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.     

The solvent effect on two competing reaction mechanisms involving hypervalent iodine reagents (λ3‐iodanes): Facing the limit of the stationary quantum chemical approach

Trifluoromethylation of acetonitrile with 3,3‐dimethyl‐1‐(trifluoromethyl)?1λ³,2‐ benziodoxol is assumed to occur via reductive elimination (RE) of the electrophilic CF₃‐ligand and MeCN bound to the hypervalent iodine. Computations in gas phase showed that the reaction might also occur via an S_N2 mechanism. There is a substantial solvent effect present for both reaction mechanisms, and their energies of activation are very sensitive toward the solvent model used (implicit, microsolvation, and cluster‐continuum). With polarizable continuum model‐based methods, the S_N2 mechanism becomes less favorable. Applying the cluster‐continuum model, using a shell of solvent molecules derived from ab initio molecular dynamics (AIMD) simulations, the gap between the two activation barriers ( ) is lowered to a few kcal mol^?1 and also shows that the activation entropies ( ) and volumes ( ) for the two mechanisms differ substantially. A quantitative assessment of will therefore only be possible using AIMD. A natural bond orbital‐analysis gives further insight into the activation of the CF₃‐reagent by protonation. © 2014 Wiley Periodicals, Inc.     

Correlation energies in open shell systems. Comparison of CEPA,PNO-CI and perturbation treatments based on the restricted Roothaan-Hartree-Fock formalism

A set of simple molecules in closed and open-shell ground states is treated by the three techniques mentioned in the title, using the same geometries and basis sets (DZ + P). It is found that for nearly all molecules treated in this study (exceptions are H₂ and CH₃) consistently about 98% of the CEPA valence shell correlation energy is obtained by third-order many-body Ray-leigh-Schrödinger perturbation theory (MB-RSPT). The CEPA and MB-RSPT results for reaction energies and barrier heights for some simple reactions differ by 0 to 30 kJ/mol, the CEPA results being in most cases closer to experiment than MB-RSPT, while CI results are much less reliable as long as CI is limited to singly and doubly substituted configurations only.     

Barrier heights of hydrogen‐transfer reactions with diffusion quantum monte carlo method

Hydrogen‐transfer reactions are an important class of reactions in many chemical and biological processes. Barrier heights of H‐transfer reactions are underestimated significantly by popular exchange–correlation functional with density functional theory (DFT), while coupled‐cluster (CC) method is quite expensive and can be applied only to rather small systems. Quantum Monte‐Carlo method can usually provide reliable results for large systems. Performance of fixed‐node diffusion quantum Monte‐Carlo method (FN‐DMC) on barrier heights of the 19 H‐transfer reactions in the HTBH38/08 database is investigated in this study with the trial wavefunctions of the single‐Slater–Jastrow form and orbitals from DFT using local density approximation. Our results show that barrier heights of these reactions can be calculated rather accurately using FN‐DMC and the mean absolute error is 1.0 kcal/mol in all‐electron calculations. Introduction of pseudopotentials (PP) in FN‐DMC calculations improves efficiency pronouncedly. According to our results, error of the employed PPs is smaller than that of the present CCSD(T) and FN‐DMC calculations. FN‐DMC using PPs can thus be applied to investigate H‐transfer reactions involving larger molecules reliably. In addition, bond dissociation energies of the involved molecules using FN‐DMC are in excellent agreement with reference values and they are even better than results of the employed CCSD(T) calculations using the aug‐cc‐pVQZ basis set. © 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.     

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.     

Distinguishing and quantifying the torquoselectivity in competitive ring‐opening reactions using the stress tensor and QTAIM

Currently the theories to explain and predict the classification of the electronic reorganization due to the torquoselectivity of a ring‐opening reaction cannot accommodate the directional character of the reaction pathway; the torquoselectivity is a type of stereoselectivity and therefore is dependent on the pathway. Therefore, in this investigation we introduced new measures from quantum theory of atoms in molecules and the stress tensor to clearly distinguish and quantify the transition states of the inward (TSIC) and outward (TSOC) conrotations of competitive ring‐opening reactions of 3‐(trifluoromethyl)cyclobut‐1‐ene and 1‐cyano‐1‐methylcyclobutene. We find the metallicity ξ( r _b) of the ring‐opening bond does not occur exactly at the transition state in agreement with transition state theory. The vector‐based stress tensor response β_σ was used to distinguish the effect of the CN, CH₃, and CF₃ groups on the TSIC and TSOC paths that was consistent with the ellipticity ε, the total local energy density H( r_b ) and the stress tensor stiffness S_σ. We determine the directional properties of the TSIC and TSOC ring‐opening reactions by constructing a stress tensor space with trajectories (s) with length l in real space, longer l correlated with the lowest density functional theory‐evaluated total energy barrier and hence will be more thermodynamically favored. © 2016 Wiley Periodicals, Inc.     

Fast and accurate determination of the relative binding affinities of small compounds to HIV‐1 protease using non‐equilibrium work

The fast pulling ligand (FPL) out of binding cavity using non‐equilibrium molecular dynamics (MD) simulations was demonstrated to be a rapid, accurate and low CPU demand method for the determination of the relative binding affinities of a large number of HIV‐1 protease (PR) inhibitors. In this approach, the ligand is pulled out of the binding cavity of the protein using external harmonic forces, and the work of pulling force corresponds to the relative binding affinity of HIV‐1 PR inhibitor. The correlation coefficient between the pulling work and the experimental binding free energy of shows that FPL results are in good agreement with experiment. It is thus easier to rank the binding affinities of HIV‐1 PR inhibitors, that have similar binding affinities because the mean error bar of pulling work amounts to . The nature of binding is discovered using the FPL approach. © 2016 Wiley Periodicals, Inc.     

Comparison of CEPA and CP-MET methods

The known CEPA variants CEPA (v) withv = 0,1,2,3 and two new ones withv = 4, 5 are compared both formally and for various numerical examples with CP-MET. The main conclusions are: 1. In those situations where both CP-MET and the CEPA variants are justified (i.e. for “good” closed shell states) the correlation energies obtained with the 7 different schemes differ very little (by something like ±2%), with CEPA (1) closest to CP-MET (difference usually a fraction of 1%) and CEPA (4) nearly as close; this is rather insensitive to whether one uses canonical or localized orbitals. Even CEPA (3) is not too far from CP-MET, which confirms an earlier suggestion of Kelly. 2. In those cases where one of the 7 schemes fails (e.g. due to near degeneracy as in covalent molecules at large internuclear distances) the other 6 usually fail as well, though CEPA (0) is then somewhat poorer than the other schemes. Then no longer CEPA (1) but rather CEPA (3) is closest to CP-MET and then all schemes converge much better in a localized representation. 3. CEPA (2) usually leads to best agreement with experiment since it simulates to some extent triple substitutions. In none of the studied examples does CP-MET show a significant superiority as compared to the other schemes. Possible improvements to extend the domain of applicability of these methods are discussed.     

Calculation of photoionization differential cross sections using complex Gauss‐type orbitals

Accurate theoretical calculation of photoelectron angular distributions for general molecules is becoming an important tool to image various chemical reactions in real time. We show in this article that not only photoionization total cross sections but also photoelectron angular distributions can be accurately calculated using complex Gauss‐type orbital (cGTO) basis functions. Our method can be easily combined with existing quantum chemistry techniques including electron correlation effects, and applied to various molecules. The so‐called two‐potential formula is applied to represent the transition dipole moment from an initial bound state to a final continuum state in the molecular coordinate frame. The two required continuum functions, the zeroth‐order final continuum state and the first‐order wave function induced by the photon field, have been variationally obtained using the complex basis function method with a mixture of appropriate cGTOs and conventional real Gauss‐type orbitals (GTOs) to represent the continuum orbitals as well as the remaining bound orbitals. The complex orbital exponents of the cGTOs are optimized by fitting to the outgoing Coulomb functions. The efficiency of the current method is demonstrated through the calculations of the asymmetry parameters and molecular‐frame photoelectron angular distributions of and . In the calculations of , the static exchange and random phase approximations are employed, and the dependence of the results on the basis functions is discussed. © 2017 Wiley Periodicals, Inc.     

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.     

Coupled‐cluster reaction barriers of : An application of the coupled‐cluster//Kohn–Sham density functional theory model chemistry

In this work, we report a theoretical investigation concerning the use of the popular coupled‐cluster//Kohn‐Sham density functional theory (CC//KS‐DFT) model chemistry, here applied to study the entrance channel of the reaction, namely by comparing CC//KS‐DFT calculations with KS‐DFT, MRPT2//CASSCF, and CC//CASSCF results from our previous investigations. This was done by performing single point energy calculations employing several coupled cluster methods and using KS‐DFT geometries optimized with six different functionals, while conducting a detailed analysis of the barrier heights and topological features of the curves and surfaces here obtained. The quality of this model chemistry is critically discussed in the context of the title reaction and also in a wider context. © 2013 Wiley Periodicals, Inc.     

Rapid QM/MM approach for biomolecular systems under periodic boundary conditions: Combination of the density‐functional tight‐binding theory and particle mesh Ewald method

A quantum mechanical/molecular mechanical (QM/MM) approach based on the density‐functional tight‐binding (DFTB) theory is a useful tool for analyzing chemical reaction systems in detail. In this study, an efficient QM/MM method is developed by the combination of the DFTB/MM and particle mesh Ewald (PME) methods. Because the Fock matrix, which is required in the DFTB calculation, is analytically obtained by the PME method, the Coulomb energy is accurately and rapidly computed. For assessing the performance of this method, DFTB/MM calculations and molecular dynamics simulation are conducted for a system consisting of two amyloid‐β(1‐16) peptides and a zinc ion in explicit water under periodic boundary conditions. As compared with that of the conventional Ewald summation method, the computational cost of the Coulomb energy by utilizing the present approach is drastically reduced, i.e., 166.5 times faster. Furthermore, the deviation of the electronic energy is less than . © 2016 Wiley Periodicals, Inc.     

Anomerization reaction of bare and microhydrated d‐erythrose via explicitly correlated coupled cluster approach. Two water molecules are optimal

We present a comprehensive benchmark computational study which has explored a complete path of the anomerization reaction of bare d ‐erythrose involving a pair of the low‐energy α‐ and β‐furanose anomers, the former of which was observed spectroscopically (Cabezas et al., Chem. Commun. 2013, 49, 10826). We find that the ring opening of the α‐anomer yields the most stable open‐chain tautomer which step is followed by the rotational interconversion of the open‐chain rotamers and final ring closing to form the β‐anomer. Our results indicate the flatness of the reaction's potential energy surface (PES) corresponding to the rotational interconversion path and its sensitivity to the computational level. By using the explicitly correlated coupled cluster CCSD(T)‐F12/cc‐pVTZ‐F12 energies, we determine the free energy barrier for the α‐furanose ring‐opening (rate‐determining) step as 170.3 kJ/mol. The question of the number of water molecules (n ) needed for optimal stabilization of the erythrose anomerization reaction rate‐determining transition state is addressed by a systematic exploration of the PES of the ring opening in the α‐anomer‐(H₂O)_n and various β‐anomer‐(H₂O)_n (n = 1–3) clusters using density functional and CCSD(T)‐F12 computations. These computations suggest the lowest free energy barrier of the ring opening for doubly hydrated α‐anomer, achieved by a mechanism that involves water‐mediated multiple proton transfer coupled with the furanose C O bond breakage. Among the methods used, the G4 performed best against the CCSD(T)‐F12 reference at estimating the ring‐opening barrier heights for both the hydrated and bare erythrose conformers. Our results for the hydrated species are most relevant to an experimental study of the anomerization reaction of d ‐erythrose to be carried out in microsolvation environment. © 2016 Wiley Periodicals, Inc.     

Ab initio potential energy surface and vibration‐rotation energy levels of sulfur dioxide

An accurate potential energy surface of sulfur dioxide, SO₂, in its ground electronic state has been determined from ab initio calculations using the coupled‐cluster approach in conjunction with the correlation‐consistent basis sets up to septuple‐zeta quality. The results obtained with the conventional and explicitly correlated coupled‐cluster methods are compared. The role of the core–electron correlation, higher‐order valence–electron correlation, scalar relativistic, and adiabatic effects in determining the structure and dynamics of the SO₂ molecule is discussed. The vibration‐rotation energy levels of the ³²SO₂ and ³⁴SO₂ isotopologues were predicted using a variational approach. It was shown that the inclusion of the aforementioned effects was mandatory to attain the “spectroscopic” accuracy. © 2017 Wiley Periodicals, Inc.     

Extension of accompanying coordinate expansion and recurrence relation method for general‐contraction basis sets

An algorithm of the accompanying coordinate expansion and recurrence relation (ACE‐RR), which is used for the rapid evaluation of the electron repulsion integral (ERI), has been extended to the general‐contraction (GC) scheme. The present algorithm, denoted by GC‐ACE‐RR, is designed for molecular calculations including heavy elements, whose orbitals consist of many primitive functions with and without higher angular momentum such as d‐ and f‐orbitals. The performance of GC‐ACE‐RR was assessed for ‐, ‐, ‐, and ‐type ERIs in terms of contraction length and the number of GC orbitals. The present algorithm was found to reduce the central processing unit time compared with the ACE‐RR algorithm, especially for higher angular momentum and highly contracted orbitals. Compared with HONDOPLUS and GAMESS program packages, GC‐ACE‐RR computations for ERIs of three‐dimensional gold clusters Au_n (n = 1, 2, …, 10, 15, 20, and 25) are more than 10 times faster. © 2014 Wiley Periodicals, Inc.     

Theoretical investigation of geometry and stability of small lithium‐iodide LinI (n = 2–6) clusters

We present theoretical investigation of the structural characteristics and stabilities of neutral and positively charged Li_nI (n = 2‐6) species. The structural isomers were found by using a randomized algorithm to search for minima structures, followed by B3LYP optimizations; the single‐point RCCSD(T)/cc‐pwCVTZ(‐PP) calculations were performed in order to compute relative energies, binding energies per atom, adiabatic and vertical ionization energies, and dissociation energies. Stability was compared to the pure lithium clusters; there is a typical odd‐even alternation; iodine doped clusters are more stable than pure lithium clusters. Lithium “cage” transfers its valence electron to the iodine atom to form neutral and cationic clusters. An electron departures the lithium cage upon ionization. An important reason for the larger stability of closed‐shell species is the existence of the HOMO 3c/2e natural bond orbitals. © 2013 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.