Structure,stability, and nature of bonding in carbon monoxide bound complexes (E = group 14 element; X = H,F, Cl,Br, I)

A density functional theory study is performed to predict the structures and stability of carbon monoxide (CO) bound (E = C, Si, Ge, Sn, Pb; X = H, F, Cl, Br, I) complexes. The possibility of bonding through both C‐ and O‐sides of CO is considered. Thermochemical analysis reveals that all the dissociation processes producing CO and are endothermic in nature whereas most of the dissociation reactions are endergonic in nature at room temperature. The nature of bonding in E? C/O bonds is analyzed via Wiberg bond index, natural population analysis, electron density, and energy decomposition analyses in conjunction with natural orbitals for chemical valence scheme. In comparison to C? O stretching frequency ( ) in free CO, while a red shift is noted in O‐side binding, the C‐side binding results in a blue shift in . The relative change in values in CO bound complexes on changing either E or X is scrutinized and possible explanation is provided in terms of polarization in the σ‐ and π‐orbitals and the relative strength of C→E or O→E σ‐donation and E→C or E→O π‐back‐donation. © 2016 Wiley Periodicals, Inc.     

Computational study of basis set and electron correlation effects on anapole magnetizabilities of chiral molecules

In the presence of a static, nonhomogeneous magnetic field, represented by the axial vector at the origin of the coordinate system and by the polar vector , assumed to be spatially uniform, the chiral molecules investigated in this paper carry an orbital electronic anapole, described by the polar vector . The electronic interaction energy of these molecules in nonordered media is a cross term, coupling and via , one third of the trace of the anapole magnetizability a_αβ tensor, that is, . Both and W^BC have opposite sign in the two enantiomeric forms, a fact quite remarkable from the conceptual point of view. The magnitude of predicted in the present computational investigation for five chiral molecules is very small and significantly biased by electron correlation contributions, estimated at the density functional level via three different functionals. © 2016 Wiley Periodicals, Inc.     

Spin–orbit effects on magnetically induced current densities in the () clusters

This study reports the spin–orbit effects on the aromaticity of the , , , , , and anionic clusters via the magnetically induced current‐density method. All‐electron density functional theory (DFT) calculations were carried out using the four‐component Dirac‐Coulomb (DC) hamiltonian, including scalar and spin–orbit relativistic effects. The magnetic index of aromaticity was calculated by numerical integration over the current flow between two atoms in the pentagonal ring. These values were compared to the spin‐free values (spin–orbit coupling switched off), in order to assess the spin–orbit effect on aromaticity. It was found that in the heavy anions, and , there is a significant influence of the spin–orbit coupling. © 2018 Wiley Periodicals, Inc.     

Low‐energy structures of benzene clusters with a novel accurate potential surface

The benzene‐benzene (Bz‐Bz) interaction is present in several chemical systems and it is known to be crucial in understanding the specificity of important biological phenomena. In this work, we propose a novel Bz‐Bz analytical potential energy surface which is fine‐tuned on accurate ab initio calculations in order to improve its reliability. Once the Bz‐Bz interaction is modeled, an analytical function for the energy of the clusters may be obtained by summing up over all pair potentials. We apply an evolutionary algorithm (EA) to discover the lowest‐energy structures of clusters (for ), and the results are compared with previous global optimization studies where different potential functions were employed. Besides the global minimum, the EA also gives the structures of other low‐lying isomers ranked by the corresponding energy. Additional ab initio calculations are carried out for the low‐lying isomers of and clusters, and the global minimum is confirmed as the most stable structure for both sizes. Finally, a detailed analysis of the low‐energy isomers of the n = 13 and 19 magic‐number clusters is performed. The two lowest‐energy isomers show S₆ and C₃ symmetry, respectively, which is compatible with the experimental results available in the literature. The structures reported here are all non‐symmetric, showing two central Bz molecules surrounded by 12 nearest‐neighbor monomers in the case of the five lowest‐energy structures. © 2015 Wiley Periodicals, Inc.     

Ab initio potential energy surface and vibration–rotation energy levels of germanium dicarbide,GeC2

The accurate ground‐state potential energy surface of germanium dicarbide, GeC₂, has been determined from ab initio calculations using the coupled‐cluster approach. The core–electron correlation, higher‐order valence‐electron correlation, and scalar relativistic effects were taken into account. The potential energy surface of GeC₂ was shown to be extraordinarily flat near the T‐shaped equilibrium configuration. The potential energy barrier to the linear CCGe configuration was predicted to be 1218 cm⁻¹. The vibration–rotation energy levels of some GeC₂ isotopologues were calculated using a variational method. The vibrational bending mode ν₃ was found to be highly anharmonic, with the fundamental wavenumber being only 58 cm⁻¹. Vibrational progressions due to this mode were predicted for the , , and states of GeC₂. © 2018 Wiley Periodicals, Inc.     

Structure and electrochemical properties for complexes of nitrocompounds with inorganic ions: A theoretical approach

Reduction and oxidation (redox) reactions are widely used for removal of nitrocompounds from contaminated soil and water. Structures and redox properties for complexes of nitrocompounds, such as 2,4,6‐trinitrotoluene (TNT), 2,4‐dinitrotoluene (DNT), 2,4‐dinitroanisole (DNAN), and 5‐nitro‐2,4‐dihydro‐3H?1,2,4‐triazol‐3‐one (NTO), with common inorganic ions (Na⁺, Cl^?, ) were investigated at the SMD(Pauling)/PCM(Pauling)/MPWB1K/TZVP level of theory. Atoms in molecules (AIM) theory was applied to analyze the topological properties of the bond critical points involved in the interactions between the nitrocompounds and the ions. Topological analyses show that intermolecular interactions of the types O(N)…Na⁺, C‐H…Cl^?( ), and C…Cl^?( ) may be discussed as noncovalent closed‐shell interactions, while N‐H···Cl^?( ) hydrogen bonds are partially covalent in nature. Complexation causes significant decrease of redox activity of the nitrocompounds. Analysis of the reduction potentials of the complexes obtained through application of the Pourbaix diagram of an iron/water system revealed that sodium complexes of NTO might be reduced by metallic iron. © 2016 Wiley Periodicals, Inc.     

Effects of zero point vibration on the reaction dynamics of water dimer cations following ionization

Reactions of water dimer cation following ionization have been investigated by means of a direct ab initio molecular dynamics method. In particular, the effects of zero point vibration and zero point energy (ZPE) on the reaction mechanism were considered in this work. Trajectories were run on two electronic potential energy surfaces (PESs) of : ground state (²A″‐like state) and the first excited state (²A′ ‐ like state). All trajectories on the ground‐state PES lead to the proton‐transferred product: H₂O⁺(Wd)‐H₂O(Wa) → OH(Wd)‐H₃O⁺(Wa), where Wd and Wa refer to the proton donor and acceptor water molecules, respectively. Time of proton transfer (PT) varied widely from 15 to 40 fs (average time of PT = 30.9 fs). The trajectories on the excited‐state PES gave two products: an intermediate complex with a face‐to‐face structure (H₂O‐OH₂)⁺ and a PT product. However, the proton was transferred to the opposite direction, and the reverse PT was found on the excited‐state PES: H₂O(Wd)‐H₂O⁺ (Wa) → H₃O⁺(Wd)‐OH(Wa). This difference occurred because the ionizing water molecule in the dimer switched between the ground and excited states. The reaction mechanism of and the effects of ZPE are discussed on the basis of the results. © 2017 Wiley Periodicals, Inc.     

Fast search algorithms for computational protein design

One of the main challenges in computational protein design (CPD) is the huge size of the protein sequence and conformational space that has to be computationally explored. Recently, we showed that state‐of‐the‐art combinatorial optimization technologies based on Cost Function Network (CFN) processing allow speeding up provable rigid backbone protein design methods by several orders of magnitudes. Building up on this, we improved and injected CFN technology into the well‐established CPD package Osprey to allow all Osprey CPD algorithms to benefit from associated speedups. Because Osprey fundamentally relies on the ability of to produce conformations in increasing order of energy, we defined new strategies combining CFN lower bounds, with new side‐chain positioning‐based branching scheme. Beyond the speedups obtained in the new ‐CFN combination, this novel branching scheme enables a much faster enumeration of suboptimal sequences, far beyond what is reachable without it. Together with the immediate and important speedups provided by CFN technology, these developments directly benefit to all the algorithms that previously relied on the DEE/ combination inside Osprey* and make it possible to solve larger CPD problems with provable algorithms. © 2016 Wiley Periodicals, Inc.     

Polygonal current models for polycyclic aromatic hydrocarbons and graphene sheets of various shapes

Assuming that graphene is an “infinite alternant” polycyclic aromatic hydrocarbon resulting from tessellation of a surface by only six‐membered carbon rings, planar fragments of various size and shape (hexagon, triangle, rectangle, and rhombus) have been considered to investigate their response to a magnetic field applied perpendicularly. Allowing for simple polygonal current models, the diatropicity of a series of polycyclic textures has been reliably determined by comparing quantitative indicators, the π‐electron contribution to I^B, the magnetic field‐induced current susceptibility of the peripheral circuit, to and to , respectively the out‐of‐plane components of the magnetizability tensor and of the magnetic shielding tensor at the center of mass. Extended numerical tests and the analysis based on the polygonal model demonstrate that (i) and yield inadequate and sometimes erroneous measures of diatropicity, as they are heavily flawed by spurious geometrical factors, (ii) I^B values computed by simple polygonal models are valid quantitative indicators of aromaticity on the magnetic criterion, preferable to others presently available, whenever current susceptibility cannot be calculated ab initio as a flux integral, (iii) the hexagonal shape is the most effective to maximize the strength of π‐electron currents over the molecular perimeter, (iv) the edge current strength of triangular and rhombic graphene fragments is usually much smaller than that of hexagonal ones, (v) doping by boron and nitrogen nuclei can regulate and even inhibit peripheral ring currents, (vi) only for very large rectangular fragments can substantial current strengths be expected. © 2017 Wiley Periodicals, Inc.     

Nuclear quantum effects induce metallization of dense solid molecular hydrogen

We present an accurate computational study of the electronic structure and lattice dynamics of solid molecular hydrogen at high pressure. The band‐gap energies of the , Pc, and structures at pressures of 250, 300, and 350 GPa are calculated using the diffusion quantum Monte Carlo (DMC) method. The atomic configurations are obtained from ab initio path‐integral molecular dynamics (PIMD) simulations at 300 K and 300 GPa to investigate the impact of zero‐point energy and temperature‐induced motion of the protons including anharmonic effects. We find that finite temperature and nuclear quantum effects reduce the band‐gaps substantially, leading to metallization of the and Pc phases via band overlap; the effect on the band‐gap of the structure is less pronounced. Our combined DMC‐PIMD simulations predict that there are no excitonic or quasiparticle energy gaps for the and Pc phases at 300 GPa and 300 K. Our results also indicate a strong correlation between the band‐gap energy and vibron modes. This strong coupling induces a band‐gap reduction of more than 2.46 eV in high‐pressure solid molecular hydrogen. Comparing our DMC‐PIMD with experimental results available, we conclude that none of the structures proposed is a good candidate for phases III and IV of solid hydrogen. © 2017 Wiley Periodicals, Inc.     

Assessment of hydrophobic interactions and their contributions through the analysis of the methane dimer

Hydrophobic Interactions (HIs) are important in many phenomena of molecular recognition in chemistry and biology. Still, the relevance of HIs is sometimes difficult to evaluate particularly in large systems and intramolecular interactions. We put forward a method to estimate the magnitude and the different contributions of a given HI of the C···C, H? C···H, and H···H type through (i) the analysis of the electron density in the intermolecular region for eleven relative orientations of the methane dimer and (ii) the subsequent decomposition of the corresponding interaction energy in physically significant contributions using Symmetry Adapted Perturbation Theory (SAPT). Strong correlations were found between the topological properties of calculated at intermolecular bond critical points and plus its different contributions with the C···C distance of the considered orientations of (CH₄)₂. These correlations were used to construct Mollier‐like diagrams of and its components as a function of the separation between two carbons and the orientation of the groups bonded to these atoms. The ethane dimer and tert‐butylcyclohexane are used as representative examples of this new approach. Overall, we anticipate that this new method might prove useful in the study of both intramolecular and intermolecular HIs particularly of those within large systems wherein SAPT or electronic structure calculations are computationally expensive or even prohibitive. © 2014 Wiley Periodicals, Inc.     

Development of spin‐orbit coupling for stochastic configuration interaction techniques

To perform spin‐orbit coupling calculations on atoms and molecules, good zeroth‐order wavefunctions are necessary. Here, we present the software development of the Monte Carlo Configuration Interaction (MCCI) method, to enable calculation of such properties, where MCCI iteratively constructs a multireference wavefunction using a stochastic procedure. In this initial work, we aim to establish the efficacy of this technique in predicting the splitting of otherwise degenerate energy levels on a range of atoms and small diatomic molecules. It is hoped that this work will subsequently act as a gateway toward using this method to investigate singlet‐triplet interactions in larger multireference molecules. We show that MCCI can generate very good results using highly compact wavefunctions compared to other techniques, with no prior knowledge of important orbitals. Higher‐order relativistic effects are neglected and spin‐orbit coupling effects are incorporated using first‐order degenerate perturbation theory with the Breit‐Pauli Hamiltonian and effective nuclear charges in the one‐electron operator. Results are obtained and presented for B, C, O, F, Si, S, and Cl atoms and OH, CN, NO, and C₂ diatomic radicals including spin‐orbit coupling constants and the relative splitting of the lowest energy degenerate state for each species. Convergence of MCCI to the full configuration interaction result is demonstrated on the multireference problem of stretched OH. We also present results from the singlet‐triplet interaction between the and both the and states of the O₂ molecule. © 2017 Wiley Periodicals, Inc.     

Quantum Monte Carlo with very large multideterminant wavefunctions

An algorithm to compute efficiently the first two derivatives of (very) large multideterminant wavefunctions for quantum Monte Carlo calculations is presented. The calculation of determinants and their derivatives is performed using the Sherman–Morrison formula for updating the inverse Slater matrix. An improved implementation based on the reduction of the number of column substitutions and on a very efficient implementation of the calculation of the scalar products involved is presented. It is emphasized that multideterminant expansions contain in general a large number of identical spin‐specific determinants: for typical configuration interaction‐type wavefunctions the number of unique spin‐specific determinants ( ) with a non‐negligible weight in the expansion is of order . We show that a careful implementation of the calculation of the N_det ‐dependent contributions can make this step negligible enough so that in practice the algorithm scales as the total number of unique spin‐specific determinants, , over a wide range of total number of determinants (here, N_det up to about one million), thus greatly reducing the total computational cost. Finally, a new truncation scheme for the multideterminant expansion is proposed so that larger expansions can be considered without increasing the computational time. The algorithm is illustrated with all‐electron fixed‐node diffusion Monte Carlo calculations of the total energy of the chlorine atom. Calculations using a trial wavefunction including about 750,000 determinants with a computational increase of ～400 compared to a single‐determinant calculation are shown to be feasible. © 2016 Wiley Periodicals, Inc.     

Horizontal vectorization of electron repulsion integrals

We present an efficient implementation of the Obara–Saika algorithm for the computation of electron repulsion integrals that utilizes vector intrinsics to calculate several primitive integrals concurrently in a SIMD vector. Initial benchmarks display a 2–4 times speedup with AVX instructions over comparable scalar code, depending on the basis set. Speedup over scalar code is found to be sensitive to the level of contraction of the basis set, and is best for quartets when l_D = 0 or , which makes such a vectorization scheme particularly suitable for density fitting. The basic Obara–Saika algorithm, how it is vectorized, and the performance bottlenecks are analyzed and discussed. © 2016 Wiley Periodicals, Inc.     

Accurate,robust, and reliable calculations of Poisson–Boltzmann binding energies

Poisson–Boltzmann (PB) model is one of the most popular implicit solvent models in biophysical modeling and computation. The ability of providing accurate and reliable PB estimation of electrostatic solvation free energy, , and binding free energy, , is important to computational biophysics and biochemistry. In this work, we investigate the grid dependence of our PB solver (MIBPB) with solvent excluded surfaces for estimating both electrostatic solvation free energies and electrostatic binding free energies. It is found that the relative absolute error of obtained at the grid spacing of 1.0 Å compared to at 0.2 Å averaged over 153 molecules is less than 0.2%. Our results indicate that the use of grid spacing 0.6 Å ensures accuracy and reliability in calculation. In fact, the grid spacing of 1.1 Å appears to deliver adequate accuracy for high throughput screening. © 2017 Wiley Periodicals, Inc.     

Accurate double many‐body expansion potential energy surface by extrapolation to the complete basis set limit and dynamics calculations for ground state of NH2

An accurate single‐sheeted double many‐body expansion potential energy surface is reported for the title system. A switching function formalism has been used to warrant the correct behavior at the and dissociation channels involving nitrogen in the ground and first excited states. The topographical features of the novel global potential energy surface are examined in detail, and found to be in good agreement with those calculated directly from the raw ab initio energies, as well as previous calculations available in the literature. The novel surface can be using to treat well the Renner–Teller degeneracy of the and states of . Such a work can both be recommended for dynamics studies of the reaction and as building blocks for constructing the double many‐body expansion potential energy surface of larger nitrogen/hydrogen‐containing systems. In turn, a test theoretical study of the reaction has been carried out with the method of quantum wave packet on the new potential energy surface. Reaction probabilities, integral cross sections, and differential cross sections have been calculated. Threshold exists because of the energy barrier (68.5 meV) along the minimum energy path. On the curve of reaction probability for total angular momentum J = 0, there are two sharp peaks just above threshold. The value of integral cross section increases quickly from zero to maximum with the increase of collision energy, and then stays stable with small oscillations. The differential cross section result shows that the reaction is a typical forward and backward scatter in agreement with experimental measurement result. © 2013 Wiley Periodicals, Inc.     

Quantum chemical study of the autoxidation of ascorbate

Reactions involved in the autoxidation of ascorbate have been investigated with quantum chemical first‐principles and ab initio methods. Reaction energies and Gibbs energies of the reactions were calculated at the density functional theory level applying the gradient‐corrected BP86 and the hybrid B3LYP functionals together with def2‐TZVP basis sets. Results of single‐point CC2, CCSD, and CCSD(T) calculations were used for calibration of the density functional theory data and show excellent agreement with the B3LYP values. Based on the Gibbs energy ascorbic acid AscH₂ is found to be the energetically lowest species in aqueous solution, whereas the monoanion ascorbate AscH is the most abundant one near pH = 7. Asc was found to be the preferred reducing agent for autoxidation and oxidation processes. The results also support a metal‐catalyzed synthesis of the reactive oxygen species H₂O₂ according to a redox cycling mechanism proposed in literature. © 2016 Wiley Periodicals, Inc.     

Revealing the physical nature and the strength of charge‐inverted hydrogen bonds by SAPT(DFT), MP2, SCS‐MP2, MP2C,and CCSD(T) methods

The physical nature of charge‐inverted hydrogen bonds in H₃XH YH₃ (X = Si, Ge; Y = Al, Ga) dimer systems is studied by means of the SAPT(DFT)‐based decomposition of interaction energies and supermolecular interaction energies based on MP2, SCS‐MP2, MP2C, and CCSD(T) methods utilizing dimer‐centered aug‐cc‐pCVnZ (n = D, T, Q) basis sets as well as an extrapolation to the complete basis set limit. It is revealed that charge‐inverted hydrogen bonds are inductive in nature, although dispersion is also important. Computed interaction energies form the following relation: . It is confirmed that the aug‐cc‐pCVDZ basis set performs poorly and that very accurate values of interaction and dispersion energies require basis sets of at least quadrupole‐ζ quality. Considerably large binding energies suggest potential usefulness of charge‐inverted hydrogen bonds as an important structural motif in molecular binding. Terminology applying to σ‐ and π‐hole interactions as well as to triel and tetrel bonds is discussed. According to this new terminology the charge‐inverted hydrogen bond would become the first described case of a hydride‐triel bond. © 2017 Wiley Periodicals, Inc.     

Aqueous acidities of primary benzenesulfonamides: Quantum chemical predictions based on density functional theory and SMD

Aqueous of selected primary benzenesulfonamides are predicted in a systematic manner using density functional theory methods and the SMD solvent model together with direct and proton exchange thermodynamic cycles. Some test calculations were also performed using high‐level composite CBS‐QB3 approach. The direct scheme generally does not yield a satisfactory agreement between calculated and measured acidities due to a severe overestimation of the Gibbs free energy changes of the gas‐phase deprotonation reaction by the used exchange‐correlation functionals. The relative values calculated using proton exchange method compare to experimental data very well in both qualitative and quantitative terms, with a mean absolute error of about 0.4 units. To achieve this accuracy, we find it mandatory to perform geometry optimization of the neutral and anionic species in the gas and solution phases separately, because different conformations are stabilized in these two cases. We have attempted to evaluate the effect of the conformer‐averaged free energies in the predictions, and the general conclusion is that this procedure is highly too costly as compared with the very small improvement we have gained. © 2015 Wiley Periodicals, Inc.