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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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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 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]

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]

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]

Energetic materials store a large amount of chemical energy. Different ignition processes, including laser ignition and shock or compression wave, initiate the energy release process by first promoting energetic molecules to the electronically excited states. This is why a full understanding of initial steps of the chemical dynamics of energetic molecules from the excited electronic states is highly desirable. In general, conical intersection (CI), which is the crossing point of multidimensional electronic potential energy surfaces, is well established as a controlling factor in the initial steps of chemical dynamics of energetic molecules following their electronic excitations. In this article, we have presented different aspects of the ultrafast unimolecular relaxation dynamics of energetic molecules through CIs. For this task, we have employed ab initio multiple spawning (AIMS) simulation using the complete active space self-consistent field (CASSCF) electronic wavefunction and frozen Gaussian-based nuclear wavefunction. The AIMS simulation results collectively reveal that the ultrafast relaxation step of the best energetic molecules (which are known to exhibit very good detonation properties) is completed in less than 500 fs. Many, however, exhibit sub-50 fs dynamics. For example, nitro-containing molecules (including C-NO2, N-NO2, and O-NO2 active moieties) relax back to the ground state in approximately 40 fs through similar (S1/S0)CI conical intersections. The N3-based energetic molecule undergoes theN2 elimination process in 40 fs through the (S1/S0)CI conical intersection. Nitramine-Fe complexes exhibit sub-50 fs Fe-O and N-O bond dissociation through the respective (S1/S0)CI conical intersection. On the other hand, tetrazine-N-oxides, which are known to exhibit better detonation properties than tetrazines, undergo internal conversion in a 400-fs time scale, while the relaxation time of tetrazine is very long (about 100 ns). Many other characteristics of sub-500 fs nonadiabatic decay of energetic molecules are discussed. In the end many unresolved issues associated with the ultrafast nonadiabatic chemical dynamics of energetic molecules are presented. [ABSTRACT FROM AUTHOR]

The unique properties of liquid water apparently arise from more than just the tetrahedral bond angle between the nuclei of a water molecule since simple three-site models of water are poor at mimicking these properties in computer simulations. Four- and five-site models add partial charges on dummy sites and are better at modeling these properties, which suggests that the shape of charge distribution is important. Since a multipole expansion of the electrostatic potential describes a charge distribution in an orthogonal basis set that is exact in the limit of infinite order, multipoles may be an even better way to model the charge distribution. In particular, molecular multipoles up to the octupole centered on the oxygen appear to describe the electrostatic potential from electronic structure calculations better than four- and five-site models, and molecular multipole models give better agreement with the temperature and pressure dependence of many liquid state properties of water while retaining the computational efficiency of three-site models. Here, the influence of the shape of the molecular charge distribution on liquid state properties is examined by correlating multipoles of non-polarizable water models with their liquid state properties in computer simulations. This will aid in the development of accurate water models for classical simulations as well as in determining the accuracy needed in quantum mechanical/molecular mechanical studies and ab initio molecular dynamics simulations of water. More fundamentally, this will lead to a greater understanding of how the charge distribution of a water molecule leads to the unique properties of liquid water. In particular, these studies indicate that p-orbital charge out of the molecular plane is important. [ABSTRACT FROM AUTHOR]

Within ab initio Quantum Monte Carlo simulations, the leading numerical cost for large systems is the computation of the values of the Slater determinants in the trial wavefunction. Each Monte Carlo step requires finding the determinant of a dense matrix. This is most commonly iteratively evaluated using a rank-1 Sherman-Morrison updating scheme to avoid repeated explicit calculation of the inverse. The overall computational cost is, therefore, formally cubic in the number of electrons or matrix size. To improve the numerical efficiency of this procedure, we propose a novel multiple rank delayed update scheme. This strategy enables probability evaluation with an application of accepted moves to the matrices delayed until after a predetermined number of moves, K. The accepted events are then applied to the matrices en bloc with enhanced arithmetic intensity and computational efficiency via matrix-matrix operations instead of matrix-vector operations. This procedure does not change the underlying Monte Carlo sampling or its statistical efficiency. For calculations on large systems and algorithms such as diffusion Monte Carlo, where the acceptance ratio is high, order of magnitude improvements in the update time can be obtained on both multi-core central processing units and graphical processing units. [ABSTRACT FROM AUTHOR]

Fermi operator expansion (FOE) methods are powerful alternatives to diagonalization type methods for solving Kohn-Sham density functional theory (KSDFT). One example is the pole expansion and selected inversion (PEXSI) method, which approximates the Fermi operator by rational matrix functions and reduces the computational complexity to at most quadratic scaling for solving KSDFT. Unlike diagonalization type methods, the chemical potential often cannot be directly read off from the result of a single step of evaluation of the Fermi operator. Hence multiple evaluations are needed to be sequentially performed to compute the chemical potential to ensure the correct number of electrons within a given tolerance. This hinders the performance of FOE methods in practice. In this paper, we develop an efficient and robust strategy to determine the chemical potential in the context of the PEXSI method. The main idea of the new method is not to find the exact chemical potential at each self-consistent-field (SCF) iteration but to dynamically and rigorously update the upper and lower bounds for the true chemical potential, so that the chemical potential reaches its convergence along the SCF iteration. Instead of evaluating the Fermi operator for multiple times sequentially, our method uses a two-level strategy that evaluates the Fermi operators in parallel. In the regime of full parallelization, the wall clock time of each SCF iteration is always close to the time for one single evaluation of the Fermi operator, even when the initial guess is far away from the converged solution. We demonstrate the effectiveness of the new method using examples with metallic and insulating characters, as well as results from ab initio molecular dynamics. [ABSTRACT FROM AUTHOR]

Using first principle calculations, we have studied the structural and electronic properties of two dimensional bilayers of indium and gallium chalcogenides. With density functional theory corrected for van derWaals interactions, the different modes of stacking were investigated in a systematic way, and several of them were found to compete in energy. Then, their band structures were obtained with the GW approximation and found to correspond to indirect bandgap semiconductors with a small dependency on the mode of stacking. Finally, by analysing the electron density, it appeared that GaSe-InS is a promising system for electron-hole separation. [ABSTRACT FROM AUTHOR]

We present an ab initio-based force-field for silver ion interactions withwater and ammonia. Compared to quantum calculations, our model allows for rather large-scale molecular dynamics simulations of silver solutions of aqueous ammonia. For a series ofNH3:H2Oratios ranging from 1 to 20 mol. %, Ag+ ions were mainly found as octahedral [Ag(NH3)x(H2O)]+ 6-x coordination complexes with preferential values of x ranging from 0 to 3. In the first coordination structure, water↔ammonia exchanges occur within a 1-3 ps time scale and, depending on the NH3 concentration, imply significant fluctuations of x covering the whole range from 0 to 6. Based on ns-scale molecular dynamics simulations, chemical potentials are derived for all Ag+ coordination species as functions of temperature and ammonia concentration. Moreover, we compare the diffusion constants of the [Ag(H2O)6]+ to [Ag(H2O)3(NH3)3+ coordination complexes, based on the solutions of the corresponding ammonia content. [ABSTRACT FROM AUTHOR]

The ab initio molecular dynamics simulations of metallic, charged and electrochemical systems require, in principle, the inclusion of unequally occupied electronic states. In this contribution, the general approach to work with fixed but arbitrary occupations within the Car-Parrinello molecular dynamics scheme is revisited, focusing on the procedure which is required to maintain the orthonormality constraints in the commonly used position-Verlet integrator. Expressions to constrain also the orbital velocities, as it is demanded by a velocity-Verlet integrator, are then derived. The generalized unequal-occupation SHAKE algorithm is compared with the standard procedure for damped dynamics (energy optimization) of systems including fully unoccupied electronic states. In turn, the proposed unequal-occupation RATTLE algorithm is validated by the corresponding microcanonical ensemble simulations. It is shown that only with the proper orthogonalization method, a correct ordering of states and energy conserving dynamics can be achieved. [ABSTRACT FROM AUTHOR]

Within the semiclassical Boltzmann transport theory in the constant relaxation-time approximation,we perform an ab initio study of the transport properties of selected systems, including crystalline solids and nanostructures. A local (Gaussian) basis set is adopted and exploited to analytically evaluate band velocities as well as to access full and range-separated hybrid functionals (such as B3LYP, PBE0 or HSE06) at a moderate computational cost. As a consequence of the analytical derivative, our approach is computationally efficient and does not suffer from problems related to band crossings.We investigate and compare the performance of a variety of hybrid functionals in evaluating Boltzmann conductivity. Demonstrative examples include silicon and aluminum bulk crystals as well as two thermoelectric materials (CoSb3, 23). We observe that hybrid functionals other than providing more realistic bandgaps--as expected--lead to larger bandwidths and hence allow for a better estimate of transport properties, also in metallic systems. As a nanostructure prototype, we also investigate conductivity in boron-nitride (BN) substituted graphene, in which nanoribbons (nanoroads) alternate with BN ones. [ABSTRACT FROM AUTHOR]

A new ab initio based chemical model for a Direct Simulation Monte Carlo (DSMC) study suitable for simulating rarefied flows with a high degree of non-equilibrium is presented. To this end, Collision Induced Dissociation (CID) cross sections for N2 +N2 → N2 + 2N are calculated and published using a global complete active space self-consistent field-complete active space second order perturbation theory N4 potential energy surface and quasi-classical trajectory algorithm for high energy collisions (up to 30 eV). CID cross sections are calculated for only a selected set of ro-vibrational combinations of the two nitrogen molecules, and a fitting scheme based on spectroscopic weights is presented to interpolate the CID cross section for all possible ro-vibrational combinations. The new chemical model is validated by calculating equilibrium reaction rate coefficients that can be compared well with existing shock tube and computational results. High-enthalpy hypersonic nitrogen flows around a cylinder in the transition flow regime are simulated using DSMC to compare the predictions of the current ab initio based chemical model with the prevailing phenomenological model (the total collision energy model). The differences in the predictions are discussed. [ABSTRACT FROM AUTHOR]

We identify by ab initio calculations a new simple cubic carbon phase in Pa3 symmetry, which has a 48-atom unit cell in all-sp³ bonding networks, thus termed SC48 carbon. It can be viewed as a crystalline form of C12 clusters or a combined structure of SC24 and BC12 carbon, but it is energetically more stable than the recently reported cubic carbon phases such as BC8, SC24, BC12, and fcc-C12. The structural stability is verified by phonon mode analysis. Electronic band and density of state calculations reveal that SC48 carbon is an insulator with a large direct band gap of 4.40 eV. Moreover, simulated x-ray diffraction patterns provide an excellent match to the distinct diffraction peaks found in milled fullerene soot. These results provide a solid foundation for further exploration of this new carbon allotrope. [ABSTRACT FROM AUTHOR]