectly spherical, but contain facets. Apart from the size of the nanocrystals, which determines the quantum confinement, the way their dangling bonds are passivated is relevant for their electronic and optical properties. For instance, the passivation with hydroxyls reduces the quantum confine-ment. On the other hand, the oxidation of the silicon nanocrys-tals increases the quantum confinement and reduces the effect of single surface terminations on the gap. Due to the oscillator strengths of the lowest-energy optical transitions, Ge nanocrys-tals are in principle more suitable for opto-electronic applica-tions than Si nanocrystals.The first author, Luis E. Ramos, is a postdoc at the Institute of Solid-State Physics and Optics (IFTO), Friedrich-Schiller University Jena, Germany. He investigates electronic and optical properties of semiconductor nanocrystallites and is a member of the European Network of Excellence NANO-QUANTA and of the European Theoretical Spectroscopy Facility (ETSF).

High-Level, First-Principles, Full-Dimensional Quantum Calculation of the Ro-vibrational Spectrum of the Simplest Criegee Intermediate (CH2OO).

PubMed

Li, Jun; Carter, Stuart; Bowman, Joel M; Dawes, Richard; Xie, Daiqian; Guo, Hua

2014-07-03

The ro-vibrational spectrum of the simplest Criegee intermediate (CH2OO) has been determined quantum mechanically based on nine-dimensional potential energy and dipole surfaces for its ground electronic state. The potential energy surface is fitted to more than 50 000 high-level ab initio points with a root-mean-square error of 25 cm(-1), using a recently proposed permutation invariant polynomial neural network method. The calculated rotational constants, vibrational frequencies, and spectral intensities of CH2OO are in excellent agreement with experiment. The potential energy surface provides a valuable platform for studying highly excited vibrational and unimolecular reaction dynamics of this important molecule.

Kinetics of Electrocatalytic Reactions from First-Principles: A Critical Comparison with the Ab Initio Thermodynamics Approach.

PubMed

Exner, Kai S; Over, Herbert

2017-05-16

Multielectron processes in electrochemistry require the stabilization of reaction intermediates (RI) at the electrode surface after every elementary reaction step. Accordingly, the bond strengths of these intermediates are important for assessing the catalytic performance of an electrode material. Current understanding of microscopic processes in modern electrocatalysis research is largely driven by theory, mostly based on ab initio thermodynamics considerations, where stable reaction intermediates at the electrode surface are identified, while the actual free energy barriers (or activation barriers) are ignored. This simple approach is popular in electrochemistry in that the researcher has a simple tool at hand in successfully searching for promising electrode materials. The ab initio TD approach allows for a rough but fast screening of the parameter space with low computational cost. However, ab initio thermodynamics is also frequently employed (often, even based on a single binding energy only) to comprehend on the activity and on the mechanism of an electrochemical reaction. The basic idea is that the activation barrier of an endergonic reaction step consists of a thermodynamic part and an additional kinetically determined barrier. Assuming that the activation barrier scales with thermodynamics (so-called Brønsted-Polanyi-Evans (BEP) relation) and the kinetic part of the barrier is small, ab initio thermodynamics may provide molecular insights into the electrochemical reaction kinetics. However, for many electrocatalytic reactions, these tacit assumptions are violated so that ab initio thermodynamics will lead to contradictions with both experimental data and ab initio kinetics. In this Account, we will discuss several electrochemical key reactions, including chlorine evolution (CER), oxygen evolution reaction (OER), and oxygen reduction (ORR), where ab initio kinetics data are available in order to critically compare the results with those derived from a simple ab initio thermodynamics treatment. We show that ab initio thermodynamics leads to erroneous conclusions about kinetic and mechanistic aspects for the CER over RuO 2 (110), while the kinetics of the OER over RuO 2 (110) and ORR over Pt(111) are reasonably well described. Microkinetics of an electrocatalyzed reaction is largely simplified by the quasi-equilibria of the RI preceding the rate-determining step (rds) with the reactants. Therefore, in ab initio kinetics the rate of an electrocatalyzed reaction is governed by the transition state (TS) with the highest free energy G rds # , defining also the rate-determining step (rds). Ab initio thermodynamics may be even more powerful, when using the highest free energy of an reaction intermediate G max (RI) rather than the highest free energy difference between consecutive reaction intermediates, ΔG loss , as a descriptor for the kinetics.

Substituent Inductive Effects on the Electrochemical Oxidation of Flavonoids Studied by Square Wave Voltammetry and Ab Initio Calculations.

PubMed

Arroyo-Currás, Netzahualcóyotl; Rosas-García, Víctor M; Videa, Marcelo

2016-10-27

Flavonoids are natural products commonly found in the human diet that show antioxidant, anti-inflammatory and anti-hepatotoxic activities. These nutraceutical properties may relate to the electrochemical activity of flavonoids. To increase the understanding of structure-electrochemical activity relations and the inductive effects that OH substituents have on the redox potential of flavonoids, we carried out square-wave voltammetry experiments and ab initio calculations of eight flavonoids selected following a systematic variation in the number of hydroxyl substituents and their location on the flavan backbone: three flavonols, three anthocyanidins, one anthocyanin and the flavonoid backbone flavone. We compared the effect that the number of -OH groups in the ring B of flavan has on the oxidation potential of the flavonoids considered, finding linear correlations for both flavonols and anthocyanidins ( R 2 = 0.98 ). We analyzed the effects that position and number of -OH substituents have on electron density distributions via ab initio quantum chemical calculations. We present direct correlations between structural features and oxidation potentials that provide a deeper insight into the redox chemistry of these molecules.

Conformational properties and electronic structure of tetrahydrotetrazines studied by photoelectron spectroscopy and quantum chemical calculations

NASA Astrophysics Data System (ADS)

Muchall, Heidi M.; Rademacher, Paul

1997-11-01

The photoelectron (PE) spectra of tetrahydro-1,2,3,4-tetrazines 1 and 2 and tetrahydro-1,2,4,5-tetrazines 3-5 have been recorded and their conformations have been investigated by ab initio SCF calculations. While v-tetrazine 2 is planar, tetrazines 1 and 3-5 each possess two low-energy conformations, according to ab initio HF and Becke3LYP methods. Attempts to assign ionization potentials to molecular orbitals obtained by semiempirical PM3 calculations indicate that this method is not suited for the compounds studied. Best results were obtained when the ab initio hybrid method Becke3LYP of the density functional theory was employed. Two conformers of 1 and 3-5 are present in the gas phase and their PE spectra are superimposed one upon the other. For v-tetrazine 1, ionizations arising from half-chair and unsymmetrical boat conformers have similar energies and cannot be separated in the PE spectrum. For s-tetrazine 3, on the other hand, the spectrum clearly shows different ionizations of both half-chairs, 3ee and 3ae.

State-of-the-art ab initio potential energy curve for the krypton atom pair and thermophysical properties of dilute krypton gas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jäger, Benjamin, E-mail: benjamin.jaeger@uni-rostock.de; Hellmann, Robert, E-mail: robert.hellmann@uni-rostock.de; Bich, Eckard

2016-03-21

A new reference krypton-krypton interatomic potential energy curve was developed by means of quantum-chemical ab initio calculations for 36 interatomic separations. Highly accurate values for the interaction energies at the complete basis set limit were obtained using the coupled-cluster method with single, double, and perturbative triple excitations as well as t-aug-cc-pV5Z and t-aug-cc-pV6Z basis sets including mid-bond functions, with the 6Z basis set being newly constructed for this study. Higher orders of coupled-cluster terms were considered in a successive scheme up to full quadruple excitations. Core-core and core-valence correlation effects were included. Furthermore, relativistic effects were studied not only atmore » a scalar relativistic level using second-order direct perturbation theory, but also utilizing full four-component and Gaunt-effect computations. An analytical pair potential function was fitted to the interaction energies, which is characterized by a depth of 200.88 K with an estimated standard uncertainty of 0.51 K. Thermophysical properties of low-density krypton were calculated for temperatures up to 5000 K. Second and third virial coefficients were obtained from statistical thermodynamics. Viscosity and thermal conductivity as well as the self-diffusion coefficient were computed using the kinetic theory of gases. The theoretical results are compared with experimental data and with results for other pair potential functions from the literature, especially with those calculated from the recently developed ab initio potential of Waldrop et al. [J. Chem. Phys. 142, 204307 (2015)]. Highly accurate experimental viscosity data indicate that both the present ab initio pair potential and the one of Waldrop et al. can be regarded as reference potentials, even though the quantum-chemical methods and basis sets differ. However, the uncertainties of the present potential and of the derived properties are estimated to be considerably lower.« less

State-of-the-art ab initio potential energy curve for the krypton atom pair and thermophysical properties of dilute krypton gas.

PubMed

Jäger, Benjamin; Hellmann, Robert; Bich, Eckard; Vogel, Eckhard

2016-03-21

A new reference krypton-krypton interatomic potential energy curve was developed by means of quantum-chemical ab initio calculations for 36 interatomic separations. Highly accurate values for the interaction energies at the complete basis set limit were obtained using the coupled-cluster method with single, double, and perturbative triple excitations as well as t-aug-cc-pV5Z and t-aug-cc-pV6Z basis sets including mid-bond functions, with the 6Z basis set being newly constructed for this study. Higher orders of coupled-cluster terms were considered in a successive scheme up to full quadruple excitations. Core-core and core-valence correlation effects were included. Furthermore, relativistic effects were studied not only at a scalar relativistic level using second-order direct perturbation theory, but also utilizing full four-component and Gaunt-effect computations. An analytical pair potential function was fitted to the interaction energies, which is characterized by a depth of 200.88 K with an estimated standard uncertainty of 0.51 K. Thermophysical properties of low-density krypton were calculated for temperatures up to 5000 K. Second and third virial coefficients were obtained from statistical thermodynamics. Viscosity and thermal conductivity as well as the self-diffusion coefficient were computed using the kinetic theory of gases. The theoretical results are compared with experimental data and with results for other pair potential functions from the literature, especially with those calculated from the recently developed ab initio potential of Waldrop et al. [J. Chem. Phys. 142, 204307 (2015)]. Highly accurate experimental viscosity data indicate that both the present ab initio pair potential and the one of Waldrop et al. can be regarded as reference potentials, even though the quantum-chemical methods and basis sets differ. However, the uncertainties of the present potential and of the derived properties are estimated to be considerably lower.

Ab initio calculation of proton-coupled electron transfer rates using the external-potential representation: A ubiquinol complex in solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yamamoto, Takeshi; Kato, Shigeki

2007-06-14

In quantum-mechanical/molecular-mechanical (QM/MM) treatment of chemical reactions in condensed phases, one solves the electronic Schroedinger equation for the solute (or an active site) under the electrostatic field from the environment. This Schroedinger equation depends parametrically on the solute nuclear coordinates R and the external electrostatic potential V. This fact suggests that one may use R and V as natural collective coordinates for describing the entire system, where V plays the role of collective solvent variables. In this paper such an (R,V) representation of the QM/MM canonical ensemble is described, with particular focus on how to treat charge transfer processes inmore » this representation. As an example, the above method is applied to the proton-coupled electron transfer of a ubiquinol analog with phenoxyl radical in acetonitrile solvent. Ab initio free-energy surfaces are calculated as functions of R and V using the reference interaction site model self-consistent field method, the equilibrium points and the minimum free-energy crossing point are located in the (R,V) space, and then the kinetic isotope effects (KIEs) are evaluated approximately. The results suggest that a stiffer proton potential at the transition state may be responsible for unusual KIEs observed experimentally for related systems.« less

Theoretical Studies of the Extraterrestrial Chemistry of Biogenic Elements and Compounds

NASA Technical Reports Server (NTRS)

Woon, D. E.

1998-01-01

The report discusses modeling gas-grain chemistry with ab initio quantum chemical cluster calculations which include heterogeneous hydrogenation of CO and H2CO on icy grain mantles, and ammonia-catalyzed, water-enhanced polymerization of formaldehyde in laboratory studies of astrophysical ices.

Software Applications on the Peregrine System | High-Performance Computing

Science.gov Websites

programming and optimization. Gaussian Chemistry Program for calculating molecular electronic structure and Materials Science Open-source classical molecular dynamics program designed for massively parallel systems framework Q-Chem Chemistry ab initio quantum chemistry package for predictin molecular structures

Theory-restricted resonant x-ray reflectometry of quantum materials

NASA Astrophysics Data System (ADS)

Fürsich, Katrin; Zabolotnyy, Volodymyr B.; Schierle, Enrico; Dudy, Lenart; Kirilmaz, Ozan; Sing, Michael; Claessen, Ralph; Green, Robert J.; Haverkort, Maurits W.; Hinkov, Vladimir

2018-04-01

The delicate interplay of competing phases in quantum materials is dominated by parameters such as the crystal field potential, the spin-orbit coupling, and, in particular, the electronic correlation strength. Whereas small quantitative variations of the parameter values can thus qualitatively change the material, these values can hitherto hardly be obtained with reasonable precision, be it theoretically or experimentally. Here we propose a solution combining resonant x-ray reflectivity (RXR) with multiplet ligand field theory (MLFT). We first perform ab initio DFT calculations within the MLFT framework to get initial parameter values, which we then use in a fit of the theoretical model to RXR. To validate our method, we apply it to NiO and SrTiO3 and obtain parameter values, which are amended by as much as 20 % compared to the ab initio results. Our approach is particularly useful to investigate topologically trivial and nontrivial correlated insulators, staggered moments in magnetically or orbitally ordered materials, and reconstructed interfaces.

Importance of nonlocal electron correlation in the BaNiS2 semimetal from quantum oscillations studies

NASA Astrophysics Data System (ADS)

Klein, Yannick; Casula, Michele; Santos-Cottin, David; Audouard, Alain; Vignolles, David; Fève, Gwendal; Freulon, Vincent; Plaçais, Bernard; Verseils, Marine; Yang, Hancheng; Paulatto, Lorenzo; Gauzzi, Andrea

2018-02-01

By means of Shubnikov-de Haas and de Haas-van Alphen oscillations, and ab initio calculations, we have studied the Fermi surface of high-quality BaNiS2 single crystals, with mean free path l ˜400 Å . The angle and temperature dependence of quantum oscillations indicates a quasi-two-dimensional Fermi surface, made of an electronlike tube centered at Γ , and of four holelike cones, generated by Dirac bands, weakly dispersive in the out-of-plane direction. Ab initio electronic structure calculations, in the density functional theory framework, show that the inclusion of screened exchange is necessary to account for the experimental Fermi pockets. Therefore, the choice of the functional becomes crucial. A modified HSE hybrid functional with 7% of exact exchange outperforms both GGA and GGA +U density functionals, signaling the importance of nonlocal screened-exchange interactions in BaNiS2, and, more generally, in 3 d compensated semimetals.

Machine learning of molecular electronic properties in chemical compound space

NASA Astrophysics Data System (ADS)

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

2013-09-01

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

Atomic resolution crystal structures and quantum chemistry meet to reveal subtleties of hydroxynitrile lyase catalysis.

PubMed

Schmidt, Andrea; Gruber, Karl; Kratky, Christoph; Lamzin, Victor S

2008-08-01

Hydroxynitrile lyases are versatile enzymes that enantiospecifically cope with cyanohydrins, important intermediates in the production of various agrochemicals or pharmaceuticals. We determined four atomic resolution crystal structures of hydroxynitrile lyase from Hevea brasiliensis: one native and three complexes with acetone, isopropyl alcohol, and thiocyanate. We observed distinct distance changes among the active site residues related to proton shifts upon substrate binding. The combined use of crystallography and ab initio quantum chemical calculations allowed the determination of the protonation states in the enzyme active site. We show that His(235) of the catalytic triad must be protonated in order for catalysis to proceed, and we could reproduce the cyanohydrin synthesis in ab initio calculations. We also found evidence for the considerable pK(a) shifts that had been hypothesized earlier. We envision that this knowledge can be used to enhance the catalytic properties and the stability of the enzyme for industrial production of enantiomerically pure cyanohydrins.

Multi-layer Lanczos iteration approach to calculations of vibrational energies and dipole transition intensities for polyatomic molecules

DOE PAGES

Yu, Hua-Gen

2015-01-28

We report a rigorous full dimensional quantum dynamics algorithm, the multi-layer Lanczos method, for computing vibrational energies and dipole transition intensities of polyatomic molecules without any dynamics approximation. The multi-layer Lanczos method is developed by using a few advanced techniques including the guided spectral transform Lanczos method, multi-layer Lanczos iteration approach, recursive residue generation method, and dipole-wavefunction contraction. The quantum molecular Hamiltonian at the total angular momentum J = 0 is represented in a set of orthogonal polyspherical coordinates so that the large amplitude motions of vibrations are naturally described. In particular, the algorithm is general and problem-independent. An applicationmore » is illustrated by calculating the infrared vibrational dipole transition spectrum of CH₄ based on the ab initio T8 potential energy surface of Schwenke and Partridge and the low-order truncated ab initio dipole moment surfaces of Yurchenko and co-workers. A comparison with experiments is made. The algorithm is also applicable for Raman polarizability active spectra.« less

Ab Initio Quantum Monte Carlo Simulation of the Warm Dense Electron Gas in the Thermodynamic Limit

DOE PAGES

Dornheim, Tobias; Groth, Simon; Sjostrom, Travis; ...

2016-10-07

Here we perform ab initio quantum Monte Carlo (QMC) simulations of the warm dense uniform electron gas in the thermodynamic limit. By combining QMC data with the linear response theory, we are able to remove finite-size errors from the potential energy over the substantial parts of the warm dense regime, overcoming the deficiencies of the existing finite-size corrections by Brown et al. [Phys. Rev. Lett. 110, 146405 (2013)]. Extensive new QMC results for up to N = 1000 electrons enable us to compute the potential energy V and the exchange-correlation free energy F xc of the macroscopic electron gas withmore » an unprecedented accuracy of | Δ V | / | V | , | Δ F xc | / | F | xc ~ 10 $-$3. Finally, a comparison of our new data to the recent parametrization of F xc by Karasiev et al. [Phys. Rev. Lett. 112, 076403 (2014)] reveals significant deviations to the latter.« less

Nonadiabatic couplings in the collisional removal of O(2)(b (1)Sigma(g) (+),v) by O(2).

PubMed

Dayou, F; Hernández, M I; Campos-Martínez, J; Hernández-Lamoneda, R

2010-01-28

The effect of nonadiabatic couplings on the collisional removal of O(2)(b (1)Sigma(g) (+),v) by O(2)(X (3)Sigma(g) (-), v=0) is investigated. Two-dimensional adiabatic and quasidiabatic potential energy surfaces for the excited dimer states and the corresponding nonadiabatic radial couplings have been computed by means of ab initio calculations. Alternately, a two-state theoretical model, based on the Landau-Zener and Rosen-Zener-Demkov assumptions, has been employed to derive analytical forms for the nonadiabatic couplings and an adiabatic-to-diabatic transformation only depending on a reduced set of adiabatic energy terms. Compared to the ab initio results, the predictions of the model are found to be highly accurate. Quantum dynamics calculations for the removal of the first ten vibrational states of O(2)(b (1)Sigma(g) (+),v) indicate a clear dominant contribution of the vibration-electronic relaxation mechanism relative to the vibration-translation energy transfer. Although the present reduced-dimensionality model precludes any quantitative comparison with experiments, it is found that the removal probabilities for v=1-3 are qualitatively consistent with the experimental observations, once the vibrational structure of the fragments is corrected with spectroscopical terms. Besides, the model served to show how the computation of the adiabatic PESs just at the crossing seam was sufficient to describe the nonadiabatic dynamics related to a given geometrical arrangement. This implies considerable savings in the calculations which will eventually allow for larger accuracy in the ab initio calculations as well as higher dimensional treatments.

Ab-initio study of pressure evolution of structural, mechanical and magnetic properties of cementite (Fe3C) phase

NASA Astrophysics Data System (ADS)

Gorai, S.; Ghosh, P. S.; Bhattacharya, C.; Arya, A.

2018-04-01

The pressure evolution of phase stability, structural and mechanical properties of Fe3C in ferro-magnetic (FM) and high pressure non magnetic (NM) phase is investigated from first principle calculations. The 2nd order FM to NM phase transition of Fe3C is identified around 60 GPa. Pressure (or density) variation of sound velocities from our ab-initio calculated single crystal elastic constants are determined to predict these parameters at Earth's outer core pressure.

Vibrations of bioionic liquids by ab initio molecular dynamics and vibrational spectroscopy.

PubMed

Tanzi, Luana; Benassi, Paola; Nardone, Michele; Ramondo, Fabio

2014-12-26

Density functional theory and vibrational spectroscopy are used to investigate a class of bioionic liquids consisting of a choline cation and carboxylate anions. Through quantum mechanical studies of motionless ion pairs and molecular dynamics of small portions of the liquid, we have characterized important structural features of the ionic liquid. Hydrogen bonding produces stable ion pairs in the liquid and induces vibrational features of the carboxylate groups comparable with experimental results. Infrared and Raman spectra of liquids have been measured, and main bands have been assigned on the basis of theoretical spectra.

The Phenalenyl Free Radical - a Jahn-Teller D3H PAH

NASA Astrophysics Data System (ADS)

O'Connor, G. D.; Troy, T. P.; Roberts, D. A.; Chalyavi, N.; Fückel, B.; Crossley, M. J.; Nauta, K.; Schmidt, T. W.; Stanton, J. F.

2012-06-01

After benzene and naphthalene, the smallest polycyclic aromatic hydrocarbon bearing six-membered rings is the threefold-symmetric phenalenyl radical. Despite the fact that it is so fundamental, its electronic spectroscopy has not been rigorously scrutinized, in spite of growing interest in graphene fragments for molecular electronic applications. Here we used complementary laser spectroscopic techniques to probe the jet-cooled phenalenyl radical in vacuo. Its spectrum reveals the interplay between four electronic states that exhibit Jahn-Teller and pseudo-Jahn-Teller (Herzberg-Teller) vibronic coupling. The coupling mechanism has been elucidated by the application of various ab initio quantum-chemical techniques.

Perspective: Quantum mechanical methods in biochemistry and biophysics.

PubMed

Cui, Qiang

2016-10-14

In this perspective article, I discuss several research topics relevant to quantum mechanical (QM) methods in biophysical and biochemical applications. Due to the immense complexity of biological problems, the key is to develop methods that are able to strike the proper balance of computational efficiency and accuracy for the problem of interest. Therefore, in addition to the development of novel ab initio and density functional theory based QM methods for the study of reactive events that involve complex motifs such as transition metal clusters in metalloenzymes, it is equally important to develop inexpensive QM methods and advanced classical or quantal force fields to describe different physicochemical properties of biomolecules and their behaviors in complex environments. Maintaining a solid connection of these more approximate methods with rigorous QM methods is essential to their transferability and robustness. Comparison to diverse experimental observables helps validate computational models and mechanistic hypotheses as well as driving further development of computational methodologies.

State-specific tunneling lifetimes from classical trajectories: H-atom dissociation in electronically excited pyrrole

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xie, Weiwei; Domcke, Wolfgang; Farantos, Stavros C.

A trajectory method of calculating tunneling probabilities from phase integrals along straight line tunneling paths, originally suggested by Makri and Miller [J. Chem. Phys. 91, 4026 (1989)] and recently implemented by Truhlar and co-workers [Chem. Sci. 5, 2091 (2014)], is tested for one- and two-dimensional ab initio based potentials describing hydrogen dissociation in the {sup 1}B{sub 1} excited electronic state of pyrrole. The primary observables are the tunneling rates in a progression of bending vibrational states lying below the dissociation barrier and their isotope dependences. Several initial ensembles of classical trajectories have been considered, corresponding to the quasiclassical and themore » quantum mechanical samplings of the initial conditions. It is found that the sampling based on the fixed energy Wigner density gives the best agreement with the quantum mechanical dissociation rates.« less

Structure and dynamics of the UO(2)(2+) ion in aqueous solution: an ab initio QMCF MD study.

PubMed

Frick, Robert J; Hofer, Thomas S; Pribil, Andreas B; Randolf, Bernhard R; Rode, Bernd M

2009-11-12

A comprehensive theoretical investigation on the structure and dynamics of the UO(2)(2+) ion in aqueous solution using double-zeta HF level quantum mechanical charge field molecular dynamics is presented. The quantum mechanical region includes two full layers of hydration and is embedded in a large box of explicitly treated water to achieve a realistic environment. A number of different functions, including segmential, radial, and angular distribution functions, are employed together with tilt- and Theta-angle distribution functions to describe the complex structural properties of this ion. These data were compared to recent experimental data obtained from LAXS and EXAFS and results of various theoretical calculations. Some properties were explained with the aid of charge distribution plots for the solute. The solvent dynamics around the ion were investigated using distance plots and mean ligand residence times and the results compared to experimental and theoretical data of related ions.

The prediction of crystal structure by merging knowledge methods with first principles quantum mechanics

NASA Astrophysics Data System (ADS)

Ceder, Gerbrand

2007-03-01

The prediction of structure is a key problem in computational materials science that forms the platform on which rational materials design can be performed. Finding structure by traditional optimization methods on quantum mechanical energy models is not possible due to the complexity and high dimensionality of the coordinate space. An unusual, but efficient solution to this problem can be obtained by merging ideas from heuristic and ab initio methods: In the same way that scientist build empirical rules by observation of experimental trends, we have developed machine learning approaches that extract knowledge from a large set of experimental information and a database of over 15,000 first principles computations, and used these to rapidly direct accurate quantum mechanical techniques to the lowest energy crystal structure of a material. Knowledge is captured in a Bayesian probability network that relates the probability to find a particular crystal structure at a given composition to structure and energy information at other compositions. We show that this approach is highly efficient in finding the ground states of binary metallic alloys and can be easily generalized to more complex systems.

AN IN SILICO INVESTIGATION OF THE ENANTIOSELECTIVE METABOLISM RATES OF TRIAZOLE FUGICIDES

EPA Science Inventory

The objective of this work is to use in silico methods such as ab initio quantum and classical force-field methods to explore and develop an understanding for the enantioselective metabolism rates experimentally observed in the triazole fungicide bromuconazole. This directed stud...

Specific interactions between mycobacterial FtsZ protein and curcumin derivatives: Molecular docking and ab initio molecular simulations

NASA Astrophysics Data System (ADS)

Fujimori, Mitsuki; Sogawa, Haruki; Ota, Shintaro; Karpov, Pavel; Shulga, Sergey; Blume, Yaroslav; Kurita, Noriyuki

2018-01-01

Filamentous temperature-sensitive Z (FtsZ) protein plays essential role in bacteria cell division, and its inhibition prevents Mycobacteria reproduction. Here we adopted curcumin derivatives as candidates of novel inhibitors and investigated their specific interactions with FtsZ, using ab initio molecular simulations based on protein-ligand docking, classical molecular mechanics and ab initio fragment molecular orbital (FMO) calculations. Based on FMO calculations, we specified the most preferable site of curcumin binding to FtsZ and highlighted the key amino acid residues for curcumin binding at an electronic level. The result will be useful for proposing novel inhibitors against FtsZ based on curcumin derivatives.

Ab Initio QM/MM Study Shows a Highly Dissociated SN2 Hydrolysis Mechanism for the cGMP-Specific Phosphodiesterase-5.

PubMed

Li, Zhe; Wu, Yinuo; Feng, Ling-Jun; Wu, Ruibo; Luo, Hai-Bin

2014-12-09

Phosphodiesterases (PDEs) are the sole enzymes hydrolyzing the important second messengers cGMP and cAMP and have been identified as therapeutic targets for several diseases. The most successful examples are PDE5 inhibitors (i.e., sildenafil and tadalafil), which have been approved for the treatment of male erectile dysfunction and pulmonary hypertension. However, the side effects mostly due to nonselective inhibition toward other PDE isoforms, set back the clinical usage of PDE5 inhibitors. Until now, the exact catalytic mechanism of the substrate cGMP by PDE5 is still unclear. Herein, the first computational study on the catalytic hydrolysis mechanism of cGMP for PDE5 (catalytic domain) is performed by employing the state-of-the-art ab initio quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations. Our simulations show a SN2 type reaction procedure via a highly dissociated transition state with a reaction barrier of 8.88 kcal/mol, which is quite different from the previously suggested hydrolysis mechanism of cAMP for PDE4. Furthermore, the subsequent ligand exchange and the release of the product GMP have also been investigated by binding energy analysis and MD simulations. It is deduced that ligand exchange would be the rate-determining step of the whole reaction, which is consistent with many previous experimental results. The obtained mechanistic insights should be valuable for not only the rational design of more specific inhibitors toward PDE5 but also understanding the general hydrolysis mechanism of cGMP-specific PDEs.

Quantum mechanical study of solvent effects in a prototype S{sub N}2 reaction in solution: Cl{sup −} attack on CH{sub 3}Cl

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuechler, Erich R.; Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455-0431; York, Darrin M., E-mail: york@biomaps.rutgers.edu

2014-02-07

The nucleophilic attack of a chloride ion on methyl chloride is an important prototype S{sub N}2 reaction in organic chemistry that is known to be sensitive to the effects of the surrounding solvent. Herein, we develop a highly accurate Specific Reaction Parameter (SRP) model based on the Austin Model 1 Hamiltonian for chlorine to study the effects of solvation into an aqueous environment on the reaction mechanism. To accomplish this task, we apply high-level quantum mechanical calculations to study the reaction in the gas phase and combined quantum mechanical/molecular mechanical simulations with TIP3P and TIP4P-ew water models and the resultingmore » free energy profiles are compared with those determined from simulations using other fast semi-empirical quantum models. Both gas phase and solution results with the SRP model agree very well with experiment and provide insight into the specific role of solvent on the reaction coordinate. Overall, the newly parameterized SRP Hamiltonian is able to reproduce both the gas phase and solution phase barriers, suggesting it is an accurate and robust model for simulations in the aqueous phase at greatly reduced computational cost relative to comparably accurate ab initio and density functional models.« less

Quantum mechanical study of solvent effects in a prototype SN2 reaction in solution: Cl- attack on CH3Cl

NASA Astrophysics Data System (ADS)

Kuechler, Erich R.; York, Darrin M.

2014-02-01

The nucleophilic attack of a chloride ion on methyl chloride is an important prototype SN2 reaction in organic chemistry that is known to be sensitive to the effects of the surrounding solvent. Herein, we develop a highly accurate Specific Reaction Parameter (SRP) model based on the Austin Model 1 Hamiltonian for chlorine to study the effects of solvation into an aqueous environment on the reaction mechanism. To accomplish this task, we apply high-level quantum mechanical calculations to study the reaction in the gas phase and combined quantum mechanical/molecular mechanical simulations with TIP3P and TIP4P-ew water models and the resulting free energy profiles are compared with those determined from simulations using other fast semi-empirical quantum models. Both gas phase and solution results with the SRP model agree very well with experiment and provide insight into the specific role of solvent on the reaction coordinate. Overall, the newly parameterized SRP Hamiltonian is able to reproduce both the gas phase and solution phase barriers, suggesting it is an accurate and robust model for simulations in the aqueous phase at greatly reduced computational cost relative to comparably accurate ab initio and density functional models.

Quantum mechanical study of solvent effects in a prototype SN2 reaction in solution: Cl- attack on CH3Cl.

PubMed

Kuechler, Erich R; York, Darrin M

2014-02-07

The nucleophilic attack of a chloride ion on methyl chloride is an important prototype SN2 reaction in organic chemistry that is known to be sensitive to the effects of the surrounding solvent. Herein, we develop a highly accurate Specific Reaction Parameter (SRP) model based on the Austin Model 1 Hamiltonian for chlorine to study the effects of solvation into an aqueous environment on the reaction mechanism. To accomplish this task, we apply high-level quantum mechanical calculations to study the reaction in the gas phase and combined quantum mechanical/molecular mechanical simulations with TIP3P and TIP4P-ew water models and the resulting free energy profiles are compared with those determined from simulations using other fast semi-empirical quantum models. Both gas phase and solution results with the SRP model agree very well with experiment and provide insight into the specific role of solvent on the reaction coordinate. Overall, the newly parameterized SRP Hamiltonian is able to reproduce both the gas phase and solution phase barriers, suggesting it is an accurate and robust model for simulations in the aqueous phase at greatly reduced computational cost relative to comparably accurate ab initio and density functional models.

Electron capture in collisions of S4+ with atomic hydrogen

NASA Astrophysics Data System (ADS)

Stancil, P. C.; Turner, A. R.; Cooper, D. L.; Schultz, D. R.; Rakovic, M. J.; Fritsch, W.; Zygelman, B.

2001-06-01

Charge transfer processes due to collisions of ground state S4+(3s2 1S) ions with atomic hydrogen are investigated for energies between 1 meV u-1 and 10 MeV u-1 using the quantum mechanical molecular-orbital close-coupling (MOCC), atomic-orbital close-coupling, classical trajectory Monte Carlo (CTMC) and continuum distorted wave methods. The MOCC calculations utilize ab initio adiabatic potentials and nonadiabatic radial coupling matrix elements obtained with the spin-coupled valence-bond approach. A number of variants of the CTMC approach were explored, including different momentum and radial distributions for the initial state, as well as effective charge and quantum-defect models to determine the corresponding quantum state after capture into final partially stripped S3+ excited classical states. Hydrogen target isotope effects are explored and rate coefficients for temperatures between 100 and 106 K are also presented.

Inverse Temperature Dependence of Nuclear Quantum Effects in DNA Base Pairs

PubMed Central

2016-01-01

Despite the inherently quantum mechanical nature of hydrogen bonding, it is unclear how nuclear quantum effects (NQEs) alter the strengths of hydrogen bonds. With this in mind, we use ab initio path integral molecular dynamics to determine the absolute contribution of NQEs to the binding in DNA base pair complexes, arguably the most important hydrogen-bonded systems of all. We find that depending on the temperature, NQEs can either strengthen or weaken the binding within the hydrogen-bonded complexes. As a somewhat counterintuitive consequence, NQEs can have a smaller impact on hydrogen bond strengths at cryogenic temperatures than at room temperature. We rationalize this in terms of a competition of NQEs between low-frequency and high-frequency vibrational modes. Extending this idea, we also propose a simple model to predict the temperature dependence of NQEs on hydrogen bond strengths in general. PMID:27195654

The nitrogen-vacancy colour centre in diamond

NASA Astrophysics Data System (ADS)

Doherty, Marcus W.; Manson, Neil B.; Delaney, Paul; Jelezko, Fedor; Wrachtrup, Jörg; Hollenberg, Lloyd C. L.

2013-07-01

The nitrogen-vacancy (NV) colour centre in diamond is an important physical system for emergent quantum technologies, including quantum metrology, information processing and communications, as well as for various nanotechnologies, such as biological and sub-diffraction limit imaging, and for tests of entanglement in quantum mechanics. Given this array of existing and potential applications and the almost 50 years of NV research, one would expect that the physics of the centre is well understood, however, the study of the NV centre has proved challenging, with many early assertions now believed false and many remaining issues yet to be resolved. This review represents the first time that the key empirical and ab initio results have been extracted from the extensive NV literature and assembled into one consistent picture of the current understanding of the centre. As a result, the key unresolved issues concerning the NV centre are identified and the possible avenues for their resolution are examined.

Specific interactions between DNA and regulatory protein controlled by ligand-binding: Ab initio molecular simulation

NASA Astrophysics Data System (ADS)

Matsushita, Y.; Murakawa, T.; Shimamura, K.; Oishi, M.; Ohyama, T.; Kurita, N.

2015-02-01

The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA.

Ab initio investigation of the thermal decomposition of n-butylcyclohexane.

PubMed

Ali, Mohamad Akbar; Dillstrom, V Tyler; Lai, Jason Y W; Violi, Angela

2014-02-13

Environmental and energy security concerns have motivated an increased focus on developing clean, efficient combustors, which increasingly relies on insight into the combustion chemistry of fuels. In particular, naphthenes (cycloalkanes and alkylcycloalkanes) are important chemical components of distillate fuels, such as diesel and jet fuels. As such, there is a growing interest in describing napthene reactivity with kinetic mechanisms. Use of these mechanisms in predictive combustion models aids in the development of combustors. This study focuses on the pyrolysis of n-butylcyclohexane (n-BCH), an important representative of naphthenes in jet fuels. Seven different unimolecular decomposition pathways of C-C bond fission were explored utilizing ab initio/DFT methods. Accurate reaction energies were computed using the high-level quantum composite G3B3 method. Variational transition state theory, Rice-Ramsperger-Kassel-Marcus/master equation simulations provided temperature- and pressure-dependent rate constants. Implementation of these pathways into an existing chemical kinetic mechanism improved the prediction of experimental OH radical and H2O speciation in shock tube oxidation. Simulations of this combustion showed a change in the expected decomposition chemistry of n-BCH, predicting increased production of cyclic alkyl radicals instead of straight-chain alkenes. The most prominent reaction pathway for the decomposition of n-BCH is n-BCH = C3H7 + C7H13. The results of this study provide insight into the combustion of n-BCH and will aid in the future development of naphthene kinetic mechanisms.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Croft, J. F. E.; Makrides, C.; Li, M.

A fundamental question in the study of chemical reactions is how reactions proceed at a collision energy close to absolute zero. This question is no longer hypothetical: quantum degenerate gases of atoms and molecules can now be created at temperatures lower than a few tens of nanokelvin. Here we consider the benchmark ultracold reaction between, the most-celebrated ultracold molecule, KRb and K. We map out an accurate ab initio ground-state potential energy surface of the K 2Rb complex in full dimensionality and report numerically-exact quantum-mechanical reaction dynamics. The distribution of rotationally resolved rates is shown to be Poissonian. An analysismore » of the hyperspherical adiabatic potential curves explains this statistical character revealing a chaotic distribution for the short-range collision complex that plays a key role in governing the reaction outcome.« less

Assessment and Validation of Machine Learning Methods for Predicting Molecular Atomization Energies.

PubMed

Hansen, Katja; Montavon, Grégoire; Biegler, Franziska; Fazli, Siamac; Rupp, Matthias; Scheffler, Matthias; von Lilienfeld, O Anatole; Tkatchenko, Alexandre; Müller, Klaus-Robert

2013-08-13

The accurate and reliable prediction of properties of molecules typically requires computationally intensive quantum-chemical calculations. Recently, machine learning techniques applied to ab initio calculations have been proposed as an efficient approach for describing the energies of molecules in their given ground-state structure throughout chemical compound space (Rupp et al. Phys. Rev. Lett. 2012, 108, 058301). In this paper we outline a number of established machine learning techniques and investigate the influence of the molecular representation on the methods performance. The best methods achieve prediction errors of 3 kcal/mol for the atomization energies of a wide variety of molecules. Rationales for this performance improvement are given together with pitfalls and challenges when applying machine learning approaches to the prediction of quantum-mechanical observables.

Accelerated path-integral simulations using ring-polymer interpolation

NASA Astrophysics Data System (ADS)

Buxton, Samuel J.; Habershon, Scott

2017-12-01

Imaginary-time path-integral (PI) molecular simulations can be used to calculate exact quantum statistical mechanical properties for complex systems containing many interacting atoms and molecules. The limiting computational factor in a PI simulation is typically the evaluation of the potential energy surface (PES) and forces at each ring-polymer "bead"; for an n-bead ring-polymer, a PI simulation is typically n times greater than the corresponding classical simulation. To address the increased computational effort of PI simulations, several approaches have been developed recently, most notably based on the idea of ring-polymer contraction which exploits either the separation of the PES into short-range and long-range contributions or the availability of a computationally inexpensive PES which can be incorporated to effectively smooth the ring-polymer PES; neither approach is satisfactory in applications to systems modeled by PESs given by on-the-fly ab initio calculations. In this article, we describe a new method, ring-polymer interpolation (RPI), which can be used to accelerate PI simulations without any prior assumptions about the PES. In simulations of liquid water modeled by an empirical PES (or force field) under ambient conditions, where quantum effects are known to play a subtle role in influencing experimental observables such as radial distribution functions, we find that RPI can accurately reproduce the results of fully-converged PI simulations, albeit with far fewer PES evaluations. This approach therefore opens the possibility of large-scale PI simulations using ab initio PESs evaluated on-the-fly without the drawbacks of current methods.

Photodissociation dynamics in the first absorption band of pyrrole. I. Molecular Hamiltonian and the Herzberg-Teller absorption spectrum for the A12(π σ* ) ←X˜ 1 A1(π π ) transition

NASA Astrophysics Data System (ADS)

Picconi, David; Grebenshchikov, Sergy Yu.

2018-03-01

This paper opens a series in which the photochemistry of the two lowest πσ* states of pyrrole and their interaction with each other and with the ground electronic state X ˜ are studied using ab initio quantum mechanics. New 24-dimensional potential energy surfaces for the photodissociation of the N-H bond and the formation of the pyrrolyl radical are calculated using the multiconfigurational perturbation theory (CASPT2) for the electronic states X ˜ (π π ) , 11A2(πσ*), and 11B1(πσ*) and locally diabatized. In this paper, the ab initio calculations are described and the photodissociation in the state 11A2(πσ*) is analyzed. The excitation 11 A2←X ˜ is mediated by the coordinate dependent transition dipole moment functions constructed using the Herzberg-Teller expansion. Nuclear dynamics, including 6, 11, and 15 active degrees of freedom, are studied using the multi-configurational time-dependent Hartree method. The focus is on the frequency resolved absorption spectrum as well as on the dissociation time scales and the resonance lifetimes. Calculations are compared with available experimental data. An approximate convolution method is developed and validated, with which absorption spectra can be calculated and assigned in terms of vibrational quantum numbers. The method represents the total absorption spectrum as a convolution of the diffuse spectrum of the detaching H-atom and the Franck-Condon spectrum of the heteroaromatic ring. Convolution calculation requires a minimal quantum chemical input and is a promising tool for studying the πσ* photodissociation in model biochromophores.

Ground and excited states of NH4: Electron propagator and quantum defect analysis

NASA Astrophysics Data System (ADS)

Ortiz, J. V.; Martín, I.; Velasco, A. M.; Lavín, C.

2004-05-01

Vertical excitation energies of the Rydberg radical NH4 are inferred from ab initio electron propagator calculations on the electron affinities of NH4+. The adiabatic ionization energy of NH4 is evaluated with coupled-cluster calculations. These predictions provide optimal parameters for the molecular-adapted quantum defect orbital method, which is used to determine Einstein emission coefficients and radiative lifetimes. Comparisons with spectroscopic data and previous calculations are discussed.

Spectroscopy of H3+ based on a new high-accuracy global potential energy surface.

PubMed

Polyansky, Oleg L; Alijah, Alexander; Zobov, Nikolai F; Mizus, Irina I; Ovsyannikov, Roman I; Tennyson, Jonathan; Lodi, Lorenzo; Szidarovszky, Tamás; Császár, Attila G

2012-11-13

The molecular ion H(3)(+) is the simplest polyatomic and poly-electronic molecular system, and its spectrum constitutes an important benchmark for which precise answers can be obtained ab initio from the equations of quantum mechanics. Significant progress in the computation of the ro-vibrational spectrum of H(3)(+) is discussed. A new, global potential energy surface (PES) based on ab initio points computed with an average accuracy of 0.01 cm(-1) relative to the non-relativistic limit has recently been constructed. An analytical representation of these points is provided, exhibiting a standard deviation of 0.097 cm(-1). Problems with earlier fits are discussed. The new PES is used for the computation of transition frequencies. Recently measured lines at visible wavelengths combined with previously determined infrared ro-vibrational data show that an accuracy of the order of 0.1 cm(-1) is achieved by these computations. In order to achieve this degree of accuracy, relativistic, adiabatic and non-adiabatic effects must be properly accounted for. The accuracy of these calculations facilitates the reassignment of some measured lines, further reducing the standard deviation between experiment and theory.

Relative stability of major types of beta-turns as a function of amino acid composition: a study based on Ab initio energetic and natural abundance data.

PubMed

Perczel, András; Jákli, Imre; McAllister, Michael A; Csizmadia, Imre G

2003-06-06

Folding properties of small globular proteins are determined by their amino acid sequence (primary structure). This holds both for local (secondary structure) and for global conformational features of linear polypeptides and proteins composed from natural amino acid derivatives. It thus provides the rational basis of structure prediction algorithms. The shortest secondary structure element, the beta-turn, most typically adopts either a type I or a type II form, depending on the amino acid composition. Herein we investigate the sequence-dependent folding stability of both major types of beta-turns using simple dipeptide models (-Xxx-Yyy-). Gas-phase ab initio properties of 16 carefully selected and suitably protected dipeptide models (for example Val-Ser, Ala-Gly, Ser-Ser) were studied. For each backbone fold most probable side-chain conformers were considered. Fully optimized 321G RHF molecular structures were employed in medium level [B3LYP/6-311++G(d,p)//RHF/3-21G] energy calculations to estimate relative populations of the different backbone conformers. Our results show that the preference for beta-turn forms as calculated by quantum mechanics and observed in Xray determined proteins correlates significantly.

Quantum-mechanical ab initio simulation of the Raman and IR spectra of Mn3Al2Si3O12 spessartine

NASA Astrophysics Data System (ADS)

Valenzano, Loredana; Meyer, Alessio; Demichelis, Raffaella; Civalleri, Bartolomeo; Dovesi, Roberto

2009-07-01

The IR and Raman spectra of spessartine garnet Mn3Al2Si3O12, are simulated with the periodic ab initio CRYSTAL code by adopting an all-electron Gaussian-type basis set and the B3LYP Hamiltonian. The frequencies of the 25 Raman active modes (3 of A 1 g , 8 of E g and 14 of F 2 g symmetry) and of the two sets of 17 F 1 u transverse-optical and longitudinal-optical frequencies are generated, as well as the IR oscillator strength. The agreement between calculated and experimental data is excellent: for the IR and Raman sets, the mean absolute difference overline{|Updelta|} is 4.0 and 6.8 cm-1, respectively. Isotopic substitution permits to highlight the Mn, Al and Si participation to the various zones of the spectrum. Graphical animation, available on the authors’ web-site ( http://www.crystal.unito.it/vibs/garnets/spessartine/ ), provides a very readable description of the movement of atoms and groups in each vibrational mode.

Spectroscopic (FT-IR and FT-Raman) investigation, first order hyperpolarizability, NBO, HOMO-LUMO and MEP analysis of 6-nitrochromone by ab initio and density functional theory calculations

NASA Astrophysics Data System (ADS)

Senthil kumar, J.; Jeyavijayan, S.; Arivazhagan, M.

2015-02-01

The vibrational spectral analysis is carried out using FT-Raman and FT-IR spectroscopy in the range 3500-50 cm-1 and 4000-400 cm-1, respectively, for 6-nitrochromone (6NC). The molecular structure, fundamental vibrational frequencies and intensity of the vibrational bands are interpreted with the aid of structure optimization and normal coordinates force field calculation based on ab initio HF and DFT gradient calculations employing the HF/6-311++G(d,p) and B3LYP/6-311++G(d,p) basis set. Stability of the molecule has been analyzed using NBO analysis. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. Thermodynamic properties like entropy, heat capacity, zero-point energy and Mulliken's charge analysis have been calculated for the 6NC. The complete assignments were performed on the basis of total energy distribution (TED) of the vibrational modes with scaled quantum mechanical (SQM) method. The MEP map shows the negative potential sites are on oxygen atoms as well as the positive potential sites are around the hydrogen atoms.

Equation of state of dense plasmas with pseudoatom molecular dynamics

DOE PAGES

Starrett, C. E.; Saumon, D.

2016-06-14

Here, we present an approximation for calculating the equation of state (EOS) of warm and hot dense matter that is built on the previously published pseudoatom molecular dynamics (PAMD) model of dense plasmas [Starrett et al., Phys. Rev. E 91, 013104 (2015)]. And while the EOS calculation with PAMD was previously limited to orbital-free density functional theory (DFT), the new approximation presented here allows a Kohn-Sham DFT treatment of the electrons. The resulting EOS thus includes a quantum mechanical treatment of the electrons with a self-consistent model of the ionic structure, while remaining tractable at high temperatures. The method ismore » validated by comparisons with pressures from ab initio simulations of Be, Al, Si, and Fe. The EOS in the Thomas-Fermi approximation shows remarkable thermodynamic consistency over a wide range of temperatures for aluminum. We also calculate the principal Hugoniots of aluminum and silicon up to 500 eV. We find that the ionic structure of the plasma has a modest effect that peaks at temperatures of a few eV and that the features arising from the electronic structure agree well with ab initio simulations.« less

5Beta,6beta-epoxy-17-oxoandrostan-3beta-yl acetate and 5beta,6beta-epoxy-20-oxopregnan-3beta-yl acetate.

PubMed

Pinto, Rui M A; Salvador, Jorge A R; Paixão, José A

2008-05-01

In the title compounds, C(21)H(30)O(4), (I), and C(23)H(34)O(4), (II), respectively, which are valuable intermediates in the synthesis of important steroid derivatives, rings A and B are cis-(5beta,10beta)-fused. The two molecules have similar conformations of rings A, B and C. The presence of the 5beta,6beta-epoxide group induces a significant twist of the steroid nucleus and a strong flattening of the B ring. The different C17 substituents result in different conformations for ring D. Cohesion of the molecular packing is achieved in both compounds only by weak intermolecular interactions. The geometries of the molecules in the crystalline environment are compared with those of the free molecules as given by ab initio Roothan Hartree-Fock calculations. We show in this work that quantum mechanical ab initio methods reproduce well the details of the conformation of these molecules, including a large twist of the steroid nucleus. The calculated twist values are comparable, but are larger than the observed values, indicating a possible small effect of the crystal packing on the twist angles.

Molecular structure, vibrational spectra, NBO analysis and molecular packing prediction of 3-nitroacetanilide by ab initio HF and density functional theory.

PubMed

Li, Xiao-Hong; Li, Tong-Wei; Ju, Wei-Wei; Yong, Yong-Liang; Zhang, Xian-Zhou

2014-01-24

Quantum chemical calculations of geometries and vibrational wavenumbers of 3-nitroacetanilide (C8H8N2O3) in the ground state were carried out by using ab initio HF and density functional theory (DFT/B3LYP) methods with 6-31+G(*) basis set. The -311++G(**) basis set is also used for B3LYP level. The scaled harmonic vibrational frequencies have been compared with experimental FT-IR spectra. Theoretical vibrational spectra of the title compound were interpreted by means of potential energies distributions (PEDs) using MOLVIB program. The theoretical spectrograms for IR spectra of the title compound have been constructed. The shortening of C-H bond length and the elongation of N-H bond length suggest the existence of weak C-H⋯O and N-H⋯O hydrogen bonds, which is confirmed by the natural bond orbital analysis. In addition, the crystal structure obtained by molecular mechanics belongs to the P2(1) space group, with lattice parameters Z=4, a=14.9989 Å, b=4.0367 Å, c=12.9913 Å, ρ=0.998 g cm(-3). Copyright © 2013 Elsevier B.V. All rights reserved.

Molecular structure, vibrational spectra, NBO analysis and molecular packing prediction of 3-nitroacetanilide by ab initio HF and density functional theory

NASA Astrophysics Data System (ADS)

Li, Xiao-Hong; Li, Tong-Wei; Ju, Wei-Wei; Yong, Yong-Liang; Zhang, Xian-Zhou

2014-01-01

Quantum chemical calculations of geometries and vibrational wavenumbers of 3-nitroacetanilide (C8H8N2O3) in the ground state were carried out by using ab initio HF and density functional theory (DFT/B3LYP) methods with 6-31+G* basis set. The -311++G** basis set is also used for B3LYP level. The scaled harmonic vibrational frequencies have been compared with experimental FT-IR spectra. Theoretical vibrational spectra of the title compound were interpreted by means of potential energies distributions (PEDs) using MOLVIB program. The theoretical spectrograms for IR spectra of the title compound have been constructed. The shortening of Csbnd H bond length and the elongation of Nsbnd H bond length suggest the existence of weak Csbnd H⋯O and Nsbnd H⋯O hydrogen bonds, which is confirmed by the natural bond orbital analysis. In addition, the crystal structure obtained by molecular mechanics belongs to the P21 space group, with lattice parameters Z = 4, a = 14.9989 Å, b = 4.0367 Å, c = 12.9913 Å, ρ = 0.998 g cm-3.

Automated first-principles mapping for phase-change materials.

PubMed

Esser, Marc; Maintz, Stefan; Dronskowski, Richard

2017-04-05

Plotting materials on bi-coordinate maps according to physically meaningful descriptors has a successful tradition in computational solid-state science spanning more than four decades. Equipped with new ab initio techniques introduced in this work, we generate an improved version of the treasure map for phase-change materials (PCMs) as introduced previously by Lencer et al. which, other than before, charts all industrially used PCMs correctly. Furthermore, we suggest seven new PCM candidates, namely SiSb 4 Te 7 , Si 2 Sb 2 Te 5 , SiAs 2 Te 4 , PbAs 2 Te 4 , SiSb 2 Te 4 , Sn 2 As 2 Te 5 , and PbAs 4 Te 7 , to be used as synthetic targets. To realize aforementioned maps based on orbital mixing (or "hybridization") and ionicity coordinates, structural information was first included into an ab initio numerical descriptor for sp 3 orbital mixing and then generalized beyond high-symmetry structures. In addition, a simple, yet powerful quantum-mechanical ionization measure also including structural information was introduced. Taken together, these tools allow for (automatically) generating materials maps solely relying on first-principles calculations. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Dielectric properties of classical and quantized ionic fluids.

PubMed

Høye, Johan S

2010-06-01

We study time-dependent correlation functions of classical and quantum gases using methods of equilibrium statistical mechanics for systems of uniform as well as nonuniform densities. The basis for our approach is the path integral formalism of quantum mechanical systems. With this approach the statistical mechanics of a quantum mechanical system becomes the equivalent of a classical polymer problem in four dimensions where imaginary time is the fourth dimension. Several nontrivial results for quantum systems have been obtained earlier by this analogy. Here, we will focus upon the presence of a time-dependent electromagnetic pair interaction where the electromagnetic vector potential that depends upon currents, will be present. Thus both density and current correlations are needed to evaluate the influence of this interaction. Then we utilize that densities and currents can be expressed by polarizations by which the ionic fluid can be regarded as a dielectric one for which a nonlocal susceptibility is found. This nonlocality has as a consequence that we find no contribution from a possible transverse electric zero-frequency mode for the Casimir force between metallic plates. Further, we establish expressions for a leading correction to ab initio calculations for the energies of the quantized electrons of molecules where now retardation effects also are taken into account.

Microwave spectra and molecular structures of (Z)-pent-2-en-4-ynenitrile and maleonitrile.

PubMed

Halter, R J; Fimmen, R L; McMahon, R J; Peebles, S A; Kuczkowski, R L; Stanton, J F

2001-12-12

Accurate equilibrium structures have been determined for (Z)-pent-2-en-4-ynenitrile (8) and maleonitrile (9) by combining microwave spectroscopy data and ab initio quantum chemistry calculations. The microwave spectra of 10 isotopomers of 8 and 5 isotopomers of 9 were obtained using a pulsed nozzle Fourier transform microwave spectrometer. The ground-state rotational constants were adjusted for vibration-rotation interaction effects calculated from force fields obtained from ab initio calculations. The resultant equilibrium rotational constants were used to determine structures that are in very good agreement with those obtained from high-level ab initio calculations (CCSD(T)/cc-pVTZ). The geometric parameters in 8 and 9 are very similar; they also do not differ significantly from the all-carbon analogue, (Z)-hex-3-ene-1,5-diyne (7), the parent molecule for the Bergman cyclization. A small deviation from linearity about the alkyne and cyano linkages is observed for 7-9 and several related species where accurate equilibrium parameters are available. The data on 7-9 should be of interest to radioastronomy and may provide insights on the formation and interstellar chemistry of unsaturated species such as the cyanopolyynes.

Summary of workshop 'Theory Meets Industry'—the impact of ab initio solid state calculations on industrial materials research

NASA Astrophysics Data System (ADS)

Wimmer, E.

2008-02-01

A workshop, 'Theory Meets Industry', was held on 12-14 June 2007 in Vienna, Austria, attended by a well balanced number of academic and industrial scientists from America, Europe, and Japan. The focus was on advances in ab initio solid state calculations and their practical use in industry. The theoretical papers addressed three dominant themes, namely (i) more accurate total energies and electronic excitations, (ii) more complex systems, and (iii) more diverse and accurate materials properties. Hybrid functionals give some improvements in energies, but encounter difficulties for metallic systems. Quantum Monte Carlo methods are progressing, but no clear breakthrough is on the horizon. Progress in order-N methods is steady, as is the case for efficient methods for exploring complex energy hypersurfaces and large numbers of structural configurations. The industrial applications were dominated by materials issues in energy conversion systems, the quest for hydrogen storage materials, improvements of electronic and optical properties of microelectronic and display materials, and the simulation of reactions on heterogeneous catalysts. The workshop is a clear testimony that ab initio computations have become an industrial practice with increasingly recognized impact.

Spectroscopic and computational studies of ionic clusters as models of solvation and atmospheric reactions

NASA Astrophysics Data System (ADS)

Kuwata, Keith T.

Ionic clusters are useful as model systems for the study of fundamental processes in solution and in the atmosphere. Their structure and reactivity can be studied in detail using vibrational predissociation spectroscopy, in conjunction with high level ab initio calculations. This thesis presents the applications of infrared spectroscopy and computation to a variety of gas-phase cluster systems. A crucial component of the process of stratospheric ozone depletion is the action of polar stratospheric clouds (PSCs) to convert the reservoir species HCl and chlorine nitrate (ClONO2) to photochemically labile compounds. Quantum chemistry was used to explore one possible mechanism by which this activation is effected: Cl- + ClONO2 /to Cl2 + NO3- eqno(1)Correlated ab initio calculations predicted that the direct reaction of chloride ion with ClONO2 is facile, which was confirmed in an experimental kinetics study. In the reaction a weakly bound intermediate Cl2-NO3- is formed, with ~70% of the charge localized on the nitrate moiety. This enables the Cl2-NO3- cluster to be well solvated even in bulk solution, allowing (1) to be facile on PSCs. Quantum chemistry was also applied to the hydration of nitrosonium ion (NO+), an important process in the ionosphere. The calculations, in conjunction with an infrared spectroscopy experiment, revealed the structure of the gas-phase clusters NO+(H2O)n. The large degree of covalent interaction between NO+ and the lone pairs of the H2O ligands is contrasted with the weak electrostatic bonding between iodide ion and H2O. Finally, the competition between ion solvation and solvent self-association is explored for the gas-phase clusters Cl/-(H2O)n and Cl-(NH3)n. For the case of water, vibrational predissociation spectroscopy reveals less hydrogen bonding among H2O ligands than predicted by ab initio calculations. Nevertheless, for n /ge 5, cluster structure is dominated by water-water interactions, with Cl- only partially solvated by the water cluster. Preliminary infrared spectra and computations on Cl- (NH3)n indicate that NH3 preferentially binds to Cl- ion instead of forming inter-solvent networks.

Ab initio perspective on the Mollwo-Ivey relation for F centers in alkali halides

NASA Astrophysics Data System (ADS)

Tiwald, Paul; Karsai, Ferenc; Laskowski, Robert; Gräfe, Stefanie; Blaha, Peter; Burgdörfer, Joachim; Wirtz, Ludger

2015-10-01

We revisit the well-known Mollwo-Ivey relation that describes the "universal" dependence of the absorption energies of F-type color centers on the lattice constant a of alkali-halide crystals, Eabs∝a-n. We perform both state-of-the-art ab initio quantum chemistry and post-DFT calculations of F-center absorption spectra. By "tuning" independently the lattice constant and the atomic species we show that the scaling with the lattice constant alone (keeping the elements fixed) would yield n =2 in agreement with the "particle-in-the-box" model. Keeping the lattice constant fixed and changing the atomic species enables us to quantify the ion-size effects which are shown to be responsible for the exponent n ≈1.8 .

Quantum Tunneling of Water in Beryl. A New State of the Water Molecule

DOE PAGES

Kolesnikov, Alexander I.; Reiter, George F.; Choudhury, Narayani; ...

2016-04-22

When using neutron scattering and ab initio simulations, we document the discovery of a new “quantum tunneling state” of the water molecule confined in 5 Å channels in the mineral beryl, characterized by extended proton and electron delocalization. We observed a number of peaks in the inelastic neutron scattering spectra that were uniquely assigned to water quantum tunneling. Additionally, the water proton momentum distribution was measured with deep inelastic neutron scattering, which directly revealed coherent delocalization of the protons in the ground state.

Quantum Tunneling of Water in Beryl. A New State of the Water Molecule

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kolesnikov, Alexander I.; Reiter, George F.; Choudhury, Narayani

When using neutron scattering and ab initio simulations, we document the discovery of a new “quantum tunneling state” of the water molecule confined in 5 Å channels in the mineral beryl, characterized by extended proton and electron delocalization. We observed a number of peaks in the inelastic neutron scattering spectra that were uniquely assigned to water quantum tunneling. Additionally, the water proton momentum distribution was measured with deep inelastic neutron scattering, which directly revealed coherent delocalization of the protons in the ground state.

Spin-orbit coupled potential energy surfaces and properties using effective relativistic coupling by asymptotic representation.

PubMed

Ndome, Hameth; Eisfeld, Wolfgang

2012-08-14

A new method has been reported recently [H. Ndome, R. Welsch, and W. Eisfeld, J. Chem. Phys. 136, 034103 (2012)] that allows the efficient generation of fully coupled potential energy surfaces (PESs) including derivative and spin-orbit (SO) coupling. The method is based on the diabatic asymptotic representation of the molecular fine structure states and an effective relativistic coupling operator and therefore is called effective relativistic coupling by asymptotic representation (ERCAR). The resulting diabatic spin-orbit coupling matrix is constant and the geometry dependence of the coupling between the eigenstates is accounted for by the diabatization. This approach allows to generate an analytical model for the fully coupled PESs without performing any ab initio SO calculations (except perhaps for the atoms) and thus is very efficient. In the present work, we study the performance of this new method for the example of hydrogen iodide as a well-established test case. Details of the diabatization and the accuracy of the results are investigated in comparison to reference ab initio calculations. The energies of the adiabatic fine structure states are reproduced in excellent agreement with reference ab initio data. It is shown that the accuracy of the ERCAR approach mainly depends on the quality of the underlying ab initio data. This is also the case for dissociation and vibrational level energies, which are influenced by the SO coupling. A method is presented how one-electron operators and the corresponding properties can be evaluated in the framework of the ERCAR approach. This allows the computation of dipole and transition moments of the fine structure states in good agreement with ab initio data. The new method is shown to be very promising for the construction of fully coupled PESs for more complex polyatomic systems to be used in quantum dynamics studies.

Anisotropic mechanoresponse of energetic crystallites: a quantum molecular dynamics study of nano-collision

NASA Astrophysics Data System (ADS)

Li, Ying; Kalia, Rajiv K.; Misawa, Masaaki; Nakano, Aiichiro; Nomura, Ken-Ichi; Shimamura, Kohei; Shimojo, Fuyuki; Vashishta, Priya

2016-05-01

At the nanoscale, chemistry can happen quite differently due to mechanical forces selectively breaking the chemical bonds of materials. The interaction between chemistry and mechanical forces can be classified as mechanochemistry. An example of archetypal mechanochemistry occurs at the nanoscale in anisotropic detonating of a broad class of layered energetic molecular crystals bonded by inter-layer van der Waals (vdW) interactions. Here, we introduce an ab initio study of the collision, in which quantum molecular dynamic simulations of binary collisions between energetic vdW crystallites, TATB molecules, reveal atomistic mechanisms of anisotropic shock sensitivity. The highly sensitive lateral collision was found to originate from the twisting and bending to breaking of nitro-groups mediated by strong intra-layer hydrogen bonds. This causes the closing of the electronic energy gap due to an inverse Jahn-Teller effect. On the other hand, the insensitive collisions normal to multilayers are accomplished by more delocalized molecular deformations mediated by inter-layer interactions. Our nano-collision studies provide a much needed atomistic understanding for the rational design of insensitive energetic nanomaterials and the detonation synthesis of novel nanomaterials.At the nanoscale, chemistry can happen quite differently due to mechanical forces selectively breaking the chemical bonds of materials. The interaction between chemistry and mechanical forces can be classified as mechanochemistry. An example of archetypal mechanochemistry occurs at the nanoscale in anisotropic detonating of a broad class of layered energetic molecular crystals bonded by inter-layer van der Waals (vdW) interactions. Here, we introduce an ab initio study of the collision, in which quantum molecular dynamic simulations of binary collisions between energetic vdW crystallites, TATB molecules, reveal atomistic mechanisms of anisotropic shock sensitivity. The highly sensitive lateral collision was found to originate from the twisting and bending to breaking of nitro-groups mediated by strong intra-layer hydrogen bonds. This causes the closing of the electronic energy gap due to an inverse Jahn-Teller effect. On the other hand, the insensitive collisions normal to multilayers are accomplished by more delocalized molecular deformations mediated by inter-layer interactions. Our nano-collision studies provide a much needed atomistic understanding for the rational design of insensitive energetic nanomaterials and the detonation synthesis of novel nanomaterials. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr08769d

Intra- and intermolecular interaction inducing pyramidalization on both sides of a proline dipeptide during isomerization: an ab initio QM/MM molecular dynamics simulation study in explicit water.

PubMed

Yonezawa, Yasushige; Nakata, Kazuto; Sakakura, Kota; Takada, Toshikazu; Nakamura, Haruki

2009-04-01

The cis-trans isomerization of the peptide bond preceding a proline plays important roles in protein folding and biological function. Although many experimental and theoretical studies have been done, the mechanism has not yet been clearly elucidated. We studied the cis-trans isomerization of the proline dipeptide (Ace-Pro-NMe) in explicit water by molecular dynamics simulations using a combined potential derived from ab initio quantum mechanics and empirical molecular mechanics. We obtained the free energy landscape during the isomerization by using the umbrella sampling method. The free energy landscape is in good accordance with previous experimental and theoretical values. We observed that in the middle of the isomerization, the prolyl nitrogen transiently takes pyramidal conformations in two polarized directions and that, simultaneously, the prolyl C-N bond extends. We show that these geometrical changes cooperatively transform the prolyl nitrogen from a sp(2)-hybridized electronic state into a sp(3)-hybridized one, and thus realize a transition state that reduces the rotational barriers separating the cis- and trans-states. We also found that the hydration of the prolyl nitrogen stabilizes the negative pyramidal conformation, while an intramolecular interaction mainly stabilizes the positive one. Fluctuations in the polarity and magnitude of the pyramidal conformation during the isomerization are interpreted as a competition between the hydrogen-bonding partners for the prolyl nitrogen between different sides of the pyrrolidine ring.

CO ADSORPTION AS A PROBE OF THE ELECTRIC FIELD IN ALKALINE-EARTH EXCHANGED ZEOLITE BETA USING FTIR AND AB INITIO QUANTUM CALCULATIONS. (R825304)

EPA Science Inventory

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Molecular simulation of the thermodynamic, structural, and vapor-liquid equilibrium properties of neon

NASA Astrophysics Data System (ADS)

Vlasiuk, Maryna; Frascoli, Federico; Sadus, Richard J.

2016-09-01

The thermodynamic, structural, and vapor-liquid equilibrium properties of neon are comprehensively studied using ab initio, empirical, and semi-classical intermolecular potentials and classical Monte Carlo simulations. Path integral Monte Carlo simulations for isochoric heat capacity and structural properties are also reported for two empirical potentials and one ab initio potential. The isobaric and isochoric heat capacities, thermal expansion coefficient, thermal pressure coefficient, isothermal and adiabatic compressibilities, Joule-Thomson coefficient, and the speed of sound are reported and compared with experimental data for the entire range of liquid densities from the triple point to the critical point. Lustig's thermodynamic approach is formally extended for temperature-dependent intermolecular potentials. Quantum effects are incorporated using the Feynman-Hibbs quantum correction, which results in significant improvement in the accuracy of predicted thermodynamic properties. The new Feynman-Hibbs version of the Hellmann-Bich-Vogel potential predicts the isochoric heat capacity to an accuracy of 1.4% over the entire range of liquid densities. It also predicts other thermodynamic properties more accurately than alternative intermolecular potentials.

Exact quantum scattering calculation of transport properties for free radicals: OH(X2Π)-helium.

PubMed

Dagdigian, Paul J; Alexander, Millard H

2012-09-07

Transport properties for OH-He are computed through quantum scattering calculations using the ab initio potential energy surfaces determined by Lee et al. [J. Chem. Phys. 113, 5736 (2000)]. To gauge the importance of the open-shell character of OH and the anisotropy of the potential on the transport properties, including the collision integrals Ω((1,1)) and Ω((2,2)), as well as the diffusion coefficient, calculations were performed with the full potential, with the difference potential V(dif) set to zero, and with only the spherical average of the potential. Slight differences (3%-5%) in the computed diffusion coefficient were found between the values obtained using the full potential and the truncated potentials. The computed diffusion coefficients were compared to recent experimental measurements and those computed with a Lennard-Jones (LJ) 12-6 potential. The values obtained with the full potential were slightly higher than the experimental values. The LJ 12-6 potential was found to underestimate the variation in temperature as compared to that obtained using the full OH-He ab initio potential.

Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector

DOE Office of Scientific and Technical Information (OSTI.GOV)

Genderen, E. van; Clabbers, M. T. B.; Center for Cellular Imaging and NanoAnalytics

A specialized quantum area detector for electron diffraction studies makes it possible to solve the structure of small organic compound nanocrystals in non-cryo conditions by direct methods. Until recently, structure determination by transmission electron microscopy of beam-sensitive three-dimensional nanocrystals required electron diffraction tomography data collection at liquid-nitrogen temperature, in order to reduce radiation damage. Here it is shown that the novel Timepix detector combines a high dynamic range with a very high signal-to-noise ratio and single-electron sensitivity, enabling ab initio phasing of beam-sensitive organic compounds. Low-dose electron diffraction data (∼0.013 e{sup −} Å{sup −2} s{sup −1}) were collected at roommore » temperature with the rotation method. It was ascertained that the data were of sufficient quality for structure solution using direct methods using software developed for X-ray crystallography (XDS, SHELX) and for electron crystallography (ADT3D/PETS, SIR2014)« less

Ab Initio Predictions of Hexagonal Zr(B,C,N) Polymorphs for Coherent Interface Design

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Chongze; Huang, Jingsong; Sumpter, Bobby G.

2017-10-27

Density functional theory calculations are used to explore hexagonal (HX) NiAs-like polymorphs of Zr(B,C,N) and compare with corresponding Zr(B,C,N) Hagg-like face-centered cubic rocksalt (B1) phases. While all predicted compounds are mechanically stable according to the Born-Huang criteria, only HX Zr(C,N) are found dynamically stable from ab initio molecular dynamics simulations and lattice dynamics calculations. HX ZrN emerges as a candidate structure with ground state energy, elastic constants, and extrinsic mechanical parameters comparable with those of B1 ZrN. Ab initio band structure and semi-classical Boltzmann transport calculations predict a metallic character and a monotonic increase in electrical conductivity with the numbermore » of valence electrons. Electronic structure calculations indicate that the HX phases gain their stability and mechanical attributes by Zr d- non-metal p hybridization and by broadening of Zr d bands. Furthermore, it is shown that the HX ZrN phase provides a low-energy coherent interface model for connecting B1 ZrN domains, with significant energetic advantage over an atomistic interface model derived from high resolution transmission electron microscopy images. The ab initio characterizations provided herein should aid the experimental identification of non-Hagg-like hard phases. Furthermore, the results can also enrich the variety of crystalline phases potentially available for designing coherent interfaces in superhard nanostructured materials and in materials with multilayer characteristics.« less

Ab initio theory of spin-orbit coupling for quantum bits in diamond exhibiting dynamic Jahn-Teller effect

NASA Astrophysics Data System (ADS)

Gali, Adam; Thiering, Gergő

Dopants in solids are promising candidates for implementations of quantum bits for quantum computing. In particular, the high-spin negatively charged nitrogen-vacancy defect (NV) in diamond has become a leading contender in solid-state quantum information processing. The initialization and readout of the spin is based on the spin-selective decay of the photo-excited electron to the ground state which is mediated by spin-orbit coupling between excited states states and phonons. Generally, the spin-orbit coupling plays a crucial role in the optical spinpolarization and readout of NV quantum bit (qubit) and alike. Strong electron-phonon coupling in dynamic Jahn-Teller (DJT) systems can substantially influence the effective strength of spin-orbit coupling. Here we show by ab initio supercell density functional theory (DFT) calculations that the intrinsic spin-orbit coupling is strongly damped by DJT effect in the triplet excited state that has a consequence on the rate of non-radiative decay. This theory is applied to the ground state of silicon-vacancy (SiV) and germanium-vacancy (GeV) centers in their negatively charged state that can also act like qubits. We show that the intrinsic spin-orbit coupling in SiV and GeV centers is in the 100 GHz region, in contrast to the NV center of 10 GHz region. Our results provide deep insight in the nature of SiV and GeV qubits in diamond. EU FP7 DIADEMS project (Contract No. 611143).

First-principles quantum-mechanical investigations of biomass conversion at the liquid-solid interfaces

NASA Astrophysics Data System (ADS)

Dang, Hongli; Xue, Wenhua; Liu, Yingdi; Jentoft, Friederike; Resasco, Daniel; Wang, Sanwu

2014-03-01

We report first-principles density-functional calculations and ab initio molecular dynamics (MD) simulations for the reactions involving furfural, which is an important intermediate in biomass conversion, at the catalytic liquid-solid interfaces. The different dynamic processes of furfural at the water-Cu(111) and water-Pd(111) interfaces suggest different catalytic reaction mechanisms for the conversion of furfural. Simulations for the dynamic processes with and without hydrogen demonstrate the importance of the liquid-solid interface as well as the presence of hydrogen in possible catalytic reactions including hydrogenation and decarbonylation of furfural. Supported by DOE (DE-SC0004600). This research used the supercomputer resources of the XSEDE, the NERSC Center, and the Tandy Supercomputing Center.

Large-Amplitude Deformation and Bond Breakage in Shock-Induced Reactions of Explosive Molecules

NASA Astrophysics Data System (ADS)

Kay, Jeffrey

The response of explosive molecules to large-amplitude mechanical deformation plays an important role in shock-induced reactions and the initiation of detonation in explosive materials. In this presentation, the response of a series of explosive molecules (nitromethane, 2,4,6-trinitrotoluene [TNT], and 2,4,6-triamino-1,3,5-trinitrobenzene [TATB]) to a variety of large-amplitude deformations are examined using ab initio quantum chemical calculations. Large-amplitude motions that result in bond breakage are described, and the insights these results provide into both previous experimental observations and previous theoretical predictions of shock-induced reactions are discussed.

Quantum mechanical calculations related to ionization and charge transfer in DNA

NASA Astrophysics Data System (ADS)

Cauët, E.; Valiev, M.; Weare, J. H.; Liévin, J.

2012-07-01

Ionization and charge migration in DNA play crucial roles in mechanisms of DNA damage caused by ionizing radiation, oxidizing agents and photo-irradiation. Therefore, an evaluation of the ionization properties of the DNA bases is central to the full interpretation and understanding of the elementary reactive processes that occur at the molecular level during the initial exposure and afterwards. Ab initio quantum mechanical (QM) methods have been successful in providing highly accurate evaluations of key parameters, such as ionization energies (IE) of DNA bases. Hence, in this study, we performed high-level QM calculations to characterize the molecular energy levels and potential energy surfaces, which shed light on ionization and charge migration between DNA bases. In particular, we examined the IEs of guanine, the most easily oxidized base, isolated and embedded in base clusters, and investigated the mechanism of charge migration over two and three stacked guanines. The IE of guanine in the human telomere sequence has also been evaluated. We report a simple molecular orbital analysis to explain how modifications in the base sequence are expected to change the efficiency of the sequence as a hole trap. Finally, the application of a hybrid approach combining quantum mechanics with molecular mechanics brings an interesting discussion as to how the native aqueous DNA environment affects the IE threshold of nucleobases.

Quantum dynamical simulation of the scattering of Ar from a frozen LiF(100) surface based on a first principles interaction potential

DOE Office of Scientific and Technical Information (OSTI.GOV)

Azuri, Asaf; Pollak, Eli, E-mail: eli.pollak@weizmann.ac.il

2015-07-07

In-plane two and three dimensional diffraction patterns are computed for the vertical scattering of an Ar atom from a frozen LiF(100) surface. Suitable collimation of the incoming wavepacket serves to reveal the quantum mechanical diffraction. The interaction potential is based on a fit to an ab initio potential calculated using density functional theory with dispersion corrections. Due to the potential coupling found between the two horizontal surface directions, there are noticeable differences between the quantum angular distributions computed for two and three dimensional scattering. The quantum results are compared to analogous classical Wigner computations on the same surface and withmore » the same conditions. The classical dynamics largely provides the envelope for the quantum diffractive scattering. The classical results also show that the corrugation along the [110] direction of the surface is smaller than along the [100] direction, in qualitative agreement with experimental observations of unimodal and bimodal scattering for the [110] and [100] directions, respectively.« less

Universality and chaoticity in ultracold K+KRb chemical reactions

DOE PAGES

Croft, J. F. E.; Makrides, C.; Li, M.; ...

2017-07-19

A fundamental question in the study of chemical reactions is how reactions proceed at a collision energy close to absolute zero. This question is no longer hypothetical: quantum degenerate gases of atoms and molecules can now be created at temperatures lower than a few tens of nanokelvin. Here we consider the benchmark ultracold reaction between, the most-celebrated ultracold molecule, KRb and K. We map out an accurate ab initio ground-state potential energy surface of the K 2Rb complex in full dimensionality and report numerically-exact quantum-mechanical reaction dynamics. The distribution of rotationally resolved rates is shown to be Poissonian. An analysismore » of the hyperspherical adiabatic potential curves explains this statistical character revealing a chaotic distribution for the short-range collision complex that plays a key role in governing the reaction outcome.« less

Sensitivity of ab Initio vs Empirical Methods in Computing Structural Effects on NMR Chemical Shifts for the Example of Peptides.

PubMed

Sumowski, Chris Vanessa; Hanni, Matti; Schweizer, Sabine; Ochsenfeld, Christian

2014-01-14

The structural sensitivity of NMR chemical shifts as computed by quantum chemical methods is compared to a variety of empirical approaches for the example of a prototypical peptide, the 38-residue kaliotoxin KTX comprising 573 atoms. Despite the simplicity of empirical chemical shift prediction programs, the agreement with experimental results is rather good, underlining their usefulness. However, we show in our present work that they are highly insensitive to structural changes, which renders their use for validating predicted structures questionable. In contrast, quantum chemical methods show the expected high sensitivity to structural and electronic changes. This appears to be independent of the quantum chemical approach or the inclusion of solvent effects. For the latter, explicit solvent simulations with increasing number of snapshots were performed for two conformers of an eight amino acid sequence. In conclusion, the empirical approaches neither provide the expected magnitude nor the patterns of NMR chemical shifts determined by the clearly more costly ab initio methods upon structural changes. This restricts the use of empirical prediction programs in studies where peptide and protein structures are utilized for the NMR chemical shift evaluation such as in NMR refinement processes, structural model verifications, or calculations of NMR nuclear spin relaxation rates.

Ab initio study of the effects of thin CsI coatings on the work function of graphite cathodes

NASA Astrophysics Data System (ADS)

Vlahos, Vasilios; Booske, John H.; Morgan, Dane

2007-10-01

Cesium-iodide (CsI)-coated graphite cathodes are promising electron sources for high power microwave generators, but the mechanism driving the improved emission is not well understood. Therefore, an ab initio modeling investigation on the effects of thin CsI coatings on graphite has been carried out. It is demonstrated that the CsI coatings reduce the work function of the system significantly through a mechanism of induced dipoles. The results suggest that work function modification is a major contribution to the improved emission seen when CsI coatings are applied to C.

The Wacker oxidation of allyl alcohol along cyclic-intermediate routes: An ab initio molecular dynamics investigation

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.

Anharmonic force field and vibrational dynamics of CH2F2 up to 5000 cm(-1) studied by Fourier transform infrared spectroscopy and state-of-the-art ab initio calculations.

PubMed

Tasinato, Nicola; Regini, Giorgia; Stoppa, Paolo; Pietropolli Charmet, Andrea; Gambi, Alberto

2012-06-07

Difluoromethane (CH(2)F(2), HFC-32) is a molecule used in refrigerant mixtures as a replacement of the more environmentally hazardous, ozone depleting, chlorofluorocarbons. On the other hand, presenting strong vibration-rotation bands in the 9 μm atmospheric window, it is a greenhouse gas which contributes to global warming. In the present work, the vibrational and ro-vibrational properties of CH(2)F(2), providing basic data for its atmospheric modeling, are studied in detail by coupling medium resolution Fourier transform infrared spectroscopy to high-level electronic structure ab initio calculations. Experimentally a full quantum assignment and accurate integrated absorption cross sections are obtained up to 5000 cm(-1). Ab initio calculations are carried out by using CCSD(T) theory and large basis sets of either the correlation consistent or atomic natural orbital hierarchies. By using vibrational perturbation theory to second order a complete set of vibrational and ro-vibrational parameters is derived from the ab initio quartic anharmonic force fields, which well compares with the spectroscopic constants retrieved experimentally. An excellent agreement between theory and experiment is achieved for vibrational energy levels and integrated absorption cross sections: transition frequencies up to four quanta of vibrational excitation are reproduced with a root mean square deviation (RMSD) of 7 cm(-1) while intensities are predicted within few km mol(-1) from the experiment. Basis set performances and core correlation effects are discussed throughout the paper. Particular attention is focused in the understanding of the anharmonic couplings which rule the vibrational dynamics of the |ν(1)>, |2ν(8)>, |2ν(2)> three levels interacting system. The reliability of the potential energy and dipole moment surfaces in reproducing the vibrational eigenvalues and intensities as well as in modeling the vibrational and ro-vibrational mixings over the whole 400-5000 cm(-1) region is also demonstrated by spectacular spectral simulations carried out by using the ro-vibrational Hamiltonian constants, and the relevant coupling terms, obtained from the perturbation treatment of the ab initio anharmonic force field. The present results suggest CH(2)F(2) as a prototype molecule to test ab initio calculations and theoretical models.

Anharmonic force field and vibrational dynamics of CH2F2 up to 5000 cm-1 studied by Fourier transform infrared spectroscopy and state-of-the-art ab initio calculations

NASA Astrophysics Data System (ADS)

Tasinato, Nicola; Regini, Giorgia; Stoppa, Paolo; Charmet, Andrea Pietropolli; Gambi, Alberto

2012-06-01

Difluoromethane (CH2F2, HFC-32) is a molecule used in refrigerant mixtures as a replacement of the more environmentally hazardous, ozone depleting, chlorofluorocarbons. On the other hand, presenting strong vibration-rotation bands in the 9 μm atmospheric window, it is a greenhouse gas which contributes to global warming. In the present work, the vibrational and ro-vibrational properties of CH2F2, providing basic data for its atmospheric modeling, are studied in detail by coupling medium resolution Fourier transform infrared spectroscopy to high-level electronic structure ab initio calculations. Experimentally a full quantum assignment and accurate integrated absorption cross sections are obtained up to 5000 cm-1. Ab initio calculations are carried out by using CCSD(T) theory and large basis sets of either the correlation consistent or atomic natural orbital hierarchies. By using vibrational perturbation theory to second order a complete set of vibrational and ro-vibrational parameters is derived from the ab initio quartic anharmonic force fields, which well compares with the spectroscopic constants retrieved experimentally. An excellent agreement between theory and experiment is achieved for vibrational energy levels and integrated absorption cross sections: transition frequencies up to four quanta of vibrational excitation are reproduced with a root mean square deviation (RMSD) of 7 cm-1 while intensities are predicted within few km mol-1 from the experiment. Basis set performances and core correlation effects are discussed throughout the paper. Particular attention is focused in the understanding of the anharmonic couplings which rule the vibrational dynamics of the |ν1⟩, |2ν8⟩, |2ν2⟩ three levels interacting system. The reliability of the potential energy and dipole moment surfaces in reproducing the vibrational eigenvalues and intensities as well as in modeling the vibrational and ro-vibrational mixings over the whole 400-5000 cm-1 region is also demonstrated by spectacular spectral simulations carried out by using the ro-vibrational Hamiltonian constants, and the relevant coupling terms, obtained from the perturbation treatment of the ab initio anharmonic force field. The present results suggest CH2F2 as a prototype molecule to test ab initio calculations and theoretical models.

Ab initio studies of dissociative recombination

NASA Technical Reports Server (NTRS)

Guberman, Steven L.

1989-01-01

Quantum chemical calculations of the dissociative recombination of O2(+) and N2(+) are reported. An approach for calculating autoionization widths from high-principal-quantum-number Rydberg states is summarized, and an example is presented for the lowest dissociative state of O2. For O2(+), the 1Sigma(+)u state is the sole source of O(1S) from the lowest 10 vibrational levels of the ion. Rate coefficients for generating O(1S) and O(1D) at ionospheric temperatures are reported.

Spin relaxation in ultracold collisions of molecular radicals with alkali-metal atoms

NASA Astrophysics Data System (ADS)

Tscherbul, Timur; Klos, Jacek; Zukowski, Piotr

2016-05-01

We present accurate quantum scattering calculations of spin relaxation in ultracold collisions of alkali-metal atoms and polar 2 Σ molecules CaH, SrF, and SrOH. The calculations employ state-of-the-art ab initio interaction potentials and a rigorous quantum theory of atom-molecule collisions in a magnetic field based on the total angular momentum representation. We will further discuss the relevance of the results to atom-molecule sympathetic cooling experiments in a magnetic trap.

Rotational Energy Transfer of N2 Determined Using a New Ab Initio Potential Energy Surface

NASA Technical Reports Server (NTRS)

Huo, Winifred M.; Stallcop, James R.; Partridge, Harry; Langhoff, Stephen R. (Technical Monitor)

1997-01-01

A new N2-N2 rigid-rotor surface has been determined using extensive Ab Initio quantum chemistry calculations together with recent experimental data for the second virial coefficient. Rotational energy transfer is studied using the new potential energy surface (PES) employing the close coupling method below 200 cm(exp -1) and coupled state approximation above that. Comparing with a previous calculation based on the PES of van der Avoird et al.,3 it is found that the new PES generally gives larger cross sections for large (delta)J transitions, but for small (delta)J transitions the cross sections are either comparable or smaller. Correlation between the differences in the cross sections and the two PES will be attempted. The computed cross sections will also be compared with available experimental data.

reaxFF Reactive Force Field for Disulfide Mechanochemistry, Fitted to Multireference ab Initio Data.

PubMed

Müller, Julian; Hartke, Bernd

2016-08-09

Mechanochemistry, in particular in the form of single-molecule atomic force microscopy experiments, is difficult to model theoretically, for two reasons: Covalent bond breaking is not captured accurately by single-determinant, single-reference quantum chemistry methods, and experimental times of milliseconds or longer are hard to simulate with any approach. Reactive force fields have the potential to alleviate both problems, as demonstrated in this work: Using nondeterministic global parameter optimization by evolutionary algorithms, we have fitted a reaxFF force field to high-level multireference ab initio data for disulfides. The resulting force field can be used to reliably model large, multifunctional mechanochemistry units with disulfide bonds as designed breaking points. Explorative calculations show that a significant part of the time scale gap between AFM experiments and dynamical simulations can be bridged with this approach.

Communication: XFAIMS—eXternal Field Ab Initio Multiple Spawning for electron-nuclear dynamics triggered by short laser pulses

DOE PAGES

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 (H 2CSO).« less

Ab Initio energetics of SiO bond cleavage.

PubMed

Hühn, Carolin; Erlebach, Andreas; Mey, Dorothea; Wondraczek, Lothar; Sierka, Marek

2017-10-15

A multilevel approach that combines high-level ab initio quantum chemical methods applied to a molecular model of a single, strain-free SiOSi bridge has been used to derive accurate energetics for SiO bond cleavage. The calculated SiO bond dissociation energy and the activation energy for water-assisted SiO bond cleavage of 624 and 163 kJ mol -1 , respectively, are in excellent agreement with values derived recently from experimental data. In addition, the activation energy for H 2 O-assisted SiO bond cleavage is found virtually independent of the amount of water molecules in the vicinity of the reaction site. The estimated reaction energy for this process including zero-point vibrational contribution is in the range of -5 to 19 kJ mol -1 . © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector.

PubMed

van Genderen, E; Clabbers, M T B; Das, P P; Stewart, A; Nederlof, I; Barentsen, K C; Portillo, Q; Pannu, N S; Nicolopoulos, S; Gruene, T; Abrahams, J P

2016-03-01

Until recently, structure determination by transmission electron microscopy of beam-sensitive three-dimensional nanocrystals required electron diffraction tomography data collection at liquid-nitrogen temperature, in order to reduce radiation damage. Here it is shown that the novel Timepix detector combines a high dynamic range with a very high signal-to-noise ratio and single-electron sensitivity, enabling ab initio phasing of beam-sensitive organic compounds. Low-dose electron diffraction data (∼ 0.013 e(-) Å(-2) s(-1)) were collected at room temperature with the rotation method. It was ascertained that the data were of sufficient quality for structure solution using direct methods using software developed for X-ray crystallography (XDS, SHELX) and for electron crystallography (ADT3D/PETS, SIR2014).

Multichannel-quantum-defect-theory treatment of preionized and predissociated triplet gerade levels of H2

NASA Astrophysics Data System (ADS)

Matzkin, A.; Jungen, Ch.; Ross, S. C.

2000-12-01

Multichannel quantum defect theory (MQDT) is used to calculate highly excited predissociated and preionized triplet gerade states of H2. The treatment is ab initio and is based on the clamped-nuclei quantum-defect matrices and dipole transition moments derived from quantum-chemical potential energy curves by Ross et al. [Can. J. Phys. (to be published)]. Level positions, predissociation or preionization widths and relative intensities are found to be in good agreement with those observed by Lembo et al. [Phys. Rev. A 38, 3447 (1988); J. Chem. Phys. 92, 2219 (1990)] by an optical-optical double resonance photoionization or depletion technique.

Chemical Studies of Free Radical Relocalization

DTIC Science & Technology

2015-01-13

Park, NC 27709-2211 combustion intermediates, rel;ocalization, infrared spectroscopy , computational quantum chemistry REPORT DOCUMENTATION PAGE 11...organotransition metal catalysis are underway. Summary of important results: I. Laboratory Spectroscopy of Gas-phase Hydrocarbon Radicals. We have carried out line...combination of gas-phase laboratory spectroscopy , photochemical studies, and ab initio computations. (1) Spectroscopy . Survey scans between 1800 and

Semiempirical and ab initio Calculations of Charged Species Used in the Physical Organic Chemistry Course.

ERIC Educational Resources Information Center

Gilliom, Richard D.

1989-01-01

Concentrates on the semiempirical methods MINDO/3, MNDO, and AMI available in the program AMPAC from the Quantum Chemistry Program Exchange at Indiana University. Uses charged ions in the teaching of computational chemistry. Finds that semiempirical methods are accurate enough for the general use of the bench chemist. (MVL)

Metal Ion Modeling Using Classical Mechanics

PubMed Central

2017-01-01

Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems. PMID:28045509

SchNet - A deep learning architecture for molecules and materials

NASA Astrophysics Data System (ADS)

Schütt, K. T.; Sauceda, H. E.; Kindermans, P.-J.; Tkatchenko, A.; Müller, K.-R.

2018-06-01

Deep learning has led to a paradigm shift in artificial intelligence, including web, text, and image search, speech recognition, as well as bioinformatics, with growing impact in chemical physics. Machine learning, in general, and deep learning, in particular, are ideally suitable for representing quantum-mechanical interactions, enabling us to model nonlinear potential-energy surfaces or enhancing the exploration of chemical compound space. Here we present the deep learning architecture SchNet that is specifically designed to model atomistic systems by making use of continuous-filter convolutional layers. We demonstrate the capabilities of SchNet by accurately predicting a range of properties across chemical space for molecules and materials, where our model learns chemically plausible embeddings of atom types across the periodic table. Finally, we employ SchNet to predict potential-energy surfaces and energy-conserving force fields for molecular dynamics simulations of small molecules and perform an exemplary study on the quantum-mechanical properties of C20-fullerene that would have been infeasible with regular ab initio molecular dynamics.

Quantum chemical modeling of the inhibition mechanism of monoamine oxidase by oxazolidinone and analogous heterocyclic compounds.

PubMed

Erdem, Safiye Sağ; Özpınar, Gül Altınbaş; Boz, Ümüt

2014-02-01

Monoamine oxidase (MAO, EC 1.4.3.4) is responsible from the oxidation of a variety of amine neurotransmitters. MAO inhibitors are used for the treatment of depression or Parkinson's disease. They also inhibit the catabolism of dietary amines. According to one hypothesis, inactivation results from the formation of a covalent adduct to a cysteine residue in the enzyme. If the adduct is stable enough, the enzyme is inhibited for a long time. After a while, enzyme can turn to its active form as a result of adduct breakdown by β-elimination. In this study, the proposed inactivation mechanism was modeled and tested by quantum chemical calculations. Eight heterocyclic methylthioamine derivatives were selected to represent the proposed covalent adducts. Activation energies related to their β-elimination reactions were calculated using ab initio and density functional theory methods. Calculated activation energies were in good agreement with the relative stabilities of the hypothetical adducts predicted in the literature by enzyme inactivation measurements.

Atomic Spectral Methods for Ab Initio Molecular Electronic Energy Surfaces: Transitioning From Small-Molecule to Biomolecular-Suitable Approaches.

PubMed

Mills, Jeffrey D; Ben-Nun, Michal; Rollin, Kyle; Bromley, Michael W J; Li, Jiabo; Hinde, Robert J; Winstead, Carl L; Sheehy, Jeffrey A; Boatz, Jerry A; Langhoff, Peter W

2016-08-25

Continuing attention has addressed incorportation of the electronically dynamical attributes of biomolecules in the largely static first-generation molecular-mechanical force fields commonly employed in molecular-dynamics simulations. We describe here a universal quantum-mechanical approach to calculations of the electronic energy surfaces of both small molecules and large aggregates on a common basis which can include such electronic attributes, and which also seems well-suited to adaptation in ab initio molecular-dynamics applications. In contrast to the more familiar orbital-product-based methodologies employed in traditional small-molecule computational quantum chemistry, the present approach is based on an "ex-post-facto" method in which Hamiltonian matrices are evaluated prior to wave function antisymmetrization, implemented here in the support of a Hilbert space of orthonormal products of many-electron atomic spectral eigenstates familiar from the van der Waals theory of long-range interactions. The general theory in its various forms incorporates the early semiempirical atoms- and diatomics-in-molecules approaches of Moffitt, Ellison, Tully, Kuntz, and others in a comprehensive mathematical setting, and generalizes the developments of Eisenschitz, London, Claverie, and others addressing electron permutation symmetry adaptation issues, completing these early attempts to treat van der Waals and chemical forces on a common basis. Exact expressions are obtained for molecular Hamiltonian matrices and for associated energy eigenvalues as sums of separate atomic and interaction-energy terms, similar in this respect to the forms of classical force fields. The latter representation is seen to also provide a long-missing general definition of the energies of individual atoms and of their interactions within molecules and matter free from subjective additional constraints. A computer code suite is described for calculations of the many-electron atomic eigenspectra and the pairwise-atomic Hamiltonian matrices required for practical applications. These matrices can be retained as functions of scalar atomic-pair separations and employed in assembling aggregate Hamiltonian matrices, with Wigner rotation matrices providing analytical representations of their angular degrees of freedom. In this way, ab initio potential energy surfaces are obtained in the complete absence of repeated evaluations and transformations of the one- and two-electron integrals at different molecular geometries required in most ab inito molecular calculations, with large Hamiltonian matrix assembly simplified and explicit diagonalizations avoided employing partitioning and Brillouin-Wigner or Rayleigh-Schrödinger perturbation theory. Illustrative applications of the important components of the formalism, selected aspects of the scaling of the approach, and aspects of "on-the-fly" interfaces with Monte Carlo and molecular-dynamics methods are described in anticipation of subsequent applications to biomolecules and other large aggregates.

The effect of sampling techniques used in the multiconfigurational Ehrenfest method

NASA Astrophysics Data System (ADS)

Symonds, C.; Kattirtzi, J. A.; Shalashilin, D. V.

2018-05-01

In this paper, we compare and contrast basis set sampling techniques recently developed for use in the ab initio multiple cloning method, a direct dynamics extension to the multiconfigurational Ehrenfest approach, used recently for the quantum simulation of ultrafast photochemistry. We demonstrate that simultaneous use of basis set cloning and basis function trains can produce results which are converged to the exact quantum result. To demonstrate this, we employ these sampling methods in simulations of quantum dynamics in the spin boson model with a broad range of parameters and compare the results to accurate benchmarks.

The effect of sampling techniques used in the multiconfigurational Ehrenfest method.

PubMed

Symonds, C; Kattirtzi, J A; Shalashilin, D V

2018-05-14

In this paper, we compare and contrast basis set sampling techniques recently developed for use in the ab initio multiple cloning method, a direct dynamics extension to the multiconfigurational Ehrenfest approach, used recently for the quantum simulation of ultrafast photochemistry. We demonstrate that simultaneous use of basis set cloning and basis function trains can produce results which are converged to the exact quantum result. To demonstrate this, we employ these sampling methods in simulations of quantum dynamics in the spin boson model with a broad range of parameters and compare the results to accurate benchmarks.

Full-dimensional quantum calculations of ground-state tunneling splitting of malonaldehyde using an accurate ab initio potential energy surface

NASA Astrophysics Data System (ADS)

Wang, Yimin; Braams, Bastiaan J.; Bowman, Joel M.; Carter, Stuart; Tew, David P.

2008-06-01

Quantum calculations of the ground vibrational state tunneling splitting of H-atom and D-atom transfer in malonaldehyde are performed on a full-dimensional ab initio potential energy surface (PES). The PES is a fit to 11 147 near basis-set-limit frozen-core CCSD(T) electronic energies. This surface properly describes the invariance of the potential with respect to all permutations of identical atoms. The saddle-point barrier for the H-atom transfer on the PES is 4.1 kcal/mol, in excellent agreement with the reported ab initio value. Model one-dimensional and ``exact'' full-dimensional calculations of the splitting for H- and D-atom transfer are done using this PES. The tunneling splittings in full dimensionality are calculated using the unbiased ``fixed-node'' diffusion Monte Carlo (DMC) method in Cartesian and saddle-point normal coordinates. The ground-state tunneling splitting is found to be 21.6 cm-1 in Cartesian coordinates and 22.6 cm-1 in normal coordinates, with an uncertainty of 2-3 cm-1. This splitting is also calculated based on a model which makes use of the exact single-well zero-point energy (ZPE) obtained with the MULTIMODE code and DMC ZPE and this calculation gives a tunneling splitting of 21-22 cm-1. The corresponding computed splittings for the D-atom transfer are 3.0, 3.1, and 2-3 cm-1. These calculated tunneling splittings agree with each other to within less than the standard uncertainties obtained with the DMC method used, which are between 2 and 3 cm-1, and agree well with the experimental values of 21.6 and 2.9 cm-1 for the H and D transfer, respectively.

Full-dimensional quantum calculations of ground-state tunneling splitting of malonaldehyde using an accurate ab initio potential energy surface.

PubMed

Wang, Yimin; Braams, Bastiaan J; Bowman, Joel M; Carter, Stuart; Tew, David P

2008-06-14

Quantum calculations of the ground vibrational state tunneling splitting of H-atom and D-atom transfer in malonaldehyde are performed on a full-dimensional ab initio potential energy surface (PES). The PES is a fit to 11 147 near basis-set-limit frozen-core CCSD(T) electronic energies. This surface properly describes the invariance of the potential with respect to all permutations of identical atoms. The saddle-point barrier for the H-atom transfer on the PES is 4.1 kcalmol, in excellent agreement with the reported ab initio value. Model one-dimensional and "exact" full-dimensional calculations of the splitting for H- and D-atom transfer are done using this PES. The tunneling splittings in full dimensionality are calculated using the unbiased "fixed-node" diffusion Monte Carlo (DMC) method in Cartesian and saddle-point normal coordinates. The ground-state tunneling splitting is found to be 21.6 cm(-1) in Cartesian coordinates and 22.6 cm(-1) in normal coordinates, with an uncertainty of 2-3 cm(-1). This splitting is also calculated based on a model which makes use of the exact single-well zero-point energy (ZPE) obtained with the MULTIMODE code and DMC ZPE and this calculation gives a tunneling splitting of 21-22 cm(-1). The corresponding computed splittings for the D-atom transfer are 3.0, 3.1, and 2-3 cm(-1). These calculated tunneling splittings agree with each other to within less than the standard uncertainties obtained with the DMC method used, which are between 2 and 3 cm(-1), and agree well with the experimental values of 21.6 and 2.9 cm(-1) for the H and D transfer, respectively.

Automated chemical kinetic modeling via hybrid reactive molecular dynamics and quantum chemistry simulations.

PubMed

Döntgen, Malte; Schmalz, Felix; Kopp, Wassja A; Kröger, Leif C; Leonhard, Kai

2018-06-13

An automated scheme for obtaining chemical kinetic models from scratch using reactive molecular dynamics and quantum chemistry simulations is presented. This methodology combines the phase space sampling of reactive molecular dynamics with the thermochemistry and kinetics prediction capabilities of quantum mechanics. This scheme provides the NASA polynomial and modified Arrhenius equation parameters for all species and reactions that are observed during the simulation and supplies them in the ChemKin format. The ab initio level of theory for predictions is easily exchangeable and the presently used G3MP2 level of theory is found to reliably reproduce hydrogen and methane oxidation thermochemistry and kinetics data. Chemical kinetic models obtained with this approach are ready-to-use for, e.g., ignition delay time simulations, as shown for hydrogen combustion. The presented extension of the ChemTraYzer approach can be used as a basis for methodologically advancing chemical kinetic modeling schemes and as a black-box approach to generate chemical kinetic models.

Ab initio study of Pd carbonyls and CO/Pd(110)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ramprasad, R.; Glassford, K.M.; Adams, J.B.

1994-12-31

Carbon monoxide chemisorption on transition metal surfaces has been one of the most extensively studied in surface science in past years due to its importance in a variety of catalytic processes, especially, automotive catalytic converters using Pt or Pd. The authors have performed ab initio studies to understand the electronic and geometric aspects of the Pd-CO bond in small carbonyl clusters and the CO covered (2 x 1)p2mg superstructure of the Pd(110) surface. They have used the standard quantum chemistry package Gaussian to study the former system and a LDA (local density approximation) formalism using ab initio pseudopotentials and amore » plane wave basis to study the latter. The latter results are preliminary; the authors intended to study thicker slabs in the future. The organization of the paper is as follows. The authors describe the methods used in their calculation in Sec. 2. In Sec. 3, they present results and discussion; here, they first look at the smallest possible clusters, viz, Pd{sub 2} and PdCO, take a brief look at the orbital chemistry involved and then move on to the study of the CO covered Pd(110) surface and examine the geometry of the near equilibrium structure.« less

Accurate virial coefficients of gaseous krypton from state-of-the-art ab initio potential and polarizability of the krypton dimer

NASA Astrophysics Data System (ADS)

Song, Bo; Waldrop, Jonathan M.; Wang, Xiaopo; Patkowski, Konrad

2018-01-01

We have developed a new krypton-krypton interaction-induced isotropic dipole polarizability curve based on high-level ab initio methods. The determination was carried out using the coupled-cluster singles and doubles plus perturbative triples method with very large basis sets up to augmented correlation-consistent sextuple zeta as well as the corrections for core-core and core-valence correlation and relativistic effects. The analytical function of polarizability and our recently constructed reference interatomic potential [J. M. Waldrop et al., J. Chem. Phys. 142, 204307 (2015)] were used to predict the thermophysical and electromagnetic properties of krypton gas. The second pressure, acoustic, and dielectric virial coefficients were computed for the temperature range of 116 K-5000 K using classical statistical mechanics supplemented with high-order quantum corrections. The virial coefficients calculated were compared with the generally less precise available experimental data as well as with values computed from other potentials in the literature {in particular, the recent highly accurate potential of Jäger et al. [J. Chem. Phys. 144, 114304 (2016)]}. The detailed examination in this work suggests that the present theoretical prediction can be applied as reference values in disciplines involving thermophysical and electromagnetic properties of krypton gas.

A review on ab initio studies of static, transport, and optical properties of polystyrene under extreme conditions for inertial confinement fusion applications

NASA Astrophysics Data System (ADS)

Hu, S. X.; Collins, L. A.; Boehly, T. R.; Ding, Y. H.; Radha, P. B.; Goncharov, V. N.; Karasiev, V. V.; Collins, G. W.; Regan, S. P.; Campbell, E. M.

2018-05-01

Polystyrene (CH), commonly known as "plastic," has been one of the widely used ablator materials for capsule designs in inertial confinement fusion (ICF). Knowing its precise properties under high-energy-density conditions is crucial to understanding and designing ICF implosions through radiation-hydrodynamic simulations. For this purpose, systematic ab initio studies on the static, transport, and optical properties of CH, in a wide range of density and temperature conditions (ρ = 0.1 to 100 g/cm3 and T = 103 to 4 × 106 K), have been conducted using quantum molecular dynamics (QMD) simulations based on the density functional theory. We have built several wide-ranging, self-consistent material-properties tables for CH, such as the first-principles equation of state, the QMD-based thermal conductivity (κQMD) and ionization, and the first-principles opacity table. This paper is devoted to providing a review on (1) what results were obtained from these systematic ab initio studies; (2) how these self-consistent results were compared with both traditional plasma-physics models and available experiments; and (3) how these first-principles-based properties of polystyrene affect the predictions of ICF target performance, through both 1-D and 2-D radiation-hydrodynamic simulations. In the warm dense regime, our ab initio results, which can significantly differ from predictions of traditional plasma-physics models, compared favorably with experiments. When incorporated into hydrocodes for ICF simulations, these first-principles material properties of CH have produced significant differences over traditional models in predicting 1-D/2-D target performance of ICF implosions on OMEGA and direct-drive-ignition designs for the National Ignition Facility. Finally, we will discuss the implications of these studies on the current small-margin ICF target designs using a CH ablator.

Wave packet and statistical quantum calculations for the He + NeH⁺ → HeH⁺ + Ne reaction on the ground electronic state.

PubMed

Koner, Debasish; Barrios, Lizandra; González-Lezana, Tomás; Panda, Aditya N

2014-09-21

A real wave packet based time-dependent method and a statistical quantum method have been used to study the He + NeH(+) (v, j) reaction with the reactant in various ro-vibrational states, on a recently calculated ab initio ground state potential energy surface. Both the wave packet and statistical quantum calculations were carried out within the centrifugal sudden approximation as well as using the exact Hamiltonian. Quantum reaction probabilities exhibit dense oscillatory pattern for smaller total angular momentum values, which is a signature of resonances in a complex forming mechanism for the title reaction. Significant differences, found between exact and approximate quantum reaction cross sections, highlight the importance of inclusion of Coriolis coupling in the calculations. Statistical results are in fairly good agreement with the exact quantum results, for ground ro-vibrational states of the reactant. Vibrational excitation greatly enhances the reaction cross sections, whereas rotational excitation has relatively small effect on the reaction. The nature of the reaction cross section curves is dependent on the initial vibrational state of the reactant and is typical of a late barrier type potential energy profile.

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2010 CFR

2010-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2014 CFR

2014-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2012 CFR

2012-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2013 CFR

2013-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2011 CFR

2011-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

Charge transfer collisions of Si^3+ with H at low energies

NASA Astrophysics Data System (ADS)

Joseph, D. C.; Gu, J. P.; Saha, B. C.

2009-11-01

Charge transfer of positively charged ions with atomic hydrogen is important not only in magnetically confined plasmas between impurity ions and H atoms from the chamber walls influences the overall ionization balance and effects the plasma cooling but also in astrophysics, where it plays a key role in determining the properties of the observed gas. It also provides a recombination mechanism for multiply charged ions in X-ray ionized astronomical environments. We report an investigation using the molecular-orbital close-coupling (MOCC) method, both quantum mechanically and semi-classically, in the adiabatic representation. Ab initio adiabatic potentials and coupling matrix elements--radial and angular--are calculated using the MRD-CI method. Comparison of our results with other theoretical as well as experimental findings will be discussed.

Role of cationic size in the optical properties of the LiCl crystal surface: theoretical study.

PubMed

Abdel Halim, Wael Salah; Abdullah, Noha; Abdel-Aal, Safaa; Shalabi, A S

2012-06-01

The size of the cations (either Ca(2+), Sr(2+), Ga(+), or Au(+)) at the F(A1)-type color centers on the (100) surface of LiCl crystal plays an important role in the optical properties of this surface. In this work, double-well potentials at this surface were investigated using ab initio quantum mechanical methods. Quantum clusters were embedded in simulated Coulomb fields that closely approximate the Madelung fields of the host surface, and the ions that were the nearest neighbors to the F(A1) site were allowed to relax to equilibrium. The calculated Stokes-shifted optical transition bands, optical-optical conversion efficiency, and relaxed excited states of the defect-containing surface, as well as the orientational destruction of the color centers, recording sensitivity, exciton (energy) transfer, and the Glasner-Tompkins empirical relation were all found to be sensitive to the size of the dopant cation.

An unscaled quantum mechanical harmonic force field for p-benzoquinone

NASA Astrophysics Data System (ADS)

Nonella, Marco; Tavan, Paul

1995-10-01

Structure and harmonic vibrational frequencies of p-benzoquinone have been calculated using quantum chemical ab initio and density functional methods. Our calculations show that a satisfactory description of fundamentals and normal mode compositions is achieved upon consideration of correlation effects by means of Møller-Plesset perturbation expansion (MP2) or by density functional theory (DFT). Furthermore, for correct prediction of CO bondlength and force constant, basis sets augmented by polarization functions are required. Applying such basis sets, MP2 and DFT calculations both give results which are generally in reasonable agreement with experimental data. The quantitatively better agreement, however, is achieved with the computationally less demanding DFT method. This method particularly allows very precise prediction of the experimentally important absorptions in the frequency region between 1500 and 1800 cm -1 and of the isotopic shifts of these vibrations due to 13C or 18O substitution.

Ab-initio quantum transport simulation of self-heating in single-layer 2-D materials

NASA Astrophysics Data System (ADS)

Stieger, Christian; Szabo, Aron; Bunjaku, Teutë; Luisier, Mathieu

2017-07-01

Through advanced quantum mechanical simulations combining electron transport and phonon transport from first-principles, self-heating effects are investigated in n-type transistors with single-layer MoS2, WS2, and black phosphorus as channel materials. The selected 2-D crystals all exhibit different phonon-limited mobility values, as well as electron and phonon properties, which have a direct influence on the increase in their lattice temperature and on the power dissipated inside their channel as a function of the applied gate voltage and electrical current magnitude. This computational study reveals (i) that self-heating plays a much more important role in 2-D materials than in Si nanowires, (ii) that it could severely limit the performance of 2-D devices at high current densities, and (iii) that black phosphorus appears less sensitive to this phenomenon than transition metal dichalcogenides.

Deep Potential Molecular Dynamics: A Scalable Model with the Accuracy of Quantum Mechanics

NASA Astrophysics Data System (ADS)

Zhang, Linfeng; Han, Jiequn; Wang, Han; Car, Roberto; E, Weinan

2018-04-01

We introduce a scheme for molecular simulations, the deep potential molecular dynamics (DPMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data. The neural network model preserves all the natural symmetries in the problem. It is first-principles based in the sense that there are no ad hoc components aside from the network model. We show that the proposed scheme provides an efficient and accurate protocol in a variety of systems, including bulk materials and molecules. In all these cases, DPMD gives results that are essentially indistinguishable from the original data, at a cost that scales linearly with system size.

Displaced path integral formulation for the momentum distribution of quantum particles.

PubMed

Lin, Lin; Morrone, Joseph A; Car, Roberto; Parrinello, Michele

2010-09-10

The proton momentum distribution, accessible by deep inelastic neutron scattering, is a very sensitive probe of the potential of mean force experienced by the protons in hydrogen-bonded systems. In this work we introduce a novel estimator for the end-to-end distribution of the Feynman paths, i.e., the Fourier transform of the momentum distribution. In this formulation, free particle and environmental contributions factorize. Moreover, the environmental contribution has a natural analogy to a free energy surface in statistical mechanics, facilitating the interpretation of experiments. The new formulation is not only conceptually but also computationally advantageous. We illustrate the method with applications to an empirical water model, ab initio ice, and one dimensional model systems.

Radiative gas dynamics of the Fire-II superorbital space vehicle

NASA Astrophysics Data System (ADS)

Surzhikov, S. T.

2016-03-01

The rates of convective and radiative heating of the Fire-II reentry vehicle are calculated, and the results are compared with experimental flight data. The computational model is based on solving a complete set of equations for (i) the radiative gas dynamics of a physically and chemically nonequilibrium viscous heatconducting gas and (ii) radiative transfer in 2D axisymmetric statement. The spectral optical parameters of high-temperature gases are calculated using ab initio quasi-classical and quantum-mechanical methods. The transfer of selective thermal radiation in terms of atomic lines is calculated using the line-by-line method on a specially generated computational grid that is nonuniform in radiation wavelength.

Quenching of Excited Na due to He Collisions

NASA Technical Reports Server (NTRS)

Lin, C. Y.; Stancil, P. C.; Liebermann, H. P.; Funke, P.; Buenker, R. J.

2006-01-01

The quenching and elastic scattering of excited Sodium by collisions with Helium have been investigated for energies between 10(exp -13) eV and 10 eV. With the ab initio adiabatic potentials and nonadiabatic radial and rotational couplings obtained from multireference single- and double-excitation configuration interaction approach, we carried out scattering calculations by the quantum-mechanical molecular-orbital close-coupling method. Cross sections for quenching reactions and elastic collisions are presented. Quenching and elastic collisional rate coefficients as a function of temperature between 1 micro-K and 10,000 K are also obtained. The results are relevant to modeling non-LTE effects on Na D absorption lines in extrasolar planets and brown dwarfs.

Ab initio characterization of coupling strength for all types of dangling-bond pairs on the hydrogen-terminated Si(100)-2 × 1 surface

NASA Astrophysics Data System (ADS)

Shaterzadeh-Yazdi, Zahra; Sanders, Barry C.; DiLabio, Gino A.

2018-04-01

Recent work has suggested that coupled silicon dangling bonds sharing an excess electron may serve as building blocks for quantum-cellular-automata cells and quantum computing schemes when constructed on hydrogen-terminated silicon surfaces. In this work, we employ ab initio density-functional theory to examine the details associated with the coupling between two dangling bonds sharing one excess electron and arranged in various configurations on models of phosphorous-doped hydrogen-terminated silicon (100) surfaces. Our results show that the coupling strength depends strongly on the relative orientation of the dangling bonds on the surface and on the separation between them. The orientation of dangling bonds is determined by the anisotropy of the silicon (100) surface, so this feature of the surface is a significant contributing factor to variations in the strength of coupling between dangling bonds. The results demonstrate that simple models for approximating tunneling, such as the Wentzel-Kramer-Brillouin method, which do not incorporate the details of surface structure, are incapable of providing reasonable estimates of tunneling rates between dangling bonds. The results provide guidance to efforts related to the development of dangling-bond based computing elements.

Potentials of Mean Force With Ab Initio Mixed Hamiltonian Models of Solvation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dupuis, Michel; Schenter, Gregory K.; Garrett, Bruce C.

2003-08-01

We give an account of a computationally tractable and efficient procedure for the calculation of potentials of mean force using mixed Hamiltonian models of electronic structure where quantum subsystems are described with computationally intensive ab initio wavefunctions. The mixed Hamiltonian is mapped into an all-classical Hamiltonian that is amenable to a thermodynamic perturbation treatment for the calculation of free energies. A small number of statistically uncorrelated (solute-solvent) configurations are selected from the Monte Carlo random walk generated with the all-classical Hamiltonian approximation. Those are used in the averaging of the free energy using the mixed quantum/classical Hamiltonian. The methodology ismore » illustrated for the micro-solvated SN2 substitution reaction of methyl chloride by hydroxide. We also compare the potential of mean force calculated with the above protocol with an approximate formalism, one in which the potential of mean force calculated with the all-classical Hamiltonian is simply added to the energy of the isolated (non-solvated) solute along the reaction path. Interestingly the latter approach is found to be in semi-quantitative agreement with the full mixed Hamiltonian approximation.« less

Atomic and electronic structure of the CdTe(111)B–(2√3 × 4) orthogonal surface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bekenev, V. L., E-mail: bekenev@ipms.kiev.ua; Zubkova, S. M.

2017-01-15

The atomic and electronic structure of four variants of Te-terminated CdTe(111)B–(2√3 × 4) orthogonal polar surface (ideal, relaxed, reconstructed, and reconstructed with subsequent relaxation) are calculated ab initio for the first time. The surface is modeled by a film composed of 12 atomic layers with a vacuum gap of ~16 Å in the layered superlattice approximation. To close Cd dangling bonds on the opposite side of the film, 24 fictitious hydrogen atoms with a charge of 1.5 electrons each are added. Ab initio calculations are performed using the Quantum Espresso program based on density functional theory. It is demonstrated thatmore » relaxation leads to splitting of the four upper layers. The band energy structures and total and layer-by-layer densities of electronic states for the four surface variants are calculated and analyzed.« less

Modeling molecule-plasmon interactions using quantized radiation fields within time-dependent electronic structure theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nascimento, Daniel R.; DePrince, A. Eugene, E-mail: deprince@chem.fsu.edu

2015-12-07

We present a combined cavity quantum electrodynamics/ab initio electronic structure approach for simulating plasmon-molecule interactions in the time domain. The simple Jaynes-Cummings-type model Hamiltonian typically utilized in such simulations is replaced with one in which the molecular component of the coupled system is treated in a fully ab initio way, resulting in a computationally efficient description of general plasmon-molecule interactions. Mutual polarization effects are easily incorporated within a standard ground-state Hartree-Fock computation, and time-dependent simulations carry the same formal computational scaling as real-time time-dependent Hartree-Fock theory. As a proof of principle, we apply this generalized method to the emergence ofmore » a Fano-like resonance in coupled molecule-plasmon systems; this feature is quite sensitive to the nanoparticle-molecule separation and the orientation of the molecule relative to the polarization of the external electric field.« less

Fully ab initio calculation of the resonant one-phonon Raman intensity of graphene

NASA Astrophysics Data System (ADS)

Reichardt, Sven; Wirtz, Ludger

We developed a fully ab initio, many-body perturbation theory approach for the calculation of resonant, one-phonon Raman spectra. Our general approach is applicable to any material and here we present its application to the case of graphene. Our diagrammatic, first-principles approach allows us to go beyond and improve on an earlier theoretical study by Basko, which relied on an analytical calculation in certain limits. We investigate the dependence of the G peak intensity on both the excitation energy and Fermi level. Furthermore, our method allows us to identify the relevant electronic quantum pathways and to demonstrate the importance of the contributions from non-resonant electronic transitions. We also applied our approach to the calculation of the resonant one-phonon Raman spectrum of MoS2, with our results being in good agreement with experimental data. SR acknowledges financial support from the National Research Fund (FNR) Luxembourg.

An ab initio study of some binary complexes containing methyl fluoride and difluoromethane: red-shifting and blue-shifting hydrogen bonds

NASA Astrophysics Data System (ADS)

Ramasami, Ponnadurai; Ford, Thomas A.

2018-07-01

The properties of a number of hydrogen-bonded complexes of methyl fluoride and difluoromethane with a range of hydrides of the first two rows of the periodic table have been computed using ab initio molecular orbital theory. The aim of this work was to identify possible examples of blue-shifting hydrogen-bonded species analogous to those formed between fluoroform and ammonia, water, phosphine and hydrogen sulphide, reported earlier. The calculations were carried out using the Gaussian-09 program, at the second-order level of Møller-Plesset perturbation theory, and with the aug-cc-pVTZ basis sets of Dunning. The properties studied include the molecular structures, the hydrogen bond energies and the vibrational spectra. The results have been interpreted with the aid of natural bond orbital theory and the quantum theory of atoms in molecules.

Quantitative structure activity relationships from optimised ab initio bond lengths: steroid binding affinity and antibacterial activity of nitrofuran derivatives

NASA Astrophysics Data System (ADS)

Smith, P. J.; Popelier, P. L. A.

2004-02-01

The present day abundance of cheap computing power enables the use of quantum chemical ab initio data in Quantitative Structure-Activity Relationships (QSARs). Optimised bond lengths are a new such class of descriptors, which we have successfully used previously in representing electronic effects in medicinal and ecological QSARs (enzyme inhibitory activity, hydrolysis rate constants and pKas). Here we use AM1 and HF/3-21G* bond lengths in conjunction with Partial Least Squares (PLS) and a Genetic Algorithm (GA) to predict the Corticosteroid-Binding Globulin (CBG) binding activity of the classic steroid data set, and the antibacterial activity of nitrofuran derivatives. The current procedure, which does not require molecular alignment, produces good r2 and q2 values. Moreover, it highlights regions in the common steroid skeleton deemed relevant to the active regions of the steroids and nitrofuran derivatives.

Quantifying Ab Initio Equation of State Errors for Hydrogen-Helium Mixtures

NASA Astrophysics Data System (ADS)

Clay, Raymond; Morales, Miguel

2017-06-01

In order to produce predictive models of Jovian planets, an accurate equation of state for hydrogen-helium mixtures is needed over pressure and temperature ranges spanning multiple orders of magnitude. While extensive theoretical work has been done in this area, previous controversies regarding the equation of state of pure hydrogen have demonstrated exceptional sensitivity to approximations commonly employed in ab initio calculations. To this end, we present the results of our quantum Monte Carlo based benchmarking studies for several major classes of density functionals. Additionally, we expand upon our published results by considering the impact that ionic finite size effects and density functional errors translate to errors in the equation of state. Sandia National Laboratories is a multi-mission laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Investigation of electronic structure and chemical bonding of intermetallic Pd2HfIn: An ab-initio study

NASA Astrophysics Data System (ADS)

Bano, Amreen; Gaur, N. K.

2018-05-01

Ab-initio calculations are carried out to study the electronic and chemical bonding properties of Intermetallic full Heusler compound Pd2HfIn which crystallizes in F-43m structure. All calculations are performed by using density functional theory (DFT) based code Quantum Espresso. Generalized gradient approximations (GGA) of Perdew- Burke- Ernzerhof (PBE) have been adopted for exchange-correlation potential. Calculated electronic band structure reveals the metallic character of the compound. From partial density of states (PDoS), we found the presence of relatively high intensity electronic states of 4d-Pd atom at Fermi level. We have found a pseudo-gap just abouve the Fermi level and N(E) at Fermi level is observed to be 0.8 states/eV, these finding indicates the existence of superconducting character in Pd2HfIn.

Ab initio calculation of a global potential, vibrational energies, and wave functions for HCN/HNC, and a simulation of the (A-tilde)-(X-tilde) emission spectrum

NASA Technical Reports Server (NTRS)

Bowman, Joel M.; Gazdy, Bela; Bentley, Joseph A.; Lee, Timothy J.; Dateo, Christopher E.

1993-01-01

A potential energy surface for the HCN/HNC system which is a fit to extensive, high-quality ab initio, coupled-cluster calculations is presented. All HCN and HNC states with energies below the energy of the first delocalized state are reported and characterized. Vibrational transition energies are compared with all available experimental data on HCN and HNC, including high CH-overtone states up to 23,063/cm. A simulation of the (A-tilde)-(X-tilde) stimulated emission pumping (SEP) spectrum is also reported, and the results are compared to experiment. Franck-Condon factors are reported for odd bending states of HCN, with one quantum of vibrational angular momentum, in order to compare with the recent assignment by Jonas et al. (1992), on the basis of axis-switching arguments of a number of previously unassigned states in the SEP spectrum.

Structure and equilibria of Ca 2+-complexes of glucose and sorbitol from multinuclear ( 1H, 13C and 43Ca) NMR measurements supplemented with molecular modelling calculations

NASA Astrophysics Data System (ADS)

Pallagi, A.; Dudás, Cs.; Csendes, Z.; Forgó, P.; Pálinkó, I.; Sipos, P.

2011-05-01

Ca 2+-complexation of D-glucose and D-sorbitol have been investigated with the aid of multinuclear ( 1H, 13C and 43Ca) NMR spectroscopy and ab initio quantum chemical calculations. Formation constants of the forming 1:1 complexes have been estimated from one-dimensional 13C NMR spectra obtained at constant ionic strength (1 M NaCl). Binding sites were identified from 2D 1H- 43Ca NMR spectra. 2D NMR measurements and ab initio calculations indicated that Ca 2+ ions were bound in a tridentate manner via the glycosidic OH, the ethereal oxygen in the ring and the OH on the terminal carbon for the α- and β-anomers of glucose and for sorbitol simultaneous binding of four hydroxide moieties (C1, C2, C4 and C6) was suggested.

Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector

PubMed Central

van Genderen, E.; Clabbers, M. T. B.; Das, P. P.; Stewart, A.; Nederlof, I.; Barentsen, K. C.; Portillo, Q.; Pannu, N. S.; Nicolopoulos, S.; Gruene, T.; Abrahams, J. P.

2016-01-01

Until recently, structure determination by transmission electron microscopy of beam-sensitive three-dimensional nanocrystals required electron diffraction tomography data collection at liquid-nitrogen temperature, in order to reduce radiation damage. Here it is shown that the novel Timepix detector combines a high dynamic range with a very high signal-to-noise ratio and single-electron sensitivity, enabling ab initio phasing of beam-sensitive organic compounds. Low-dose electron diffraction data (∼0.013 e− Å−2 s−1) were collected at room temperature with the rotation method. It was ascertained that the data were of sufficient quality for structure solution using direct methods using software developed for X-ray crystallography (XDS, SHELX) and for electron crystallography (ADT3D/PETS, SIR2014). PMID:26919375

Quantum-chemical study of model chemisorption structures on copper-containing catalysts. Communicat ion 1. ab-initio calculations of CuCo and CuCo/sup +/

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuzminskii, M.B.; Bagator'yants, A.A.; Kazanskii, V.B.

1986-08-01

The authors perform ab-initio calculations, by the SCF MO LCAO method, of the electronic and geometric structure of the systems CuCO /SUP n+/ (n=0, 1) and potential curves of CO, depending on the charge state of the copper, with variation of all geometric parameters. The calculations of open-shell electronic states were performed by the unrestricted SCF method in a minimal basis set (I, STO-3G for the C and O, and MINI-1' for the Cu) and in a valence two-exponential basis set (II, MIDI-1 for the C and O, and MIDI'2' for the Cu). The principal results from the calculation inmore » the more flexible basis II are presented and the agreement between the results obtained in the minimal basis I and these data is then analyzed qualitatively.« less

On the Origin of Quantum Diffusion Coefficient and Quantum Potential

NASA Astrophysics Data System (ADS)

Gupta, Aseem

2016-03-01

Synchronizability of space and time experiences between different inhabitants of a spacetime is abstracted as a fundamental premise of Classical physics. Absence thereof i.e. desynchronization between space and time experiences of a system under study and the observer is then studied for a single dimension single particle system. Desynchronization fundamentally makes probability concepts enter physics ab-initio and not as secondary tools to deal with situations wherein incomplete information in situation following perfectly deterministic dynamics demands its introduction. Desynchronization model based on Poisson distribution of events vis-à-vis an observer, leads to expectation of particle's motion as a Brownian motion deriving Nelson's quantum diffusion coefficient naturally, without needing to postulate it. This model also incorporates physical effects akin to those of Bohm's Quantum Potential, again without needing any sub-quantum medium. Schrodinger's equation is shown to be derivable incorporating desynchronization only of space while Quantum Field Theory is shown to model desynchronization of time as well. Fundamental suggestion of the study is that it is desynchronization that is at the root of quantum phenomena rather than sub-micro scales of spacetime. Absence of possibility of synchronization between system's space and time and those of observer is studied. Mathematical modeling of desynchronized evolution explains some intriguing aspects of Quantum Mechanical theory.

Nonadiabatic Ab Initio Molecular Dynamics with the Floating Occupation Molecular Orbital-Complete Active Space Configuration Interaction Method [Non-Adiabatic Ab Initio Molecular Dynamics with Floating Occupation Molecular Orbitals CASCI Method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hollas, Daniel; Sistik, Lukas; Hohenstein, Edward G.

Here, we show that the floating occupation molecular orbital complete active space configuration interaction (FOMO-CASCI) method is a promising alternative to the widely used complete active space self-consistent field (CASSCF) method in direct nonadiabatic dynamics simulations. We have simulated photodynamics of three archetypal molecules in photodynamics: ethylene, methaniminium cation, and malonaldehyde. We compared the time evolution of electronic populations and reaction mechanisms as revealed by the FOMO-CASCI and CASSCF approaches. Generally, the two approaches provide similar results. Some dynamical differences are observed, but these can be traced back to energetically minor differences in the potential energy surfaces. We suggest thatmore » the FOMO-CASCI method represents, due to its efficiency and stability, a promising approach for direct ab initio dynamics in the excited state.« less

Multi-level Quantum Mechanics and Molecular Mechanics Study of Ring Opening Process of Guanine Damage by Hydroxyl Radical in Aqueous Solution.

PubMed

Liu, Peng; Wang, Qiong; Niu, Meixing; Wang, Dunyou

2017-08-10

Combining multi-level quantum mechanics theories and molecular mechanics with an explicit water model, we investigated the ring opening process of guanine damage by hydroxyl radical in aqueous solution. The detailed, atomic-level ring-opening mechanism along the reaction pathway was revealed in aqueous solution at the CCSD(T)/MM levels of theory. The potentials of mean force in aqueous solution were calculated at both the DFT/MM and CCSD(T)/MM levels of the theory. Our study found that the aqueous solution has a significant effect on this reaction in solution. In particular, by comparing the geometries of the stationary points between in gas phase and in aqueous solution, we found that the aqueous solution has a tremendous impact on the torsion angles much more than on the bond lengths and bending angles. Our calculated free-energy barrier height 31.6 kcal/mol at the CCSD(T)/MM level of theory agrees well with the one obtained based on gas-phase reaction profile and free energies of solvation. In addition, the reaction path in gas phase was also mapped using multi-level quantum mechanics theories, which shows a reaction barrier at 19.2 kcal/mol at the CCSD(T) level of theory, agreeing very well with a recent ab initio calculation result at 20.8 kcal/mol.

Comparing Vibrationally Averaged Nuclear Shielding Constants by Quantum Diffusion Monte Carlo and Second-Order Perturbation Theory.

PubMed

Ng, Yee-Hong; Bettens, Ryan P A

2016-03-03

Using the method of modified Shepard's interpolation to construct potential energy surfaces of the H2O, O3, and HCOOH molecules, we compute vibrationally averaged isotropic nuclear shielding constants ⟨σ⟩ of the three molecules via quantum diffusion Monte Carlo (QDMC). The QDMC results are compared to that of second-order perturbation theory (PT), to see if second-order PT is adequate for obtaining accurate values of nuclear shielding constants of molecules with large amplitude motions. ⟨σ⟩ computed by the two approaches differ for the hydrogens and carbonyl oxygen of HCOOH, suggesting that for certain molecules such as HCOOH where big displacements away from equilibrium happen (internal OH rotation), ⟨σ⟩ of experimental quality may only be obtainable with the use of more sophisticated and accurate methods, such as quantum diffusion Monte Carlo. The approach of modified Shepard's interpolation is also extended to construct shielding constants σ surfaces of the three molecules. By using a σ surface with the equilibrium geometry as a single data point to compute isotropic nuclear shielding constants for each descendant in the QDMC ensemble representing the ground state wave function, we reproduce the results obtained through ab initio computed σ to within statistical noise. Development of such an approach could thereby alleviate the need for any future costly ab initio σ calculations.

Bound state potential energy surface construction: ab initio zero-point energies and vibrationally averaged rotational constants.

PubMed

Bettens, Ryan P A

2003-01-15

Collins' method of interpolating a potential energy surface (PES) from quantum chemical calculations for reactive systems (Jordan, M. J. T.; Thompson, K. C.; Collins, M. A. J. Chem. Phys. 1995, 102, 5647. Thompson, K. C.; Jordan, M. J. T.; Collins, M. A. J. Chem. Phys. 1998, 108, 8302. Bettens, R. P. A.; Collins, M. A. J. Chem. Phys. 1999, 111, 816) has been applied to a bound state problem. The interpolation method has been combined for the first time with quantum diffusion Monte Carlo calculations to obtain an accurate ground state zero-point energy, the vibrationally average rotational constants, and the vibrationally averaged internal coordinates. In particular, the system studied was fluoromethane using a composite method approximating the QCISD(T)/6-311++G(2df,2p) level of theory. The approach adopted in this work (a) is fully automated, (b) is fully ab initio, (c) includes all nine nuclear degrees of freedom, (d) requires no assumption of the functional form of the PES, (e) possesses the full symmetry of the system, (f) does not involve fitting any parameters of any kind, and (g) is generally applicable to any system amenable to quantum chemical calculations and Collins' interpolation method. The calculated zero-point energy agrees to within 0.2% of its current best estimate. A0 and B0 are within 0.9 and 0.3%, respectively, of experiment.

Mechanism of fast lattice diffusion of hydrogen in palladium: Interplay of quantum fluctuations and lattice strain

NASA Astrophysics Data System (ADS)

Kimizuka, Hajime; Ogata, Shigenobu; Shiga, Motoyuki

2018-01-01

Understanding the underlying mechanism of the nanostructure-mediated high diffusivity of H in Pd is of recent scientific interest and also crucial for industrial applications. Here, we present a decisive scenario explaining the emergence of the fast lattice-diffusion mode of interstitial H in face-centered cubic Pd, based on the quantum mechanical natures of both electrons and nuclei under finite strains. Ab initio path-integral molecular dynamics was applied to predict the temperature- and strain-dependent free energy profiles for H migration in Pd over a temperature range of 150-600 K and under hydrostatic tensile strains of 0.0%-2.4%; such strain conditions are likely to occur in real systems, especially around the elastic fields induced by nanostructured defects. The simulated results revealed that, for preferential H location at octahedral sites, as in unstrained Pd, the activation barrier for H migration (Q ) was drastically increased with decreasing temperature owing to nuclear quantum effects. In contrast, as tetrahedral sites increased in stability with lattice expansion, nuclear quantum effects became less prominent and ceased impeding H migration. This implies that the nature of the diffusion mechanism gradually changes from quantum- to classical-like as the strain is increased. For H atoms in Pd at the hydrostatic strain of ˜2.4 % , we determined that the mechanism promoted fast lattice diffusion (Q =0.11 eV) of approximately 20 times the rate of conventional H diffusion (Q =0.23 eV) in unstrained Pd at a room temperature of 300 K.

Single-ion 4f element magnetism: an ab-initio look at Ln(COT)2(-).

PubMed

Gendron, Frédéric; Pritchard, Benjamin; Bolvin, Hélène; Autschbach, Jochen

2015-12-14

The electron densities associated with the Ln 4f shell, and spin and orbital magnetizations ('magnetic moment densities'), are investigated for the Ln(COT)2(-) series. The densities are obtained from ab-initio calculations including spin-orbit coupling. For Ln = Ce, Pr the magnetizations are also derived from crystal field models and shown to agree with the ab-initio results. Analysis of magnetizations from ab-initio calculations may be useful in assisting research on single molecule magnets.

A coupled two-dimensional main chain torsional potential for protein dynamics: generation and implementation.

PubMed

Li, Yongxiu; Gao, Ya; Zhang, Xuqiang; Wang, Xingyu; Mou, Lirong; Duan, Lili; He, Xiao; Mei, Ye; Zhang, John Z H

2013-09-01

Main chain torsions of alanine dipeptide are parameterized into coupled 2-dimensional Fourier expansions based on quantum mechanical (QM) calculations at M06 2X/aug-cc-pvtz//HF/6-31G** level. Solvation effect is considered by employing polarizable continuum model. Utilization of the M06 2X functional leads to precise potential energy surface that is comparable to or even better than MP2 level, but with much less computational demand. Parameterization of the 2D expansions is against the full main chain torsion space instead of just a few low energy conformations. This procedure is similar to that for the development of AMBER03 force field, except unique weighting factor was assigned to all the grid points. To avoid inconsistency between quantum mechanical calculations and molecular modeling, the model peptide is further optimized at molecular mechanics level with main chain dihedral angles fixed before the calculation of the conformational energy on molecular mechanical level at each grid point, during which generalized Born model is employed. Difference in solvation models at quantum mechanics and molecular mechanics levels makes this parameterization procedure less straightforward. All force field parameters other than main chain torsions are taken from existing AMBER force field. With this new main chain torsion terms, we have studied the main chain dihedral distributions of ALA dipeptide and pentapeptide in aqueous solution. The results demonstrate that 2D main chain torsion is effective in delineating the energy variation associated with rotations along main chain dihedrals. This work is an implication for the necessity of more accurate description of main chain torsions in the future development of ab initio force field and it also raises a challenge to the development of quantum mechanical methods, especially the quantum mechanical solvation models.

Quantum fluctuations of a fullerene cage modulate its internal magnetic environment.

PubMed

Kawatsu, Tsutomu; Tachikawa, Masanori

2018-01-17

To investigate the effect of quantum fluctuations on the magnetic environment inside a C 60 fullerene cage, we have calculated the nuclear magnetic shielding constant of protons in H 2 @C 60 and HD@C 60 systems by on-the-fly ab initio path integral simulation, including both thermal and nuclear quantum effects. The most dominant upfield from an isolated hydrogen molecule occurs due to the diamagnetic current of the C 60 cage, which is partly cancelled by the paramagnetic current, where the paramagnetic contribution is enlarged by the zero-point vibrational fluctuation of the C 60 carbon backbone structure via a widely distributed HOMO-LUMO gap. This quantum modulation mechanism of the nuclear magnetic shielding constant is newly proposed. Because this quantum effect is independent of the difference between H 2 and HD, the H 2 /HD isotope shift occurs in spite of the C 60 cage. The nuclear magnetic constants computed for H 2 @C 60 and HD@C 60 are 32.047 and 32.081 ppm, respectively, which are in reasonable agreement with the corresponding values of 32.19 and 32.23 ppm estimated from the experimental values of the chemical shifts.

Nuclear quantum effects on adsorption of H2 and isotopologues on metal ions

NASA Astrophysics Data System (ADS)

Savchenko, Ievgeniia; Gu, Bing; Heine, Thomas; Jakowski, Jacek; Garashchuk, Sophya

2017-02-01

The nuclear quantum effects on the zero-point energy (ZPE), influencing adsorption of H2 and isotopologues on metal ions, are examined using normal mode analysis of ab initio electronic structure results for complexes with 17 metal cations. The lightest metallic nuclei, Li and Be, are found to be the most 'quantum'. The largest selectivity in adsorption is predicted for Cu, Ni and Co ions. Analysis of the nuclear wavepacket dynamics on the ground state electronic potential energy surfaces (PES) performed for complexes of Li+ and Cu+2 with H2/D2/HD shows that the PES anharmonicity changes the ZPE by up to 9%.

Ab initio molecular dynamics simulations of the initial stages of solid-electrolyte interphase formation on lithium ion battery graphitic anodes.

PubMed

Leung, Kevin; Budzien, Joanne L

2010-07-07

The decomposition of ethylene carbonate (EC) during the initial growth of solid-electrolyte interphase (SEI) films at the solvent-graphitic anode interface is critical to lithium ion battery operations. Ab initio molecular dynamics simulations of explicit liquid EC/graphite interfaces are conducted to study these electrochemical reactions. We show that carbon edge terminations are crucial at this stage, and that achievable experimental conditions can lead to surprisingly fast EC breakdown mechanisms, yielding decomposition products seen in experiments but not previously predicted.

Ab initio nonadiabatic molecular dynamics of the ultrafast electron injection from a PbSe quantum dot into the TiO2 surface.

PubMed

Long, Run; Prezhdo, Oleg V

2011-11-30

Following recent experiments [Science 2010, 328, 1543; PNAS 2011, 108, 965], we report an ab initio nonadiabatic molecular dynamics (NAMD) simulation of the ultrafast photoinduced electron transfer (ET) from a PbSe quantum dot (QD) into the rutile TiO(2) (110) surface. The system forms the basis for QD-sensitized semiconductor solar cells and demonstrates that ultrafast interfacial ET is instrumental for achieving high efficiencies in solar-to-electrical energy conversion. The simulation supports the observation that the ET successfully competes with energy losses due to electron-phonon relaxation. The ET proceeds by the adiabatic mechanism because of strong donor-acceptor coupling. High frequency polar vibrations of both QD and TiO(2) promote the ET, since these modes can rapidly influence the donor-acceptor state energies and coupling. Low frequency vibrations generate a distribution of initial conditions for ET, which shows a broad variety of scenarios at the single-molecule level. Compared to the molecule-TiO(2) interfaces, the QD-TiO(2) system exhibits pronounced differences that arise due to the larger size and higher rigidity of QDs relative to molecules. Both donor and acceptor states are more delocalized in the QD system, and the ET is promoted by optical phonons, which have relatively low frequencies in the QD materials composed of heavy elements. In contrast, in molecular systems, optical phonons are not thermally accessible under ambient conditions. Meanwhile, TiO(2) acceptor states resemble surface impurities due to the local influence of molecular chromophores. At the same time, the photoinduced ET at both QD-TiO(2) and molecule-TiO(2) interfaces is ultrafast and occurs by the adiabatic mechanism, as a result of strong donor-acceptor coupling. The reported state-of-the-art simulation generates a detailed time-domain atomistic description of the interfacial ET process that is fundamental to a wide variety of applications.

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2010 CFR

2010-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2010 CFR

2010-07-01

... conditions specified in § 86.1843-01, the Administrator may deem such certificate void ab initio. (e) When the Administrator denies, suspends, revokes, or voids ab initio a certificate, EPA will provide the... that makes the certification void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2014 CFR

2014-07-01

... conditions specified in § 86.1843-01, the Administrator may deem such certificate void ab initio. (e) When the Administrator denies, suspends, revokes, or voids ab initio a certificate, EPA will provide the... that makes the certification void ab initio. ...

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2013 CFR

2013-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2011 CFR

2011-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2012 CFR

2012-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2012 CFR

2012-07-01

... conditions specified in § 86.1843-01, the Administrator may deem such certificate void ab initio. (e) When the Administrator denies, suspends, revokes, or voids ab initio a certificate, EPA will provide the... that makes the certification void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2013 CFR

2013-07-01

... conditions specified in § 86.1843-01, the Administrator may deem such certificate void ab initio. (e) When the Administrator denies, suspends, revokes, or voids ab initio a certificate, EPA will provide the... that makes the certification void ab initio. ...

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2014 CFR

2014-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2011 CFR

2011-07-01

... conditions specified in § 86.1843-01, the Administrator may deem such certificate void ab initio. (e) When the Administrator denies, suspends, revokes, or voids ab initio a certificate, EPA will provide the... that makes the certification void ab initio. ...

High-throughput materials discovery and development: breakthroughs and challenges in the mapping of the materials genome

NASA Astrophysics Data System (ADS)

Buongiorno Nardelli, Marco

High-Throughput Quantum-Mechanics computation of materials properties by ab initio methods has become the foundation of an effective approach to materials design, discovery and characterization. This data driven approach to materials science currently presents the most promising path to the development of advanced technological materials that could solve or mitigate important social and economic challenges of the 21st century. In particular, the rapid proliferation of computational data on materials properties presents the possibility to complement and extend materials property databases where the experimental data is lacking and difficult to obtain. Enhanced repositories such as AFLOWLIB open novel opportunities for structure discovery and optimization, including uncovering of unsuspected compounds, metastable structures and correlations between various properties. The practical realization of these opportunities depends almost exclusively on the the design of efficient algorithms for electronic structure simulations of realistic material systems beyond the limitations of the current standard theories. In this talk, I will review recent progress in theoretical and computational tools, and in particular, discuss the development and validation of novel functionals within Density Functional Theory and of local basis representations for effective ab-initio tight-binding schemes. Marco Buongiorno Nardelli is a pioneer in the development of computational platforms for theory/data/applications integration rooted in his profound and extensive expertise in the design of electronic structure codes and in his vision for sustainable and innovative software development for high-performance materials simulations. His research activities range from the design and discovery of novel materials for 21st century applications in renewable energy, environment, nano-electronics and devices, the development of advanced electronic structure theories and high-throughput techniques in materials genomics and computational materials design, to an active role as community scientific software developer (QUANTUM ESPRESSO, WanT, AFLOWpi)

Electronic and mechanical properties of ZnX (X = S, Se and Te)—An ab initio study

NASA Astrophysics Data System (ADS)

Verma, Ajay Singh; Sharma, Sheetal; Sarkar, Bimal Kumar; Jindal, Vijay Kumar

2011-12-01

Zinc chalcogenides (ZnX, X = S, Se and Te) have been increasing attention as wide and direct band gap semiconductor for blue and ultraviolet optical devices. This paper analyzes electronic and mechanical properties of these materials by ab initio pseudo-potential method that uses non conserving pseudopotentials in fully nonlocal form, as implemented in SIESTA code. In this approach the local density approximation (LDA) is used for the exchange-correlation (XC) potential. The calculations are given for band gap, elastic constants (C11, C12 and C44), shear modulus, and Young's modulus. The results are in very good agreement with previous theoretical calculations and available experimental data.

Merging first principle structure studies and few-body reaction formalism

NASA Astrophysics Data System (ADS)

Crespo, R.; Cravo, E.; Arriaga, A.; Wiringa, R.; Deltuva, A.; Diego, R.

2018-02-01

Calculations for nucleon knockout from a 7Li beam due to the collision with a proton target at 400 MeV/u are shown based on ab initio Quantum Monte Carlo (QMC) and conventional shell-model nuclear structure approaches to describe the relative motion between the knockout particle and the heavy fragment of the projectile. Structure effects on the total cross section are shown.

Initial-State Quantum Fluctuations in the Little Bang

DOE PAGES

Gelis, François; Schenke, Björn

2016-06-01

In this work, we review recent developments in the ab initio theoretical description of the initial state in heavy-ion collisions. We emphasize the importance of fluctuations, both for the phenomenological description of experimental data from the Relativistic Heavy Ion Collider (RHIC) and the Large Hadron Collider (LHC) and for the theoretical understanding of the nonequilibrium early-time dynamics and thermalization of the medium.

Ab initio joint density-functional theory of solvated electrodes, with model and explicit solvation

NASA Astrophysics Data System (ADS)

Arias, Tomas

2015-03-01

First-principles guided design of improved electrochemical systems has the potential for great societal impact by making non-fossil-fuel systems economically viable. Potential applications include improvements in fuel-cells, solar-fuel systems (``artificial photosynthesis''), supercapacitors and batteries. Economical fuel-cell systems would enable zero-carbon footprint transportation, solar-fuel systems would directly convert sunlight and water into hydrogen fuel for such fuel-cell vehicles, supercapacitors would enable nearly full recovery of energy lost during vehicle braking thus extending electric vehicle range and acceptance, and economical high-capacity batteries would be central to mitigating the indeterminacy of renewable resources such as wind and solar. Central to the operation of all of the above electrochemical systems is the electrode-electrolyte interface, whose underlying physics is quite rich, yet remains remarkably poorly understood. The essential underlying technical challenge to the first principles studies which could explore this physics is the need to properly represent simultaneously both the interaction between electron-transfer events at the electrode, which demand a quantum mechanical description, and multiscale phenomena in the liquid environment such as the electrochemical double layer (ECDL) and its associated shielding, which demand a statistical description. A direct ab initio approach to this challenge would, in principle, require statistical sampling and thousands of repetitions of already computationally demanding quantum mechanical calculations. This talk will begin with a brief review of a recent advance, joint density-functional theory (JDFT), which allows for a fully rigorous and, in principle, exact representation of the thermodynamic equilibrium between a system described at the quantum-mechanical level and a liquid environment, but without the need for costly sampling. We then shall demonstrate how this approach applies in the electrochemical context and how it is needed for realistic description of solvated electrode systems [], and how simple ``implicit'' polarized continuum methods fail radically in this context. Finally, we shall present a series of results relevant to battery, supercapacitor, and solar-fuel systems, one of which has led to a recent invention disclosure for improving battery cycle lifetimes. Supported as a part of the Energy Materials Center at Cornell, an Energy Frontier Research Center funded by DOE/BES (award de-sc0001086) and by the New York State Division of Science, Technology and Innovation (NYSTAR, award 60923).

DOE Office of Scientific and Technical Information (OSTI.GOV)

Makhov, Dmitry V.; Shalashilin, Dmitrii V.; Glover, William J.

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 MCEmore » 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.« less

Transferability of polarizable models for ion-water electrostatic interaction

NASA Astrophysics Data System (ADS)

Masia, Marco

2009-06-01

Studies of ion-water systems at condensed phase and at interfaces have pointed out that molecular and ionic polarization plays an important role for many phenomena ranging from hydrogen bond dynamics to water interfaces' structure. Classical and ab initio Molecular Dynamics simulations reveal that induced dipole moments at interfaces (e.g. air-water and water-protein) are usually high, hinting that polarizable models to be implemented in classical force fields should be very accurate in reproducing the electrostatic properties of the system. In this paper the electrostatic properties of three classical polarizable models for ion-water interaction are compared with ab initio results both at gas and condensed phase. For Li+- water and Cl--water dimers the reproducibility of total dipole moments obtained with high level quantum chemical calculations is studied; for the same ions in liquid water, Car-Parrinello Molecular Dynamics simulations are used to compute the time evolution of ionic and molecular dipole moments, which are compared with the classical models. The PD2-H2O model developed by the author and coworkers [Masia et al. J. Chem. Phys. 2004, 121, 7362] together with the gaussian intermolecular damping for ion-water interaction [Masia et al. J. Chem. Phys. 2005, 123, 164505] showed to be the fittest in reproducing the ab initio results from gas to condensed phase, allowing for force field transferability.

How does the trans-cis photoisomerization of azobenzene take place in organic solvents?

PubMed

Tiberio, Giustiniano; Muccioli, Luca; Berardi, Roberto; Zannoni, Claudio

2010-04-06

The trans-cis photoisomerization of azobenzene-containing materials is key to a number of photomechanical applications, but the actual conversion mechanism in condensed phases is still largely unknown. Herein, we study the n, pi* isomerization in a vacuum and in various solvents via a modified molecular dynamics simulation adopting an ab initio torsion-inversion force field in the ground and excited states, while allowing for electronic transitions and a stochastic decay to the fundamental state. We determine the trans-cis photoisomerization quantum yield and decay times in various solvents (n-hexane, anisole, toluene, ethanol, and ethylene glycol), and obtain results comparable with experimental ones where available. A profound difference between the isomerization mechanism in vacuum and in solution is found, with the often neglected mixed torsional-inversion pathway being the most important in solvents.

Quantum Dynamics Scattering Study of AB+CDE Reactions: A Seven Dimensional Treatment for the H2+C2H Reaction

NASA Technical Reports Server (NTRS)

Wang, Dunyou

2003-01-01

A time-dependent wave-packet approach is presented for the quantum dynamics study of the AB+CDE reaction system for zero total angular momentum. A seven-degree-of-freedom calculation is employed to study the chemical reaction of H2+C2H yields H + C2H2 by treating C2H as a linear molecule. Initial state selected reaction probabilities are presented for various initial ro-vibrational states. This study shows that vibrational excitation of H2 enhances the reaction probability, whereas the excitation of C2H has only a small effect on the reactivity. An integral cross section is also reported for the initial ground states of H2 and C2H. The theoretical and experimental results agree with each other very well when the calculated seven dimensional results are adjusted to account for the lower transition state barrier heights found in recent ab initio calculations.

40 CFR 86.004-30 - Certification.

Code of Federal Regulations, 2010 CFR

2010-07-01

... determined in accordance with this part. The certificate shall be void ab initio for those vehicles causing... the certificate was issued, and the certificate may be deemed void ab initio. (C) The manufacturer... determined in accordance with this part. The certificate shall be void ab initio for those vehicles causing...

40 CFR 86.004-30 - Certification.

Code of Federal Regulations, 2012 CFR

2012-07-01

... determined in accordance with this part. The certificate shall be void ab initio for those vehicles causing... the certificate was issued, and the certificate may be deemed void ab initio. (C) The manufacturer... determined in accordance with this part. The certificate shall be void ab initio for those vehicles causing...

40 CFR 86.007-30 - Certification.

Code of Federal Regulations, 2014 CFR

2014-07-01

... certificate may be deemed void ab initio. (C) The manufacturer shall bear the burden of establishing to the... be deemed void ab initio. (C) The manufacturer shall bear the burden of establishing to the... of conformity, the Administrator may deem such certificate void ab initio. (4) In any case in which...

40 CFR 86.004-30 - Certification.

Code of Federal Regulations, 2013 CFR

2013-07-01

... determined in accordance with this part. The certificate shall be void ab initio for those vehicles causing... the certificate was issued, and the certificate may be deemed void ab initio. (C) The manufacturer... determined in accordance with this part. The certificate shall be void ab initio for those vehicles causing...

Structural modeling of Ge6.25As32.5Se61.25 using a combination of reverse Monte Carlo and Ab initio molecular dynamics.

PubMed

Opletal, George; Drumm, Daniel W; Wang, Rong P; Russo, Salvy P

2014-07-03

Ternary glass structures are notoriously difficult to model accurately, and yet prevalent in several modern endeavors. Here, a novel combination of Reverse Monte Carlo (RMC) modeling and ab initio molecular dynamics (MD) is presented, rendering these complicated structures computationally tractable. A case study (Ge6.25As32.5Se61.25 glass) illustrates the effects of ab initio MD quench rates and equilibration temperatures, and the combined approach's efficacy over standard RMC or random insertion methods. Submelting point MD quenches achieve the most stable, realistic models, agreeing with both experimental and fully ab initio results. The simple approach of RMC followed by ab initio geometry optimization provides similar quality to the RMC-MD combination, for far fewer resources.

ParFit: A Python-Based Object-Oriented Program for Fitting Molecular Mechanics Parameters to ab Initio Data

DOE PAGES

Zahariev, Federico; De Silva, Nuwan; Gordon, Mark S.; ...

2017-02-23

Here, a newly created object-oriented program for automating the process of fitting molecular-mechanics parameters to ab initio data, termed ParFit, is presented. ParFit uses a hybrid of deterministic and stochastic genetic algorithms. ParFit can simultaneously handle several molecular-mechanics parameters in multiple molecules and can also apply symmetric and antisymmetric constraints on the optimized parameters. The simultaneous handling of several molecules enhances the transferability of the fitted parameters. ParFit is written in Python, uses a rich set of standard and nonstandard Python libraries, and can be run in parallel on multicore computer systems. As an example, a series of phosphine oxides,more » important for metal extraction chemistry, are parametrized using ParFit.« less

ParFit: A Python-Based Object-Oriented Program for Fitting Molecular Mechanics Parameters to ab Initio Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zahariev, Federico; De Silva, Nuwan; Gordon, Mark S.

Here, a newly created object-oriented program for automating the process of fitting molecular-mechanics parameters to ab initio data, termed ParFit, is presented. ParFit uses a hybrid of deterministic and stochastic genetic algorithms. ParFit can simultaneously handle several molecular-mechanics parameters in multiple molecules and can also apply symmetric and antisymmetric constraints on the optimized parameters. The simultaneous handling of several molecules enhances the transferability of the fitted parameters. ParFit is written in Python, uses a rich set of standard and nonstandard Python libraries, and can be run in parallel on multicore computer systems. As an example, a series of phosphine oxides,more » important for metal extraction chemistry, are parametrized using ParFit.« less

Comparing ab initio density-functional and wave function theories: the impact of correlation on the electronic density and the role of the correlation potential.

PubMed

Grabowski, Ireneusz; Teale, Andrew M; Śmiga, Szymon; Bartlett, Rodney J

2011-09-21

The framework of ab initio density-functional theory (DFT) has been introduced as a way to provide a seamless connection between the Kohn-Sham (KS) formulation of DFT and wave-function based ab initio approaches [R. J. Bartlett, I. Grabowski, S. Hirata, and S. Ivanov, J. Chem. Phys. 122, 034104 (2005)]. Recently, an analysis of the impact of dynamical correlation effects on the density of the neon atom was presented [K. Jankowski, K. Nowakowski, I. Grabowski, and J. Wasilewski, J. Chem. Phys. 130, 164102 (2009)], contrasting the behaviour for a variety of standard density functionals with that of ab initio approaches based on second-order Møller-Plesset (MP2) and coupled cluster theories at the singles-doubles (CCSD) and singles-doubles perturbative triples [CCSD(T)] levels. In the present work, we consider ab initio density functionals based on second-order many-body perturbation theory and coupled cluster perturbation theory in a similar manner, for a range of small atomic and molecular systems. For comparison, we also consider results obtained from MP2, CCSD, and CCSD(T) calculations. In addition to this density based analysis, we determine the KS correlation potentials corresponding to these densities and compare them with those obtained for a range of ab initio density functionals via the optimized effective potential method. The correlation energies, densities, and potentials calculated using ab initio DFT display a similar systematic behaviour to those derived from electronic densities calculated using ab initio wave function theories. In contrast, typical explicit density functionals for the correlation energy, such as VWN5 and LYP, do not show behaviour consistent with this picture of dynamical correlation, although they may provide some degree of correction for already erroneous explicitly density-dependent exchange-only functionals. The results presented here using orbital dependent ab initio density functionals show that they provide a treatment of exchange and correlation contributions within the KS framework that is more consistent with traditional ab initio wave function based methods.

Ab initio characterization of electron transfer coupling in photoinduced systems: generalized Mulliken-Hush with configuration-interaction singles.

PubMed

Chen, Hung-Cheng; Hsu, Chao-Ping

2005-12-29

To calculate electronic couplings for photoinduced electron transfer (ET) reactions, we propose and test the use of ab initio quantum chemistry calculation for excited states with the generalized Mulliken-Hush (GMH) method. Configuration-interaction singles (CIS) is proposed to model the locally excited (LE) and charge-transfer (CT) states. When the CT state couples with other high lying LE states, affecting coupling values, the image charge approximation (ICA), as a simple solvent model, can lower the energy of the CT state and decouple the undesired high-lying local excitations. We found that coupling strength is weakly dependent on many details of the solvent model, indicating the validity of the Condon approximation. Therefore, a trustworthy value can be obtained via this CIS-GMH scheme, with ICA used as a tool to improve and monitor the quality of the results. Systems we tested included a series of rigid, sigma-linked donor-bridge-acceptor compounds where "through-bond" coupling has been previously investigated, and a pair of molecules where "through-space" coupling was experimentally demonstrated. The calculated results agree well with experimentally inferred values in the coupling magnitudes (for both systems studied) and in the exponential distance dependence (for the through-bond series). Our results indicate that this new scheme can properly account for ET coupling arising from both through-bond and through-space mechanisms.

Ab initio chemical kinetic study on Cl + ClO and related reverse processes.

PubMed

Xu, Z F; Lin, M C

2010-11-04

The reaction of ClO with Cl and its related reverse processes have been studied theoretically by ab initio quantum chemical and statistical mechanical calculations. The geometric parameters of the reactants, products, and transition states are optimized by both UMPW1PW91 and unrestricted coupled-cluster single and double excitation (UCCSD) methods with the 6-311+G(3df) basis set. The potential energy surface has been further refined (with triple excitations, T) at the UCCSD(T)/6-311+G(3df) level of theory. The results show that Cl(2) and O ((3)P) can be produced by chlorine atom abstraction via a tight transition state, while ClOCl ((1)A(1)) and ClClO ((1)A') can be formed by barrierless association processes with exothermicities of 31.8 and 16.0 kcal/mol, respectively. In principle the O ((1)D) atom can be generated with a large endothermicity of 56.9 kcal/mol; on the other hand, its barrierless reaction with Cl(2) can readily form ClClO ((1)A'), which fragments rapidly to give ClO + Cl. The rate constants of both forward and reverse processes have been predicted at 150-2000 K by the microcanonical variational transition state theory (VTST)/Rice-Ramsperger-Kassel-Marcus (RRKM) theory. The predicted rate constants are in good agreement with available experimental data within reported errors.

Large scale Full QM-MD investigation of small peptides and insulin adsorption on ideal and defective TiO2 (1 0 0) surfaces. Influence of peptide size on interfacial bonds

NASA Astrophysics Data System (ADS)

Dubot, Pierre; Boisseau, Nicolas; Cenedese, Pierre

2018-05-01

Large biomolecule interaction with oxide surface has attracted a lot of attention because it drives behavior of implanted devices in the living body. To investigate the role of TiO2 surface structure on a large polypeptide (insulin) adsorption, we use a homemade mixed Molecular Dynamics-Full large scale Quantum Mechanics code. A specific re-parameterized (Ti) and globally convergent NDDO method fitted on high level ab initio method (coupled cluster CCSD(T) and DFT) allows us to safely describe the electronic structure of the whole insulin-TiO2 surface system (up to 4000 atoms). Looking specifically at carboxylate residues, we demonstrate in this work that specific interfacial bonds are obtained from the insulin/TiO2 system that are not observed in the case of smaller peptides (tripeptides, insulin segment chains with different configurations). We also demonstrate that a large part of the adsorption energy is compensated by insulin conformational energy changes and surface defects enhanced this trend. Large slab dimensions allow us to take into account surface defects that are actually beyond ab initio capabilities owing to size effect. These results highlight the influence of the surface structure on the conformation and therefore of the possible inactivity of an adsorbed polypeptides.

On the Origins of the Linear Free Energy Relationships: Exploring the Nature of the Off-Diagonal Coupling Elements in SN2 Reactions

PubMed Central

Rosta, Edina; Warshel, Arieh

2012-01-01

Understanding the relationship between the adiabatic free energy profiles of chemical reactions and the underlining diabatic states is central to the description of chemical reactivity. The diabatic states form the theoretical basis of Linear Free Energy Relationships (LFERs) and thus play a major role in physical organic chemistry and related fields. However, the theoretical justification for some of the implicit LFER assumptions has not been fully established by quantum mechanical studies. This study follows our earlier works1,2 and uses the ab initio frozen density functional theory (FDFT) method3 to evaluate both the diabatic and adiabatic free energy surfaces and to determine the corresponding off-diagonal coupling matrix elements for a series of SN2 reactions. It is found that the off-diagonal coupling matrix elements are almost the same regardless of the nucleophile and the leaving group but change upon changing the central group. Furthermore, it is also found that the off diagonal elements are basically the same in gas phase and in solution, even when the solvent is explicitly included in the ab initio calculations. Furthermore, our study establishes that the FDFT diabatic profiles are parabolic to a good approximation thus providing a first principle support to the origin of LFER. These findings further support the basic approximation of the EVB treatment. PMID:23329895

Revisiting structure and dynamics of preferential solvation of K(I) ion in aqueous ammonia using QMCF-MD simulation

NASA Astrophysics Data System (ADS)

Hidayat, Yuniawan; Pranowo, Harno Dwi; Armunanto, Ria

2018-05-01

Structure and dynamics of preferential solvation of K(I) ion in aqueous ammonia have been reinvestigated using ab initio quantum mechanical charge field (QMCF) molecular dynamics (MD) simulation. The average coordination number of the first solvation consists of 2 ammonia and 4 waters. The mean residence time is less than 2 ps confirming the rapid mobility of ligands. The distance evolution data shows the frequent of ligand exchanges. The second solvation shell shows a more labile structure. The NBO analysis of the first shell structure emphasizes that interaction of K(I)-H2O is stronger than K(I)-NH3. The Wiberg bond confirms a weak electrostatic of ion-ligand interaction.

Computational study of alkali-metal-noble gas collisions in the presence of nonresonant lasers - Na + Xe + h/2/pi/omega sub 1 + h/2/pi/omega sub 2 system

NASA Technical Reports Server (NTRS)

Devries, P. L.; Chang, C.; George, T. F.; Laskowski, B.; Stallcop, J. R.

1980-01-01

The collision of Na with Xe in the presence of both the rhodamine-110 dye laser and the Nd-glass laser is investigated within a quantum-mechanical close-coupled formalism, utilizing ab initio potential curves and transition dipole matrix elements. Both one- and two-photon processes are investigated; the Na + Xe system is not asymptotically resonant with the radiation fields, so that these processes can only occur in the molecular collision region. The one-photon processes are found to have measurable cross sections at relatively low intensities; even the two-photon process has a significant section for field intensities as low as 10 MW/sq cm.

The role of atomic lines in radiation heating of the experimental space vehicle Fire-II

NASA Astrophysics Data System (ADS)

Surzhikov, S. T.

2015-10-01

The results of calculating the convective and radiation heating of the Fire-II experimental space vehicle allowing for atomic lines of atoms and ions using the NERAT-ASTEROID computer platform are presented. This computer platform is intended to solve the complete set of equations of radiation gas dynamics of viscous, heat-conductive, and physically and chemically nonequilibrium gas, as well as radiation transfer. The spectral optical properties of high temperature gases are calculated using ab initio quasi-classical and quantum-mechanical methods. The calculation of the transfer of selective thermal radiation is performed using a line-by-line method using specially generated computational grids over the radiation wavelengths, which make it possible to attain a noticeable economy of computational resources.

Ab initio single and multideterminant methods used in the determination of reduction potentials and magnetic properties of Rieske ferredoxins

NASA Astrophysics Data System (ADS)

Powers, Nathan Lee

2008-10-01

The [Fe2S2]2+/[Fe2S 2]+ electronic structure of seven Rieske protein active sites (bovine mitochondrial cytochrome bc1 complex, spinach chloroplast cytochrome b6f complex, Rieske-type ferredoxin associated with biphenyl dioxygenase from Burkholderia cepacia, yeast cytochrome bcl complex from Saccharomyces cerevisiae, Rieske subunit of arsenite oxidase from Alcaligenes faecalis, respiratory-type Rieske protein from Thermus thermophilus, and Rieske protein II (soxF) from Sulfolobus acidocaldarius), which lie in a reduction potential range from -150 mV to 375 mV, have been studied by both single and multi-determinant quantum mechanical methods. Calculated reduction potentials and magnetic properties are found comparable to experimental values.

Electronic Structure of Energetic Molecules and Crystals Under Compression

NASA Astrophysics Data System (ADS)

Kay, Jeffrey

Understanding how the electronic structure of energetic materials change under compression is important to elucidating mechanisms of shock-induced reactions and detonation. In this presentation, the electronic structure of prototypical energetic crystals are examined under high degrees of compression using ab initio quantum chemical calculations. The effects of compression on and interactions between the constituent molecules are examined in particular. The insights these results provide into previous experimental observations and theoretical predictions of energetic materials under high pressure are discussed. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. DOE's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Giant magnetic anisotropy of heavy p-elements on high-symmetry substrates: a new paradigm for supported nanostructures

NASA Astrophysics Data System (ADS)

Pang, Rui; Deng, Bei; Shi, Xingqiang; Zheng, Xiaohong

2018-04-01

Nanostructures with giant magnetic anisotropy energies (MAEs) are desired in designing miniaturized magnetic storage and quantum computing devices. Previous works focused mainly on materials or elements with d electrons. Here, by taking Bi–X(X = In, Tl, Ge, Sn, Pb) adsorbed on nitrogenized divacancy of graphene and Bi atoms adsorbed on MgO(100) as examples, through ab initio and model calculations, we propose that special p-element dimers and single-adatoms on symmetry-matched substrates possess giant atomic MAEs of 72–200 meV, and has room temperature structural stability. The huge MAEs originate from the p-orbital degeneracy around the Fermi level in a symmetry-matched surface ligand field and the lifting of this degeneracy when spin–orbit interaction (SOI) is taken into account. Especially, we developed a simplified quantum mechanical model for the design principles of giant MAEs of supported magnetic adatoms and dimers. Thus, our discoveries and mechanisms provide a new paradigm to design giant atomic MAE of p electrons in supported nanostructures.

Photodissociation dynamics in the first absorption band of pyrrole. II. Photofragment distributions for the 1A2(π σ* ) ←X˜ 1A1(π π ) transition

NASA Astrophysics Data System (ADS)

Picconi, David; Grebenshchikov, Sergy Yu.

2018-03-01

The analysis of the total kinetic energy release (TKER) of the photofragments pyrrolyl + H-atom formed in the photodissociation of pyrrole in the low-lying state 1A2(πσ*) is presented. The TKER distributions contain complementary and often more precise information on the fragmentation process than the broad diffuse absorption spectra. The distributions are calculated quantum mechanically for the diabatic state 1A2(πσ*) either isolated or coupled to the ground electronic state at an exit channel conical intersection. The calculations use the novel ab initio quasi-diabatic potential energy matrix constructed in the work of Picconi and Grebenshchikov [J. Chem. Phys. 148, 104103 (2018)]. The approximate overlap integral-based adiabatic mapping approach is introduced with which the quantum mechanical TKER distributions can be efficiently and accurately reproduced. Finally, the calculated TKERs are compared with the experimental results. The main features of the measured vibrationally resolved distributions are reproduced, and the spectral peaks are assigned and interpreted in detail.

Quantum mechanical effects in zwitterionic amino acids: The case of proline, hydroxyproline, and alanine in water

NASA Astrophysics Data System (ADS)

Ulman, Kanchan; Busch, Sebastian; Hassanali, Ali A.

2018-06-01

In this work, we use ab initio molecular dynamics simulations to elucidate the electronic properties of three hydrated zwitterionic amino acids, namely proline, hydroxyproline, and alanine, the former two forming an important constituent of collagen. In all three systems, we find a substantial amount of charge transfer between the amino acids and surrounding solvent, which, rather surprisingly, also involves the reorganization of electron density near the hydrophobic non-polar groups. Water around proline appears to be slightly more polarized, as reflected by the enhanced water dipole moment in its hydration shell. This observation is also complemented by an examination of the IR spectra of the three systems where there is a subtle red and blue shift in the O-H stretch and bend regions, respectively, for proline. We show that polarizability of these amino acids as revealed by a dipole moment analysis involves a significant enhancement from the solvent and that this also involves non-polar groups. Our results suggest that quantum mechanical effects are likely to be important in understanding the coupling between biomolecules and water in general and in hydrophobic interactions.

Accuracy of Protein Embedding Potentials: An Analysis in Terms of Electrostatic Potentials.

PubMed

Olsen, Jógvan Magnus Haugaard; List, Nanna Holmgaard; Kristensen, Kasper; Kongsted, Jacob

2015-04-14

Quantum-mechanical embedding methods have in recent years gained significant interest and may now be applied to predict a wide range of molecular properties calculated at different levels of theory. To reach a high level of accuracy in embedding methods, both the electronic structure model of the active region and the embedding potential need to be of sufficiently high quality. In fact, failures in quantum mechanics/molecular mechanics (QM/MM)-based embedding methods have often been associated with the QM/MM methodology itself; however, in many cases the reason for such failures is due to the use of an inaccurate embedding potential. In this paper, we investigate in detail the quality of the electronic component of embedding potentials designed for calculations on protein biostructures. We show that very accurate explicitly polarizable embedding potentials may be efficiently designed using fragmentation strategies combined with single-fragment ab initio calculations. In fact, due to the self-interaction error in Kohn-Sham density functional theory (KS-DFT), use of large full-structure quantum-mechanical calculations based on conventional (hybrid) functionals leads to less accurate embedding potentials than fragment-based approaches. We also find that standard protein force fields yield poor embedding potentials, and it is therefore not advisable to use such force fields in general QM/MM-type calculations of molecular properties other than energies and structures.

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.

A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein.

PubMed

Xu, Mingyuan; Zhu, Tong; Zhang, John Z H

2018-01-01

A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC) method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA) 9 -NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

Ab initio potential-energy surfaces for complex, multichannel systems using modified novelty sampling and feedforward neural networks

NASA Astrophysics Data System (ADS)

Raff, L. M.; Malshe, M.; Hagan, M.; Doughan, D. I.; Rockley, M. G.; Komanduri, R.

2005-02-01

A neural network/trajectory approach is presented for the development of accurate potential-energy hypersurfaces that can be utilized to conduct ab initio molecular dynamics (AIMD) and Monte Carlo studies of gas-phase chemical reactions, nanometric cutting, and nanotribology, and of a variety of mechanical properties of importance in potential microelectromechanical systems applications. The method is sufficiently robust that it can be applied to a wide range of polyatomic systems. The overall method integrates ab initio electronic structure calculations with importance sampling techniques that permit the critical regions of configuration space to be determined. The computed ab initio energies and gradients are then accurately interpolated using neural networks (NN) rather than arbitrary parametrized analytical functional forms, moving interpolation or least-squares methods. The sampling method involves a tight integration of molecular dynamics calculations with neural networks that employ early stopping and regularization procedures to improve network performance and test for convergence. The procedure can be initiated using an empirical potential surface or direct dynamics. The accuracy and interpolation power of the method has been tested for two cases, the global potential surface for vinyl bromide undergoing unimolecular decomposition via four different reaction channels and nanometric cutting of silicon. The results show that the sampling methods permit the important regions of configuration space to be easily and rapidly identified, that convergence of the NN fit to the ab initio electronic structure database can be easily monitored, and that the interpolation accuracy of the NN fits is excellent, even for systems involving five atoms or more. The method permits a substantial computational speed and accuracy advantage over existing methods, is robust, and relatively easy to implement.

Ab initio simulation of elastic and mechanical properties of Zn- and Mg-doped hydroxyapatite (HAP).

PubMed

Aryal, Sitaram; Matsunaga, Katsuyuki; Ching, Wai-Yim

2015-07-01

Hydroxyapatite (HAP) is an important bioceramic which constitutes the mineral components of bones and hard tissues in mammals. It is bioactive and used as bioceramic coatings for metallic implants and bone fillers. HAP readily absorbs a large amount of impurities. Knowledge on the elastic and mechanical properties of impurity-doped HAP is a subject of great importance to its potential for biomedical applications. Zn and Mg are the most common divalent cations HAP absorbs. Using density function theory based ab initio methods, we have carried out a large number of ab initio calculations to obtain the bulk elastic and mechanical properties of HAP with Zn or Mg doped in different concentration at the Ca1 and Ca2 sites using large 352-atom supercells. Detailed information on their dependece on the concetraion of the substitued impurity is obtained. Our results show that Mg enhances overall elastic and bulk mechanical properties whereas Zn tends to degrade except at low concentrations. At a higher concentration, the mechanical properties of Zn and Mg doped HAP also depend significantly on impurity distribution between the Ca1 and Ca2 sites. There is a strong evidence that Zn prefers Ca2 site for substituion whereas Mg has no such preference. These results imply that proper control of dopant concentration and their site preference must carefully considered in using doped HAP for specific biomedical applications. Copyright © 2015 Elsevier Ltd. All rights reserved.

Ab initio molecular simulations on specific interactions between amyloid beta and monosaccharides

NASA Astrophysics Data System (ADS)

Nomura, Kazuya; Okamoto, Akisumi; Yano, Atsushi; Higai, Shin'ichi; Kondo, Takashi; Kamba, Seiji; Kurita, Noriyuki

2012-09-01

Aggregation of amyloid β (Aβ) peptides, which is a key pathogenetic event in Alzheimer's disease, can be caused by cell-surface saccharides. We here investigated stable structures of the solvated complexes of Aβ with some types of monosaccharides using molecular simulations based on protein-ligand docking and classical molecular mechanics methods. Moreover, the specific interactions between Aβ and the monosaccharides were elucidated at an electronic level by ab initio fragment molecular orbital calculations. Based on the results, we proposed which type of monosaccharide prefers to have large binding affinity to Aβ and inhibit the Aβ aggregation.

Ab-initio study of liquid systems: Concentration dependence of electrical resistivity of binary liquid alloy Rb1-xCsx

NASA Astrophysics Data System (ADS)

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

2013-02-01

The electrical resistivity (ρL) of Rb1-XCsX binary alloys has been made calculated using Troullier Martins ab-initio pseudopotentials. The present results of the electrical resistivity (ρL) of Rb1-XCsX binary alloys have been found in good agreement with the experimental results. These results suggest that ab-initio approach for calculating electrical resistivity is quite successful in explaining the electronic transport properties of binary Liquid alloys. Hence ab-initio pseudopotentials can be used instead of model pseudopotentials having problem of transferability.

Topological Semimetals Studied by Ab Initio Calculations

NASA Astrophysics Data System (ADS)

Hirayama, Motoaki; Okugawa, Ryo; Murakami, Shuichi

2018-04-01

In topological semimetals such as Weyl, Dirac, and nodal-line semimetals, the band gap closes at points or along lines in k space which are not necessarily located at high-symmetry positions in the Brillouin zone. Therefore, it is not straightforward to find these topological semimetals by ab initio calculations because the band structure is usually calculated only along high-symmetry lines. In this paper, we review recent studies on topological semimetals by ab initio calculations. We explain theoretical frameworks which can be used for the search for topological semimetal materials, and some numerical methods used in the ab initio calculations.

Use of Biodescriptors and Chemodescriptors in Predictive Toxicology: A Mathematical/Computational Approach

DTIC Science & Technology

2005-01-01

proteomic gel analyses. The research group has explored the use of chemodescriptors calculated using high-level ab initio quantum chemical basis sets...descriptors that characterize the entire proteomics map, local descriptors that characterize a subset of the proteins present in the gel, and spectrum...techniques for analyzing the full set of proteins present in a proteomics map. 14. SUBJECT TERMS 1S. NUMBER OF PAGES Topological indices

Solvent Dependence of Double Proton Transfer in the Formic Acid-Formamidine Complex: Path Integral Molecular Dynamics Investigation.

PubMed

Kungwan, Nawee; Ngaojampa, Chanisorn; Ogata, Yudai; Kawatsu, Tsutomu; Oba, Yuki; Kawashima, Yukio; Tachikawa, Masanori

2017-10-05

Solvent dependence of double proton transfer in the formic acid-formamidine (FA-FN) complex at room temperature was investigated by means of ab initio path integral molecular dynamics (AIPIMD) simulation with taking nuclear quantum and thermal effects into account. The conductor-like screening model (COSMO) was applied for solvent effect. In comparison with gas phase, double proton delocalization between two heavy atoms (O and N) in FA-FN were observed with reduced proton transfer barrier height in low dielectric constant medium (<4.8). For dielectric constant medium at 4.8, the chance of finding these two protons are more pronounced due to the solvent effect which completely washes out the proton transfer barrier. In the case of higher dielectric constant medium (>4.8), the ionic species becomes more stable than the neutral ones and the formate anion and formamidium cation are thermodynamically stable. For ab initio molecular dynamics simulation, in low dielectric constant medium (<4.8) a reduction of proton transfer barrier with solvent effect is found to be less pronounced than the AIPIMD due to the absence of nuclear quantum effect. Moreover, the motions of FA-FN complex are significantly different with increasing dielectric constant medium. Such a difference is revealed in detail by the principal component analysis.

Network-Forming Nanoclusters in Binary As-S/Se Glasses: From Ab Initio Quantum Chemical Modeling to Experimental Evidences.

PubMed

Hyla, M

2017-12-01

Network-forming As 2 (S/Se) m nanoclusters are employed to recognize expected variations in a vicinity of some remarkable compositions in binary As-Se/S glassy systems accepted as signatures of optimally constrained intermediate topological phases in earlier temperature-modulated differential scanning calorimetry experiments. The ab initio quantum chemical calculations performed using the cation-interlinking network cluster approach show similar oscillating character in tendency to local chemical decomposition but obvious step-like behavior in preference to global phase separation on boundary chemical compounds (pure chalcogen and stoichiometric arsenic chalcogenides). The onsets of stability are defined for chalcogen-rich glasses, these being connected with As 2 Se 5 (Z = 2.29) and As 2 S 6 (Z = 2.25) nanoclusters for As-Se and As-S glasses, respectively. The physical aging effects result preferentially from global phase separation in As-S glass system due to high localization of covalent bonding and local demixing on neighboring As 2 Se m+1 and As 2 Se m-1 nanoclusters in As-Se system. These nanoclusters well explain the lower limits of reversibility windows in temperature-modulated differential scanning calorimetry, but they cannot be accepted as signatures of topological phase transitions in respect to the rigidity theory.

Rotational Quenching Study in Isovalent H+ + CO and H+ + CS Systems

NASA Astrophysics Data System (ADS)

Kaur, Rajwant; Dhilip Kumar, T. J.

2016-06-01

Cooling and trapping of polar molecules has attracted attention at cold and ultracold temperatures. Extended study of molecular inelastic collision processes of polar interstellar species with proton finds an important astrophysical application to model interstellar medium. Present study includes computation of rate coefficient for molecular rotational quenching process in proton collision with isovalent CO and CS molecules using quantum dynamical close-coupling calculations. Full dimensional ab initio potential energy surfaces have been computed for the ground state for both the systems using internally contracted multireference configuration interaction method and basis sets. Quantum scattering calculations for rotational quenching of isovalent species are studied in the rigid-rotor approximation with CX (X=O, S) bond length fixed at an experimental equilibrium value of 2.138 and 2.900 a.u., respectively. Asymptotic potentials are computed using the dipole and quadrupole moments, and the dipole polarizability components. The resulting long-range potentials with the short-range ab initio interaction potentials have been fitted to study the anisotropy of the rigid-rotor surface using the multipolar expansion coefficients. Rotational quenching cross-section and corresponding rates from j=4 level of CX to lower j' levels have been obtained and found to obey Wigner's threshold law at ultra cold temperatures.

Vibrational cooling of spin-stretched dimer states by He buffer gas: quantum calculations for Li2(a 3Sigma(u)+) at ultralow energies.

PubMed

Bovino, S; Bodo, E; Yurtsever, E; Gianturco, F A

2008-06-14

The interaction between the triplet state of the lithium dimer, (7)Li(2), with (4)He is obtained from accurate ab initio calculations where the vibrational dependence of the potential is newly computed. Vibrational quenching dynamics within a coupled-channel quantum treatment is carried out at ultralow energies, and large differences in efficiency as a function of the initial vibrational state of the targets are found as one compares the triplet results with those of the singlet state of the same target.

On the origin of the gauche effect. A quantum chemical study of 1,2-difluoroethane

NASA Astrophysics Data System (ADS)

Engkvist, O.; Karlström, G.; Widmark, P.-O.

1997-01-01

The conformational equilibrium of 1,2-difluoroethane has been investigated using ab initio quantum chemical calculations at the SCF, MP2 and CCSD(T) levels, with ANO basis sets. The relative stability of the gauche-conformation of 1,2-difluoroethane is found to be a consequence of the nodal structure of the singly occupied orbital in the CFH 2 radical. It is also shown that the nodal structure of the singly occupied orbitals in the CFH biradical can explain the stability of the cis conformation of 1,2-difluoroethene.

Neutron matter with Quantum Monte Carlo: chiral 3N forces and static response

DOE PAGES

Buraczynski, M.; Gandolfi, S.; Gezerlis, A.; ...

2016-03-14

Neutron matter is related to the physics of neutron stars and that of neutron-rich nuclei. Moreover, Quantum Monte Carlo (QMC) methods offer a unique way of solving the many-body problem non-perturbatively, providing feedback on features of nuclear interactions and addressing scenarios that are inaccessible to other approaches. Our contribution goes over two recent accomplishments in the theory of neutron matter: a) the fusing of QMC with chiral effective field theory interactions, focusing on local chiral 3N forces, and b) the first attempt to find an ab initio solution to the problem of static response.

Towards accurate ab initio predictions of the vibrational spectrum of methane

NASA Technical Reports Server (NTRS)

Schwenke, David W.

2002-01-01

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.

A review on ab initio studies of static, transport, and optical properties of polystyrene under extreme conditions for inertial confinement fusion applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Collins, L. A.; Boehly, T. R.; Ding, Y. H.

Polystyrene (CH), commonly known as “plastic,” has been one of the widely used ablator materials for capsule designs in inertial confinement fusion (ICF). Knowing its precise properties under high-energy-density conditions is crucial to understanding and designing ICF implosions through radiation–hydrodynamic simulations. For this purpose, systematic ab initio studies on the static, transport, and optical properties of CH, in a wide range of density and temperature conditions (ρ= 0.1 to 100 g/cm 3 and T = 10 3 to 4 × 10 6K), have been conducted using quantum molecular dynamics (QMD) simulations based on the density functional theory. We have builtmore » several wide-ranging, self-consistent material-properties tables for CH, such as the first-principles equation of state (FPEOS), the QMD-based thermal conductivity (Κ QMD) and ionization, and the first-principles opacity table (FPOT). This paper is devoted to providing a review on (1) what results were obtained from these systematic ab initio studies; (2) how these self-consistent results were compared with both traditional plasma-physics models and available experiments; and (3) how these first-principles–based properties of polystyrene affect the predictions of ICF target performance, through both 1-D and 2-D radiation–hydrodynamic simulations. In the warm dense regime, our ab initio results, which can significantly differ from predictions of traditional plasma-physics models, compared favorably with experiments. When incorporated into hydrocodes for ICF simulations, these first-principles material properties of CH have produced significant differences over traditional models in predicting 1-D/2-D target performance of ICF implosions on OMEGA and direct-drive–ignition designs for the National Ignition Facility. Lastly, we will discuss the implications of these studies on the current small-margin ICF target designs using a CH ablator.« less

A review on ab initio studies of static, transport, and optical properties of polystyrene under extreme conditions for inertial confinement fusion applications

DOE PAGES

Collins, L. A.; Boehly, T. R.; Ding, Y. H.; ...

2018-03-23

Polystyrene (CH), commonly known as “plastic,” has been one of the widely used ablator materials for capsule designs in inertial confinement fusion (ICF). Knowing its precise properties under high-energy-density conditions is crucial to understanding and designing ICF implosions through radiation–hydrodynamic simulations. For this purpose, systematic ab initio studies on the static, transport, and optical properties of CH, in a wide range of density and temperature conditions (ρ= 0.1 to 100 g/cm 3 and T = 10 3 to 4 × 10 6K), have been conducted using quantum molecular dynamics (QMD) simulations based on the density functional theory. We have builtmore » several wide-ranging, self-consistent material-properties tables for CH, such as the first-principles equation of state (FPEOS), the QMD-based thermal conductivity (Κ QMD) and ionization, and the first-principles opacity table (FPOT). This paper is devoted to providing a review on (1) what results were obtained from these systematic ab initio studies; (2) how these self-consistent results were compared with both traditional plasma-physics models and available experiments; and (3) how these first-principles–based properties of polystyrene affect the predictions of ICF target performance, through both 1-D and 2-D radiation–hydrodynamic simulations. In the warm dense regime, our ab initio results, which can significantly differ from predictions of traditional plasma-physics models, compared favorably with experiments. When incorporated into hydrocodes for ICF simulations, these first-principles material properties of CH have produced significant differences over traditional models in predicting 1-D/2-D target performance of ICF implosions on OMEGA and direct-drive–ignition designs for the National Ignition Facility. Lastly, we will discuss the implications of these studies on the current small-margin ICF target designs using a CH ablator.« less

A general method for constructing multidimensional molecular potential energy surfaces from {ital ab} {ital initio} calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ho, T.; Rabitz, H.

1996-02-01

A general interpolation method for constructing smooth molecular potential energy surfaces (PES{close_quote}s) from {ital ab} {ital initio} data are proposed within the framework of the reproducing kernel Hilbert space and the inverse problem theory. The general expression for an {ital a} {ital posteriori} error bound of the constructed PES is derived. It is shown that the method yields globally smooth potential energy surfaces that are continuous and possess derivatives up to second order or higher. Moreover, the method is amenable to correct symmetry properties and asymptotic behavior of the molecular system. Finally, the method is generic and can be easilymore » extended from low dimensional problems involving two and three atoms to high dimensional problems involving four or more atoms. Basic properties of the method are illustrated by the construction of a one-dimensional potential energy curve of the He{endash}He van der Waals dimer using the exact quantum Monte Carlo calculations of Anderson {ital et} {ital al}. [J. Chem. Phys. {bold 99}, 345 (1993)], a two-dimensional potential energy surface of the HeCO van der Waals molecule using recent {ital ab} {ital initio} calculations by Tao {ital et} {ital al}. [J. Chem. Phys. {bold 101}, 8680 (1994)], and a three-dimensional potential energy surface of the H{sup +}{sub 3} molecular ion using highly accurate {ital ab} {ital initio} calculations of R{umlt o}hse {ital et} {ital al}. [J. Chem. Phys. {bold 101}, 2231 (1994)]. In the first two cases the constructed potentials clearly exhibit the correct asymptotic forms, while in the last case the constructed potential energy surface is in excellent agreement with that constructed by R{umlt o}hse {ital et} {ital al}. using a low order polynomial fitting procedure. {copyright} {ital 1996 American Institute of Physics.}« less

Simulating biochemical physics with computers: 1. Enzyme catalysis by phosphotriesterase and phosphodiesterase; 2. Integration-free path-integral method for quantum-statistical calculations

NASA Astrophysics Data System (ADS)

Wong, Kin-Yiu

We have simulated two enzymatic reactions with molecular dynamics (MD) and combined quantum mechanical/molecular mechanical (QM/MM) techniques. One reaction is the hydrolysis of the insecticide paraoxon catalyzed by phosphotriesterase (PTE). PTE is a bioremediation candidate for environments contaminated by toxic nerve gases (e.g., sarin) or pesticides. Based on the potential of mean force (PMF) and the structural changes of the active site during the catalysis, we propose a revised reaction mechanism for PTE. Another reaction is the hydrolysis of the second-messenger cyclic adenosine 3'-5'-monophosphate (cAMP) catalyzed by phosphodiesterase (PDE). Cyclicnucleotide PDE is a vital protein in signal-transduction pathways and thus a popular target for inhibition by drugs (e.g., ViagraRTM). A two-dimensional (2-D) free-energy profile has been generated showing that the catalysis by PDE proceeds in a two-step SN2-type mechanism. Furthermore, to characterize a chemical reaction mechanism in experiment, a direct probe is measuring kinetic isotope effects (KIEs). KIEs primarily arise from internuclear quantum-statistical effects, e.g., quantum tunneling and quantization of vibration. To systematically incorporate the quantum-statistical effects during MD simulations, we have developed an automated integration-free path-integral (AIF-PI) method based on Kleinert's variational perturbation theory for the centroid density of Feynman's path integral. Using this analytic method, we have performed ab initio pathintegral calculations to study the origin of KIEs on several series of proton-transfer reactions from carboxylic acids to aryl substituted alpha-methoxystyrenes in water. In addition, we also demonstrate that the AIF-PI method can be used to systematically compute the exact value of zero-point energy (beyond the harmonic approximation) by simply minimizing the centroid effective potential.

Prospect of quantum anomalous Hall and quantum spin Hall effect in doped kagome lattice Mott insulators.

PubMed

Guterding, Daniel; Jeschke, Harald O; Valentí, Roser

2016-05-17

Electronic states with non-trivial topology host a number of novel phenomena with potential for revolutionizing information technology. The quantum anomalous Hall effect provides spin-polarized dissipation-free transport of electrons, while the quantum spin Hall effect in combination with superconductivity has been proposed as the basis for realizing decoherence-free quantum computing. We introduce a new strategy for realizing these effects, namely by hole and electron doping kagome lattice Mott insulators through, for instance, chemical substitution. As an example, we apply this new approach to the natural mineral herbertsmithite. We prove the feasibility of the proposed modifications by performing ab-initio density functional theory calculations and demonstrate the occurrence of the predicted effects using realistic models. Our results herald a new family of quantum anomalous Hall and quantum spin Hall insulators at affordable energy/temperature scales based on kagome lattices of transition metal ions.

Relating Ab Initio Mechanical Behavior of Intergranular Glassy Films in Γ-Si3N4 to Continuum Scales

NASA Astrophysics Data System (ADS)

Ouyang, L.; Chen, J.; Ching, W.; Misra, A.

2006-05-01

Nanometer thin intergranular glassy films (IGFs) form in polycrystalline ceramics during sintering at high temperatures. The structure and properties of these IGFs are significantly changed by doping with rare earth elements. We have performed highly accurate large-scale ab initio calculations of the mechanical properties of both undoped and Yittria doped (Y-IGF) model by theoretical uniaxial tensile experiments. Uniaxial strain was applied by incrementally stretching the super cell in one direction, while the other two dimensions were kept constant. At each strain, all atoms in the model were fully relaxed using Vienna Ab initio Simulation Package VASP. The relaxed model at a given strain serves as the starting position for the next increment of strain. This process is carried on until the total energy (TE) and stress data show that the "sample" is fully fractured. Interesting differences are seen between the stress-strain response of undoped and Y-doped models. For the undoped model, the stress-strain behavior indicates that the initial atomic structure of the IGF is such that there is negligible coupling between the x- and the y-z directions. However, once the behavior becomes non- linear the lateral stresses increase, indicating that the atomic structure evolves with loading [1]. To relate the ab initio calculations to the continuum scales we analyze the atomic-scale deformation field under this uniaxial loading [1]. The applied strain in the x-direction is mostly accommodated by the IGF part of the model and the crystalline part experiences almost negligible strain. As the overall strain on the sample is incrementally increased, the local strain field evolves such that locations proximal to the softer spots attract higher strains. As the load progresses, the strain concentration spots coalesce and eventually form persistent strain localization zone across the IGF. The deformation pattern obtained through ab initio calculations indicates that it is possible to construct discrete grain-scale models that may be used to bridge these calculations to the continuum scale for finite element analysis. Reference: 1. J. Chen, L. Ouyang, P. Rulis, A. Misra, W. Y. Ching, Phys. Rev. Lett. 95, 256103 (2005)

NH2- in a cold ion trap with He buffer gas: Ab initio quantum modeling of the interaction potential and of state-changing multichannel dynamics

NASA Astrophysics Data System (ADS)

Hernández Vera, Mario; Yurtsever, Ersin; Wester, Roland; Gianturco, Franco A.

2018-05-01

We present an extensive range of accurate ab initio calculations, which map in detail the spatial electronic potential energy surface that describes the interaction between the molecular anion NH2 - (1A1) in its ground electronic state and the He atom. The time-independent close-coupling method is employed to generate the corresponding rotationally inelastic cross sections, and then the state-changing rates over a range of temperatures from 10 to 30 K, which is expected to realistically represent the experimental trapping conditions for this ion in a radio frequency ion trap filled with helium buffer gas. The overall evolutionary kinetics of the rotational level population involving the molecular anion in the cold trap is also modelled during a photodetachment experiment and analyzed using the computed rates. The present results clearly indicate the possibility of selectively detecting differences in behavior between the ortho- and para-anions undergoing photodetachment in the trap.

An ab initio investigation of possible intermediates in the reaction of the hydroxyl and hydroperoxyl radicals

NASA Technical Reports Server (NTRS)

Jackels, C. F.

1985-01-01

Ab initio quantum chemical techniques are used to investigate covalently-bonded and hydrogen-bonded species that may be important intermediates in the reaction of hydroxyl and hydroperoxyl radicals. Stable structures of both types are identified. Basis sets of polarized double zeta quality and large scale configuration interaction wave functions are utilized. Based on electronic energies, the covalently bonded HOOOH species is 26.4 kcal/mol more stable than the OH and HO2 radicals. Similarly, the hydrogen bonded HO---HO2 species has an electronic energy 4.7 kcal/mol below that of the component radicals, after correction is made for the basis set superposition error. The hydrogen bonded form is planar, possesses one relatively normal hydrogen bond, and has the lowest energy 3A' and 1A' states that are essentially degenerate. The 1A" and 3A" excited states produced by rotation of the unpaired OH electron into the molecular plane are very slightly bound.

Interfacing the Ab initio multiple spawning method with electronic structure methods in GAMESS: Photodecay of trans-Azomethane

DOE PAGES

Gaenko, Alexander; DeFusco, Albert; Varganov, Sergey A.; ...

2014-10-20

This work presents a nonadiabatic molecular dynamics study of the nonradiative decay of photoexcited trans-azomethane, using the ab initio multiple spawning (AIMS) program that has been interfaced with the General Atomic and Molecular Electronic Structure System (GAMESS) quantum chemistry package for on-the-fly electronic structure evaluation. The interface strategy is discussed, and the capabilities of the combined programs are demonstrated with a nonadiabatic molecular dynamics study of the nonradiative decay of photoexcited trans-azomethane. Energies, gradients, and nonadiabatic coupling matrix elements were obtained with the state-averaged complete active space self-consistent field method, as implemented in GAMESS. The influence of initial vibrational excitationmore » on the outcome of the photoinduced isomerization is explored. Increased vibrational excitation in the CNNC torsional mode shortens the excited state lifetime. Depending on the degree of vibrational excitation, the excited state lifetime varies from ~60–200 fs. As a result, these short lifetimes are in agreement with time-resolved photoionization mass spectroscopy experiments.« less

Ab Initio Vibrational Levels For HO2 and Vibrational Splittings for Hydrogen Atom Transfer

NASA Technical Reports Server (NTRS)

Barclay, V. J.; Dateo, Christopher E.; Hamilton, I. P.; Arnold, James O. (Technical Monitor)

1994-01-01

We calculate vibrational levels and wave functions for HO2 using the recently reported ab initio potential energy surface of Walch and Duchovic. There is intramolecular hydrogen atom transfer when the hydrogen atom tunnels through a T-shaped saddle point separating two equivalent equilibrium geometries, and correspondingly, the energy levels are split. We focus on vibrational levels and wave functions with significant splitting. The first three vibrational levels with splitting greater than 2/cm are (15 0), (0 7 1) and (0 8 0) where V(sub 2) is the O-O-H bend quantum number. We discuss the dynamics of hydrogen atom transfer; in particular, the O-O distances at which hydrogen atom transfer is most probable for these vibrational levels. The material of the proposed presentation was reviewed and the technical content will not reveal any information not already in the public domain and will not give any foreign industry or government a competitive advantage.

Ab initio calculation of resonant Raman intensities of transition metal dichalcogenides

NASA Astrophysics Data System (ADS)

Miranda, Henrique; Reichardt, Sven; Molina-Sanchez, Alejandro; Wirtz, Ludger

Raman spectroscopy is used to characterize optical and vibrational properties of materials. Its computational simulation is important for the interpretation of experimental results. Two approaches are the bond polarizability model and density functional perturbation theory. However, both are known to not capture resonance effects. These resonances and quantum interference effects are important to correctly reproduce the intensities as a function of laser energy as, e.g., reported for the case of multi-layer MoTe21.We present two fully ab initio approaches that overcome this limitation. In the first, we calculate finite difference derivatives of the dielectric susceptibility with the phonon displacements2. In the second we calculate electron-light and electron-phonon matrix elements from density functional theory and use them to evaluate expressions for the Raman intensity derived from time-dependent perturbation theory. These expressions are implemented in a computer code that performs the calculations as a post-processing step. We compare both methods and study the case of triple-layer MoTe2. Luxembourg National Research Fund (FNR).

Ab initio predictions of the symmetry energy and recent constraints

NASA Astrophysics Data System (ADS)

Sammarruca, Francesca

2017-01-01

The symmetry energy plays a crucial role in the structure and the dynamics of neutron-rich systems, including the formation of neutron skins, the location of neutron drip lines, as well as intriguing correlations with the structure of compact stars. With experimental efforts in progress or being planned to shed light on the less known aspects of the nuclear chart, microscopic predictions based on ab initio approaches are very important. In recent years, chiral effective field theory has become popular because of its firm connection with quantum chromodynamics and its systematic approach to the development of nuclear forces. Predictions of the symmetry energy obtained from modern chiral interactions will be discussed in the light of recent empirical constraints extracted from heavy ion collisions at 400 MeV per nucleon at GSI. Applications of our equations of state to neutron-rich systems will also be discussed, with particular emphasis on neutron skins, which are sensitive to the density dependence of the symmetry energy.

Calculations on the rate of the ion-molecule reaction between NH3(+) and H2

NASA Technical Reports Server (NTRS)

Herbst, Eric; Defrees, D. J.; Talbi, D.; Pauzat, F.; Koch, W.

1991-01-01

The rate coefficient for the ion-molecule reaction NH3(+) + H2 yields NH4(+) + H has been calculated as a function of temperature with the use of the statistical phase space approach. The potential surface and reaction complex and transition state parameters used in the calculation have been taken from ab initio quantum chemical calculations. The calculated rate coefficient has been found to mimic the unusual temperature dependence measured in the laboratory, in which the rate coefficient decreases with decreasing temperature until 50-100 K and then increases at still lower temperatures. Quantitative agreement between experimental and theoretical rate coefficients is satisfactory given the uncertainties in the ab initio results and in the dynamics calculations. The rate coefficient for the unusual three-body process NH3(+) + H2 + He yields NH4(+) + H + He has also been calculated as a function of temperature and the result found to agree well with a previous laboratory determination.

Ab initio prediction of the vibration-rotation-tunneling spectrum of HCl-(H2O)2

NASA Astrophysics Data System (ADS)

Wormer, P. E. S.; Groenenboom, G. C.; van der Avoird, A.

2001-08-01

Quantum calculations of the vibration-rotation-tunneling (VRT) levels of the trimer HCl-(H2O)2 are presented. Two internal degrees of freedom are considered—the rotation angles of the two nonhydrogen-bonded (flipping) hydrogens in the complex—together with the overall rotation of the trimer in space. The kinetic energy expression of van der Avoird et al. [J. Chem. Phys. 105, 8034 (1996)] is used in a slightly modified form. The experimental microwave geometry of Kisiel et al. [J. Chem. Phys. 112, 5767 (2000)] served as input in the generation of a planar reference structure. The two-dimensional potential energy surface is generated ab initio by the iterative coupled-cluster method based on singly and doubly excited states with triply excited states included noniteratively [CCSD(T)]. Frequencies of vibrations and tunnel splittings are predicted for two isotopomers. The effect of the nonadditive three-body forces is considered and found to be important.

Free Quantum Field Theory from Quantum Cellular Automata

NASA Astrophysics Data System (ADS)

Bisio, Alessandro; D'Ariano, Giacomo Mauro; Perinotti, Paolo; Tosini, Alessandro

2015-10-01

After leading to a new axiomatic derivation of quantum theory (see D'Ariano et al. in Found Phys, 2015), the new informational paradigm is entering the domain of quantum field theory, suggesting a quantum automata framework that can be regarded as an extension of quantum field theory to including an hypothetical Planck scale, and with the usual quantum field theory recovered in the relativistic limit of small wave-vectors. Being derived from simple principles (linearity, unitarity, locality, homogeneity, isotropy, and minimality of dimension), the automata theory is quantum ab-initio, and does not assume Lorentz covariance and mechanical notions. Being discrete it can describe localized states and measurements (unmanageable by quantum field theory), solving all the issues plaguing field theory originated from the continuum. These features make the theory an ideal framework for quantum gravity, with relativistic covariance and space-time emergent solely from the interactions, and not assumed a priori. The paper presents a synthetic derivation of the automata theory, showing how the principles lead to a description in terms of a quantum automaton over a Cayley graph of a group. Restricting to Abelian groups we show how the automata recover the Weyl, Dirac and Maxwell dynamics in the relativistic limit. We conclude with some new routes about the more general scenario of non-Abelian Cayley graphs. The phenomenology arising from the automata theory in the ultra-relativistic domain and the analysis of corresponding distorted Lorentz covariance is reviewed in Bisio et al. (Found Phys 2015, in this same issue).

Torsional anharmonicity in the conformational thermodynamics of flexible molecules

NASA Astrophysics Data System (ADS)

Miller, Thomas F., III; Clary, David C.

We present an algorithm for calculating the conformational thermodynamics of large, flexible molecules that combines ab initio electronic structure theory calculations with a torsional path integral Monte Carlo (TPIMC) simulation. The new algorithm overcomes the previous limitations of the TPIMC method by including the thermodynamic contributions of non-torsional vibrational modes and by affordably incorporating the ab initio calculation of conformer electronic energies, and it improves the conventional ab initio treatment of conformational thermodynamics by accounting for the anharmonicity of the torsional modes. Using previously published ab initio results and new TPIMC calculations, we apply the algorithm to the conformers of the adrenaline molecule.

HPAM: Hirshfeld Partitioned Atomic Multipoles

PubMed Central

Elking, Dennis M.; Perera, Lalith; Pedersen, Lee G.

2011-01-01

An implementation of the Hirshfeld (HD) and Hirshfeld-Iterated (HD-I) atomic charge density partitioning schemes is described. Atomic charges and atomic multipoles are calculated from the HD and HD-I atomic charge densities for arbitrary atomic multipole rank lmax on molecules of arbitrary shape and size. The HD and HD-I atomic charges/multipoles are tested by comparing molecular multipole moments and the electrostatic potential (ESP) surrounding a molecule with their reference ab initio values. In general, the HD-I atomic charges/multipoles are found to better reproduce ab initio electrostatic properties over HD atomic charges/multipoles. A systematic increase in precision for reproducing ab initio electrostatic properties is demonstrated by increasing the atomic multipole rank from lmax = 0 (atomic charges) to lmax = 4 (atomic hexadecapoles). Both HD and HD-I atomic multipoles up to rank lmax are shown to exactly reproduce ab initio molecular multipole moments of rank L for L ≤ lmax. In addition, molecular dipole moments calculated by HD, HD-I, and ChelpG atomic charges only (lmax = 0) are compared with reference ab initio values. Significant errors in reproducing ab initio molecular dipole moments are found if only HD or HD-I atomic charges used. PMID:22140274

On the incorporation of the geometric phase in general single potential energy surface dynamics: A removable approximation to ab initio data.

PubMed

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.

Dynamical importance of van der Waals saddle and excited potential surface in C(1D)+D2 complex-forming reaction

PubMed Central

Shen, Zhitao; Ma, Haitao; Zhang, Chunfang; Fu, Mingkai; Wu, Yanan; Bian, Wensheng; Cao, Jianwei

2017-01-01

Encouraged by recent advances in revealing significant effects of van der Waals wells on reaction dynamics, many people assume that van der Waals wells are inevitable in chemical reactions. Here we find that the weak long-range forces cause van der Waals saddles in the prototypical C(1D)+D2 complex-forming reaction that have very different dynamical effects from van der Waals wells at low collision energies. Accurate quantum dynamics calculations on our highly accurate ab initio potential energy surfaces with van der Waals saddles yield cross-sections in close agreement with crossed-beam experiments, whereas the same calculations on an earlier surface with van der Waals wells produce much smaller cross-sections at low energies. Further trajectory calculations reveal that the van der Waals saddle leads to a torsion then sideways insertion reaction mechanism, whereas the well suppresses reactivity. Quantum diffraction oscillations and sharp resonances are also predicted based on our ground- and excited-state potential energy surfaces. PMID:28094253

Habituation based synaptic plasticity and organismic learning in a quantum perovskite

DOE PAGES

Zuo, Fan; Panda, Priyadarshini; Kotiuga, Michele; ...

2017-08-14

A central characteristic of living beings is the ability to learn from and respond to their environment leading to habit formation and decision making. This behavior, known as habituation, is universal among all forms of life with a central nervous system, and is also observed in single-cell organisms that do not possess a brain. Here, we report the discovery of habituation-based plasticity utilizing a perovskite quantum system by dynamical modulation of electron localization. Microscopic mechanisms and pathways that enable this organismic collective charge-lattice interaction are elucidated by first-principles theory, synchrotron investigations, ab initio molecular dynamics simulations, and in situ environmentalmore » breathing studies. In conclusion, we implement a learning algorithm inspired by the conductance relaxation behavior of perovskites that naturally incorporates habituation, and demonstrate learning to forget: a key feature of animal and human brains. Incorporating this elementary skill in learning boosts the capability of neural computing in a sequential, dynamic environment.« less

Habituation based synaptic plasticity and organismic learning in a quantum perovskite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zuo, Fan; Panda, Priyadarshini; Kotiuga, Michele

A central characteristic of living beings is the ability to learn from and respond to their environment leading to habit formation and decision making. This behavior, known as habituation, is universal among all forms of life with a central nervous system, and is also observed in single-cell organisms that do not possess a brain. Here, we report the discovery of habituation-based plasticity utilizing a perovskite quantum system by dynamical modulation of electron localization. Microscopic mechanisms and pathways that enable this organismic collective charge-lattice interaction are elucidated by first-principles theory, synchrotron investigations, ab initio molecular dynamics simulations, and in situ environmentalmore » breathing studies. In conclusion, we implement a learning algorithm inspired by the conductance relaxation behavior of perovskites that naturally incorporates habituation, and demonstrate learning to forget: a key feature of animal and human brains. Incorporating this elementary skill in learning boosts the capability of neural computing in a sequential, dynamic environment.« less

Raman bandshape analysis on CH and CSC stretching modes of dimethyl sulfoxide in liquid binary mixture: comparative study with quantum-chemical calculations.

PubMed

Upadhyay, Ganesh; Gomti Devi, Th

2014-12-10

The interacting nature of dimethyl sulfoxide (DMSO) in binary mixtures has been carried out on CH and CSC stretching modes of vibration using chloroform (CLF), chloroform-d (CLFd), acetonitrile (ACN) and acetonitrile-d3 (ACNd) solvents. Peak frequencies of both the stretching modes show blue shift with the increase in solvent concentration. Variation of Raman bandwidth with the solvent concentration was discussed using different mechanisms. Ab initio calculation for geometry optimization and vibrational wavenumber calculation have been performed on monomer and dimer structures of DMSO to explain the experimentally observed Raman spectra. Theoretically calculated values are found in good agreement with the experimental results. Vibrational and reorientational relaxation times have been studied corresponding to solvent concentrations to elucidate the interacting mechanisms of binary mixtures. Copyright © 2014 Elsevier B.V. All rights reserved.

Modeling, Measurements, and Fundamental Database Development for Nonequilibrium Hypersonic Aerothermodynamics

NASA Technical Reports Server (NTRS)

Bose, Deepak

2012-01-01

The design of entry vehicles requires predictions of aerothermal environment during the hypersonic phase of their flight trajectories. These predictions are made using computational fluid dynamics (CFD) codes that often rely on physics and chemistry models of nonequilibrium processes. The primary processes of interest are gas phase chemistry, internal energy relaxation, electronic excitation, nonequilibrium emission and absorption of radiation, and gas-surface interaction leading to surface recession and catalytic recombination. NASAs Hypersonics Project is advancing the state-of-the-art in modeling of nonequilibrium phenomena by making detailed spectroscopic measurements in shock tube and arcjets, using ab-initio quantum mechanical techniques develop fundamental chemistry and spectroscopic databases, making fundamental measurements of finite-rate gas surface interactions, implementing of detailed mechanisms in the state-of-the-art CFD codes, The development of new models is based on validation with relevant experiments. We will present the latest developments and a roadmap for the technical areas mentioned above

Molecular dynamics simulations of fluid cyclopropane with MP2/CBS-fitted intermolecular interaction potentials

NASA Astrophysics Data System (ADS)

Ho, Yen-Ching; Wang, Yi-Siang; Chao, Sheng D.

2017-08-01

Modeling fluid cycloalkanes with molecular dynamics simulations has proven to be a very challenging task partly because of lacking a reliable force field based on quantum chemistry calculations. In this paper, we construct an ab initio force field for fluid cyclopropane using the second-order Møller-Plesset perturbation theory. We consider 15 conformers of the cyclopropane dimer for the orientation sampling. Single-point energies at important geometries are calibrated by the coupled cluster with single, double, and perturbative triple excitation method. Dunning's correlation consistent basis sets (up to aug-cc-pVTZ) are used in extrapolating the interaction energies at the complete basis set limit. The force field parameters in a 9-site Lennard-Jones model are regressed by the calculated interaction energies without using empirical data. With this ab initio force field, we perform molecular dynamics simulations of fluid cyclopropane and calculate both the structural and dynamical properties. We compare the simulation results with those using an empirical force field and obtain a quantitative agreement for the detailed atom-wise radial distribution functions. The experimentally observed gross radial distribution function (extracted from the neutron scattering measurements) is well reproduced in our simulation. Moreover, the calculated self-diffusion coefficients and shear viscosities are in good agreement with the experimental data over a wide range of thermodynamic conditions. To the best of our knowledge, this is the first ab initio force field which is capable of competing with empirical force fields for simulating fluid cyclopropane.

Ultrafast non-adiabatic dynamics of methyl substituted ethylenes: the π3s Rydberg state.

PubMed

Wu, Guorong; Boguslavskiy, Andrey E; Schalk, Oliver; Schuurman, Michael S; Stolow, Albert

2011-10-28

Excited state unimolecular reactions of some polyenes exhibit localization of their dynamics at a single ethylenic double bond. Here we present studies of the fundamental photophysical processes in the ethylene unit itself. Combined femtosecond time-resolved photoelectron spectroscopy (TRPES) and ab initio quantum chemical calculations was applied to the study of excited state dynamics in cis-butene, trans-butene, trimethylethylene, and tetramethylethylene, following initial excitation to their respective π3s Rydberg states. The wavelength dependence of the π3s Rydberg state dynamics of tetramethylethylene was investigated in more detail. The π3s Rydberg to ππ(∗) valence state decay rate varies greatly with substituent: the 1,2-di- and tri-methyl substituted ethylenes (cis-butene, trans-butene, and trimethylethylene) show an ultrafast decay (∼20 fs), whereas the fully methylated tetramethylethylene shows a decay rate of 2 to 4 orders of magnitude slower. These observations are rationalized in terms of topographical trends in the relevant potential energy surfaces, as found from ab initio calculations: (1) the barrier between the π3s state and the ππ∗ state increases with increasing methylation, and (2) the π3s∕ππ∗ minimum energy conical intersection displaces monotonically away from the π3s Franck-Condon region with increasing methylation. The use of systematic methylation in combination with TRPES and ab initio computation is emerging as an important tool in discerning the excited state dynamics of unsaturated hydrocarbons.

Ultrafast non-adiabatic dynamics of methyl substituted ethylenes: The π3s Rydberg state

NASA Astrophysics Data System (ADS)

Wu, Guorong; Boguslavskiy, Andrey E.; Schalk, Oliver; Schuurman, Michael S.; Stolow, Albert

2011-10-01

Excited state unimolecular reactions of some polyenes exhibit localization of their dynamics at a single ethylenic double bond. Here we present studies of the fundamental photophysical processes in the ethylene unit itself. Combined femtosecond time-resolved photoelectron spectroscopy (TRPES) and ab initio quantum chemical calculations was applied to the study of excited state dynamics in cis-butene, trans-butene, trimethylethylene, and tetramethylethylene, following initial excitation to their respective π3s Rydberg states. The wavelength dependence of the π3s Rydberg state dynamics of tetramethylethylene was investigated in more detail. The π3s Rydberg to ππ* valence state decay rate varies greatly with substituent: the 1,2-di- and tri-methyl substituted ethylenes (cis-butene, trans-butene, and trimethylethylene) show an ultrafast decay (˜20 fs), whereas the fully methylated tetramethylethylene shows a decay rate of 2 to 4 orders of magnitude slower. These observations are rationalized in terms of topographical trends in the relevant potential energy surfaces, as found from ab initio calculations: (1) the barrier between the π3s state and the ππ* state increases with increasing methylation, and (2) the π3s/ππ* minimum energy conical intersection displaces monotonically away from the π3s Franck-Condon region with increasing methylation. The use of systematic methylation in combination with TRPES and ab initio computation is emerging as an important tool in discerning the excited state dynamics of unsaturated hydrocarbons.

Theoretical determination of chemical rate constants using novel time-dependent methods

NASA Technical Reports Server (NTRS)

Dateo, Christopher E.

1994-01-01

The work completed within the grant period 10/1/91 through 12/31/93 falls primarily in the area of reaction dynamics using both quantum and classical mechanical methodologies. Essentially four projects have been completed and have been or are in preparation of being published. The majority of time was spent in the determination of reaction rate coefficients in the area of hydrocarbon fuel combustion reactions which are relevant to NASA's High Speed Research Program (HSRP). These reaction coefficients are important in the design of novel jet engines with low NOx emissions, which through a series of catalytic reactions contribute to the deterioration of the earth's ozone layer. A second area of research studied concerned the control of chemical reactivity using ultrashort (femtosecond) laser pulses. Recent advances in pulsed-laser technologies have opened up a vast new field to be investigated both experimentally and theoretically. The photodissociation of molecules adsorbed on surfaces using novel time-independent quantum mechanical methods was a third project. And finally, using state-of-the-art, high level ab initio electronic structure methods in conjunction with accurate quantum dynamical methods, the rovibrational energy levels of a triatomic molecule with two nonhydrogen atoms (HCN) were calculated to unprecedented levels of agreement between theory and experiment.

A hybrid approach to simulation of electron transfer in complex molecular systems

PubMed Central

Kubař, Tomáš; Elstner, Marcus

2013-01-01

Electron transfer (ET) reactions in biomolecular systems represent an important class of processes at the interface of physics, chemistry and biology. The theoretical description of these reactions constitutes a huge challenge because extensive systems require a quantum-mechanical treatment and a broad range of time scales are involved. Thus, only small model systems may be investigated with the modern density functional theory techniques combined with non-adiabatic dynamics algorithms. On the other hand, model calculations based on Marcus's seminal theory describe the ET involving several assumptions that may not always be met. We review a multi-scale method that combines a non-adiabatic propagation scheme and a linear scaling quantum-chemical method with a molecular mechanics force field in such a way that an unbiased description of the dynamics of excess electron is achieved and the number of degrees of freedom is reduced effectively at the same time. ET reactions taking nanoseconds in systems with hundreds of quantum atoms can be simulated, bridging the gap between non-adiabatic ab initio simulations and model approaches such as the Marcus theory. A major recent application is hole transfer in DNA, which represents an archetypal ET reaction in a polarizable medium. Ongoing work focuses on hole transfer in proteins, peptides and organic semi-conductors. PMID:23883952

Quantum mechanical force fields for condensed phase molecular simulations

NASA Astrophysics Data System (ADS)

Giese, Timothy J.; York, Darrin M.

2017-09-01

Molecular simulations are powerful tools for providing atomic-level details into complex chemical and physical processes that occur in the condensed phase. For strongly interacting systems where quantum many-body effects are known to play an important role, density-functional methods are often used to provide the model with the potential energy used to drive dynamics. These methods, however, suffer from two major drawbacks. First, they are often too computationally intensive to practically apply to large systems over long time scales, limiting their scope of application. Second, there remain challenges for these models to obtain the necessary level of accuracy for weak non-bonded interactions to obtain quantitative accuracy for a wide range of condensed phase properties. Quantum mechanical force fields (QMFFs) provide a potential solution to both of these limitations. In this review, we address recent advances in the development of QMFFs for condensed phase simulations. In particular, we examine the development of QMFF models using both approximate and ab initio density-functional models, the treatment of short-ranged non-bonded and long-ranged electrostatic interactions, and stability issues in molecular dynamics calculations. Example calculations are provided for crystalline systems, liquid water, and ionic liquids. We conclude with a perspective for emerging challenges and future research directions.

Pressure broadening of the electric dipole and Raman lines of CO2 by argon: Stringent test of the classical impact theory at different temperatures on a benchmark system

NASA Astrophysics Data System (ADS)

Ivanov, Sergey V.; Buzykin, Oleg G.

2016-12-01

A classical approach is applied to calculate pressure broadening coefficients of CO2 vibration-rotational spectral lines perturbed by Ar. Three types of spectra are examined: electric dipole (infrared) absorption; isotropic and anisotropic Raman Q branches. Simple and explicit formulae of the classical impact theory are used along with exact 3D Hamilton equations for CO2-Ar molecular motion. The calculations utilize vibrationally independent most accurate ab initio potential energy surface (PES) of Hutson et al. expanded in Legendre polynomial series up to lmax = 24. New improved algorithm of classical rotational frequency selection is applied. The dependences of CO2 half-widths on rotational quantum number J up to J=100 are computed for the temperatures between 77 and 765 K and compared with available experimental data as well as with the results of fully quantum dynamical calculations performed on the same PES. To make the picture complete, the predictions of two independent variants of the semi-classical Robert-Bonamy formalism for dipole absorption lines are included. This method. however, has demonstrated poor accuracy almost for all temperatures. On the contrary, classical broadening coefficients are in excellent agreement both with measurements and with quantum results at all temperatures. The classical impact theory in its present variant is capable to produce quickly and accurately the pressure broadening coefficients of spectral lines of linear molecules for any J value (including high Js) using full-dimensional ab initio - based PES in the cases where other computational methods are either extremely time consuming (like the quantum close coupling method) or give erroneous results (like semi-classical methods).

On the R-Dependence of the Spin-Orbit Coupling Constant: Potential Energy Functions of Xe2+ by High-Resolution Photoelectron Spectroscopy and ab initio Quantum Chemistry

DTIC Science & Technology

2008-01-01

ORGANIZATION NAME(S) AND ADDRESS(ES) 8. PERFORMING ORGANIZATION REPORT NUMBER Air Force Research Laboratory /RVBXR AFRL-RV-HA-TR-2008-1053 29 Randolph...the umn 2 in Table I) features a very similiar behavior of a(R) g states so that the asymptotic value of a(R) exactly coffe - although these a(R) curves

Raman spectrum, quantum mechanical calculations and vibrational assignments of (95% alpha-TeO2/5% Sm2O3) glass.

PubMed

Shaltout, I; Mohamed, Tarek A

2007-06-01

Chozen system of tellurite glasses doped with rare earth oxides (95% alpha-TeO(2)+5% Sm2O3) was prepared by melt quenching. Consequently, the Raman spectrum (150-1250 cm(-1)) of the modified tellurite have been recorded. As a continuation to our normal coordinate analysis, force constants and quantum mechanical (QM) calculations for tbp TeO4(4-) (triagonal bipyramid, C(2v)) and TeO(3+1); Te2O7(6-) (bridged tetrahedral), we have carried out ab initio frequency calculations for tpy TeO3(2-) (triagonal pyramidal, C(3v) and C(s)) and tp TeO3(2-) (triagonal planar, D(3h)) ions. The quantum mechanical calculations at the levels of RHF, B3LYP and MP2 allow confident vibrational assignments and structural identification in the binary oxide glass (95% alpha-TeO2 +5% Sm2O3). The dominant three-dimensional network structures in the modified glass are triagonal pyramidal TeO3 with minor features of short range distorted tbp TeO4 and bridged tetrahedral unit of TeO(3+1), leading to a structure of infinite chain. Therefore, alpha-TeO2/Sm2O3 (95/5%) glass experience structural changes from TeO4 (tbp); Te2O7 (TeO(3+1))-->TeO3 (tpy).

Effects of molecular packing in organic crystals on singlet fission with ab initio many body perturbation theory

NASA Astrophysics Data System (ADS)

Haber, Jonah; Refaely-Abramson, Sivan; da Jornada, Felipe H.; Louie, Steven G.; Neaton, Jeffrey B.

Multi-exciton generation processes, in which multiple charge carriers are generated from a single photon, are mechanisms of significant interest for achieving efficiencies beyond the Shockley-Queisser limit of conventional p-n junction solar cells. One well-studied multiexciton process is singlet fission, whereby a singlet decays into two spin-correlated triplet excitons. Here, we use a newly developed computational approach to calculate singlet-fission coupling terms and rates with an ab initio Green's function formalism based on many-body perturbation theory (MBPT) within the GW approximation and the Bethe-Salpeter equation approach. We compare results for crystalline pentacene and TIPS-pentacene and explore the effect of molecular packing on the singlet fission mechanism. This work is supported by the Department of Energy.

Effects of boron-nitride substrates on Stone-Wales defect formation in graphene: An ab initio molecular dynamics study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jin, K.; Xiao, H. Y.; Zhang, Y.

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 recoverymore » process. This study indicates that the BN substrate enhances the irradiation resistance of graphene.« less

Quantum Simulation of Helium Hydride Cation in a Solid-State Spin Register.

PubMed

Wang, Ya; Dolde, Florian; Biamonte, Jacob; Babbush, Ryan; Bergholm, Ville; Yang, Sen; Jakobi, Ingmar; Neumann, Philipp; Aspuru-Guzik, Alán; Whitfield, James D; Wrachtrup, Jörg

2015-08-25

Ab initio computation of molecular properties is one of the most promising applications of quantum computing. While this problem is widely believed to be intractable for classical computers, efficient quantum algorithms exist which have the potential to vastly accelerate research throughput in fields ranging from material science to drug discovery. Using a solid-state quantum register realized in a nitrogen-vacancy (NV) defect in diamond, we compute the bond dissociation curve of the minimal basis helium hydride cation, HeH(+). Moreover, we report an energy uncertainty (given our model basis) of the order of 10(-14) hartree, which is 10 orders of magnitude below the desired chemical precision. As NV centers in diamond provide a robust and straightforward platform for quantum information processing, our work provides an important step toward a fully scalable solid-state implementation of a quantum chemistry simulator.

Theoretical calculations of physico-chemical and spectroscopic properties of bioinorganic systems: current limits and perspectives.

PubMed

Rokob, Tibor András; Srnec, Martin; Rulíšek, Lubomír

2012-05-21

In the last decade, we have witnessed substantial progress in the development of quantum chemical methodologies. Simultaneously, robust solvation models and various combined quantum and molecular mechanical (QM/MM) approaches have become an integral part of quantum chemical programs. Along with the steady growth of computer power and, more importantly, the dramatic increase of the computer performance to price ratio, this has led to a situation where computational chemistry, when exercised with the proper amount of diligence and expertise, reproduces, predicts, and complements the experimental data. In this perspective, we review some of the latest achievements in the field of theoretical (quantum) bioinorganic chemistry, concentrating mostly on accurate calculations of the spectroscopic and physico-chemical properties of open-shell bioinorganic systems by wave-function (ab initio) and DFT methods. In our opinion, the one-to-one mapping between the calculated properties and individual molecular structures represents a major advantage of quantum chemical modelling since this type of information is very difficult to obtain experimentally. Once (and only once) the physico-chemical, thermodynamic and spectroscopic properties of complex bioinorganic systems are quantitatively reproduced by theoretical calculations may we consider the outcome of theoretical modelling, such as reaction profiles and the various decompositions of the calculated parameters into individual spatial or physical contributions, to be reliable. In an ideal situation, agreement between theory and experiment may imply that the practical problem at hand, such as the reaction mechanism of the studied metalloprotein, can be considered as essentially solved.

Hybrid Quantum Mechanics/Molecular Mechanics Solvation Scheme for Computing Free Energies of Reactions at Metal-Water Interfaces.

PubMed

Faheem, Muhammad; Heyden, Andreas

2014-08-12

We report the development of a quantum mechanics/molecular mechanics free energy perturbation (QM/MM-FEP) method for modeling chemical reactions at metal-water interfaces. This novel solvation scheme combines planewave density function theory (DFT), periodic electrostatic embedded cluster method (PEECM) calculations using Gaussian-type orbitals, and classical molecular dynamics (MD) simulations to obtain a free energy description of a complex metal-water system. We derive a potential of mean force (PMF) of the reaction system within the QM/MM framework. A fixed-size, finite ensemble of MM conformations is used to permit precise evaluation of the PMF of QM coordinates and its gradient defined within this ensemble. Local conformations of adsorbed reaction moieties are optimized using sequential MD-sampling and QM-optimization steps. An approximate reaction coordinate is constructed using a number of interpolated states and the free energy difference between adjacent states is calculated using the QM/MM-FEP method. By avoiding on-the-fly QM calculations and by circumventing the challenges associated with statistical averaging during MD sampling, a computational speedup of multiple orders of magnitude is realized. The method is systematically validated against the results of ab initio QM calculations and demonstrated for C-C cleavage in double-dehydrogenated ethylene glycol on a Pt (111) model surface.

Multiscale QM/MM molecular dynamics study on the first steps of guanine damage by free hydroxyl radicals in solution.

PubMed

Abolfath, Ramin M; Biswas, P K; Rajnarayanam, R; Brabec, Thomas; Kodym, Reinhard; Papiez, Lech

2012-04-19

Understanding the damage of DNA bases from hydrogen abstraction by free OH radicals is of particular importance to understanding the indirect effect of ionizing radiation. Previous studies address the problem with truncated DNA bases as ab initio quantum simulations required to study such electronic-spin-dependent processes are computationally expensive. Here, for the first time, we employ a multiscale and hybrid quantum mechanical-molecular mechanical simulation to study the interaction of OH radicals with a guanine-deoxyribose-phosphate DNA molecular unit in the presence of water, where all of the water molecules and the deoxyribose-phosphate fragment are treated with the simplistic classical molecular mechanical scheme. Our result illustrates that the presence of water strongly alters the hydrogen-abstraction reaction as the hydrogen bonding of OH radicals with water restricts the relative orientation of the OH radicals with respect to the DNA base (here, guanine). This results in an angular anisotropy in the chemical pathway and a lower efficiency in the hydrogen-abstraction mechanisms than previously anticipated for identical systems in vacuum. The method can easily be extended to single- and double-stranded DNA without any appreciable computational cost as these molecular units can be treated in the classical subsystem, as has been demonstrated here. © 2012 American Chemical Society

Trapping hydrogen atoms from a neon-gas matrix: a theoretical simulation.

PubMed

Bovino, S; Zhang, P; Kharchenko, V; Dalgarno, A

2009-08-07

Hydrogen is of critical importance in atomic and molecular physics and the development of a simple and efficient technique for trapping cold and ultracold hydrogen atoms would be a significant advance. In this study we simulate a recently proposed trap-loading mechanism for trapping hydrogen atoms released from a neon matrix. Accurate ab initio quantum calculations are reported of the neon-hydrogen interaction potential and the energy- and angular-dependent elastic scattering cross sections that control the energy transfer of initially cold atoms are obtained. They are then used to construct the Boltzmann kinetic equation, describing the energy relaxation process. Numerical solutions of the Boltzmann equation predict the time evolution of the hydrogen energy distribution function. Based on the simulations we discuss the prospects of the technique.

Determining the phase diagram of lithium via ab initio calculation and ramp compression

NASA Astrophysics Data System (ADS)

Shulenburger, Luke; Seagle, Chris; Haill, Thomas; Harding, Eric

2015-06-01

Diamond anvil cell experiments have shown elemental lithium to have an extraordinarily complex phase diagram under pressure exhibiting numerous solid phases at pressures below 1 Mbar, as well as a complicated melting behavior. We explore this phase diagram utilizing a combination of quantum mechanical calculations and ramp compression experiments performed on Sandia National Laboratories' Z-machine. We aim to extend our knowledge of the high pressure behavior to moderate temperatures at pressures above 50 GPa with a specific focus on the melt line above 70 GPa. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Company, for the US Dept of Energy's Natl. Nuclear Security Administration under Contract DE-AC04-94AL85000.

On the theory of Carriers's Electrostatic Interaction near an Interface

NASA Astrophysics Data System (ADS)

Waters, Michael; Hashemi, Hossein; Kieffer, John

2015-03-01

Heterojunction interfaces are common in non-traditional photovoltaic device designs, such as those based small molecules, polymers, and perovskites. We have examined a number of the effects of the heterojunction interface region on carrier/exciton energetics using a mixture of both semi-classical and quantum electrostatic methods, ab initio methods, and statistical mechanics. Our theoretical analysis has yielded several useful relationships and numerical recipes that should be considered in device design regardless of the particular materials system. As a demonstration, we highlight these formalisms as applied to carriers and polaron pairs near a C60/subphthalocyanine interface. On the regularly ordered areas of the heterojunction, the effect of the interface is a significant set of corrections to the carrier energies, which in turn directly affects device performance.

Electron-phonon interaction within classical molecular dynamics

DOE PAGES

Tamm, A.; Samolyuk, G.; Correa, A. A.; ...

2016-07-14

Here, we present a model for nonadiabatic classical molecular dynamics simulations that captures with high accuracy the wave-vector q dependence of the phonon lifetimes, in agreement with quantum mechanics calculations. It is based on a local view of the e-ph interaction where individual atom dynamics couples to electrons via a damping term that is obtained as the low-velocity limit of the stopping power of a moving ion in a host. The model is parameter free, as its components are derived from ab initio-type calculations, is readily extended to the case of alloys, and is adequate for large-scale molecular dynamics computermore » simulations. We also show how this model removes some oversimplifications of the traditional ionic damped dynamics commonly used to describe situations beyond the Born-Oppenheimer approximation.« less

Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems.

PubMed

Tanaka, Shigenori; Mochizuki, Yuji; Komeiji, Yuto; Okiyama, Yoshio; Fukuzawa, Kaori

2014-06-14

Recent developments in the fragment molecular orbital (FMO) method for theoretical formulation, implementation, and application to nano and biomolecular systems are reviewed. The FMO method has enabled ab initio quantum-mechanical calculations for large molecular systems such as protein-ligand complexes at a reasonable computational cost in a parallelized way. There have been a wealth of application outcomes from the FMO method in the fields of biochemistry, medicinal chemistry and nanotechnology, in which the electron correlation effects play vital roles. With the aid of the advances in high-performance computing, the FMO method promises larger, faster, and more accurate simulations of biomolecular and related systems, including the descriptions of dynamical behaviors in solvent environments. The current status and future prospects of the FMO scheme are addressed in these contexts.

DCA_Tools

DOE Office of Scientific and Technical Information (OSTI.GOV)

Summers, Michael S

2017-11-08

HPC software for ab-initio, condensed-matter physics, quantum mechanics calculations needs to be built on top of well tested libraries some of which address requirements unique to the programming domain. During the development of the DCA++ code, that we use in our research, we have developed a collection of libraries that may be of use to other computational scientists working in the same or similar domains. The libraries include: a) a pythonic input-language system, b) tensors whose shape is constructed from generalized dimension objects such at time domains. frequency domains, momentum domains, vertex domains et. al. and c) linear algebra operationsmore » that resolve to BLA/LAPACK operations when possible. This supports the implementation of Greens functions and operations on them such as are used in condensed matter physics.« less

ParFit: A Python-Based Object-Oriented Program for Fitting Molecular Mechanics Parameters to ab Initio Data.

PubMed

Zahariev, Federico; De Silva, Nuwan; Gordon, Mark S; Windus, Theresa L; Dick-Perez, Marilu

2017-03-27

A newly created object-oriented program for automating the process of fitting molecular-mechanics parameters to ab initio data, termed ParFit, is presented. ParFit uses a hybrid of deterministic and stochastic genetic algorithms. ParFit can simultaneously handle several molecular-mechanics parameters in multiple molecules and can also apply symmetric and antisymmetric constraints on the optimized parameters. The simultaneous handling of several molecules enhances the transferability of the fitted parameters. ParFit is written in Python, uses a rich set of standard and nonstandard Python libraries, and can be run in parallel on multicore computer systems. As an example, a series of phosphine oxides, important for metal extraction chemistry, are parametrized using ParFit. ParFit is in an open source program available for free on GitHub ( https://github.com/fzahari/ParFit ).

Novel view on the mechanism of water-assisted proton transfer in the DNA bases: bulk water hydration.

PubMed

Furmanchuk, Al'ona; Isayev, Olexandr; Gorb, Leonid; Shishkin, Oleg V; Hovorun, Dmytro M; Leszczynski, Jerzy

2011-03-14

In the present work, the conventional static ab initio picture of a water-assisted mechanism of the tautomerization of Nucleic Acid Bases (NABs) in an aqueous environment is enhanced by the classical and Car-Parrinello molecular dynamics simulations. The inclusion of the dynamical contribution is vital because the formation and longevity of the NAB-water bridge complexes represent decisive factors for further tautomerization. The results of both molecular dynamic techniques indicate that the longest time when such complexes exist is significantly shorter than the time required for proton transfer suggested by the static ab initio level of theory. New rate constants of tautomerization corrected for the dynamic effect of environment are proposed based on the first principles molecular dynamics data. Those values are used for the evaluation of a water-assisted mechanism that is feasible in such biological systems as E. coli cell.

Comment on "Comparative study of ab initio nonradiative recombination rate calculations under different formalisms"

NASA Astrophysics Data System (ADS)

Wickramaratne, Darshana; Shen, Jimmy-Xuan; Alkauskas, Audrius; Van de Walle, Chris G.

2018-02-01

In a recent article [Phys. Rev. B 91, 205315 (2015), 10.1103/PhysRevB.91.205315] Shi, Xu, and Wang presented a comparison of several formalisms to calculate nonradiative recombination rates and concluded the "one-dimensional (1D) quantum formula" that was used by Alkauskas et al. [Phys. Rev. B 90, 075202 (2014), 10.1103/PhysRevB.90.075202] is insufficient to accurately describe nonradiative capture rates. Our analysis of the results of Shi, Xu, and Wang indicates that their conclusions about the 1D quantum formula are unfounded and stem from an error in their calculations. Our own calculations demonstrate that the 1D quantum formula approach yields reliable and accurate results for nonradiative recombination rates.

Evidence for a first-order liquid-liquid transition in high-pressure hydrogen from ab initio simulations.

PubMed

Morales, Miguel A; Pierleoni, Carlo; Schwegler, Eric; Ceperley, D M

2010-07-20

Using quantum simulation techniques based on either density functional theory or quantum Monte Carlo, we find clear evidence of a first-order transition in liquid hydrogen, between a low conductivity molecular state and a high conductivity atomic state. Using the temperature dependence of the discontinuity in the electronic conductivity, we estimate the critical point of the transition at temperatures near 2,000 K and pressures near 120 GPa. Furthermore, we have determined the melting curve of molecular hydrogen up to pressures of 200 GPa, finding a reentrant melting line. The melting line crosses the metalization line at 700 K and 220 GPa using density functional energetics and at 550 K and 290 GPa using quantum Monte Carlo energetics.

Determination of Quantum Chemistry Based Force Fields for Molecular Dynamics Simulations of Aromatic Polymers

NASA Technical Reports Server (NTRS)

Jaffe, Richard; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).

A note on AB INITIO semiconductor band structures

NASA Astrophysics Data System (ADS)

Fiorentini, Vincenzo

1992-09-01

We point out that only the internal features of the DFT ab initio theoretical picture of a crystal should be used in a consistent ab initio calculation of the band structure. As a consequence, we show that ground-state band structure calculations should be performed for the system in equilibrium at zero pressure, i.e. at the computed equilibrium cell volume ω th. Examples of consequences of this attitude are considered.

Computational Chemistry Comparison and Benchmark Database

National Institute of Standards and Technology Data Gateway

SRD 101 NIST Computational Chemistry Comparison and Benchmark Database (Web, free access)   The NIST Computational Chemistry Comparison and Benchmark Database is a collection of experimental and ab initio thermochemical properties for a selected set of molecules. The goals are to provide a benchmark set of molecules for the evaluation of ab initio computational methods and allow the comparison between different ab initio computational methods for the prediction of thermochemical properties.

Sampling the potential energy surface of a DNA duplex damaged by a food carcinogen: Force field parameterization by ab initio quantum calculations and conformational searching using molecular mechanics computations

NASA Astrophysics Data System (ADS)

Wu, Xiangyang

1999-07-01

The heterocyclic amine 2-amino-3-methylimidazo (4, 5-f) quinoline (IQ) is one of a number of carcinogens found in barbecued meat and fish. It induces tumors in mammals and is probably involved in human carcinogenesis, because of great exposure to such food carcinogens. IQ is biochemically activated to a derivative which reacts with DNA to form a covalent adduct. This adduct may deform the DNA and consequently cause a mutation. which may initiate carcinogenesis. To understand this cancer initiating event, it is necessary to obtain atomic resolution structures of the damaged DNA. No such structures are available experimentally due to synthesis difficulties. Therefore, we employ extensive molecular mechanics and dynamics calculations for this purpose. The major IQ-DNA adduct in the specific DNA sequence d(5'G1G2C G3CCA3') - d(5'TGGCGCC3') with IQ modified at G3 is studied. The d(5'G1G2C G3CC3') sequence has recently been shown to be a hot-spot for mutations when IQ modification is at G3. Although this sequence is prone to -2 deletions via a ``slippage mechanism'' even when unmodified, a key question is why IQ increases the mutation frequency of the unmodified DNA by about 104 fold. Is there a structural feature imposed by IQ that is responsible? The molecular mechanics and dynamics program AMBER for nucleic acids with the latest force field was chosen for this work. This force field has been demonstrated to reproduce well the B-DNA structure. However, some parameters, the partial charges, bond lengths and angles, dihedral parameters of the modified residue, are not available in the AMBER database. We parameterized the force field using high level ab initio quantum calculations. We created 800 starting conformations which uniformly sampled in combination at 18° intervals three torsion angles that govern the IQ-DNA orientations, and energy minimized them. The most important structures are abnormal; the IQ damaged guanine is rotated out of its standard B-DNA orientations, compromising its ability to act as a faithful template during DNA replication.

Multiobjective evolutionary algorithm with many tables for purely ab initio protein structure prediction.

PubMed

Brasil, Christiane Regina Soares; Delbem, Alexandre Claudio Botazzo; da Silva, Fernando Luís Barroso

2013-07-30

This article focuses on the development of an approach for ab initio protein structure prediction (PSP) without using any earlier knowledge from similar protein structures, as fragment-based statistics or inference of secondary structures. Such an approach is called purely ab initio prediction. The article shows that well-designed multiobjective evolutionary algorithms can predict relevant protein structures in a purely ab initio way. One challenge for purely ab initio PSP is the prediction of structures with β-sheets. To work with such proteins, this research has also developed procedures to efficiently estimate hydrogen bond and solvation contribution energies. Considering van der Waals, electrostatic, hydrogen bond, and solvation contribution energies, the PSP is a problem with four energetic terms to be minimized. Each interaction energy term can be considered an objective of an optimization method. Combinatorial problems with four objectives have been considered too complex for the available multiobjective optimization (MOO) methods. The proposed approach, called "Multiobjective evolutionary algorithms with many tables" (MEAMT), can efficiently deal with four objectives through the combination thereof, performing a more adequate sampling of the objective space. Therefore, this method can better map the promising regions in this space, predicting structures in a purely ab initio way. In other words, MEAMT is an efficient optimization method for MOO, which explores simultaneously the search space as well as the objective space. MEAMT can predict structures with one or two domains with RMSDs comparable to values obtained by recently developed ab initio methods (GAPFCG , I-PAES, and Quark) that use different levels of earlier knowledge. Copyright © 2013 Wiley Periodicals, Inc.

Ground and excited states of the Rydberg radical H3O: Electron propagator and quantum defect analysis

NASA Astrophysics Data System (ADS)

Melin, Junia; Ortiz, J. V.; Martín, I.; Velasco, A. M.; Lavín, C.

2005-06-01

Vertical excitation energies of the Rydberg radical H3O are inferred from ab initio electron propagator calculations on the electron affinities of H3O+. The adiabatic ionization energy of H3O is evaluated with coupled-cluster calculations. These predictions provide optimal parameters for the molecular-adapted quantum defect orbital method, which is used to determine oscillator strengths. Given that the experimental spectrum of H3O does not seem to be available, comparisons with previous calculations are discussed. A simple model Hamiltonian, suitable for the study of bound states with arbitrarily high energies is generated by these means.

QED Tests and Search for New Physics in Molecular Hydrogen

NASA Astrophysics Data System (ADS)

Salumbides, E. J.; Niu, M. L.; Dickenson, G. D.; Eikema, K. S. E.; Komasa, J.; Pachucki, K.; Ubachs, W.

2013-06-01

The hydrogen molecule has been the benchmark system for quantum chemistry, and may provide a test ground for new physics. We present our high-resolution spectroscopic studies on the X ^1Σ^+_g electronic ground state rotational series and fundamenal vibrational tones in molecular hydrogen. In combination with recent accurate ab initio calculations, we demonstrate systematic tests of quantum electrodynamical (QED) effects in molecules. Moreover, the precise comparison between theory and experiment can provide stringent constraints on possible new interactions that extend beyond the Standard Model. E. J. Salumbides, G. D. Dickenson, T. I. Ivanov and W. Ubachs, Phys. Rev. Lett. 107, 043005 (2011).

Employing OpenCL to Accelerate Ab Initio Calculations on Graphics Processing Units.

PubMed

Kussmann, Jörg; Ochsenfeld, Christian

2017-06-13

We present an extension of our graphics processing units (GPU)-accelerated quantum chemistry package to employ OpenCL compute kernels, which can be executed on a wide range of computing devices like CPUs, Intel Xeon Phi, and AMD GPUs. Here, we focus on the use of AMD GPUs and discuss differences as compared to CUDA-based calculations on NVIDIA GPUs. First illustrative timings are presented for hybrid density functional theory calculations using serial as well as parallel compute environments. The results show that AMD GPUs are as fast or faster than comparable NVIDIA GPUs and provide a viable alternative for quantum chemical applications.

The spectroscopic (FTIR, FT-IR gas phase and FT-Raman), first order hyperpolarizabilities, NMR analysis of 2,4-dichloroaniline by ab initio HF and density functional methods.

PubMed

Sundaraganesan, N; Karpagam, J; Sebastian, S; Cornard, J P

2009-07-01

In this work, the experimental and theoretical study on molecular structure and vibrational spectra of 2,4-dichloroaniline (2,4-DCA) were studied. The Fourier transform infrared (gas phase) and Fourier transform Raman spectra of 2,4-DCA were recorded. The molecular geometry and vibrational frequencies of 2,4-DCA in the ground state were calculated by using the Hartree-Fock (HF) and density functional (DF) methods (BLYP, B3LYP and SVWN) with 6-31G(d,p) as basis set. Comparison of the observed fundamental vibrational frequencies of 2,4-DCA with calculated results by HF and density functional methods indicates that BLYP is superior to other methods for molecular vibrational problems. The difference between the observed and scaled wave number values of most of the fundamentals is very small. The electric dipole moment (micro) and the first hyperpolarizability (beta) values of the investigated molecule were computed using ab initio quantum mechanical calculations. The calculated results also show that the 2,4-DCA molecule might have microscopic nonlinear optical (NLO) behavior with non-zero values. Natural atomic charges of 2,4-DCA and 4-chloroaniline was calculated and compared. The isotropic chemical shift computed by (13)C NMR analyses also shows good agreement with experimental observations. The theoretically predicted FTIR and FT-Raman spectra of the title molecule have been constructed.

Vivek S. Bharadwaj | NREL

Science.gov Websites

Interests Vivek's interests broadly span across protein structure and dynamics, reaction mechanisms, and energetics and kinetics from first principles Protein structure prediction and docking Education PhD structure on the fumarate addition mechanism - a gas-phase ab initio study," Physical Chemistry

Control of Electronic Structures and Phonon Dynamics in Quantum Dot Superlattices by Manipulation of Interior Nanospace.

PubMed

Chang, I-Ya; Kim, DaeGwi; Hyeon-Deuk, Kim

2016-07-20

Quantum dot (QD) superlattices, periodically ordered array structures of QDs, are expected to provide novel photo-optical functions due to their resonant couplings between adjacent QDs. Here, we computationally demonstrated that electronic structures and phonon dynamics of a QD superlattice can be effectively and selectively controlled by manipulating its interior nanospace, where quantum resonance between neighboring QDs appears, rather than by changing component QD size, shape, compositions, etc. A simple H-passivated Si QD was examined to constitute one-, two-, and three-dimensional QD superlattices, and thermally fluctuating band energies and phonon modes were simulated by finite-temperature ab initio molecular dynamics (MD) simulations. The QD superlattice exhibited a decrease in the band gap energy enhanced by thermal modulations and also exhibited selective extraction of charge carriers out of the component QD, indicating its advantage as a promising platform for implementation in solar cells. Our dynamical phonon analyses based on the ab initio MD simulations revealed that THz-frequency phonon modes were created by an inter-QD crystalline lattice formed in the QD superlattice, which can contribute to low energy thermoelectric conversion and will be useful for direct observation of the dimension-dependent superlattice. Further, we found that crystalline and ligand-originated phonon modes inside each component QD can be independently controlled by asymmetry of the superlattice and by restriction of the interior nanospace, respectively. Taking into account the thermal effects at the finite temperature, we proposed guiding principles for designing efficient and space-saving QD superlattices to develop functional photovoltaic and thermoelectric devices.

Density functional calculations on structural materials for nuclear energy applications and functional materials for photovoltaic energy applications (abstract only).

PubMed

Domain, C; Olsson, P; Becquart, C S; Legris, A; Guillemoles, J F

2008-02-13

Ab initio density functional theory calculations are carried out in order to predict the evolution of structural materials under aggressive working conditions such as cases with exposure to corrosion and irradiation, as well as to predict and investigate the properties of functional materials for photovoltaic energy applications. Structural metallic materials used in nuclear facilities are subjected to irradiation which induces the creation of large amounts of point defects. These defects interact with each other as well as with the different elements constituting the alloys, which leads to modifications of the microstructure and the mechanical properties. VASP (Vienna Ab initio Simulation Package) has been used to determine the properties of point defect clusters and also those of extended defects such as dislocations. The resulting quantities, such as interaction energies and migration energies, are used in larger scale simulation methods in order to build predictive tools. For photovoltaic energy applications, ab initio calculations are used in order to search for new semiconductors and possible element substitutions for existing ones in order to improve their efficiency.

Frontiers of Theoretical Research on Shape Memory Alloys: A General Overview

NASA Astrophysics Data System (ADS)

Chowdhury, Piyas

2018-03-01

In this concise review, general aspects of modeling shape memory alloys (SMAs) are recounted. Different approaches are discussed under four general categories, namely, (a) macro-phenomenological, (b) micromechanical, (c) molecular dynamics, and (d) first principles models. Macro-phenomenological theories, stemming from empirical formulations depicting continuum elastic, plastic, and phase transformation, are primarily of engineering interest, whereby the performance of SMA-made components is investigated. Micromechanical endeavors are generally geared towards understanding microstructural phenomena within continuum mechanics such as the accommodation of straining due to phase change as well as role of precipitates. By contrast, molecular dynamics, being a more recently emerging computational technique, concerns attributes of discrete lattice structures, and thus captures SMA deformation mechanism by means of empirically reconstructing interatomic bonding forces. Finally, ab initio theories utilize quantum mechanical framework to peek into atomistic foundation of deformation, and can pave the way for studying the role of solid-sate effects. With specific examples, this paper provides concise descriptions of each category along with their relative merits and emphases.

Two-state model based on the block-localized wave function method

NASA Astrophysics Data System (ADS)

Mo, Yirong

2007-06-01

The block-localized wave function (BLW) method is a variant of ab initio valence bond method but retains the efficiency of molecular orbital methods. It can derive the wave function for a diabatic (resonance) state self-consistently and is available at the Hartree-Fock (HF) and density functional theory (DFT) levels. In this work we present a two-state model based on the BLW method. Although numerous empirical and semiempirical two-state models, such as the Marcus-Hush two-state model, have been proposed to describe a chemical reaction process, the advantage of this BLW-based two-state model is that no empirical parameter is required. Important quantities such as the electronic coupling energy, structural weights of two diabatic states, and excitation energy can be uniquely derived from the energies of two diabatic states and the adiabatic state at the same HF or DFT level. Two simple examples of formamide and thioformamide in the gas phase and aqueous solution were presented and discussed. The solvation of formamide and thioformamide was studied with the combined ab initio quantum mechanical and molecular mechanical Monte Carlo simulations, together with the BLW-DFT calculations and analyses. Due to the favorable solute-solvent electrostatic interaction, the contribution of the ionic resonance structure to the ground state of formamide and thioformamide significantly increases, and for thioformamide the ionic form is even more stable than the covalent form. Thus, thioformamide in aqueous solution is essentially ionic rather than covalent. Although our two-state model in general underestimates the electronic excitation energies, it can predict relative solvatochromic shifts well. For instance, the intense π →π* transition for formamide upon solvation undergoes a redshift of 0.3eV, compared with the experimental data (0.40-0.5eV).

Exploring Nuclear Photorelaxation of Pyranine in Aqueous Solution: an Integrated Ab-Initio Molecular Dynamics and Time Resolved Vibrational Analysis Approach.

PubMed

Chiariello, Maria Gabriella; Rega, Nadia

2018-03-22

Advances in time-resolved vibrational spectroscopy techniques provided a new stimulus for understanding the transient molecular dynamics triggered by the electronic excitation. The detailed interpretation of such time-dependent spectroscopic signals is a challenging task from both experimental and theoretical points of view. We simulated and analyzed the transient photorelaxation of the pyranine photoacid in aqueous solution, with special focus on structural parameters and low frequency skeleton modes that are possibly preparatory for the photoreaction occurring at later time, as suggested by experimental spectroscopic studies. To this aim, we adopted an accurate computational protocol that combines excited state ab initio molecular dynamics within an hybrid quantum mechanical/molecular mechanics framework and a time-resolved vibrational analysis based on the Wavelet transform. According to our results, the main nuclear relaxation on the excited potential energy surface is completed in about 500 fs, in agreement with experimental data. The rearrangement of C-C bonds occurs according to a complex vibrational dynamics, showing oscillatory patterns that are out of phase and modulated by modes below 200 cm -1 . We also analyzed in both the ground and the excited state the evolution of some structural parameters involved in excited state proton transfer reaction, namely, those involving the pyranine and the water molecule hydrogen bonded to the phenolic O-H group. Both the hydrogen bond distance and the intermolecular orientation are optimized in the excited state, resulting in a tighter proton donor-acceptor couple. Indeed, we found evidence that collective low frequency skeleton modes, such as the out of plane wagging at 108 cm -1 and the deformation at 280 cm -1 , are photoactivated by the ultrafast part of the relaxation and modulate the pyranine-water molecule rearrangement, favoring the preparatory step for the photoreactivity.

Investigation of base pairs containing oxidized guanine using ab initio method and ABEEMσπ polarizable force field.

PubMed

Liu, Cui; Wang, Yang; Zhao, Dongxia; Gong, Lidong; Yang, Zhongzhi

2014-02-01

The integrity of the genetic information is constantly threatened by oxidizing agents. Oxidized guanines have all been linked to different types of cancers. Theoretical approaches supplement the assorted experimental techniques, and bring new sight and opportunities to investigate the underlying microscopic mechanics. Unfortunately, there is no specific force field to DNA system including oxidized guanines. Taking high level ab initio calculations as benchmark, we developed the ABEEMσπ fluctuating charge force field, which uses multiple fluctuating charges per atom. And it was applied to study the energies, structures and mutations of base pairs containing oxidized guanines. The geometries were obtained in reference to other studies or using B3LYP/6-31+G* level optimization, which is more rational and timesaving among 24 quantum mechanical methods selected and tested by this work. The energies were determined at MP2/aug-cc-pVDZ level with BSSE corrections. Results show that the constructed potential function can accurately simulate the change of H-bond and the buckled angle formed by two base planes induced by oxidized guanine, and it provides reliable information of hydrogen bonding, stacking interaction and the mutation processes. The performance of ABEEMσπ polarizable force field in predicting the bond lengths, bond angles, dipole moments etc. is generally better than those of the common force fields. And the accuracy of ABEEMσπ PFF is close to that of the MP2 method. This shows that ABEEMσπ model is a reliable choice for further research of dynamics behavior of DNA fragment including oxidized guanine. Copyright © 2013 Elsevier Inc. All rights reserved.

Influence of metal cofactors and water on the catalytic mechanism of creatininase-creatinine in aqueous solution from molecular dynamics simulation and quantum study

NASA Astrophysics Data System (ADS)

Lee, Vannajan Sanghiran; Kodchakorn, Kanchanok; Jitonnom, Jitrayut; Nimmanpipug, Piyarat; Kongtawelert, Prachya; Premanode, Bhusana

2010-10-01

The reaction mechanism of creatinine-creatininase binding to form creatine as a final product has been investigated by using a combined ab initio quantum mechanical/molecular mechanical approach and classical molecular dynamics (MD) simulations. In MD simulations, an X-ray crystal structure of the creatininase/creatinine was modified for creatininase/creatinine complexes and the MD simulations were run for free creatininase and creatinine in water. MD results reveal that two X-ray water molecules can be retained in the active site as catalytic water. The binding free energy from Molecular Mechanics Poisson-Boltzmann Surface Area calculation predicted the strong binding of creatinine with Zn2+, Asp45 and Glu183. Two step mechanisms via Mn2+/Zn2+ (as in X-ray structure) and Zn2+/Zn2+ were proposed for water adding step and ring opening step with two catalytic waters. The pathway using synchronous transit methods with local density approximations with PWC functional for the fragment in the active region were obtained. Preferable pathway Zn2+/Zn2+ was observed due to lower activation energy in water adding step. The calculated energy in the second step for both systems were comparable with the barrier of 26.03 and 24.44 kcal/mol for Mn2+/Zn2+ and Zn2+/Zn2+, respectively.

Lamb Shift of n = 1 and n = 2 States of Hydrogen-like Atoms, 1 ≤ Z ≤ 110

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yerokhin, V. A.; Shabaev, V. M.

2015-09-15

Theoretical energy levels of the n = 1 and n = 2 states of hydrogen-like atoms with the nuclear charge numbers 1 ≤ Z ≤ 110 are tabulated. The tabulation is based on ab initio quantum electrodynamics calculations performed to all orders in the nuclear binding strength parameter Zα, where α is the fine structure constant. Theoretical errors due to various effects are critically examined and estimated.

Applicability of PM3 to transphosphorylation reaction path: Toward designing a minimal ribozyme

NASA Technical Reports Server (NTRS)

Manchester, John I.; Shibata, Masayuki; Setlik, Robert F.; Ornstein, Rick L.; Rein, Robert

1993-01-01

A growing body of evidence shows that RNA can catalyze many of the reactions necessary both for replication of genetic material and the possible transition into the modern protein-based world. However, contemporary ribozymes are too large to have self-assembled from a prebiotic oligonucleotide pool. Still, it is likely that the major features of the earliest ribozymes have been preserved as molecular fossils in the catalytic RNA of today. Therefore, the search for a minimal ribozyme has been aimed at finding the necessary structural features of a modern ribozyme (Beaudry and Joyce, 1990). Both a three-dimensional model and quantum chemical calculations are required to quantitatively determine the effects of structural features of the ribozyme on the reaction it catalyzes. Using this model, quantum chemical calculations must be performed to determine quantitatively the effects of structural features on catalysis. Previous studies of the reaction path have been conducted at the ab initio level, but these methods are limited to small models due to enormous computational requirements. Semiempirical methods have been applied to large systems in the past; however, the accuracy of these methods depends largely on a simple model of the ribozyme-catalyzed reaction, or hydrolysis of phosphoric acid. We find that the results are qualitatively similar to ab initio results using large basis sets. Therefore, PM3 is suitable for studying the reaction path of the ribozyme-catalyzed reaction.

Energy barriers and rates of tautomeric transitions in DNA bases: ab initio quantum chemical study.

PubMed

Basu, Soumalee; Majumdar, Rabi; Das, Gourab K; Bhattacharyya, Dhananjay

2005-12-01

Tautomeric transitions of DNA bases are proton transfer reactions, which are important in biology. These reactions are involved in spontaneous point mutations of the genetic material. In the present study, intrinsic reaction coordinates (IRC) analyses through ab initio quantum chemical calculations have been carried out for the individual DNA bases A, T, G, C and also A:T and G:C base pairs to estimate the kinetic and thermodynamic barriers using MP2/6-31G** method for tautomeric transitions. Relatively higher values of kinetic barriers (about 50-60 kcal/mol) have been observed for the single bases, indicating that tautomeric alterations of isolated single bases are quite unlikely. On the other hand, relatively lower values of the kinetic barriers (about 20-25 kcal/mol) for the DNA base pairs A:T and G:C clearly suggest that the tautomeric shifts are much more favorable in DNA base pairs than in isolated single bases. The unusual base pairing A':C, T':G, C':A or G':T in the daughter DNA molecule, resulting from a parent DNA molecule with tautomeric shifts, is found to be stable enough to result in a mutation. The transition rate constants for the single DNA bases in addition to the base pairs are also calculated by computing the free energy differences between the transition states and the reactants.

Interaction energies for the purine inhibitor roscovitine with cyclin-dependent kinase 2: correlated ab initio quantum-chemical, DFT and empirical calculations.

PubMed

Dobes, Petr; Otyepka, Michal; Strnad, Miroslav; Hobza, Pavel

2006-05-24

The interaction between roscovitine and cyclin-dependent kinase 2 (cdk2) was investigated by performing correlated ab initio quantum-chemical calculations. The whole protein was fragmented into smaller systems consisting of one or a few amino acids, and the interaction energies of these fragments with roscovitine were determined by using the MP2 method with the extended aug-cc-pVDZ basis set. For selected complexes, the complete basis set limit MP2 interaction energies, as well as the coupled-cluster corrections with inclusion of single, double and noninteractive triples contributions [CCSD(T)], were also evaluated. The energies of interaction between roscovitine and small fragments and between roscovitine and substantial sections of protein (722 atoms) were also computed by using density-functional tight-binding methods covering dispersion energy (DFTB-D) and the Cornell empirical potential. Total stabilisation energy originates predominantly from dispersion energy and methods that do not account for the dispersion energy cannot, therefore, be recommended for the study of protein-inhibitor interactions. The Cornell empirical potential describes reasonably well the interaction between roscovitine and protein; therefore, this method can be applied in future thermodynamic calculations. A limited number of amino acid residues contribute significantly to the binding of roscovitine and cdk2, whereas a rather large number of amino acids make a negligible contribution.

Polarization effects on quantum levels in InN/GaN quantum wells.

PubMed

Lin, Wei; Li, Shuping; Kang, Junyong

2009-12-02

Polarization effects on quantum states in InN/GaN quantum wells have been investigated by means of ab initio calculation and spectroscopic ellipsometry. Through the position-dependent partial densities of states, our results show that the polarization modified by the strain with different well thickness leads to an asymmetry band bending of the quantum well. The quantum levels are identified via the band structures and their square wave function distributions are analyzed by the partial charge densities. Further theoretical and experimental comparison of the imaginary part of the dielectric function show that the overall transition probability increases under larger polarization fields, which can be attributable to the fact that the excited quantum states of 2h have a greater overlap with 1e states and enhance other hole quantum states in the well by a hybridization. These results would provide a new approach to improve the transition probability and light emission by enhancing the polarization fields in a proper way.

An ab initio study of the conformational energy map of acetylcholine

NASA Astrophysics Data System (ADS)

Segall, M. D.; Payne, M. C.; Boyes, R. N.

An ab initio density functional theory study is reported of the conformational energy map of acetylcholine, with respect to the two central dihedral angles of the molecule. The acetylcholine molecule pays a central role in neurotransmission and has been studied widely using semi-empirical computational modelling. The ab initio results are compared with a number of previous investigations and with experiment. The ab initio data indicate that the most stable conformation of acetylcholine is the trans , gauche arrangement of the central dihedral angles. Furthermore, Mulliken population analysis of the electronic structure of the molecule in this conformation indicates that the positive charge of the molecule is spread over the exterior of the cationic head of the molecule.

Quantum delocalization of protons in the hydrogen-bond network of an enzyme active site.

PubMed

Wang, Lu; Fried, Stephen D; Boxer, Steven G; Markland, Thomas E

2014-12-30

Enzymes use protein architectures to create highly specialized structural motifs that can greatly enhance the rates of complex chemical transformations. Here, we use experiments, combined with ab initio simulations that exactly include nuclear quantum effects, to show that a triad of strongly hydrogen-bonded tyrosine residues within the active site of the enzyme ketosteroid isomerase (KSI) facilitates quantum proton delocalization. This delocalization dramatically stabilizes the deprotonation of an active-site tyrosine residue, resulting in a very large isotope effect on its acidity. When an intermediate analog is docked, it is incorporated into the hydrogen-bond network, giving rise to extended quantum proton delocalization in the active site. These results shed light on the role of nuclear quantum effects in the hydrogen-bond network that stabilizes the reactive intermediate of KSI, and the behavior of protons in biological systems containing strong hydrogen bonds.

Quantum delocalization of protons in the hydrogen-bond network of an enzyme active site

PubMed Central

Wang, Lu; Fried, Stephen D.; Boxer, Steven G.; Markland, Thomas E.

2014-01-01

Enzymes use protein architectures to create highly specialized structural motifs that can greatly enhance the rates of complex chemical transformations. Here, we use experiments, combined with ab initio simulations that exactly include nuclear quantum effects, to show that a triad of strongly hydrogen-bonded tyrosine residues within the active site of the enzyme ketosteroid isomerase (KSI) facilitates quantum proton delocalization. This delocalization dramatically stabilizes the deprotonation of an active-site tyrosine residue, resulting in a very large isotope effect on its acidity. When an intermediate analog is docked, it is incorporated into the hydrogen-bond network, giving rise to extended quantum proton delocalization in the active site. These results shed light on the role of nuclear quantum effects in the hydrogen-bond network that stabilizes the reactive intermediate of KSI, and the behavior of protons in biological systems containing strong hydrogen bonds. PMID:25503367

Ice Ih anomalies: Thermal contraction, anomalous volume isotope effect, and pressure-induced amorphization.

PubMed

Salim, Michael A; Willow, Soohaeng Yoo; Hirata, So

2016-05-28

Ice Ih displays several anomalous thermodynamic properties such as thermal contraction at low temperatures, an anomalous volume isotope effect (VIE) rendering the volume of D2O ice greater than that of H2O ice, and a pressure-induced transition to the high-density amorphous (HDA) phase. Furthermore, the anomalous VIE increases with temperature, despite its quantum-mechanical origin. Here, embedded-fragment ab initio second-order many-body perturbation (MP2) theory in the quasiharmonic approximation (QHA) is applied to the Gibbs energy of an infinite, proton-disordered crystal of ice Ih at wide ranges of temperatures and pressures. The quantum effect of nuclei moving in anharmonic potentials is taken into account from first principles without any empirical or nonsystematic approximation to either the electronic or vibrational Hamiltonian. MP2 predicts quantitatively correctly the thermal contraction at low temperatures, which is confirmed to originate from the volume-contracting hydrogen-bond bending modes (acoustic phonons). It qualitatively reproduces (but underestimates) the thermal expansion at higher temperatures, caused by the volume-expanding hydrogen-bond stretching (and to a lesser extent librational) modes. The anomalous VIE is found to be the result of subtle cancellations among closely competing isotope effects on volume from all modes. Consequently, even ab initio MP2 with the aug-cc-pVDZ and aug-cc-pVTZ basis sets has difficulty reproducing this anomaly, yielding qualitatively varied predictions of the sign of the VIE depending on such computational details as the choice of the embedding field. However, the temperature growth of the anomalous VIE is reproduced robustly and is ascribed to the librational modes. These solid-state MP2 calculations, as well as MP2 Born-Oppenheimer molecular dynamics, find a volume collapse and a loss of symmetry and long-range order in ice Ih upon pressure loading of 2.35 GPa or higher. Concomitantly, rapid softening of acoustic phonons is observed starting around 2 GPa. They constitute a computational detection of a mechanical instability in ice Ih and the resulting pressure-induced amorphization to HDA.

Ice Ih anomalies: Thermal contraction, anomalous volume isotope effect, and pressure-induced amorphization

NASA Astrophysics Data System (ADS)

Salim, Michael A.; Willow, Soohaeng Yoo; Hirata, So

2016-05-01

Ice Ih displays several anomalous thermodynamic properties such as thermal contraction at low temperatures, an anomalous volume isotope effect (VIE) rendering the volume of D2O ice greater than that of H2O ice, and a pressure-induced transition to the high-density amorphous (HDA) phase. Furthermore, the anomalous VIE increases with temperature, despite its quantum-mechanical origin. Here, embedded-fragment ab initio second-order many-body perturbation (MP2) theory in the quasiharmonic approximation (QHA) is applied to the Gibbs energy of an infinite, proton-disordered crystal of ice Ih at wide ranges of temperatures and pressures. The quantum effect of nuclei moving in anharmonic potentials is taken into account from first principles without any empirical or nonsystematic approximation to either the electronic or vibrational Hamiltonian. MP2 predicts quantitatively correctly the thermal contraction at low temperatures, which is confirmed to originate from the volume-contracting hydrogen-bond bending modes (acoustic phonons). It qualitatively reproduces (but underestimates) the thermal expansion at higher temperatures, caused by the volume-expanding hydrogen-bond stretching (and to a lesser extent librational) modes. The anomalous VIE is found to be the result of subtle cancellations among closely competing isotope effects on volume from all modes. Consequently, even ab initio MP2 with the aug-cc-pVDZ and aug-cc-pVTZ basis sets has difficulty reproducing this anomaly, yielding qualitatively varied predictions of the sign of the VIE depending on such computational details as the choice of the embedding field. However, the temperature growth of the anomalous VIE is reproduced robustly and is ascribed to the librational modes. These solid-state MP2 calculations, as well as MP2 Born-Oppenheimer molecular dynamics, find a volume collapse and a loss of symmetry and long-range order in ice Ih upon pressure loading of 2.35 GPa or higher. Concomitantly, rapid softening of acoustic phonons is observed starting around 2 GPa. They constitute a computational detection of a mechanical instability in ice Ih and the resulting pressure-induced amorphization to HDA.

Ice Ih anomalies: Thermal contraction, anomalous volume isotope effect, and pressure-induced amorphization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salim, Michael A.; Willow, Soohaeng Yoo; Hirata, So, E-mail: sohirata@illinois.edu

Ice Ih displays several anomalous thermodynamic properties such as thermal contraction at low temperatures, an anomalous volume isotope effect (VIE) rendering the volume of D{sub 2}O ice greater than that of H{sub 2}O ice, and a pressure-induced transition to the high-density amorphous (HDA) phase. Furthermore, the anomalous VIE increases with temperature, despite its quantum-mechanical origin. Here, embedded-fragment ab initio second-order many-body perturbation (MP2) theory in the quasiharmonic approximation (QHA) is applied to the Gibbs energy of an infinite, proton-disordered crystal of ice Ih at wide ranges of temperatures and pressures. The quantum effect of nuclei moving in anharmonic potentials ismore » taken into account from first principles without any empirical or nonsystematic approximation to either the electronic or vibrational Hamiltonian. MP2 predicts quantitatively correctly the thermal contraction at low temperatures, which is confirmed to originate from the volume-contracting hydrogen-bond bending modes (acoustic phonons). It qualitatively reproduces (but underestimates) the thermal expansion at higher temperatures, caused by the volume-expanding hydrogen-bond stretching (and to a lesser extent librational) modes. The anomalous VIE is found to be the result of subtle cancellations among closely competing isotope effects on volume from all modes. Consequently, even ab initio MP2 with the aug-cc-pVDZ and aug-cc-pVTZ basis sets has difficulty reproducing this anomaly, yielding qualitatively varied predictions of the sign of the VIE depending on such computational details as the choice of the embedding field. However, the temperature growth of the anomalous VIE is reproduced robustly and is ascribed to the librational modes. These solid-state MP2 calculations, as well as MP2 Born–Oppenheimer molecular dynamics, find a volume collapse and a loss of symmetry and long-range order in ice Ih upon pressure loading of 2.35 GPa or higher. Concomitantly, rapid softening of acoustic phonons is observed starting around 2 GPa. They constitute a computational detection of a mechanical instability in ice Ih and the resulting pressure-induced amorphization to HDA.« less

Spin-dependent Otto quantum heat engine based on a molecular substance

NASA Astrophysics Data System (ADS)

Hübner, W.; Lefkidis, G.; Dong, C. D.; Chaudhuri, D.; Chotorlishvili, L.; Berakdar, J.

2014-07-01

We explore the potential of single molecules for thermodynamic cycles. To this end we propose two molecular heat engines based on the Ni2 dimer in the presence of a static magnetic field: (a) a quantum Otto engine and (b) a modified quantum Otto engine for which optical excitations induced by a laser pulse substitute for one of the heat-exchange points. For reliable predictions and to inspect the role of spin and electronic correlations we perform fully correlated ab initio calculations of the molecular electronic structure including spin-orbital effects. We analyze the efficiency of the engines in dependence of the electronic level scheme and the entanglement and find a significant possible enhancement connected to the quantum nature and the heat capacity of the dimer, as well as to the zero-field triplet states splitting.

Role of Quantum Vibrations on the Structural, Electronic, and Optical Properties of 9-Methylguanine.

PubMed

Law, Yu Kay; Hassanali, Ali A

2015-11-05

In this work, we report theoretical predictions of the UV-absorption spectra of 9-methylguanine using time dependent density functional theory (TDDFT). Molecular dynamics simulations of the hydrated DNA base are peformed using an empirical force field, Born-Oppenheimer ab initio molecular dynamics (AIMD), and finally path-integral AIMD to understand the role of the underlying electronic potential, solvation, and nuclear quantum vibrations on the absorption spectra. It is shown that the conformational distributions, including hydrogen bonding interactions, are perturbed by the inclusion of nuclear quantum effects, leading to significant changes in the total charge and dipole fluctuations of the DNA base. The calculated absorption spectra using the different sampling protocols shows that the inclusion of nuclear quantum effects causes a significant broadening and red shift of the spectra bringing it into closer agreement with experiments.

Toward understanding the roaming mechanism in H + MgH → Mg + HH reaction

DOE PAGES

Mauguiere, Frederic A. L.; Collins, Peter; Stamatiadis, Stamatis; ...

2016-02-26

The roaming mechanism in the reaction H + MgH →Mg + HH is investigated by classical and quantum dynamics employing an accurate ab initio threedimensional ground electronic state potential energy surface. The reaction dynamics are explored by running trajectories initialized on a four-dimensional dividing surface anchored on three-dimensional normally hyperbolic invariant manifold associated with a family of unstable orbiting periodic orbits in the entrance channel of the reaction (H + MgH). By locating periodic orbits localized in the HMgH well or involving H orbiting around the MgH diatom, and following their continuation with the total energy, regions in phase spacemore » where reactive or nonreactive trajectories may be trapped are found. In this way roaming reaction pathways are deduced in phase space. Patterns similar to periodic orbits projected into configuration space are found for the quantum bound and resonance eigenstates. Roaming is attributed to the capture of the trajectories in the neighborhood of certain periodic orbits. As a result, the complex forming trajectories in the HMgH well can either return to the radical channel or “roam” to the MgHH minimum from where the molecule may react.« less

Habituation based synaptic plasticity and organismic learning in a quantum perovskite.

PubMed

Zuo, Fan; Panda, Priyadarshini; Kotiuga, Michele; Li, Jiarui; Kang, Mingu; Mazzoli, Claudio; Zhou, Hua; Barbour, Andi; Wilkins, Stuart; Narayanan, Badri; Cherukara, Mathew; Zhang, Zhen; Sankaranarayanan, Subramanian K R S; Comin, Riccardo; Rabe, Karin M; Roy, Kaushik; Ramanathan, Shriram

2017-08-14

A central characteristic of living beings is the ability to learn from and respond to their environment leading to habit formation and decision making. This behavior, known as habituation, is universal among all forms of life with a central nervous system, and is also observed in single-cell organisms that do not possess a brain. Here, we report the discovery of habituation-based plasticity utilizing a perovskite quantum system by dynamical modulation of electron localization. Microscopic mechanisms and pathways that enable this organismic collective charge-lattice interaction are elucidated by first-principles theory, synchrotron investigations, ab initio molecular dynamics simulations, and in situ environmental breathing studies. We implement a learning algorithm inspired by the conductance relaxation behavior of perovskites that naturally incorporates habituation, and demonstrate learning to forget: a key feature of animal and human brains. Incorporating this elementary skill in learning boosts the capability of neural computing in a sequential, dynamic environment.Habituation is a learning mechanism that enables control over forgetting and learning. Zuo, Panda et al., demonstrate adaptive synaptic plasticity in SmNiO 3 perovskites to address catastrophic forgetting in a dynamic learning environment via hydrogen-induced electron localization.

Polarizabilities and van der Waals C{sub 6} coefficients of fullerenes from an atomistic electrodynamics model: Anomalous scaling with number of carbon atoms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saidi, Wissam A., E-mail: alsaidi@pitt.edu; Norman, Patrick

2016-07-14

The van der Waals C{sub 6} coefficients of fullerenes are shown to exhibit an anomalous dependence on the number of carbon atoms N such that C{sub 6} ∝ N{sup 2.2} as predicted using state-of-the-art quantum mechanical calculations based on fullerenes with small sizes, and N{sup 2.75} as predicted using a classical-metallic spherical-shell approximation of the fullerenes. We use an atomistic electrodynamics model where each carbon atom is described by a polarizable object to extend the quantum mechanical calculations to larger fullerenes. The parameters of this model are optimized to describe accurately the static and complex polarizabilities of the fullerenes bymore » fitting against accurate ab initio calculations. This model shows that C{sub 6} ∝ N{sup 2.8}, which is supportive of the classical-metallic spherical-shell approximation. Additionally, we show that the anomalous dependence of the polarizability on N is attributed to the electric charge term, while the dipole–dipole term scales almost linearly with the number of carbon atoms.« less

Ab initio and classical molecular dynamics studies of the structural and dynamical behavior of water near a hydrophobic graphene sheet.

PubMed

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.

Revisiting the Electronic Structure of FeS Monomers Using ab Initio Ligand Field Theory and the Angular Overlap Model.

PubMed

Chilkuri, Vijay Gopal; DeBeer, Serena; Neese, Frank

2017-09-05

Iron-sulfur (FeS) proteins are universally found in nature with actives sites ranging in complexity from simple monomers to multinuclear sites from two up to eight iron atoms. These sites include mononuclear (rubredoxins), dinuclear (ferredoxins and Rieske proteins), trinuclear (e.g., hydrogenases), and tetranuclear (various ferredoxins and high-potential iron-sulfur proteins). The electronic structure of the higher-nuclearity clusters is inherently extremely complex. Hence, it is reasonable to take a bottom-up approach in which clusters of increasing nuclearity are analyzed in terms of the properties of their lower nuclearity constituents. In the present study, the first step is taken by an in-depth analysis of mononuclear FeS systems. Two different FeS molecules with phenylthiolate and methylthiolate as ligands are studied in their oxidized and reduced forms using modern wave function-based ab initio methods. The ab initio electronic spectra and wave function are presented and analyzed in detail. The very intricate electronic structure-geometry relationship in these systems is analyzed using ab initio ligand field theory (AILFT) in conjunction with the angular overlap model (AOM) parametrization scheme. The simple AOM model is used to explain the effect of geometric variations on the electronic structure. Through a comparison of the ab initio computed UV-vis absorption spectra and the available experimental spectra, the low-energy part of the many-particle spectrum is carefully analyzed. We show ab initio calculated magnetic circular dichroism spectra and present a comparison with the experimental spectrum. Finally, AILFT parameters and the ab initio spectra are compared with those obtained experimentally to understand the effect of the increased covalency of the thiolate ligands on the electronic structure of FeS monomers.

Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches.

PubMed

Antipov, Sergey V; Bhattacharyya, Swarnendu; El Hage, Krystel; Xu, Zhen-Hao; Meuwly, Markus; Rothlisberger, Ursula; Vaníček, Jiří

2017-11-01

Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quantum, semiclassical, and classical approaches to describe the ultrafast molecular dynamics, including the multiconfiguration time-dependent Hartree method, Bohmian dynamics, local control theory, semiclassical thawed Gaussian approximation, phase averaging, dephasing representation, molecular mechanics with proton transfer, and multipolar force fields. In addition to the general overview, some focus is given to the description of nuclear quantum effects and to the direct dynamics, in which the ab initio energies and forces acting on the nuclei are evaluated on the fly. Several practical applications, performed within the framework of the Swiss National Center of Competence in Research "Molecular Ultrafast Science and Technology," are presented: These include Bohmian dynamics description of the collision of H with H 2 , local control theory applied to the photoinduced ultrafast intramolecular proton transfer, semiclassical evaluation of vibrationally resolved electronic absorption, emission, photoelectron, and time-resolved stimulated emission spectra, infrared spectroscopy of H-bonding systems, and multipolar force fields applications in the condensed phase.

Solid-state electron spin lifetime limited by phononic vacuum modes.

PubMed

Astner, T; Gugler, J; Angerer, A; Wald, S; Putz, S; Mauser, N J; Trupke, M; Sumiya, H; Onoda, S; Isoya, J; Schmiedmayer, J; Mohn, P; Majer, J

2018-04-01

Longitudinal relaxation is the process by which an excited spin ensemble decays into its thermal equilibrium with the environment. In solid-state spin systems, relaxation into the phonon bath usually dominates over the coupling to the electromagnetic vacuum 1-9 . In the quantum limit, the spin lifetime is determined by phononic vacuum fluctuations 10 . However, this limit was not observed in previous studies due to thermal phonon contributions 11-13 or phonon-bottleneck processes 10, 14,15 . Here we use a dispersive detection scheme 16,17 based on cavity quantum electrodynamics 18-21 to observe this quantum limit of spin relaxation of the negatively charged nitrogen vacancy (NV - ) centre 22 in diamond. Diamond possesses high thermal conductivity even at low temperatures 23 , which eliminates phonon-bottleneck processes. We observe exceptionally long longitudinal relaxation times T 1 of up to 8 h. To understand the fundamental mechanism of spin-phonon coupling in this system we develop a theoretical model and calculate the relaxation time ab initio. The calculations confirm that the low phononic density of states at the NV - transition frequency enables the spin polarization to survive over macroscopic timescales.

Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches

PubMed Central

Antipov, Sergey V.; Bhattacharyya, Swarnendu; El Hage, Krystel; Xu, Zhen-Hao; Meuwly, Markus; Rothlisberger, Ursula; Vaníček, Jiří

2018-01-01

Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quantum, semiclassical, and classical approaches to describe the ultrafast molecular dynamics, including the multiconfiguration time-dependent Hartree method, Bohmian dynamics, local control theory, semiclassical thawed Gaussian approximation, phase averaging, dephasing representation, molecular mechanics with proton transfer, and multipolar force fields. In addition to the general overview, some focus is given to the description of nuclear quantum effects and to the direct dynamics, in which the ab initio energies and forces acting on the nuclei are evaluated on the fly. Several practical applications, performed within the framework of the Swiss National Center of Competence in Research “Molecular Ultrafast Science and Technology,” are presented: These include Bohmian dynamics description of the collision of H with H2, local control theory applied to the photoinduced ultrafast intramolecular proton transfer, semiclassical evaluation of vibrationally resolved electronic absorption, emission, photoelectron, and time-resolved stimulated emission spectra, infrared spectroscopy of H-bonding systems, and multipolar force fields applications in the condensed phase. PMID:29376107

Quantum Reactive Scattering of Ultracold K+KRb Reaction: Universality and Chaotic Dynamics

NASA Astrophysics Data System (ADS)

Croft, J. F. E.; Makrides, C.; Li, M.; Petrov, A.; Kendrick, B. K.; Balakrishnan, N.; Kotochigova, S.

2017-04-01

A fundamental question in the study of chemical reactions is how reactions proceed at a collision energy close to absolute zero. This question is no longer hypothetical: quantum degenerate gases of atoms and molecules can now be created at temperatures lower than a few tens of nanoKelvin. In this talk, we discuss the benchmark ultracold reaction between, the most-celebrated ultracold molecule, KRb and K. We report numerically exact quantum-mechanical calculations of the K+KRb reaction on an accurate ab initio ground state potential energy surface of the K2Rb system and compare our results with available experimental data and predictions of universal models. The role of non-additive three-body contributions to the interaction potential is examined and is found to be small for the total reaction rates. However, the rotationally resolved rate coefficients are shown to be sensitive to the short-range interaction potential and follow a Poissonian distribution. This work was supported in part by NSF Grants PHY-1505557 (N.B.), PHY-1619788 (S.K.), ARO MURI Grant No. W911NF-12-1-0476 (N.B. & S.K.), and DOE LDRD Grant No. 20170221ER (B.K.).

Dynamics of Photoexcited State of Semiconductor Quantum Dots

NASA Astrophysics Data System (ADS)

Trivedi, Dhara J.

In this thesis, non-adiabatic molecular dynamics (NAMD) of excited states in semiconductor quantum dots are investigated. Nanoscale systems provide important opportunities for theory and computation for research because the experimental tools often provide an incomplete picture of the structure and/or function of nanomaterials, and theory can often fill in missing features crucial in understanding what is being measured. The simulation of NAMD is an indispensable tool for understanding complex ultrafast photoinduced processes such as charge and energy transfer, thermal relaxation, and charge recombination. Based on the state-of-the-art ab initio approaches in both the energy and time domains, the thesis presents a comprehensive discussion of the dynamical processes in quantum dots, ranging from the initial photon absorption to the final emission. We investigate the energy relaxation and transfer rates in pure and surface passivated quantum dots of different sizes. The study establishes the fundamental mechanisms of the electron and hole relaxation processes with and without hole traps. We develop and implement more accurate and efficient methods for NAMD. These methods are advantageous over the traditional ones when one encounters classically forbidden transitions. We also explore the effect of decoherence and non-adiabatic couplings on the dynamics. The results indicate significant influence on the accuracy and related computational cost of the simulated dynamics.

Ab initio investigation of the surface properties of dispenser B-type and scandate thermionic emission cathodes

NASA Astrophysics Data System (ADS)

Vlahos, Vasilios; Lee, Yueh-Lin; Booske, John H.; Morgan, Dane; Turek, Ladislav; Kirshner, Mark; Kowalczyk, Richard; Wilsen, Craig

2009-05-01

Scandate cathodes (BaxScyOz on W) are important thermionic electron emission materials whose emission mechanism remains unclear. Ab initio modeling is used to investigate the surface properties of both scandate and traditional B-type (Ba-O on W) cathodes. We demonstrate that the Ba-O dipole surface structure believed to be present in active B-type cathodes is not thermodynamically stable, suggesting that a nonequilibrium steady state dominates the active cathode's surface structure. We identify a stable, low work function BaxScyOz surface structure, which may be responsible for some scandate cathode properties and demonstrate that multicomponent surface coatings can lower cathode work functions.

Analysis of Borderline Substitution/Electron Transfer Pathways from Direct ab initio MD Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yamataka, H; Aida, M A.; Dupuis, Michel

Ab initio molecular dynamics simulations were carried out for the borderline reaction pathways in the reaction of CH2O?- with CH3Cl. The simulations reveal distinctive features of three types of mechanisms passing through the SN2-like transition state (TS): (i) a direct formation of SN2 products, (ii) a direct formation of ET products, and (iii) a 2-step formation of ET products via the SN2 valley. The direct formation of the ET product through the SN2-like TS appears to be more favorable at higher temperatures. The 2-step process depends on the amount of energy that goes into the C-C stretching mode.

Electronic excitation induced amorphization in titanate pyrochlores: an ab initio molecular dynamics study

PubMed Central

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