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In this article, the theoretical photoionization spectroscopy of the aziridine (C2H5N) molecule is investigated. To start with, we have optimized the geometry of this molecule at the neutral electronic ground state at the density functional theory/augmented correlation-consistent polarized valence triple zeta level of theory using the G09 program. The electronic structure calculations were restricted to the first six low-lying electronic states in order to account for the experimental photoelectron spectrum of the C2H5N molecule. The first six low-lying electronic states ( X ̃ 2 A ′ , A ̃ 2 A ′ , B ̃ 2 A ″ , C ̃ 2 A ″ , D ̃ 2 A ′ , and E ̃ 2 A ′ ) of the potential energy surfaces (PESs) are calculated by both equation of motion-ionization potential-coupled cluster singles and doubles and multi-configuration quasi-degenerate perturbation theory ab initio quantum chemistry methods along the dimensionless normal displacement coordinates in which multiple conical intersections were established among the considered electronic states. A (6 × 6) model vibronic Hamiltonian is constructed on a diabatic electronic basis, using the symmetry selection rules and Taylor series expansion. The Cs symmetry point group of the aziridine molecule leads to electronic states symmetry of either A′ or A″, and these states are close in energy, due to which the same symmetry electronic states avoid each other. To get a smooth diabatic PES, a fourfold diabatization scheme is used, which is implemented in the General Atomic and Molecular Electronic Structure Systems suite of programs. All the parameters used in the diabatic vibronic coupling model Hamiltonian are calculated in terms of the normal modes of vibrational coordinates. Finally, the vibronic model Hamiltonian constructed for the coupled six electronic states is used to solve both time-independent and time-dependent Schrödinger equations using the multi-configuration time-dependent Hartree program module to obtain the dynamical observables. The theoretical vibronic band structure is found to be in good accord with the available experimental results. [ABSTRACT FROM AUTHOR]

The rate constants of elementary processes in the atom–diatom system O (3 P) + H 2 (v) , including the processes of vibrational relaxation and dissociation, were studied using the quasiclassical trajectory method. All calculations were carried out along the ground potential energy surface (PES) 3 A ″ that was approximated by a neural network. Approximation data were obtained using ab initio quantum chemistry methods at the extended multi-configuration quasi-degenerate second-order perturbation theory XMCQDPT2 in a basis set limit. The calculated cross-sections of the reaction channels are in good agreement with the literature data. A complete set of state-to-state rate constants was obtained for the metathesis reaction, the dissociation and relaxation of the H2 molecule upon collision with an O atom. According to these data, Arrhenius approximations over a wide temperature range were obtained for the thermal rate constants of considered processes. Data obtained on the dissociation constants and VT relaxation of vibrationally excited H2 molecules can be used in constructing kinetic models describing the oxidation of hydrogen at high temperatures or highly nonequilibrium conditions. [ABSTRACT FROM AUTHOR]

Accurately modeling large biomolecules such as DNA from first principles is fundamentally challenging due to the steep computational scaling of ab initio quantum chemistry methods. This limitation becomes even more prominent when modeling biomolecules in solution due to the need to include large numbers of solvent molecules. We present a machine-learned electron density model based on a Euclidean neural network framework that includes a built-in understanding of equivariance to model explicitly solvated double-stranded DNA. By training the machine learning model using molecular fragments that sample the key DNA and solvent interactions, we show that the model predicts electron densities of arbitrary systems of solvated DNA accurately, resolves polarization effects that are neglected by classical force fields, and captures the physics of the DNA-solvent interaction at the ab initio level. [ABSTRACT FROM AUTHOR]

Heusler alloy is a ferromagnetic alloy based on the Heusler phase. It is an intermetallic alloy between metallic and non-metallic elements that can be non-ferromagnetic and has a BCC crystal structure. This paper presents the theory of thermodynamics and elastic deformation of full-Heusler A2BC alloy with BCC structure built on the basis of statistical moment method (SMM). The paper presents numerical results for the temperature and pressure dependence of the mean nearest neighbor distance between two atoms, the density, the volume, the thermal expansion coefficient, the isotherm and adiabatic compressibilities, the isothermal elastic modulus, the heat capacities at constant volume and pressure, Young's modulus, the bulk modulus, longitudinal and transverse wave velocities of alloys Co2TaGa and Co2VGa when using the coordination sphere method and the Mie–Lennard-Jones pair interaction potential. Some SMM calculation results agree well with available ab initio calculation results. [ABSTRACT FROM AUTHOR]

An alternative formulation of the non-orthogonal molecular orbital model of electronic structure theory is developed based on the expansion of the inverse molecular orbital overlap matrix. From this model, a hierarchy of ab initio fragment-based quantum chemistry methods, referred to as the nth-order expanded non-orthogonal molecular orbital methods, are developed using a minimal number of approximations, each of which is frequently employed in intermolecular interaction theory. These novel methods are compared to existing fragment-based quantum chemistry methods, and the implications of those significant differences, where they exist, between the methods developed herein and those already existing methods are examined in detail. Computational complexities and theoretical scaling are also analyzed and discussed. Future extensions for the hierarchy of methods, to account for additional intrafragment and interfragment interactions, are outlined. [ABSTRACT FROM AUTHOR]

Using the ab initio methods of quantum chemistry, a detailed theoretical investigation of oligomeric products, that reproduce some features of the structure for typical fragments of lignin macromolecules have been carried out. The structuring of individual sections has done on the basis of trans-coniferyl alcohol as a prototype with its subsequent dimerization for three pairs of isomeric compounds with different types of linkages. Their ranking according to the level of relative thermodynamic stability showed, that the forms (α-O-4), (β-β) and (5-5) are the most stable, while the structures (β-O-4), (β-5) and (4-O-5) turned out to be the less stable ones. When substantiating of the spectral characteristics for these systems with the calculation of vibrational frequencies in the harmonic approximation, considerable attention was paid to the intramolecular hydrogen bonding effects, which occur with some participation of spatially complicated hydroxyl groups of the alcohol or phenolic type, as well as the analysis of the rigid chain of pinoresinol system, which contains a bicyclic cage fragment. The results of calculations are in good agreement with the IR spectral data obtained experimentally, and may be of fundamental importance from the point of view about searching of potential precursor compounds for further structuring of this irregular biopolymer. [ABSTRACT FROM AUTHOR]

Motivation Ab initio gene prediction in nonmodel organisms is a difficult task. While many ab initio methods have been developed, their average accuracy over long segments of a genome, and especially when assessed over a wide range of species, generally yields results with sensitivity and specificity levels in the low 60% range. A common weakness of most methods is the tendency to learn patterns that are species-specific to varying degrees. The need exists for methods to extract genetic features that can distinguish coding and noncoding regions that are not sensitive to specific organism characteristics. Results A new method based on a neural network (NN) that uses a collection of sensors to create input features is presented. It is shown that accurate predictions are achieved even when trained on organisms that are significantly different phylogenetically than test organisms. A consensus prediction algorithm for a CoDing Sequence (CDS) is subsequently applied to the first nucleotide level of NN predictions that boosts accuracy through a data-driven procedure that optimizes a CDS/non-CDS threshold. An aggregate accuracy benchmark at the nucleotide level shows that this new approach performs better than existing ab initio methods, while requiring significantly less training data. Availability and implementation https://github.com/BioMolecularPhysicsGroup-UNCC/MachineLearning. [ABSTRACT FROM AUTHOR]

The main effort in this study is focused on devising a numerical model procedure capable of providing reliable values of collisionally induced microscopic properties of importance in processes of light radiation interactions with molecular media. Special attention is devoted to the anisotropic polarizability of the weakly bound H2-H compounds, although broader applicability of the routines proposed is anticipated as well. To this end, Cartesian components of the collision-induced anisotropic polarizability, Δ α i j [ − ] , are obtained for the L- (linear, 0°), S- (45°), and T-shape (90°) configurations of the supermolecular systems. The quantum chemistry ab initio numerical method is applied to determine the values of the quantities within the range of the separations between H2 and H moieties reaching 3 < R < 20 bohrs. This approach is then combined with long-range approximate computing routines in order to formulate an overall uniform modeling algorithm including the influence of the exchange, dispersion, and induction interactions on the collisional induced (CI) effects. The validity and precision of the tool is thoroughly assessed. The polarizabilities are then transformed so as to be expressed in terms of the so-called symmetry adapted (SA) components of the spherical tensor representation, Δ α λ L (2) . Applicability of the modeling scheme is evidenced with regard to the effective evaluation of symmetry adapted parameters for an extended range of intramolecular angularities, separations, and indices. The importance of the procedure for foreseeable CI spectral profile analyses is discussed. [ABSTRACT FROM AUTHOR]

In this work, the structural and electronic properties of two-dimensional (2D) atomically thick (100) diamond nanofilms are investigated by first-principles calculations. The results of phonon dispersion curves and ab initio molecular dynamics simulations indicate that the nanofilms are dynamically and thermally stable with three types of reconstructed surfaces (named 5-MR, 5-7-MR, and 5/5-7-MR). The bandgaps (Eg) of the nanofilms with 5-MR and 5-7-MR patterns are in regions of 1.02–1.40 eV and 0.32–0.55 eV, respectively, and an oscillatory phenomenon of Eg appears related to parity of the layer number. The nanofilms with the 5/5-7-MR pattern show a metallic feature. The variations in Eg are determined by surface states with different configurations. These novel diamond-based structures may be useful for applications such as 2D semiconductors in diamond-based electronic devices. [ABSTRACT FROM AUTHOR]

Ab initio calculation and Boltzmann transport equation have been integrated to find the fundamental influences of trigonal transformation on band structures and thermoelectric performances of antimony. Calculations reveal that antimony could keep its semimetal feature within the c/a range of 2.27–2.82 and that two transitions of band structures of antimony under trigonal transformation are revealed for the first time. Moreover, trigonal transformation has a significant influence on the thermoelectric performances of antimony, and the Seebeck coefficients for the electrons and holes of antimony reach the peaks at the c/a points of 2.72 and 2.57, respectively. The calculated results are in good agreement with the values from experiments in the literature and could deepen the comprehension of the intrinsic relationship between trigonal transformation, band structures, and Seebeck coefficients of antimony. [ABSTRACT FROM AUTHOR]

The role of the coherent interference of phonons on thermal transport in artificial materials such as superlattices is of intense interest. Recent experimental studies report a non-monotonic trend in thermal conductivity with interface density which is attributed to band-folding of thermal phonons. Various models have been proposed to interpret these measurements, but most make simplifying assumptions that make definitively attributing the trends to the coherent transport difficult. Here, we investigate thermal transport in superlattices in the incoherent limit using the Boltzmann equation with intrinsic phonon dispersions and lifetimes calculated from first-principles. We find that the Boltzmann equation is unable to predict the non-monotonic behavior of thermal conductivity versus superlattice period, supporting the interpretation of phonon interference in recent experiments. [ABSTRACT FROM AUTHOR]

The 2 1Π state of NaH has been observed up to the last bound vibrational level using pulsed optical-optical double resonance fluorescence depletion spectroscopy. A total of 20 rovibrational energy levels (v = 2–4 and J = 1–9) were assigned to this electronic state by means of comparing the successive rovibrational spectra to the eigenvalues of the ab initio potential energy curve. The decrease of background fluorescence near the atomic asymptotic limit Na(3d) + H(1s) is an indication of reaching the dissociation limit of the NaH 2 1Π state. Unobserved rovibrational levels (v = 0 and 1) are due to poor Franck-Condon overlap of 2 1Π ← A1Σ+ transition within the accessible rovibrational levels of intermediate A1Σ+ state of this work. [ABSTRACT FROM AUTHOR]

Ab initio calculations of the energy level structure of H 2 + that include relativistic and radiative corrections to nonrelativistic energies and the diagonal part of the hyperfine interaction have predicted the existence of four bound rovibrational levels [(v = 0, N = 0 − 2) and (v = 1, N = 0)] of the first electronically excited ( A + Σ u + 2 ) state of H 2 + , the (v = 1, N = 0) level having a calculated binding energy of only Eb = 1.082 219 8(4)·10−9 Eh and leading to an extremely large scattering length of 750(5) a0 for the H+ + H collision [J. Carbonell et al., J. Phys. B: At., Mol. Opt. Phys. 37, 2997 (2004)]. We present an investigation of the nonadiabatic coupling between the first two electronic states ( X + Σ g + 2 and A + Σ u + 2 ) of H 2 + induced by the Fermi-contact term of the hyperfine-coupling Hamiltonian. This interaction term, which mixes states of total spin quantum number G = 1/2, is rigorously implemented in a close-coupling approach to solve the spin-rovibronic Schrödinger equation. We show that it mixes states of gerade and ungerade electronic symmetry, that it shifts the positions of all weakly bound rovibrational states of H 2 + , and that it affects both the positions and widths of its shape resonances. The calculations demonstrate that the G = 1/2 hyperfine component of the A+ (v = 1, N = 0) state does not exist and that, for G = 1/2, the s-wave scattering lengths of the H+ + H(1s) collision are −578(6) a0 and −43(4) a0 for the F = 0 and F = 1 hyperfine components of the H(1s) atom, respectively. The binding energy of the G = 3/2 hyperfine component of the A+ (v = 1, N = 0) state is not significantly affected by the hyperfine interaction and the corresponding scattering length for the H+ + H(1s, F = 1) collision is 757(7) a0. [ABSTRACT FROM AUTHOR]

Fanpy is a free and open‐source Python library for developing and testing multideterminant wavefunctions and related ab initio methods in electronic structure theory. The main use of Fanpy is to quickly prototype new methods by making it easier to convert the mathematical formulation of a new wavefunction ansätze to a working implementation. Fanpy is designed based on our recently introduced Flexible Ansatz for N‐electron Configuration Interaction (FANCI) framework, where multideterminant wavefunctions are represented by their overlaps with Slater determinants of orthonormal spin‐orbitals. In the simplest case, a new wavefunction ansatz can be implemented by simply writing a function for evaluating its overlap with an arbitrary Slater determinant. Fanpy is modular in both implementation and theory: the wavefunction model, the system's Hamiltonian, and the choice of objective function are all independent modules. This modular structure makes it easy for users to mix and match different methods and for developers to quickly explore new ideas. Fanpy is written purely in Python with standard dependencies, making it accessible for various operating systems. In addition, it adheres to principles of modern software development, including comprehensive documentation, extensive testing, quality assurance, and continuous integration and delivery protocols. This article is considered to be the official release notes for the Fanpy library. [ABSTRACT FROM AUTHOR]

Attempts at the theoretical interpretation of NMR spectra have a very long and fascinating history. Present quantum chemical calculations of shielding and indirect spin-spin couplings permit modeling NMR spectra when small, isolated molecules are studied. Similar data are also available from NMR experiments if investigations are performed in the gas phase. An interesting set of molecules is formed when a methane molecule is sequentially substituted by fluorine atoms—CH4-nFn, where n = 0, 1, 2, 3, or 4. The small molecules contain up to three magnetic nuclei, each with a one-half spin number. The spectral parameters of CH4-nFn can be easily observed in the gas phase and calculated with high accuracy using the most advanced ab initio methods of quantum chemistry. However, the presence of fluorine atoms makes the calculations of shielding and spin-spin coupling constants extremely demanding. Appropriate experimental 19F NMR parameters are good but also require some further improvements. Therefore, there is a real need for the comparison of existing NMR measurements with available state-of-the-art theoretical results for a better understanding of actual limits in the determination of the best shielding and spin-spin coupling values, and CH4-nFn molecules are used here as the exceptionally important case. [ABSTRACT FROM AUTHOR]

Carbon possesses an important ability to be in a valence state of IV, which is essential for organic chemistry and all carbon-based life forms. In turn, tin is usually observed in the valence state of II, although it is a carbon group element. This creates an open question about the possibility of the existence of tin-based "organic" molecules. In this work, we investigate hydro-tin compounds Sn2Hx (x = 1–6) and Sn3Hy (y = 1–8) via DFT and ab initio quantum chemistry methods, studying their global minimum geometry, thermodynamic stability, and chemical bonding patterns. We show that hydrogen-saturated stoichiometries (Sn2H6 and Sn3H8) are exact analogs of hydrocarbons, while unsaturated stoichiometries are characterized by multi-center bonds, aromaticity, and different valence states of tin. In addition, a refined procedure of global geometry minimization based on simulated annealing and ab initio molecular dynamics is proposed. [ABSTRACT FROM AUTHOR]

Boron hydrides have been an object of intensive theoretical and experimental investigation for many decades due to their unusual and somewhat unique bonding patterns. Despite boron being a neighboring element to carbon, boron hydrides almost always form non-classical structures with multi-center bonds. However, we expect indium to form its interesting molecules with non-classical patterns, though such molecules still need to be extensively studied theoretically. In this work, we investigated indium hydrides of In2Hx (x = 0–4,6) and In3Hy (y = 0–5) series via DFT and ab initio quantum chemistry methods, performing a global minimum search, chemical bonding analysis, and studies of their thermodynamical stability. We found that the bonding pattern of indium hydrides differs from the classical structures composed of 1c-2e lone pairs and 2c-2e bonds and the bonding pattern of earlier investigated boron hydrides of the BnHn+2 series. The studied stoichiometries are characterized by multi-center bonds, aromaticity, and the tendency for indium to preserve the 1c-2e lone pair. [ABSTRACT FROM AUTHOR]

The structure of tin(II) is not well known in aqueous solution. The energies, structures, and vibrational frequencies of [Sn(H2O)n,]2+ n = 0–9, 18 have been calculated at the Hartree–Fock and second order Møller–Plesset levels of theory using the CEP, LANL2, and SDD effective core potentials in combination with their associated basis sets, or with the 6-31G* and 6-31+G* basis sets. The tin–oxygen distances and totally symmetric stretching frequency of the aquatin(II) ions were compared with each other, and with solution measurements where available. [ABSTRACT FROM AUTHOR]

A new diabatization method based on artificial neural networks (ANNs) is presented, which is capable of reproducing high-quality ab initio data with excellent accuracy for use in quantum dynamics studies. The diabatic potential matrix is expanded in terms of a set of basic coupling matrices and the expansion coefficients are made geometry-dependent by the output neurons of the ANN. The ANN is trained with respect to ab initio data using a modified Marquardt-Levenberg back-propagation algorithm. Due to its setup, this approach combines the stability and straightforwardness of a standard low-order vibronic coupling model with the accuracy by the ANN, making it particularly advantageous for problems with a complicated electronic structure. This approach combines the stability and straightforwardness of a standard low-order vibronic coupling model with the accuracy by the ANN, making it particularly advantageous for problems with a complicated electronic structure. This novel ANN diabatization approach has been applied to the low-lying electronic states of NO3 as a prototypical and notoriously difficult Jahn-Teller system in which the accurate description of the very strong non-adiabatic coupling is of paramount importance. Thorough tests show that an ANN with a single hidden layer is sufficient to achieve excellent results and the use of a "deeper" layering shows no clear benefit. The newly developed diabatic ANN potential energy surface (PES) model accurately reproduces a set of more than 90 000 Multi-configuration Reference Singles and Doubles Configuration Interaction (MR-SDCI) energies for the five lowest PES sheets. [ABSTRACT FROM AUTHOR]

Size-selected anion photoelectron spectroscopy and theoretical calculations were used to investigate the structural evolution and bonding properties of BSin−/0 (n = 4–12) clusters. The results showed that the B atom in BSi4–12−/0 prefers to occupy the high coordination sites to form more B–Si bonds. The lowest-lying isomers of BSi4–7−/0 primarily adopt bowl-shaped based geometries, while those of BSi8–12−/0 are mainly dominated by prismatic based geometries. For anionic clusters, BSi11− is the critical size of the endohedral structure, whereas BSin neutrals form the B-endohedral structure at n = 9. Interestingly, both anionic and neutral BSi11 have a D3h symmetric tricapped tetragonal antiprism structure with the B atom at the center and exhibit 3D aromaticity. The BSi11− anion possesses σ plus π doubly delocalized bonding characters. The natural population analysis charge distributions on the B atom are related with the structural evolution of BSin− and the B–Si interactions. [ABSTRACT FROM AUTHOR]

The 1, 2, 3, 4-tetrafluorobenzene-water complex was investigated by pulsed-jet Fourier transform microwave spectroscopy. One isomer was detected in the jet expansion. Ab initio calculations and non-covalent interaction (NCI) analysis were performed to characterize the intermolecular NCIs. In the observed isomer, the water molecule lies almost in the plane of the benzene ring acting as a proton donor to one of the fluorine atoms and as an acceptor to one of the hydrogen atoms forming a six-membered ring structure. The CH⋯O and H⋯FC bonding distances are determined to be 2.385(1) Å and 2.429(1) Å, respectively. The interaction energy is calculated to be −18.0 kJ mol−1 at the SAPT2+(3)/aug-cc-pVDZ level of theory. The observed transitions exhibit splitting in the order of tens to hundreds of kHz due to the internal rotation of water moiety. The possible tunneling paths of water were investigated by ab initio calculations resulting in a barrier for an internal rotation of about 201 cm−1. [ABSTRACT FROM AUTHOR]

The stable low energy states of the HPS and DPS molecules have been studied through multi-reference ab initio methods in conjunction with large atomic basis sets. Stable states for these species have been examined up to 7 eV above the ground state minimum. We found six stable electronic states that are mostly mono-configurational. These states may be involved in the photodynamics and photodissociation of this molecule. In particular, the 2 1A′ state presents two minima on the potential energy surface, one of them close to linear configuration. This state may be populated after the absorption of a visible photon from the ground state and gives rise to large amplitude motions that may eventually induce isomerization to electronically excited HSP. Moreover, we characterized these states spectroscopically to facilitate the assignment of the vibronic spectra of the HPS and DPS species. For these low-energy states, we thus computed vertical and adiabatic excitation energies, and for the stable ones, a full set of spectroscopic constants including harmonic frequencies and anharmonic vibrational, rotational, and centrifugal distortion constants. The calculated potential energy surfaces for these states have been used in a variational procedure to deduce the pattern of vibrational levels up to 4000 cm−1 above the corresponding vibrationless level. Our data may serve for the assignment of the IR and Vis spectra of HPS and DPS. [ABSTRACT FROM AUTHOR]

The single-sheeted potential energy surface (PES) of H 2 S + (X 2 A ′ ′ ) is developed based on the ab initio energies calculated by the multi-reference configuration interaction method including the Davidson correction. All the ab initio energies are first calculated using aug-cc-pVQdZ and aug-cc-pV5dZ basis sets, which are then extrapolated to the complete basis set (CBS) limit. A switching function is developed to model the transition of S + D 2 to S + S 4 . The many-body expansion formalism is employed to obtain the H 2 S + (X 2 A ′ ′ ) PES by fitting such CBS energies and the root-mean square derivation is 0.0367 eV. The topographical features of the present PES are examined in detail, which are well consistent with previous studies. The quasiclassical trajectory method is subsequently utilized to study the S + D 2 + H 2 ( X 1 Σ g + ) → S H + (X 3 Σ − ) + H (S 2 ) reaction. The capture time, integral cross sections, and rovibrational distributions are calculated. By examining the capture time, it can be concluded that the title reaction is mainly controlled by the indirect mechanism for lower collision energies, while the direct and indirect mechanisms coexist and the latter plays a dominant role for higher collision energies. [ABSTRACT FROM AUTHOR]

Magic-angle-spinning (MAS) dynamic nuclear polarization (DNP) has recently emerged as a powerful technology enabling otherwise unrealistic solid-state NMR experiments. The simulation of DNP processes which might, for example, aid in refining the experimental conditions or the design of better performing polarizing agents, is, however, plagued with significant challenges, often limiting the system size to only 3 spins. Here, we present the first approach to fully ab initio large-scale simulations of MAS DNP enhancements. The Landau-Zener equation is used to treat all interactions concerning electron spins, and the low-order correlations in the Liouville space method is used to accurately treat the spin diffusion, as well as its MAS speed dependence. As the propagator cannot be stored, a Monte Carlo optimization method is used to determine the steady-state enhancement factors. This new software is employed to investigate the MAS speed dependence of the enhancement factors in large spin systems where spin diffusion is of importance, as well as to investigate the impacts of solvent and polarizing agent deuteration on the performance of MAS DNP. [ABSTRACT FROM AUTHOR]

An adaptive modeling method (AMM) that couples a deep neural network potential and a classical force field is introduced to address the accuracy-efficiency dilemma faced by the molecular simulation community. The AMM simulated system is decomposed into three types of regions. The first type captures the important phenomena in the system and requires high accuracy, for which we use the Deep Potential Molecular Dynamics (DeePMD) model in this work. The DeePMD model is trained to accurately reproduce the statistical properties of the ab initio molecular dynamics. The second type does not require high accuracy, and a classical force field is used to describe it in an efficient way. The third type is used for a smooth transition between the first and the second types of regions. By using a force interpolation scheme and imposing a thermodynamics force in the transition region, we make the DeePMD region embedded in the AMM simulated system as if it were embedded in a system that is fully described by the accurate potential. A representative example of the liquid water system is used to show the feasibility and promise of this method. [ABSTRACT FROM AUTHOR]

By means of ab initio computations and the global minimum structure search method, we have investigated structural, mechanical, and electronic properties of D-carbon, a crystalline orthorhombic sp³ carbon allotrope (space group Pmma [D2h5] with 6 atoms per cell). Total-energy calculations demonstrate that D-carbon is energetically more favorable than the previously proposed T6 structure (with 6 atoms per cell) as well as many others. This novel phase is dynamically, mechanically, and thermally stable at zero pressure and more stable than graphite beyond 63.7 GPa. D-carbon is a semiconductor with a bandgap of 4.33 eV, less than diamond's gap (5.47 eV). The simulated X-ray diffraction pattern is in satisfactory agreement with previous experimental data in chimney or detonation soot, suggesting its possible presence in the specimen. Published by AIP Publishing. [ABSTRACT FROM AUTHOR]

A new global and highly accurate ab initio dipole moment surface (DMS) for water vapour is presented. This DMS is based on a set of 17 628 multi-reference configuration interaction data points that were calculated with the aug-cc-pCV6Z basis set with the Douglas-Kroll-Hess Hamiltonian; tests are performed at several other levels of ab initio theory. This new “CKAPTEN” DMS improves agreement with recent experimental measurements compared with previous models that poorly predicted some bands in the infrared while also maintaining or improving on the agreement for all remaining strong lines. For high overtones located in both the visible and the near ultraviolet regions, our predicted intensities all lie within 10% of recent atmospheric observations. A crossing of energy levels in the ν1 fundamental and 2ν2 states is seen to offset transition intensities in the ν1 fundamental band; residual inaccuracies within the potential energy surface used is the cause of this problem. [ABSTRACT FROM AUTHOR]

A series of 20 composite structures, consisting of superhalogen and noble gas (Ng) hydrides, was explored via high-level coupled-cluster single, double and perturbative triple excitations calculations in this work. The existence of these composites, as local minima on the potential energy surface, arises from the charge transfer from the Ng hydride part to the superhalogen moiety. Clearly, this transfer could lead to stabilizing the interaction of the ionic type between the two components. The driving force of the charge transfer should be the high vertical electron detachment energy (VDE) of the superhalogen part leading to its enough capability of extracting the electron from the Ng hydride moiety. However, except triggering the ionic attractive interaction, there is nomonotonic correlation between the VDE value and the thermodynamic stability of the whole composite. This counterintuitive result actually originates from the fact that, irrespective of various superhalogens, only two of their F ligands interact with the Ng atoms directly. Thus, although leading to higher VDE values, the increase in the number of electronegative ligands of the superhalogen moiety does not affect the stabilizing interaction of the composites here directly. In other words, with the necessary charge transfer generated, further increase of theVDEdoes not ensure the improvement of the thermodynamic stabilities of the whole composite. Moreover, in the transition state of the exothermic dissociation channel, more F atoms will give rise to higher probability of additional attractions between the F and H atoms which should lower the energy barrier. That is to say, increasing VDE, i.e., having more F atoms in many cases, will probably reduce the kinetic stability. Knowing the inevitable existence of the exothermic channel, kinetic stability is crucial to the ultimate goal of experimental observation of these Ng hydrides. Thus, in some cases, only the superhalogen itself may not provide enough information for the correct prediction on the properties of the whole composites. The understanding of the superhalogen-based composites will provide valuable information on the functional properties as well as the application potential of superhalogen clusters. Thus, the corresponding researches should focus on not only the superhalogen itself but also other related aspects, especially the details of the interaction between different parts. [ABSTRACT FROM AUTHOR]

Autoionization spectra of CH2Cl2 and CD2Cl2 molecules after Cl 2p excitation are studied. The two molecular and atomic Auger transitions are examined and assigned. The contribution of atomic Auger transitions is lower in the deuterated molecule. In addition, to support the presence of the ultrafast dissociation mechanism in the dichloromethane molecule, a series of high-level ab initio quantum mechanical calculations were performed at multiconfigurational self-consistent field (MCSCF) and multireference configuration interaction (MRCI) levels of theory. Minimum energy pathways for the dissociation of the dichloromethane molecule have been calculated by taking into account the spin-orbit splitting between the singlet and triplet transitions in the Cl 2p edge. [ABSTRACT FROM AUTHOR]

The selectivity of electrically detected magnetic resonance (EDMR) is utilized to probe the dominant recombination defect at the Si-face 4H-SiC/SiO2 interface. The nature of this defect has long been debated with the two main candidates being the Si vacancy (VSi) or the C-dangling bond (PbC). Through comparison between experimental EDMR measurements and ab initio calculations, an important performance limiting recombination defect observed with EDMR in the current generation of nMOSFETs is reasonably explained as a combination of the PbC and the dual-PbC defects. These defects match the symmetry, hyperfine interaction, and isotopic abundance observed in the experimental EDMR spectrum. [ABSTRACT FROM AUTHOR]

We present a comparison of ab initio molecular dynamics calculations for CHD3 dissociation on Pt(111) using the Perdew, Burke and Ernzerhof (PBE) functional and a specific reaction parameter (SRP) functional. Despite the two functionals predicting approximately the same activation barrier for the reaction, the calculations using the PBE functional consistently overestimate the experimentally determined dissociation probability, whereas the SRP functional reproduces the experimental values within a chemical accuracy (4.2 kJ/mol). We present evidence that suggests that this difference in reactivity can at least in part be attributed to the presence of a van derWaals well in the potential of the SRP functional which is absent from the PBE description. This leads to the CHD3 molecules being accelerated and spending less time near the surface for the trajectories run with the SRP functional, as well as more energy being transferred to the surface atoms.We suggest that both these factors reduce the reactivity observed in the SRP calculations compared to the PBE calculations. [ABSTRACT FROM AUTHOR]

A valence bond (VB) block-diagonalization approach, named VBBDA, is proposed to construct the charge-localized diabatic state explicitly within the framework of ab initio VB theory. Since the VB structure built upon the localized orbitals represents the charge localized character of the diabatic state faithfully, we are able to obtain accurate electronic coupling between diabatic states by using a very compact VB wave function. Moreover, the potential energy curves of the diabatic states and hence the crossing points of them can be accurately evaluated. The pilot applications showed that the electronic couplings computed by the VB method are consistent with the complete active space self-consistent field method and may even be close to the results of other high-level ab initio methods such as full configuration interaction and multireference configuration interaction. In addition, the computed electronic couplings show the expected exponential attenuation for the donor-acceptor systems as the distance increases. Moreover, VBBDA has the capability for handling complicated systems based on either two-state or multi-state treatment. Finally, because of the outstanding performance of the Xiamen Valence Bond software package, which is an ab initio VB program, VBBDA is capable for systems consisting more than 1000 basis functions. [ABSTRACT FROM AUTHOR]

In this paper, the electronically nonadiabatic Landau-Zener (LZ) mechanism for the vibrational relaxation v = 1 → v = 0 of NO ( X 2 Π ) in collisions with Ar ( S 0 1 ) is discussed. It corresponds to nonadiabatic transitions between two crossing vibronic potential energy surfaces (PESs) originating from vibrational states of the collision complex and supported by two coupled electronic PESs. The LZ rate coefficients k 10 LZ are calculated within the uniform Airy approach in the reaction coordinate approximation with parameters derived from ab initio PESs and an asymptotic estimation of the Franck–Condon factor in the nonadiabatic coupling region. The rate coefficients are close to the experimental rate coefficients available over the range of 900–2500 K, where the electronically adiabatic Landau-Teller (LT) mechanism with the rate coefficients k 10 LT does not make a noticeable contribution to the total relaxation rate. The ratio k 10 LZ / k 10 LT increases with temperature and the LZ and LT mechanisms have comparable rates at about 4000 K. [ABSTRACT FROM AUTHOR]

Using density functional theory method, the linear optical absorption spectra and nonlinear optical susceptibilities of hydrogen passivated armchair and zigzag Phosphorous Nanoribbons (aPNR and zPNR) as well as α-phase phosphorous monolayer were calculated. It was observed that the crystallographic direction has a strong effect on the band edge absorption which in turn leads to optical anisotropy as well as a red shift of the absorption spectra by increasing the width. The calculated absorption values are in the order of 105 cm−1 and are very close to the experimentally measured ones. It was also observed that the 2nd order nonlinear optical susceptibility, χ(2), in the nanoribbons is enhanced by two orders of magnitude. This effect is caused by breaking the centro-symmetric structure of monolayer phosphorene as a result of hydrogen surface termination. The calculated 3rd order susceptibilities, χ(3), are in the order of ≈10−13 esu (≈10−21 m2/V2) which are in close agreement with experimentally reported values as well as those computed based on the relativistic picture of electron. The closeness of our results to experimental values strongly supports the reliability of our method in calculating the nonlinear optical susceptibilities of phosphorene and other nanostructures in general. The enhanced 2nd order optical nonlinearity in phosphorene promises a better second harmonic and frequency difference (THz) generation. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

We propose a new scheme to parameterize effective potentials that can be used to simulate atomic systems such as oxide glasses. As input data for the optimization, we use the radial distribution functions of the liquid and the vibrational density of state of the glass, both obtained from ab initio simulations, as well as experimental data on the pressure dependence of the density of the glass. For the case of silica, we find that this new scheme facilitates finding pair potentials that are significantly more accurate than the previous ones even if the functional form is the same, thus demonstrating that even simple two-body potentials can be superior to more complex three-body potentials. We have tested the new potential by calculating the pressure dependence of the elastic moduli and found a good agreement with the corresponding experimental data. [ABSTRACT FROM AUTHOR]

In the calculations of tetragonal BaTiO3, some exchange-correlation (XC) energy functionals such as local density approximation (LDA) have shown good agreement with experiments at room temperature (RT), e.g., spontaneous polarization (PS), and superiority compared with other XC functionals. This is due to the error compensation of the RT effect and, hence, will be ineffective in the heavily strained case such as domain boundaries. Here, ferroelectrics under large strain at RT are approximated as those at 0 K because the strain effect surpasses the RT effects. To find effective XC energy functionals for strained BaTiO3, we propose a new comparison, i.e., a criterion. This criterion is the properties at 0 K given by the Ginzburg-Landau (GL) theory because GL theory is a thermodynamic description of experiments working under the same symmetry-constraints as ab initio calculations. With this criterion, we examine LDA, generalized gradient approximations (GGA), meta-GGA, meta-GGA + local correlation potential (U), and hybrid functionals, which reveals the high accuracy of some XC functionals superior to XC functionals that have been regarded as accurate. This result is examined directly by the calculations of homogenously strained tetragonal BaTiO3, confirming the validity of the new criterion. In addition, the data points of theoretical PS vs. certain crystallographic parameters calculated with different XC functionals are found to lie on a single curve, despite their wide variations. Regarding these theoretical data points as corresponding to the experimental results, analytical expressions of the local PS using crystallographic parameters are uncovered. These expressions show the primary origin of BaTiO3 ferroelectricity as oxygen displacements. Elastic compliance and electrostrictive coefficients are estimated. For the comparison of strained results, we show that the effective critical temperature TC under strain <−0.01 is >1000 K from an approximate method combining ab initio results with GL theory. In addition, in a definite manner, the present results show much more enhanced ferroelectricity at large strain than the previous reports. [ABSTRACT FROM AUTHOR]

Gamma-aminobutyric acid (GABA), a primary neurotransmitter, accomplishes its activities by binding to different receptor sites in different conformations. It is known to have two major conformers: the closed and open forms. Earlier studies on preferred conformation of GABA in water revealed differing results with some reporting the open form while others inferring the closed form to be more stable. We found the existence of many open forms and only one closed form of GABA in water through ab initio metadynamics simulation. Some of the open conformers are equally or more stable while others are less stable than the closed form. Free energy barriers reveal that different conformers are interconvertible at room temperature in typical experimental time scales. Ab initio molecular dynamics simulations are performed to further investigate the inter-conversion of various conformers of GABA in water and their dipole moments and also to make connections to experiments on the conformation of GABA in water. [ABSTRACT FROM AUTHOR]

The excited state non-adiabatic dynamics of the smallest polyene, trans 1,3-butadiene (BD), has long been the subject of controversy due to its strong coupling, ultrafast time scales and the difficulties that theory faces in describing the relevant electronic states in a balanced fashion. Here we apply Ab Initio Multiple Spawning (AIMS) using state-averaged complete active space multistate second order perturbation theory [SA-3-CAS(4/4)-MSPT2] which describes both static and dynamic electron correlation effects, providing a balanced description of both the initially prepared bright 1¹Bu (ππ*) state and non-adiabatically coupled dark 2¹Ag state of BD. Importantly, AIMS allows for on-the-fly calculations of experimental observables. We validate our approach by directly simulating the time resolved photoelectron-photoion coincidence spectroscopy results presented in Paper I [A. E. Boguslavskiy et al., J. Chem. Phys. 148, 164302 (2018)], demonstrating excellent agreement with experiment. Our simulations reveal that the initial excitation to the 1¹Bu state rapidly evolves via wavepacket dynamics that follow both bright- and dark-state pathways as well as mixtures of these. In order to test the sensitivity of the AIMS results to the relative ordering of states, we considered two hypothetical scenarios biased toward either the bright ¹Bu or the dark 2¹Ag state. In contrast with AIMS/SA-3-CAS(4/4)-MSPT2 simulations, neither of these scenarios yields favorable agreement with experiment. Thus, we conclude that the excited state non-adiabatic dynamics in BD involves both of these ultrafast pathways. [ABSTRACT FROM AUTHOR]

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 thiswork, 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 hydrogenterminated 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. [ABSTRACT FROM AUTHOR]

A highly accurate, consistent set of ab initio interaction potentials is obtained for the title systems at the coupled cluster with singles, doubles, and non-iterative triples level of theory with extrapolation to the complete basis set limit. These potentials are shown to be more reliable than the previous potentials based on their long-range behavior, equilibrium properties, collision cross sections, and transport properties. [ABSTRACT FROM AUTHOR]

The potential energy surface (PES) describing the interaction of the ethynyl (C2H) radical in its ground X ²Σ+ electronic state with molecular hydrogen has been computed through restricted coupled cluster calculations including single, double, and (perturbative) triple excitations [RCCSD(T)], with the assumption of fixed molecular geometries. The computed points were fit to an analytical form suitable for time-independent quantum scattering calculations of rotationally inelastic cross sections and rate constants. A representative set of energy dependent state-to-state cross sections is presented and discussed. The PES and cross sections for collisions of H2(j = 0) are compared with a previous study [F. Najar et al., Chem. Phys. Lett. 614, 251 (2014)] of collisions of C2H with H2 treated as a spherical collision partner. Good agreement is found between the two sets of calculations when the H2 molecule in the present calculation is spherically averaged. [ABSTRACT FROM AUTHOR]

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 fin particular, the recent highly accurate potential of Jäger et al. [J. Chem. Phys. 144, 114304 (2016)]g. 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. [ABSTRACT FROM AUTHOR]

The reaction between an impinging H atom and a Cl atom adsorbed on Au(111), which is a prototype for the Eley-Rideal mechanism, is investigated using ab initio molecular dynamics at different incidence angles. The reaction yielding gaseous HCl with large internal excitation proceeds via both direct and hot-atom mechanisms. Significant energy exchange with both surface phonons and electron-hole pairs has been observed. However, their impact on the reactivity and final state distributions was found to be limited, thanks to the large exothermicity and small barrier of the reaction. [ABSTRACT FROM AUTHOR]

Computational studies have revealed that the photo-excitation of these compounds involve a strongly allowed S SB 0 sb ->S SB 2 sb transition which is subsequently followed by S SB 2 sb /S SB 1 sb and S SB 0 sb /S SB 1 sb conical intersections to form the photo-product oxaziridine. However, the S SB 2 sb /S SB 1 sb crossing may certainly populate this state and the S SB 1 sb minimum can come to the picture following this deactivation channel of the S SB 2 sb state. However, as mentioned for the TMIO system, the S SB 2 sb /S SB 1 sb crossing may increase the S SB 1 sb state population and such minimum energy geometry on S SB 1 sb can be reached. Keywords: photochemistry; 2H-imidazole 1-oxide; excited states; oxaziridine EN photochemistry 2H-imidazole 1-oxide excited states oxaziridine 1 7 7 11/10/22 20221107 NES 221107 The photochemistry of 2H-imidazole-1-oxides has been explored using the two well-known spin-trapping agents, TMIO and DMPIO as the representative systems of this cyclic nitrone category. [Extracted from the article]

Hydrated zinc(II) cations, due to their importance in biological systems, are the subject of ongoing research concerning their hydration shell structure and dynamics. Here, ab initio molecular dynamics (AIMD) simulations are used to study solvent exchange events around aqueous Zn2+, for which observation in detail is possible owing to the considerable length of the generated trajectory. While the hexacoordinated Zn(H2O)62+ is the dominant form of Zn(II) in an aqueous solution, there is a non-negligible contribution of the pentacoordinated Zn(H2O)52+ complex which presence is linked to the dissociative solvent exchange events around Zn2+. The pentacoordinated Zn(II) has a much tighter hydration sphere and is characterized by a trigonal bipyramidal structure, in contrast to the usual octahedral symmetry of the hexacoordinated complex. In total, two full exchange events are registered in the analyzed trajectory. AIMD simulations on an adequate length scale thus provide a direct way of studying such solvent exchange events around ions in molecular detail. [ABSTRACT FROM AUTHOR]

Sulfur crosslinked polyisoprene (rubber) is used in important material components for a number of technical tasks (e.g., in tires and sealings). If mechanical stress, like tension or shear, is applied on these material components, the sulfur crosslinks suffer from homolytic bond breaking. In thiswork, we have simulated the bond breaking mechanism of sulfur crosslinks between polyisoprene chains using Car- Parrinello molecular dynamic simulations and investigated the maximum forces which can be resisted by the crosslinks. Small model systems with crosslinks formed by chains of N = 1 to N = 6 sulfur atoms have been simulated with the slow growth-technique, known from the literature. The maximum force can be thereby determined from the calculated energies as a function of strain (elongation). The stability of the crosslink under strain is quantified in terms of the maximum force that can be resisted by the system before the crosslink breaks. As shown by our simulations, this maximum force decreases with the sulfur crosslink length N in a step like manner. Our findings indicate that in bridges with N = 1, 2, and 3 sulfur atoms predominantly, carbon-sulfur bonds break, while in crosslinks with N > 3, the breaking of a sulfur-sulfur bond is the dominant failure mechanism. The results are explained within a simple chemical bond model, which describes how the delocalization of the electrons in the generated radicals can lower their electronic energy and decrease the activation barriers. It is described which of the double bonds in the isoprene units are involved in the mechanochemistry of crosslinked rubber. [ABSTRACT FROM AUTHOR]

Quantitative chemical reaction data, including activation energies and reaction rates, are crucial for developing detailed kinetic mechanisms and accurately predicting reaction outcomes. However, such data are often difficult to find, and high-quality datasets are especially rare. Here, we use CCSD(T)-F12a/cc-pVDZ-F12//ωB97X-D3/def2-TZVP to obtain high-quality single point calculations for nearly 22,000 unique stable species and transition states. We report the results from these quantum chemistry calculations and extract the barrier heights and reaction enthalpies to create a kinetics dataset of nearly 12,000 gas-phase reactions. These reactions involve H, C, N, and O, contain up to seven heavy atoms, and have cleaned atom-mapped SMILES. Our higher-accuracy coupled-cluster barrier heights differ significantly (RMSE of ∼5 kcal mol−1) relative to those calculated at ωB97X-D3/def2-TZVP. We also report accurate transition state theory rate coefficients k ∞ (T) between 300 K and 2000 K and the corresponding Arrhenius parameters for a subset of rigid reactions. We believe this data will accelerate development of automated and reliable methods for quantitative reaction prediction. Measurement(s) Barrier Heights • Enthalpies • Rate Coefficients Technology Type(s) ab initio quantum chemistry computational method [ABSTRACT FROM AUTHOR]

Laser irradiation of materials induces changes in their structure and functional properties. In this work, lattice heating and electronic excitation on silver bromide (AgBr), provoked by femtosecond laser irradiation, have been investigated by finite-temperature density functional theory and ab initio molecular dynamics calculations by using the two-temperature model. According to our results, the electronic temperature of 0.25 eV is enough to excite the electrons from the valence to the conduction band, whereas 1.00 eV changes the structural properties of the irradiated AgBr material. Charge density simulations also show that an Ag clustering process and the formation of Br3− complexes take place when the electronic temperature reaches 2.00 eV and 5.00 eV, respectively. The present results can be used to obtain coherent control of the extreme nonequilibrium conditions due to femtosecond laser irradiation for designing new functional materials. [ABSTRACT FROM AUTHOR]