We introduce a simple but computationally very efficient harmonic force field, which works for all fullerene structures and includes bond stretching, bending, and torsional motions as implemented into our open-source code *Fullerene*. This gives accurate geometries and reasonably accurate vibrational frequencies with root mean square deviations of up to 0.05 Å for bond distances and 45.5 cm^{−1} for vibrational frequencies compared with more elaborate density functional calculations. The structures obtained were used for density functional calculations of Goldberg–Coxeter fullerenes up to C_{980}. This gives a rather large range of fullerenes making it possible to extrapolate to the graphene limit. Periodic boundary condition calculations using density functional theory (DFT) within the projector augmented wave method gave an energy difference between −8.6 and −8.8 kcal/mol at various levels of DFT for the reaction C_{60}graphene (per carbon atom) in excellent agreement with the linear extrapolation to the graphene limit (−8.6 kcal/mol at the Perdew–Burke–Ernzerhof level of theory). © 2015 Wiley Periodicals, Inc.

A general force field is introduced which works for all fullerene isomers. It leads to structures and zero-point vibrational energy contributions in very good agreement to more expensive quantum theoretical calculations. The graphene limit is well represented by the growth of Goldberg-Coxeter transforms of C_{20}.

Pentacene derivative 6,13-dichloropentacene (DCP) is one of the latest additions to the family of organic semiconductors with a great potential for use in transistors. We carry out a detailed theoretical calculation for DCP, with systematical comparison to pentacene, pentathienoacene (PTA, the thiophene equivalent of pentacene), to gain insights in the theoretical design of organic transport materials. The charge transport parameters and carrier mobilities are investigated from the first-principles calculations, based on the widely used Marcus electron transfer theory and quantum nuclear tunneling model, coupled with random walk simulation. Molecular structure and the crystal packing type are essential to understand the differences in their transport behaviors. With the effect of molecule modification, significant one-dimensional *π-*stacks are found within the molecular layer in PTA and DCP crystals. The charge transport along the *a-*axis plays a dominant role for the carrier mobilities in the DCP crystal due to the strong transfer integrals within the *a-*axis. Pentacene shows a relatively large 3D mobility. This is attributed to the relatively uniform electronic couplings, which thus provides more transport pathways. PTA has a much smaller 3D mobility than pentacene and DCP for the obvious increase of the reorganization energy with the introduction of thiophene. It is found that PTA and DCP exhibit lower HOMO (highest occupied molecular orbital) levels and better environmental stability, indicating the potential applications in organic electronics. © 2015 Wiley Periodicals, Inc.

The hole and electron transport properties are theoretically studied for pentacene, pentathienoacene and 6,13-dichloropentacene. A detailed comparative calculation is carried out to gain insights in the theoretical design of organic transport materials.

This article reports a combined quantum mechanics/molecular mechanics (QM/MM) investigation on the acid hydrolysis of cellulose in water using two different models, cellobiose and a 40-unit cellulose chain. The explicitly treated solvent molecules strongly influence the conformations, intramolecular hydrogen bonds, and exoanomeric effects in these models. As these features are largely responsible for the barrier to cellulose hydrolysis, the present QM/MM results for the pathways and reaction intermediates in water are expected to be more realistic than those from a former density functional theory (DFT) study with implicit solvent (CPCM). However, in a qualitative sense, there is reasonable agreement between the DFT/CPCM and QM/MM predictions for the reaction mechanism. Differences arise mainly from specific solute–solvent hydrogen bonds that are only captured by QM/MM and not by DFT/CPCM. © 2015 Wiley Periodicals, Inc.

Acid hydrolysis of cellulose yields glucose. This process is investigated computationally in water using two cellulose models (cellobiose and a 40-unit glucose chain) and explicit solvation. Hydrogen bonding is found to have a large impact on the reaction mechanism and on the barriers to hydrolysis. The results are compared to those from to a previous study with implicit solvation.

We illustrate solving the protein alignment problem exactly using the algorithm VESPA (very efficient search for protein alignment). We have compared our result with the approximate solution obtained with BLAST (basic local alignment search tool) software, which is currently the most widely used for searching for protein alignment. We have selected human and mouse proteins having around 170 amino acids for comparison. The exact solution has found 78 pairs of amino acids, to which one should add 17 *individual* amino acid alignments giving a total of 95 aligned amino acids. BLAST has identified 64 aligned amino acids which involve pairs of more than two adjacent amino acids. However, the difference between the two outputs is not as large as it may appear, because a number of amino acids that are adjacent have been reported by BLAST as *single* amino acids. So if one counts all amino acids, whether isolated (*single*) or in a group of two and more amino acids, then the count for BLAST is 89 and for VESPA is 95, a difference of only six. © 2015 Wiley Periodicals, Inc.

From the list of sequential labels for each adjacent pair of amino acid of two proteins one finds for all pairs of amino acids locations at which they have the same difference in labels. By ordering pairs having the same difference one finds segments at which two proteins have the same amino acids fragments. This information allows construction of the exact alignment of two proteins.

In this work, we aim at optimizing the performance of the anisotropic GBEMP model, which adopts a framework by combining a Gay–Berne (GB) anisotropic potential with an electric multipole (EMP) potential, in simulating a DMPC lipid bilayer in an implicit solvent model. First, the Gay–Berne parameters were initially obtained by fitting to atomistic profiles of van der Waals interactions between homodimers of molecular fragments while EMP parameters was directly derived from the expansion of point multipoles at predefined EMP sites. Second, the GB and EMP parameters for DMPC molecule were carefully optimized to be comparable to AMBER atomistic model in the calculations of the dipole moments of DMPC monomers adopting different conformations as well as the nonbonded interactions between two DMPC molecules adopting different conformations and separated at various distances. Finally, the GB parameters for DMPC were slightly adjusted in simulating a 72 DMPC bilayer system so that our GBEMP model would be able to reproduce a few important structural properties, namely, thickness ( ), area per lipid ( ) and volume per lipid ( ). Meanwhile, the atomistic and experimental results for electron density profiles and order parameters were reproduced reasonably well by the GBEMP model, demonstrating the promising feature of GBEMP model in modeling lipid systems. Finally, we have shown that current GBEMP model is more efficient by a factor of about 25 than AMBER atomistic point charge model. © 2015 Wiley Periodicals, Inc.

The promising performance of an anisotropic coarse-grained model (so-called GBEMP) has been demonstrated in modeling a DMPC lipid bilayer. A 72-DMPC bilayer system was used for testing the performance of the GBEMP model, and it has shown a few important structural properties. In addition, the atomistic and experimental results for electron density profiles and order parameters can be reproduced reasonably well by this GBEMP model.

Previous calculations suggested that di-tetrazine-tetroxide (DTTO), aka tetrazino-tetrazine-tetraoxide, might have a particularly large density (2.3 g/cm^{3}) and high energy release (8.8 kJ/kg), but it has not yet been synthesized successfully. We report here density functional theory (DFT) (M06, B3LYP, and PBE-ulg) on 20 possible isomers of DTTO. For the two most stable isomers, **c1** and **c2** we predict the best packings (i.e., polymorphs) among the 10 most common space groups for organic molecular crystal using the Universal force field and Dreiding force field with Monte Carlo sampling. This was followed by DFT calculations at the PBE-ulg level to optimize the crystal packing. We conclude that the **c1** isomer has the *P2 _{1}2_{1}2_{1}* space group with a density of 1.96 g/cm

The two most stable isomers of Di-tetrazine-tetroxide (DTTO), **c1** and **c2,** were used to predict the most stable polymorphs of DTTO. For the **c1** isomer, the most stable polymorph has *P2 _{1}2_{1}2_{1}* space group with a density of 1.96 g/cm

A method is proposed to study protein–ligand binding in a system governed by specific and nonspecific interactions. Strong associations lead to narrow distributions in the proteins configuration space; weak and ultraweak associations lead instead to broader distributions, a manifestation of nonspecific, sparsely populated binding modes with multiple interfaces. The method is based on the notion that a discrete set of preferential first-encounter modes are metastable states from which stable (prerelaxation) complexes at equilibrium evolve. The method can be used to explore alternative pathways of complexation with statistical significance and can be integrated into a general algorithm to study protein interaction networks. The method is applied to a peptide–protein complex. The peptide adopts several low-population conformers and binds in a variety of modes with a broad range of affinities. The system is thus well suited to analyze general features of binding, including conformational selection, multiplicity of binding modes, and nonspecific interactions, and to illustrate how the method can be applied to study these problems systematically. The equilibrium distributions can be used to generate biasing functions for simulations of multiprotein systems from which bulk thermodynamic quantities can be calculated. © 2015 Wiley Periodicals, Inc.

A method is developed to study protein complexation in a system governed by specific and nonspecific interactions. Strong associations lead to narrow distributions in the configuration space; weak and ultraweak associations lead instead to broader distributions, a manifestation of nonspecific sparsely populated binding modes. The method can be used to explore alternative pathways of complexation with statistical significance and can be integrated into a general algorithm to study protein interaction networks in concentrated multispecies, multiprotein systems.

The adaptation of novel techniques developed in the field of computational chemistry to solve the concerned problems for large and flexible molecules is taking the center stage with regard to efficient algorithm, computational cost and accuracy. In this article, the gradient-based gravitational search (GGS) algorithm, using analytical gradients for a fast minimization to the next local minimum has been reported. Its efficiency as metaheuristic approach has also been compared with Gradient Tabu Search and others like: Gravitational Search, Cuckoo Search, and Back Tracking Search algorithms for global optimization. Moreover, the GGS approach has also been applied to computational chemistry problems for finding the minimal value potential energy of two-dimensional and three-dimensional off-lattice protein models. The simulation results reveal the relative stability and physical accuracy of protein models with efficient computational cost. © 2015 Wiley Periodicals, Inc.

The adaptation of novel techniques developed in the field of computational chemistry to solve the concerned problems for large and flexible molecules is taking center stage with regard to efficient algorithms, computational cost, and accuracy. The gradient-based gravitational search (GGS) algorithm, using analytical gradients for a fast minimization to the next local minimum, has been reported. The GGS approach has been applied to computational chemistry problems for finding the minimal value potential energy of two-dimensional and three-dimensional off-lattice protein models.

Charge transfer among individual atoms is the key concept in modern electronic theory of chemical bonding. In this work, we present a first-principles approach to calculating the charge transfer. Based on the effects of perturbations of an individual atom or a group of atoms on the electron charge density, we determine unambiguously the amount of electron charge associated with a particular atom or a group of atoms. We computed the topological electron loss versus gain using ethylene, graphene, MgO, and SrTiO_{3} as examples. Our results verify the nature of chemical bonds in these materials at the atomic level. © 2015 Wiley Periodicals, Inc.

Charge transfer among individual atoms is the key concept in modern electronic theory of chemical bonding. A first-principles approach to calculating the charge transfer is presented. Based on the effects of perturbations of an individual atom or a group of atoms on the electron charge density, the amount of electron charge associated with a particular atom or a group of atoms is determined. The topological electron loss versus gain is demonstrated using ethylene, graphene, MgO, and SrTiO3 as examples.

A cascaded model is proposed to establish the quantitative structure–activity relationship (QSAR) between the overall power conversion efficiency (PCE) and quantum chemical molecular descriptors of all-organic dye sensitizers. The cascaded model is a two-level network in which the outputs of the first level (*J*_{SC}, *V*_{OC}, and FF) are the inputs of the second level, and the ultimate end-point is the overall PCE of dye-sensitized solar cells (DSSCs). The model combines quantum chemical methods and machine learning methods, further including quantum chemical calculations, data division, feature selection, regression, and validation steps. To improve the efficiency of the model and reduce the redundancy and noise of the molecular descriptors, six feature selection methods (multiple linear regression, genetic algorithms, mean impact value, forward selection, backward elimination, and +*n-m* algorithm) are used with the support vector machine. The best established cascaded model predicts the PCE values of DSSCs with a MAE of 0.57 (%), which is about 10% of the mean value PCE (5.62%). The validation parameters according to the OECD principles are *R*^{2}(0.75), *Q*^{2}(0.77), and
(0.76), which demonstrate the great goodness-of-fit, predictivity, and robustness of the model. Additionally, the applicability domain of the cascaded QSAR model is defined for further application. This study demonstrates that the established cascaded model is able to effectively predict the PCE for organic dye sensitizers with very low cost and relatively high accuracy, providing a useful tool for the design of dye sensitizers with high PCE. © 2015 Wiley Periodicals, Inc.

A cascaded support vector machine CasSVM model is built to establish the relationship between structures of all-organic dye molecules and the overall power conversion efficiency (PCE) of dye sensitized solar cells (DSSCs). The prediction mean absolute error (MAE) is about 10% of the mean value of experimental PCE. The validation parameters show the unique model could efficiently predict the PCE values of DSSCs with little cost, which may be practically useful for developing novel organic dyes.

We introduce a software package for the analysis of biomolecular solvation. The package collects computer codes that implement numerical methods for a variational implicit-solvent model (VISM). The input of the package includes the atomic data of biomolecules under consideration and the macroscopic parameters such as solute–solvent surface tension, bulk solvent density and ionic concentrations, and the dielectric coefficients. The output includes estimated solvation free energies and optimal macroscopic solute–solvent interfaces that are obtained by minimizing the VISM solvation free-energy functional among all possible solute–solvent interfaces enclosing the solute atoms. We review the VISM with various descriptions of electrostatics. We also review our numerical methods that consist mainly of the level-set method for relaxing the VISM free-energy functional and a compact coupling interface method for the dielectric Poisson–Boltzmann equation. Such numerical methods and algorithms constitute the central modules of the software package. We detail the structure of the package, format of input and output files, workflow of the codes, and the postprocessing of output data. Our demo application to a host–guest system illustrates how to use the package to perform solvation analysis for biomolecules, including ligand–receptor binding systems. The package is simple and flexible with respect to minimum adjustable parameters and a wide range of applications. Future extensions of the package use can include the efficient identification of ligand binding pockets on protein surfaces. © 2015 Wiley Periodicals, Inc.

Recent development of a dielectric boundary-based, variational implicit-solvent approach and its robust level-set method implementation have enabled efficient and accurate predictions of the solvation free energies and stable conformations of biomolecules in aqueous solution. This article reviews the new implicit solvation theory and numerical methods, and introduces and details the resulting level-set variational implicit-solvent model, a software package for analysis of biomolecular interactions.

Water is an extremely important liquid for chemistry and the search for more accurate force fields for liquid water continues unabated. Neglect of diatomic differential overlap (NDDO) molecular orbital methods provide and intriguing generalization of classical force fields in this regard because they can account both for bond breaking and electronic polarization of molecules. However, we show that most standard NDDO methods fail for water because they give an incorrect description of hydrogen bonding, water's key structural feature. Using force matching, we design a reparameterized NDDO model and find that it qualitatively reproduces the experimental radial distribution function of water, as well as various monomer, dimer, and bulk properties that PM6 does not. This suggests that the apparent limitations of NDDO models are primarily due to poor parameterization and not to the NDDO approximations themselves. Finally, we identify the physical parameters that most influence the condensed phase properties. These results help to elucidate the chemistry that a semiempirical molecular orbital picture of water must capture. We conclude that properly parameterized NDDO models could be useful for simulations that require electronically detailed explicit solvent, including the calculation of redox potentials and simulation of charge transfer and photochemistry. © 2015 Wiley Periodicals, Inc.

Semiempirical methods offer a cheap, yet physically accurate description of electronic effects in liquid water. However, the popular neglect of diatomic differential overlap (NDDO) method PM6 incorrectly describes water's basic structure. This work examines why PM6 fails for water, and uses force matching to create an improved NDDO model of water.

The topology of the Ehrenfest force density was studied with Slater-type orbitals (STO). At larger distances from the nuclei, STOs generate similar artefacts as noticed before with Gaussian-type orbitals. The topology of the Ehrenfest force density was found to be mainly homeomorphic with the topology of the electron density. For the first time, reliable integrations of several properties over force density atomic basins were performed successfully. Integration of the electron density of a number of hydrides, fluorides, and chlorides of first row elements over force density basins indicate substantial differences between the partial charges of the atoms as compared with those obtained from electron density basins. Calculations on saturated hydrocarbons confirm that the electronegativity of carbon atoms increases with increasing geometrical strain. Atomic interaction lines are observed to exist in the Ehrenfest force density between the hydrogen atoms of several so-called “congested” molecules, and also in some inclusion complexes of alkanes with helium. However, interaction lines are lacking in several other controversial cases. © 2015 Wiley Periodicals, Inc.

The topology of the Ehrenfest force density is studied with Slater-type orbitals and is found to be mainly homeomorphic with the topology of the electron density. Atomic interaction lines are observed to exist in support of the hydrogen–hydrogen bond and are also found in some inclusion complexes of alkanes with helium. However, interaction lines are lacking in several other controversial cases.

The growth of commercial cloud computing (CCC) as a viable means of computational infrastructure is largely unexplored for the purposes of quantum chemistry. In this work, the PSI4 suite of computational chemistry programs is installed on five different types of Amazon World Services CCC platforms. The performance for a set of electronically excited state single-point energies is compared between these CCC platforms and typical, “in-house” physical machines. Further considerations are made for the number of cores or virtual CPUs (vCPUs, for the CCC platforms), but no considerations are made for full parallelization of the program (even though parallelization of the BLAS library is implemented), complete high-performance computing cluster utilization, or steal time. Even with this most pessimistic view of the computations, CCC resources are shown to be more cost effective for significant numbers of typical quantum chemistry computations. Large numbers of large computations are still best utilized by more traditional means, but smaller-scale research may be more effectively undertaken through CCC services. © 2015 Wiley Periodicals, Inc.

Cloud computing is currently a viable alternative to the purchase of in-house hardware for quantum chemistry. As cloud technology improves and the costs of such stabilize or decrease, it is expected that its usage in this field will continue to climb while traditional means may decrease relative to current levels of cloud usage.

In this article, implementation of periodic boundary conditions (PBC) into physics-based coarse-grained UNited RESidue (UNRES) force field is presented, which replaces droplet-like restraints previously used. Droplet-like restraints are necessary to keep multichain systems together and prevent them from dissolving to infinitely low concentration. As an alternative for droplet-like restrains cuboid PBCs with imaging of the molecules were introduced. Owing to this modification, artificial forces which arose from restraints keeping a droplet together were eliminated what leads to more realistic trajectories. Due to computational reasons cutoff and smoothing functions were introduced on the long range interactions. The UNRES force field with PBC was tested by performing microcanonical simulations. Moreover, to asses the behavior of the thermostat in PBCs Langevin and Berendsen thermostats were studied. The influence of PBCs on association pattern was compared with droplet-like restraints on the *ββα* hetero tetramer 1 protein system. © 2015 Wiley Periodicals, Inc.

The implementation of translational periodic conditions allowed for the simulation of multichain system in a UNRES force field with greater reality in association pattern and a removal of the colliding course trajectories.

We present the molecular dynamics study of benzene molecules confined into the single wall carbon nanotube. The local structure and orientational ordering of benzene molecules are investigated. It is found that the molecules mostly group in the middle distance from the axis of the tube to the wall. The molecules located in the vicinity of the wall demonstrate some deviation from planar shape. There is a tilted orientational ordering of the molecules which depends on the location of the molecule. It is shown that the diffusion coefficient of the benzene molecules is very small at the conditions we report here. © 2015 Wiley Periodicals, Inc.

The behavior of benzene confined in single wall carbon nanotube is studied by means of molecular dynamics simulation. Structural and dynamical properties are considered. The density and the temperature effects on the structure and diffusion of benzene are considered.

QuickFF is a software package to derive accurate force fields for isolated and complex molecular systems in a quick and easy manner. Apart from its general applicability, the program has been designed to generate force fields for metal-organic frameworks in an automated fashion. The force field parameters for the covalent interaction are derived from *ab initio* data. The mathematical expression of the covalent energy is kept simple to ensure robustness and to avoid fitting deficiencies as much as possible. The user needs to produce an equilibrium structure and a Hessian matrix for one or more building units. Afterward, a force field is generated for the system using a three-step method implemented in QuickFF. The first two steps of the methodology are designed to minimize correlations among the force field parameters. In the last step, the parameters are refined by imposing the force field parameters to reproduce the *ab initio* Hessian matrix in Cartesian coordinate space as accurate as possible. The method is applied on a set of 1000 organic molecules to show the easiness of the software protocol. To illustrate its application to metal-organic frameworks (MOFs), QuickFF is used to determine force fields for MIL-53(Al) and MOF-5. For both materials, accurate force fields were already generated in literature but they requested a lot of manual interventions. QuickFF is a tool that can easily be used by anyone with a basic knowledge of performing *ab initio* calculations. As a result, accurate force fields are generated with minimal effort. © 2015 Wiley Periodicals, Inc.

QuickFF is a software package to derive accurate force fields for isolated and complex molecular systems in a quick and easy manner. Apart from its general applicability, the program has been designed to generate force fields for metal-organic frameworks in an automated fashion. The force field parameters for the covalent terms are derived from *ab initio* data. As a result, accurate force fields are generated with minimal effort.

Adaptation of improved virtual orbitals (IVOs) in state-specific multireference perturbation theory using Møller–Plesset multipartitioning of the Hamiltonian (IVO-SSMRPT) is examined in which the IVO-complete active space configuration interaction (CASCI) is used as an inexpensive alternative to the more involved CAS-self-consistent field (CASSCF) orbitals. Unlike the CASSCF approach, IVO-CASCI does not bear tedious and costly iterations beyond those in the initial SCF calculation. The IVO-SSMRPT is intruder-free, and explicitly size-extensive. In the present preliminary study, the IVO-SSMRPT method which relies on a small reference space is applied to study potential energy surfaces (PES) of the ground state of challenging, multiconfigurational F_{2}, Be_{2}, and N_{2} molecules. These systems provide a serious challenge to any *ab initio* methodology due to the presence of an intricate interplay of nondynamical and dynamical correlations to the entire PES. The quality of the computed PES has been judged by extracting spectroscopic parameters and vibrational levels. The reported results illustrate that the IVO-SSMRPT method has a potential to yield accuracies as good as the CASSCF-SSMRPT one with reduced computational labor. Even with small reference spaces, our estimates demonstrate a good agreement with the available experimental values, and some benchmark computations. The blend of accuracy and low computational cost of IVO-SSMRPT should deserve future attention for the accurate treatment of electronic states of small to large molecular systems for which the wavefunction is characterized by various configurations. © 2015 Wiley Periodicals, Inc.

Improved virtual orbital-complete active space configuration interaction-based state-specific multireference perturbation theory in the frame of Rayleigh–Schrödinger perturbative expansion has been used to investigate the spectroscopic constants and vibrational spectrum of F_{2}, Be_{2}, and N_{2} through the computation of dissociation energy surfaces.

The prevalence of Mg^{2+} ions in biology and their essential role in nucleic acid structure and function has motivated the development of various Mg^{2+} ion models for use in molecular simulations. Currently, the most widely used models in biomolecular simulations represent a nonbonded metal ion as an ion-centered point charge surrounded by a nonelectrostatic pairwise potential that takes into account dispersion interactions and exchange effects that give rise to the ion's excluded volume. One strategy toward developing improved models for biomolecular simulations is to first identify a Mg^{2+} model that is consistent with the simulation force fields that closely reproduces a range of properties in aqueous solution, and then, in a second step, balance the ion–water and ion–solute interactions by tuning parameters in a pairwise fashion where necessary. The present work addresses the first step in which we compare 17 different nonbonded single-site Mg^{2+} ion models with respect to their ability to simultaneously reproduce structural, thermodynamic, kinetic and mass transport properties in aqueous solution. None of the models based on a 12-6 nonelectrostatic nonbonded potential was able to reproduce the experimental radial distribution function, solvation free energy, exchange barrier and diffusion constant. The models based on a 12-6-4 potential offered improvement, and one model in particular, in conjunction with the SPC/E water model, performed exceptionally well for all properties. The results reported here establish useful benchmark calculations for Mg^{2+} ion models that provide insight into the origin of the behavior in aqueous solution, and may aid in the development of next-generation models that target specific binding sites in biomolecules. © 2015 Wiley Periodicals, Inc.

Mg^{2+} ions are essential for nucleic acid structure and function and this has motivated the development of several Mg^{2+} models for use in molecular simulations. As a first step in developing improved Mg^{2+} models for biomolecular simulations, we focus on the ability to which 17 different pairwise potential Mg^{2+} models, which belong to the most mature force fields for modeling nucleic acid dynamics, can simultaneously reproduce structural, thermodynamic, kinetic and mass transport properties in aqueous solution. These represent a balanced set of solution properties that serve as a useful departure point from which robust models for molecular dynamics simulations of biological processes can be developed by tuning pairwise interaction parameters.

The reduction and oxidation properties of four nitrocompounds (trinitrotoluene [TNT], 2,4-dinitrotoluene, 2,4-dinitroanisole, and 5-nitro-2,4-dihydro-3*H*-1,2,4-triazol-3-one [NTO]) dissolved in water as compared with the same properties for compounds adsorbed on a silica surface were studied. To consider the influence of adsorption, cluster models were developed at the M05/tzvp level. A hydroxylated silica (001) surface was chosen to represent a key component of soil. The PCM(Pauling) and SMD solvation models were used to model water bulk influence. The following properties were analyzed: electron affinity, ionization potential, reduction Gibbs free energy, oxidation Gibbs free energy, and reduction and oxidation potentials. It was found that adsorption and solvation decrease gas phase electron affinity, ionization potential, and Gibbs free energy of reduction and oxidation, and thus, promote redox transformation of nitrocompounds. However, in case of solvation, the changes are more significant than for adsorption. This means that nitrocompounds dissolved in water are easier to transform by reduction or oxidation than adsorbed ones. Among the considered compounds, TNT was found to be the most reactive in an electron attachment process and the least reactive for an electron detachment transformation. During ionization, a deprotonation of adsorbed NTO was found to occur. © 2015 Wiley Periodicals, Inc.

Reduction and oxidation properties of trinitrotoluene (TNT), 2,4-dinitrotoluene (DNT), 2,4-dinitroanisole (DNAN), and 5-nitro-2,4-dihydro-3*H*-1,2,4-triazol-3-one (NTO) were studied in gas phase, in water, and adsorbed on a silica surface state. It was found that adsorption and solvation promote redox transformation of nitrocompounds. Nitrocompounds dissolved in water are easier to transform than adsorbed ones. Reactivity in an electron attachment and electron detachment processes increases in the rows: DNT < DNAN ≈ NTO < TNT and TNT < DNT < DNAN < NTO, respectively.

Procedure for deriving Wyckoff positions for nanowires (NWs) and nanotubes (NTs) from Wyckoff positions of ambient space group is described. It is proposed how to use SITESYM code available on Bilbao Crystallographic Server to calculate representations induced from orbit stabilizers for 1-periodic groups. This procedure is demonstrated on the example of TiO_{2} rutile-based NWs. General analytic expressions for Line group representations induced from irreps of their orbit stabilizers are obtained. This approach presupposes the use of the standard (crystallographic) factorization of Line groups. Computer construction of orbits and induced representations can be efficiently implemented and the corresponding computer code SITESYML, which can be considered as a certain elaboration of the existing code SITESYM is written. The application of the code is demonstrated on the example of TiO_{2} anatase-based NTs with the rectangular and hexagonal morphology. © 2015 Wiley Periodicals, Inc.

General approach to the phonon symmetry analysis for nanowires and nanotubes is outlined. It is illustrated on the example of TiO_{2} rutile-based nanorods and TiO_{2} anatase-based nanotubes with the hexagonal and rectangular morphology, respectively. The number and symmetry of Infrared active, Raman active, and silent modes is found, which is important for the vibrational spectra interpretations of the systems in consideration. There are four acoustic modes with zero frequencies for **k** = 0: three longitudinal acoustic and one twisting.

The dynamics of complex systems with many degrees of freedom can be analyzed by projecting it onto one or few coordinates (collective variables). The dynamics is often described then as diffusion on a free energy landscape associated with the coordinates. Fep1d is a script for the analysis of such one-dimensional coordinates. The script allows one to construct conventional and cut-based free energy profiles, to assess the optimality of a reaction coordinate, to inspect whether the dynamics projected on the coordinate is diffusive, to transform (rescale) the reaction coordinate to more convenient ones, and to compute such quantities as the mean first passage time, the transition path times, the coordinate dependent diffusion coefficient, and so forth. Here, we describe the implemented functionality together with the underlying theoretical framework. © 2015 Wiley Periodicals, Inc.

Multidimensional dynamical processes can be analyzed by projecting them onto one or few coordinates (collective variables). The dynamics is often described then as diffusion on a free energy landscape associated with the coordinates. Fep1d is a script which can be used to answer questions appearing during such an analysis. In particular, the determination of the associated free energy profile and the diffusion coefficient and establishing whether the used coordinate is optimal.

In this study, we use a very simple scheme to achieve range separation of a total exchange–correlation functional. We have utilized this methodology to combine a short-range pure density functional theory (DFT) functional with a corresponding long-range pure DFT, leading to a “Range-separated eXchange–Correlation” (RXC) scheme. By examining the performance of a range of standard exchange–correlation functionals for prototypical short- and long-range properties, we have chosen B-LYP as the short-range functional and PBE-B95 as the long-range counterpart. The results of our testing using a more diverse range of data sets show that, for properties that we deem to be short-range in nature, the performance of this prescribed RXC-DFT protocol does resemble that of B-LYP in most cases, and *vice versa*. Thus, this RXC-DFT protocol already provides meaningful numerical results. Furthermore, we envisage that the general RXC scheme can be easily implemented in computational chemistry software packages. This study paves a way for further refinement of such a range-separation technique for the development of better performing DFT procedures. © 2015 Wiley Periodicals, Inc.

Range separation for the exchanged functional has contributed significantly to the advancement of DFT. A simple “Range-separated eXchange–Correlation” (RXC) scheme is used to divide a total exchange–correlation functional. For properties that are short-range in nature, the performance of the RXC-DFT protocol resembles that of the short-range component, and vice versa. The general RXC scheme can be easily implemented in computational chemistry software packages.

In nanopore force spectroscopy (NFS) a charged polymer is threaded through a channel of molecular dimensions. When an electric field is applied across the insulating membrane, the ionic current through the nanopore reports on polymer translocation, unzipping, dissociation, and so forth. We present a new model that can be applied in molecular dynamics simulations of NFS. Although simplified, it does reproduce experimental trends and all-atom simulations. The scaled conductivities in bulk solution are consistent with experimental results for NaCl for a wide range of electrolyte concentrations and temperatures. The dependence of the ionic current through a nanopore on the applied voltage is symmetric and, in the voltage range used in experiments (up to 2 V), linear and in good agreement with experimental data. The thermal stability and geometry of DNA is well represented. The model was applied to simulations of DNA hairpin unzipping in nanopores. The results are in good agreement with all-atom simulations: the scaled translocation times and unzipping sequence are similar. © 2015 Wiley Periodicals, Inc.

In nanopore force spectroscopy (NFS), a charged polymer is threaded through a channel of molecular dimensions. When an electric field is applied across the insulating membrane, the ionic current through the nanopore reports on polymer translocation, unzipping, dissociation, and so forth. A new model is presented that can be applied in molecular dynamics simulations of NFS. Although simplified, it does reproduce experimental trends and all-atom simulations. The model was applied to simulations of DNA hairpin unzipping in nanopores.

On page 861 (DOI: 10.1002/jcc.23871), Alex Domingo, Celestino Angeli, Coen de Graaf, and Vincent Robert report the intervalence charge transfer (IVCT) between the metal centers of a bi-iron complex induces a response of the whole electronic structure of the compound. The response effects consist of an electronic reorganization that affects each molecular orbital of the complex differently. The π- and n-type orbitals localized on coordinating atoms undergo the largest polarization, being even larger than that of the Fe 3d-like orbitals involved in the transfer. The electronic reorganization follows the induced dipole moment by the IVCT, but having a weaker effect on the orbitals close to the Fe center accepting the transferring electron.

Can allenes and their derivatives perform as efficient leaving groups in catalysis processes? This is the question addressed on page 795 (DOI: 10.1002/jcc.23855) by Nishamol Kuriakose and Kumar Vanka. Specifically, the possibility of these interesting compounds acting as leaving groups in the case of olefin metathesis with the Grubbs catalyst is explored. The investigation is performed with high level quantum chemical calculations using density functional theory (DFT). The results for a range of different allene and substituted allene cases indicate that these compounds would be better by several orders of magnitude in comparison to currently employed leaving groups. This interesting result showcases the potential of this important new class of compounds.

According to high accuracy quantum chemical computations up to the CCSDTQ level, both ^{1}*A*_{1} and ^{3}*A ^{′}*

The electrophilic *N*-trifluoromethylation of MeCN with a hypervalent iodine reagent to form a nitrilium ion, that is rapidly trapped by an azole nucleophile, is thought to occur via reductive elimination (RE). A recent study showed that, depending on the solvent representation, the S_{N}2 is favoured to a different extent over the RE. However, there is a discriminative solvent effect present, which calls for a statistical mechanics approach to fully account for the entropic contributions. In this study, we perform metadynamic simulations for two trifluoromethylation reactions (with *N*- and *S*-nucleophiles), showing that the RE mechanism is always favoured in MeCN solution. These computations also indicate that a radical mechanism (single electron transfer) may play an important role. The computational protocol based on accelerated molecular dynamics for the exploration of the free energy surface is transferable and will be applied to similar reactions to investigate other electrophiles on the reagent. Based on the activation parameters determined, this approach also gives insight into the mechanistic details of the trifluoromethylation and shows that these commonly known mechanisms mark the limits within which the reaction proceeds. © 2015 Wiley Periodicals, Inc.

Hypervalent iodine reagents such as *λ*^{3}-iodanes are frequently used for electrophilic atom/group-transfers. However, little is known about the mechanistic details of these reactions. Based on *ab initio* molecular dynamic simulations of the trifluoromethylation of two different nucleophiles with a *λ*^{3}-iodane in acetonitrile solution, it is shown that the reaction may occur via three concomitant mechanisms (reductive elimination, nucleophilic substitution, radical mechanism), thus each one defining the limits in which the reaction may occur.

There is considerable interest presently in the chemistry of allenes. The current computational investigation looks into the possibility of using allenes and their derivatives as leaving groups. As it is well known, leaving groups are significant in catalytic processes for generating the active site. A full quantum mechanical study using density functional theory shows that allenes and their derivatives can function as excellent leaving groups. Indeed, the calculations show that they can be several orders of magnitude more effective than existing ligands for this purpose. The modification of second generation Grubbs' catalysts with these ligands suggests that the allene ligand cases that would be most effective are those having electron withdrawing groups, especially those that have the potential for supramolecular interactions between the substituent groups in the free state. © 2015 Wiley Periodicals, Inc.

Can allenes and their derivatives perform as efficient leaving groups in catalysis processes? This is the question that is addressed in this study. The results for a range of different allene and substituted allene cases indicate that these compounds would be better by several orders of magnitude in comparison to currently employed leaving groups. This interesting result showcases the potential of this important new class of compounds.

We revisit the singlet–triplet energy gap (Δ*E*_{ST}) of silicon trimer and evaluate the gaps of its derivatives by attachment of a cation (H^{+}, Li^{+}, Na^{+}, and K^{+}) using the wavefunction-based methods including the composite G4, coupled-cluster theory CCSD(T)/CBS, CCSDT and CCSDTQ, and CASSCF/CASPT2 (for Si_{3}) computations. Both ^{1}A_{1} and ^{3}
states of Si_{3} are determined to be degenerate. An intersystem crossing between both states appears to be possible at a point having an apex bond angle of around *α* = 68 ± 2° which is 16 ± 4 kJ/mol above the ground state. The proton, Li^{+} and Na^{+} cations tend to favor the low-spin state, whereas the K^{+} cation favors the high-spin state. However, they do not modify significantly the Δ*E*_{ST}. The proton affinity of silicon trimer is determined as PA(Si_{3}) = 830 ± 4 kJ/mol at 298 K. The metal cation affinities are also predicted to be LiCA(Si_{3}) = 108 ± 8 kJ/mol, NaCA(Si_{3}) = 79 ± 8 kJ/mol and KCA(Si_{3}) = 44 ± 8 kJ/mol. The chemical bonding is probed using the electron localization function, and ring current analyses show that the singlet three-membered ring Si_{3} is, at most, nonaromatic. Attachment of the proton and Li^{+} cation renders it anti-aromatic. © 2015 Wiley Periodicals, Inc.

Both ^{1}A_{1} and ^{3}A^{′}_{2} states of Si_{3} are degenerate. The H^{+}, Li^{+}, and Na^{+} cations favor the singlet state, whereas K^{+} favors the triplet. Some thermochemical parameters are predicted: PA(Si_{3}) = 830 ± 4, LiCA(Si_{3}) =108 ± 8, NaCA(Si_{3}) = 79 ± 8, and KCA(Si_{3}) = 44 ± 8 kJ/mol. The ring current shows that the singlet three-membered Si_{3} ring is, at most, nonaromatic. Attachment of H^{+} and Li^{+} renders it anti-aromatic.

We investigate the accuracy of two-component Douglas–Kroll–Hess (DKH) methods in calculations of the nuclear volume term (≡ lnK_{nv}) in the isotope fractionation coefficient. lnK_{nv} is a main term in the chemical equilibrium constant for isotope exchange reactions in heavy element. Previous work based on the four-component method reasonably reproduced experimental lnK_{nv} values of uranium isotope exchange. In this work, we compared uranium reaction lnK_{nv} values obtained from the two-component and four-component methods. We find that both higher-order relativistic interactions and spin-orbit interactions are essential for quantitative description of lnK_{nv}. The best alternative is the infinite-order Douglas–Kroll–Hess method with infinite-order spin-orbit interactions for the one-electron term and atomic-mean-field spin-same-orbit interaction for the two-electron term (IODKH-IOSO-MFSO). This approach provides almost equivalent results for the four-component method, while being 30 times faster. The IODKH-IOSO-MFSO methodology should pave the way toward computing larger and more general molecules beyond the four-component method limits. © 2015 Wiley Periodicals, Inc.

Nuclear volume term is a main term in the chemical equilibrium constants of isotope fractionations with heavy-element isotopes. The nuclear volume term can be calculated by the four-component Dirac-Hartree-Fock method. In this work, various types of two-component quasi-relativistic methods are performed in an attempt to find alternatives to the time-consuming four-component method. One of the infinite-order Douglass-Kroll-Hess methods is found to be accurate, but 30 times faster than the four-component method.

The halogen bonded complexes between six carbonyl bases and molecular chlorine are investigated theoretically. The interaction energies calculated at the CCSD(T)/aug-cc-pVTZ level range between −1.61 and −3.50 kcal mol^{−1}. These energies are related to the ionization potential, proton affinity, and also to the most negative values (*V*_{s,min}) on the electrostatic potential surface of the carbonyl bases. A symmetry adapted perturbation theory decomposition of the energies has been performed. The interaction results in an elongation of the ClCl bond and a contraction of the CF and CH bonds accompanied by a blue shift of the ν(CH) vibrations. The properties of the Cl_{2} molecules are discussed as a function of the σ*(ClCl) occupation, the hybridization, and the occupation of the Rydberg orbitals of the two chlorine atoms. Our calculations predict a large enhancement of the infrared and Raman intensities of the ν(ClCl) vibration on going from isolated to complexed Cl_{2}. © 2015 Wiley Periodicals, Inc.

The halogen-bonded complexes between six carbonyl bases and molecular chlorine are investigated theoretically. The study includes the optimized geometries and the interaction energies along with an extended natural bond orbital analysis. The interaction energies calculated at the CCSD(T)/aug-cc-pVTZ level range between −1.61 and −3.50 kcal mol^{−1}. These energies are related to the ionization potential and the proton affinity of the carbonyl bases.

We introduce a general procedure to construct a set of one-electron functions in chemical bonding theory, which remain physically sound both for correlated and noncorrelated electronic structure descriptions. These functions, which we call natural adaptive orbitals, decompose the *n*-center bonding indices used in real space theories of the chemical bond into one-electron contributions. For the *n* = 1 case, they coincide with the domain natural orbitals used in domain-averaged Fermi hole analyses. We examine their interpretation in the two-center case, and show how they behave and evolve in simple cases. Orbital pictures obtained through this technique converge onto the chemist's molecular orbital toolbox if electron correlation may be ignored, and provide new insight if it may not. © 2015 Wiley Periodicals, Inc.

A hierarchical set of one-electron functions called natural adaptive orbitals (NAdOs) is introduced. *n*-Center NAdOs decompose real space *n*-center bonding indices into one-electron contributions. NAdOs maintain their meaning both for correlated and noncorrelated descriptions.

To probe the kinetic performance of microsolvated α-nucleophile, the G2(+)_{M} calculations were carried out for the gas-phase S_{N}2 reactions of monohydrated and dihydrated α-oxy-nucleophiles XO^{−}(H_{2}O)_{n}_{ = 1,2} (X = HO, CH_{3}O, F, Cl, Br), and α-sulfur-nucleophile, HSS^{−}(H_{2}O)_{n}_{ = 1,2}, toward CH_{3}Cl. We compared the reactivities of hydrated α-nucleophiles to those of hydrated normal nucleophiles. Our calculations show that the α-effect of monohydrated and dihydrated α-oxy-nucleophiles will become weaker than those of unhydrated ones if we apply a plot of activation barrier as a function of anion basicity. Whereas the enhanced reactivity of monohydrated and dihydrated ROO^{−} (R = H, Me) could be observed if compared them with the specific normal nucleophiles, RO^{−} (R = H, Me). This phenomena can not be seen in the comparisons of XO^{−}(H_{2}O)_{n}_{ = 1,2} (X = F, Cl, Br) with ClC_{2}H_{4}O^{−}(H_{2}O)_{n}_{ = 1,2}, a normal nucleophile with similar gas basicity to XO^{−}(H_{2}O)_{n}_{ = 1,2}. These results have been carefully analyzed by natural bond orbital theory and activation strain model. Meanwhile, the relationships between activation barriers with reaction energies and the ionization energies of α-nucleophile are also discussed. © 2015 Wiley Periodicals, Inc.

The α-effect (ΔΔ*G*_{α}^{≠}; normal for *n* = 0, **bold** for *n* = 1, and *italic* for *n* = 2) exhibited by α-oxy-Nus becomes weaker with microsolvation of nucleophiles, whereas the reactivity of ROO^{−}(H_{2}O)_{n}_{ = 1,2} are enhanced compared with RO^{−}(H_{2}O)_{n}_{ = 1,2} (R = H, CH_{3}), which may be induced by the significant reduction of basicity difference between them from *n* = 0 to *n* = 1 to *n* = 2.

Despite the relatively small size of molecular bromine and iodine, the physicochemical behavior in different solvents is not yet fully understood, in particular when excited-state properties are sought. In this work, we investigate isolated halogen molecules trapped in clathrate hydrate cages. Relativistic supermolecular calculations reveal that the environment shift to the excitation energies of the (nondegenerate) states and lie within a spread of 0.05 eV, respectively, suggesting that environment shifts can be estimated with scalar-relativistic treatments. As even scalar-relativistic calculations are problematic for excited-state calculations for clathrates with growing size and basis sets, we have applied the subsystem-based scheme frozen-density embedding, which avoids a supermolecular treatment. This allows for the calculation of excited states for extended clusters with coupled-cluster methods and basis sets of triple-zeta quality with additional diffuse functions mandatory for excited-state properties, as well as a facile treatment at scalar-relativistic exact two-component level of theory for the heavy atoms bromine and iodine. This simple approach yields scalar-relativistic estimates for solvatochromic shifts introduced by the clathrate cages. © 2015 Wiley Periodicals, Inc.

Solvatochromic shifts are estimated for molecular bromine and iodine trapped in selected clathrate hydrate cages using frozen-density embedding, allowing for the combination of scalar-relativistic and nonrelativistic methods for heavy halogens and light water molecules, respectively.

The key role of the molecular orbitals in describing electron transfer processes is put in evidence for the intervalence charge transfer (IVCT) of a synthetic nonheme binuclear mixed-valence Fe^{3+}/Fe^{2+} compound. The electronic reorganization induced by the IVCT can be quantified by controlling the adaptation of the molecular orbitals to the charge transfer process. We evaluate the transition energy and its polarization effects on the molecular orbitals by means of *ab initio* calculations. The resulting energetic profile of the IVCT shows strong similarities to the Marcus' model, suggesting a response behaviour of the ensemble of electrons analogue to that of the solvent. We quantify the extent of the electronic reorganization induced by the IVCT process to be 11.74 eV, a very large effect that induces the crossing of states reducing the total energy of the transfer to 0.89 eV. © 2015 Wiley Periodicals, Inc.

The electronic reorganization induced by the intervalence charge transfer of a synthetic nonheme binuclear mixed-valence Fe^{3+}/Fe^{2+} complex determines the energy cost of the electron transfer. The largest electronic reorganization occurs in the pyrimidinic N atoms and the bridge O of the first coordination shell, being weaker in the metal centres. The adaptation of the molecular orbitals to the electron transfer is sufficient to inverse the spectroscopy and generate a metastable electron transfer state.