Ab Initio Potential Research Articles

Diffusion of Cu adatoms and dimers on Cu(111) and Ag(111) surfaces

Diffusion of Cu adatoms and dimers on Cu(111) and Ag(111) surfaces is analyzed based on ab initio surface potentials. Single adatom diffusion is compared with dimer diffusion on both surfaces. Surface geometry makes the adatoms jump alternately between two states in the same way in both systems, whereas dimers undergo more complex diffusion process that combines translational and rotational motion. Small difference in the surface lattice constant between Cu and Ag crystals results in a completely different energy landscape for dimer jumps. As an effect the character of diffusion process changes. Homogeneous Cu dimer diffusion is more difficult and dimers rather rotate within single surface cell, whereas diffusion over Ag surface is faster and happens more smoothly. The temperature dependence of diffusion coefficient and its parameters: energy barrier and prefactor is calculated and compared for both surfaces.

Effect of O2 + O ab initio and Morse additive pairwise potentials on dissociation and relaxation rates for nonequilibrium flow calculations

This work quantifies the sensitivity of O2 + O dissociation rates and relaxation to interatomic potential energy surfaces at high-enthalpy, nonequilibrium flow conditions. State-to-state cross sections are obtained by quasi-classical trajectory (QCT) calculations with two potential surfaces. The first is a Morse additive pairwise potential for O3 that is constructed based on O2(3Σg−) spectroscopic measurements and the second is a double many-body expansion potential by Varandas and Pais [Mol. Phys. 65, 843–860 (1988)]. The QCT calculations of cross sections and rates with the two surfaces are compared to each other and shock tube measurements. It is found that, at temperatures between 2500 K and 20 000 K, the equilibrium dissociation rates predicted by the two potentials agree within 12%, and they are bound by experimental dissociation measurements. In contrast, above 10 000 K, ab initio based equilibrium dissociation rates are about a factor of two higher than the widely used Park’s model. The nonequilibrium dissociation rates calculated by the two potentials are within 70% while phenomenological models differ by two orders of magnitude for vibrationally cold conditions of shocks. The analyses provide an approach for improving accuracy of nonequilibrium high-enthalpy flow modeling when ab initio potentials are not available.

Communication: The ground electronic state of Si2C: Rovibrational level structure, quantum monodromy, and astrophysical implications.

We report the gas-phase optical detection of Si2C near 390 nm and the first experimental investigation of the rovibrational structure of its (1)A1 ground electronic state using mass-resolved and fluorescence spectroscopy and variational calculations performed on a high-level ab initio potential. From this joint study, it is possible to assign all observed Ka = 1 vibrational levels up to 3800 cm(-1) with confidence, as well as a number of levels in the Ka = 0, 2, and 3 manifolds. Dixon-dip plots for the bending coordinate (ν2) allow an experimental determination of a barrier to linearity of 783(48) cm(-1) (2σ), in good agreement with theory (802(9) cm(-1)). The calculated (Ka, ν2) eigenvalue lattice shows an archetypal example of quantum monodromy (absence of a globally valid set of quantum numbers) that is reflected by the experimentally observed rovibrational levels. The present study provides a solid foundation for infrared and optical surveys of Si2C in astronomical objects, particularly in the photosphere of N- and J-type carbon stars where the isovalent SiC2 molecule is known to be abundant.

Quantum chemistry and nuclear dynamics as diagnostic tools for stellar atmosphere modeling

We report full quantum scattering calculations of inelastic cross sections and rate coefficients for Mg in collision with H atoms. Transitions until the Mg(3s3d) 3D level were considered, as well as mutual neutralization and ion-pair production. These calculations are based on new ab initio potentials and nonadiabatic couplings for the nine 2Σ+ and five 2Π lowest electronic states of MgH. The collision energy range is from threshold up to 10eV. The main mechanisms underlying the scattering processes are discussed. An extension of these calculations is performed by means of a multichannel model approach. Rate coefficients are thus obtained for all processes between the 12 lowest atomic states of Mg in collisions with H, plus the ionic channel. Those data permit to model spectral lines in stellar atmospheres. Their impact on statistical equilibrium of Mg populations through the non-LTE departure coefficients is investigated for the Sun and the HD122563 metal-poor star.

State-Selective Differential Cross Section Measurements for the One-Electron Capture Process in C3+–He and C3+–Ne Systems at Elab = 33 eV

Using a crossed-beam apparatus, we measured the relative state-selective differential cross sections (DCSs) for the following reactions: C3+ (1s2 2s 2S) + He (1s2 1S) → C2+ (1s2 2s2p 1P) + He+ (1s 2S) + 10.6 eV and C3+ (1s2 2s 2S) + Ne (2p6 1S) → C2+ (1s2 2p2 1D) + Ne+ (2p5 2P) + 8.2 eV. The scattering angle studied in the laboratory frame, θlab, was from −3.0 to 24°, and the laboratory collision energy Elab was 33 eV. In both systems, the DCSs for the reaction are zero at the center-of-mass angle θcm = 0, and show a peak at a certain angle and a broad hump at larger angles. A classical trajectory analysis within the two-state approximation based on the ab initio potentials for (CHe)3+ revealed that these structures observed are ascribed to the reactions that occur in different trajectories. The peak corresponds to the reactions occurring in the outgoing part of the trajectory, and the hump is associated with the reactions occurring mainly in the incoming part of the trajectory.

Ab Initio and Molecular Dynamics-Based Pair Potentials for Lanthanum Hexaboride

Lanthanum hexaboride (LaB6) is a well-known refractory ceramic with unique mechanical and electrochemical behavior, leading to a diverse array of possible attractive applications. In this work, we present and discuss the development of interatomic potentials for LaB6 using a combination of density functional theory with molecular dynamics simulations. Density functional theory is employed to acquire energetic and dynamic data of the atoms in various configurations and environments. Lattice inversion techniques are then combined with other optimization procedures to yield potentials which can accurately capture the lattice dynamics–mean-square displacements and equilibrium energetics of the system as a function of temperature.

Perspectives of Halogen Bonding Description in Scoring Functions and QSAR/QSPR: Substituent Effects in Aromatic Core.

Halogen bonding (XB) is a new promising interaction pattern in medicinal chemistry. It has predominantly electrostatic nature - high electrostatic potential anisotropy. However to fully unleash the potential of XB in rational drug design fast and robust empirical methods of XB description should be developed. Current approaches rely heavily on ab initio calculation for each molecule studied. Thus fast prediction of electrostatic parameters for description of XB for arbitrary organic molecules is of paramount importance to promptly establish QSAR/QSPR, virtual screening and molecular docking pipelines suitable for today's agile development requirements. The two most promising approaches to describe anisotropic electrostatic models - the extra point (EP) charge model and the multipole expansion (ME) model - were studied on their ability (1) to describe ab initio molecular electrostatic potential (MEP) and (2) to produce parameters that can be predicted for each molecule empirically rather than estimated via ab initio calculations. The reference ab initio MEP was calculated for a set of 730 substituted halobenzenes. Parameters for anisotropic electrostatics of both empirical models (EP and ME) studied were extracted from ab initio MEP. The FreeWilson and Hansch type QSPR models relating XB parameters with aromatic substituents were built and analyzed, providing the guidelines for further development.

Strong competition between velocity-changing and phase- or state-changing collisions inH2spectra perturbed by Ar

A collisional inhomogeneous broadening of the H2 Q(1) line perturbed by Ar was observed for the first time 25 years ago. Several attempts were made to explain the line broadening from ab initio calculations , which however resulted in fundamental discrepancies between the theory and experiment. To resolve this problem we investigate two possible sources of these differences. First, we repeat the ab initio calculations of the broadening and shifting speed dependence, using in the scattering calculations a new, highly-accurate ab initio H2-Ar interaction potential. Second, we replace the previous phenomenological models of velocity-changing collisions with a more physical one based on the interaction potential. This allows us to properly reproduce the experimental broadening over a wide range of temperatures and pressures. We show that this abnormal broadening is caused by strong competition between the velocity-changing collisions and speed-dependent shifting, especially at high pressures.

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

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.

A multi-scale approach to characterize pure CH4, CF4, and CH4/CF4 mixtures.

In this study, we develop three intermolecular potentials for methane (CH4), tetrafluoromethane (CF4), and CH4/CF4 dimers using a novel ab initio method. The ultimate goal is to understand microscopically the phase-separation in CH4/CF4 systems, which takes place in the liquid states near their freezing points. Monte-Carlo (MC) simulations of the pure CH4 system are performed using the ab initio energies to verify the potential. The simulations reproduce quite well the experimentally known liquid densities, the internal energies, the second virial coefficients, and the radial distribution function. The essentially six-dimensional (6D) ab initio potential is then reduced to a one-dimensional (1D) effective potential using the inverse Monte-Carlo technique. This potential, too, successfully reproduces the experimental results. Interestingly, the MC study cannot be extended to the pure CF4 system and the CH4/CF4 mixed system because the two respective ab initio potentials present very rough potential landscapes. This renders the interpolation of energies for the MC simulations and thus the multi-scale approach unreliable. It suggests, however, a possible driving force for the experimentally observed phase separation of the CH4/CF4 system at low temperatures. Furthermore, we carefully study the determination of 1D effective potentials via inverse MC techniques. We argue that to a good approximation the temperature dependence of the 1D potentials can be estimated via reweighting techniques for a fixed temperature.

AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain-domain interaction prediction.

Most proteins consist of multiple domains, independent structural and evolutionary units that are often reshuffled in genomic rearrangements to form new protein architectures. Template-based modeling methods can often detect homologous templates for individual domains, but templates that could be used to model the entire query protein are often not available. We have developed a fast docking algorithm ab initio domain assembly (AIDA) for assembling multi-domain protein structures, guided by the ab initio folding potential. This approach can be extended to discontinuous domains (i.e. domains with 'inserted' domains). When tested on experimentally solved structures of multi-domain proteins, the relative domain positions were accurately found among top 5000 models in 86% of cases. AIDA server can use domain assignments provided by the user or predict them from the provided sequence. The latter approach is particularly useful for automated protein structure prediction servers. The blind test consisting of 95 CASP10 targets shows that domain boundaries could be successfully determined for 97% of targets. The AIDA package as well as the benchmark sets used here are available for download at http://ffas.burnham.org/AIDA/. adam@sanfordburnham.org Supplementary data are available at Bioinformatics online.

Recommended gas transport properties of argon at low density using ab initio potential

The most important transport properties of argon have been calculated using classical kinetic theory expressions in conjunction with high-quality ab initio potential energy values computed by Patkowski and Szalewicz. Dilute gas transport properties have been calculated for the viscosity, thermal conductivity, self-diffusion coefficient and thermal diffusion factor from 83 to 10,000 K. Comparisons between experimental transport property data and values presently calculated indicate that the present theoretical predictions may be employed as recommended values for this set of transport properties over a wide temperature range.

Ab initio Intermolecular Potential Energy Surface and Calculation of Second Virial Coefficients for the Cl2-Cl2 Dimer

The results presented in this paper are the ab initio intermolecular potentials and the second virial coefficient, B2 (T) of the dimer Cl2-Cl2. These ab initio potentials were proposed by the quantum chemical calculations at high level of theory CCSD (T) with basis sets of Dunning's valence correlation-consistent aug-cc-pVmZ (m = 2, 3); these results were extrapolated to complete basis set limit aug-cc-pV23Z. The ab initio energies of complete basis set limit aug-cc-pV23Z resulted from the exponential extrapolation were used to construct the 5-site pair potential functions. The second virial coefficients for this dimer were predicted from those with four-dimensional integration. The second virial coefficients were also corrected to first-order quantum effects. The results turn out to be in good agreement with experimental data, if available, or with those from empirical correlation. The quality of ab initio 5-site potentials proved the reliability for prediction of molecular thermodynamic properties.

1304 アルゴン気液系の表面張力の分子動力学シミュレーション : Ab initioポテンシャルに基づく計算(流体工学V)

1304 アルゴン気液系の表面張力の分子動力学シミュレーション : Ab initioポテンシャルに基づく計算(流体工学V)

The role of the shape resonance state in low energy electron induced single strand break in 2'-deoxycytidine-5'-monophosphate.

Low energy electron (LEE) induced single strand break (SSB) has been studied for 2'-deoxycytidine-5'-monophosphate (5'-dCMPH) molecules in the gas phase by means of ab initio electronic structure methods and local complex potential based time-dependent wavepacket quantum mechanical calculations. We have found that the LEE attachment to this cytidine nucleotide results in the formation of a transient metastable anion. The results obtained here show that the electron attachment takes place at the cytosine nucleobase center and within 18-20 fs, the LEE transfers to the σ* orbital of the sugar-phosphate 5' C-O bond. The characteristic electron attachment cross section spectrum is found at ∼1 eV, which is in good agreement with the available experimental observations. Quantum mechanical tunneling of the 5' C-O bound vibrational energy levels may contribute to SSB only above 1.5 eV energy regimes.

Sub-femtosecond quantum dynamics of the strong-field ionization of water to the X ̃(2)B1 and Ã(2)A1 states of the cation.

Motivated by recent efforts to achieve sub-femtosecond structural resolution in various molecular systems, we have performed a femtosecond quantum dynamics study of the water cation in the X ̃(2)B1 and Ã(2)A1 electronic states. Autocorrelation functions for H2O(+) and D2O(+) are calculated for such electronic states by solving numerically the time-dependent Schrödinger equation. From the ratio of the squared autocorrelation functions of D2O(+) and H2O(+), the high-order harmonic generation signals are calculated. Substantial vibrational dynamics is found in the Ã(2)A1 state as compared to the one in X ̃(2)B1, which supports recent experimental findings of Farrell et al., Phys. Rev. Lett., 2011, 107, 083001. Maxima in the above ratio are also predicted at ∼1.1 fs and ∼1.6 fs for the X ̃(2)B1 and Ã(2)A1 states, respectively. The expectation values of the positions of the atoms in H2O(+) as a function of time reveal a strong excitation of the bending mode in the Ã(2)A1 state, which explains the observed vibrational dynamics. The peaks in the ratios of the squared autocorrelation functions are also explained in terms of the evolving geometries of the water cation.

Cold magnetically trapped2Dgscandium atoms. II. Scattering dynamics

The binary collision dynamics of ${}^{2}{D}_{g,3/2}$ ground state scandium atoms is studied from first principles. We employ 30 coupled diabatic ab initio potentials in a coupled-channels study of the scattering dynamics of cold and ultracold scandium atoms in external magnetic fields. Due to the long-ranged magnetic dipolar interaction, the field dependence of the cross section does not follow the threshold laws derived by Volpi and Bohn [Phys. Rev. A 65, 052712 (2002)]. In the field-free case, the near-threshold cross section is independent of the collision energy, and hence the cross section does not follow the well-established Wigner threshold laws. The observed threshold behavior is explained in the Born approximation. For energies above $1\phantom{\rule{4pt}{0ex}}\ensuremath{\mu}\mathrm{K}$, inelastic collisions are driven by the anisotropic nonrelativistic electronic interaction. For energies below $100\phantom{\rule{4pt}{0ex}}\ensuremath{\mu}\mathrm{K}$, the ratio of elastic-to-inelastic collisions is likely to be favorable for evaporative cooling. Both anisotropy in the long-range interaction and in the short-range potential contribute to large cross sections for inelastic collisions at higher energies and lead to a small ratio of elastic-to-inelastic collisions. This is in agreement with the large rates for Zeeman relaxation of submerged-shell atoms observed experimentally. The effect of the uncertainty in the ab initio potential is sampled by scaling the reduced mass and is found to have little influence on the conclusions drawn from this work.

Beryllium monohydride (BeH): Where we are now, after 86 years of spectroscopy

BeH is one of the most important benchmark systems for ab initio methods and for studying Born–Oppenheimer breakdown. However the best empirical potential and best ab initio potential for the ground electronic state to date give drastically different predictions in the long-range region between where the highest measurements have been made, and the dissociation energy; a region which is about ∼1000cm−1 for 9BeH, ∼3000cm−1 for 9BeD, and ∼13000cm−1 for 9BeT. Improved empirical potentials and Born–Oppenheimer breakdown corrections have now been built in this work for the ground electronic states X(12Σ+) of all three isotopologues. The predicted dissociation energy for 9BeH from the new empirical potential is now in agreement with the current best ab initio prediction in all 5 digits of the former’s precision, while the previous best empirical potential was in disagreement by 74cm−1. The previous best empirical potential predicted the existence of unobserved vibrational levels for all three isotopologues, and the current best ab initio study also predicted the existence of all of these levels, and 7 more in total. With the exception of two, the present empirical potential agrees with the existence of all of the ab initio potentials’ extra levels not predicted by the earlier empirical potential. With one exception, all energy spacings between vibrational energy levels for which measurements have been made, are predicted with an agreement of better than 1cm−1 between the new empirical potential and the current best ab initio potential, but some predictions for unobserved levels are still in great disagreement, and the equilibrium bond lengths are different by orders of magnitude.

Combined experimental and theoretical study of fast atom diffraction on theβ2(2×4)reconstructed GaAs(001) surface

A grazing incidence fast atom diffraction (GIFAD or FAD) setup, installed on a molecular beam epitaxy chamber, has been used to characterize the ${\ensuremath{\beta}}_{2}(2\ifmmode\times\else\texttimes\fi{}4)$ reconstruction of a GaAs(001) surface at $530{\phantom{\rule{0.16em}{0ex}}}^{\ensuremath{\circ}}\mathrm{C}$ under an ${\mathrm{As}}_{4}$ overpressure. Using a 400-eV ${}^{4}\mathrm{He}$ beam, high-resolution diffraction patterns with up to eighty well-resolved diffraction orders are observed simultaneously, providing a detailed fingerprint of the surface structure. Experimental diffraction data are in good agreement with results from quantum scattering calculations based on an ab initio projectile-surface interaction potential. Along with exact calculations, we show that a straightforward semiclassical analysis allows the features of the diffraction chart to be linked to the main characteristics of the surface reconstruction topography. Our results demonstrate that GIFAD is a technique suitable for measuring in situ the subtle details of complex surface reconstructions. We have performed measurements at very small incidence angles, where the kinetic energy of the projectile motion perpendicular to the surface can be reduced to less than 1 meV. This allowed the depth of the attractive van der Waals potential well to be estimated as $\ensuremath{-}8.7$ meV in very good agreement with results reported in literature.

Ab initio study of the Ar–CS2(V1B2) intermolecular potential surface: effect of van der Waals interaction on the emission of CS2 molecule

In this work, the excited state intermolecular potential energy surface of the Ar–CS2(V1B2) van der Waals complex was evaluated for the first time. The calculation of more than 4000 single-point interaction energies for the complex using an equation-of-motion coupled-cluster model with single and double substitutions level of theory with extended basis set involving bond functions has been performed. After fitting the interaction energies to analytical functions, the emission spectra of the Ar–CS2(V1B2) complex related to the different stationary points on the potential energy surface were calculated. It was seen that the intensity and the position of the emission spectra are dependent on the orientation of the Ar atom around the bent excited CS2 and the distance between two components. The information about the structural parameters of the complex related to the global minimum was obtained under the pseudodiatomic approximation with assistance of ab initio potential. The presented investigation could be useful for further theoretical and experimental studies of Ar–CS2(V1B2) complex.