The recent σ-hole concept emphasizes the contribution of electrostatic attraction to noncovalent bonds, and implies that the electrostatic force has an angular dependency. Here a set of clusters, which includes hydrogen bonding, halogen bonding, chalcogen bonding, and pnicogen bonding systems, is investigated to probe the magnitude of covalency and its contribution to the directionality in noncovalent bonding. The study is based on the block-localized wavefunction (BLW) method that decomposes the binding energy into the steric and the charge transfer (CT) (hyperconjugation) contributions. One unique feature of the BLW method is its capability to derive optimal geometries with only steric effect taken into account, while excluding the CT interaction. The results reveal that the overall steric energy exhibits angular dependency notably in halogen bonding, chalcogen bonding, and pnicogen bonding systems. Turning on the CT interactions further shortens the intermolecular distances. This bond shortening enhances the Pauli repulsion, which in turn offsets the electrostatic attraction, such that in the final sum, the contribution of the steric effect to bonding is diminished, leaving the CT to dominate the binding energy. In several other systems particularly hydrogen bonding systems, the steric effect nevertheless still plays the major role whereas the CT interaction is minor. However, in all cases, the CT exhibits strong directionality, suggesting that the linearity or near linearity of noncovalent bonds is largely governed by the charge-transfer interaction whose magnitude determines the covalency in noncovalent bonds. © 2015 Wiley Periodicals, Inc.

The block-localized wavefunction method, which can derive hypothetical structures without the charge transfer effect and conduct intermolecular energy decomposition analysis, is used to probe the origins of the directionality of weak noncovalent bonds. While the overall steric energy exhibits certain angular dependency, in all cases the charge transfer exhibits the strongest directionality, suggesting that the linearity or near linearity of noncovalent bonds is largely governed by the charge-transfer interaction whose magnitude determines the bond covalency.

Despite the fact that the complexation of ammonium cations with ionophores like crown ethers plays an important role in biological and industrial processes, there is still a lack of theoretical methods to reproduce or even predict the host–guest complex structures or their thermodynamic stabilities in an accurate manner. Hence, the development of ionophores has often relied on a trial-and-error approach and the synthetic efforts associated with this have been enormous, so far. Therefore, theoretical methods for the reliable prediction of binding affinities of crown ether derivatives with ammonium ions would be an indispensable tool for the rational design of new receptors with tailored properties. Here, we suggest a computationally efficient but still accurate theoretical approach. It is tested for a model system consisting of 18-crown-6 ether and an ammonium cation, but is invented for application to much larger complexes. The accuracy of various approximate quantum-chemical methods, based on density functional theory (DFT) and many-body perturbation theory, is evaluated against the gold standard CCSD(T) in the basis set limit as internal reference. An important aspect is the consideration of dispersion interactions in DFT methods, for which the dispersion-correction by Grimme was employed. For all selected methods, the basis-set dependence of calculated interaction energies was investigated. © 2015 Wiley Periodicals, Inc.

A protocol for the efficient calculation of supramolecular binding affinities of crown ether derivatives with ammonium cations is presented. The performance of various density functionals and the MP2 method is investigated and the influence of dispersion interaction is analyzed. CCSD(T) binding energies extrapolated to the basis set limit served as internal reference.

Metadynamics (MTD) is a powerful enhanced sampling method for systems with rugged energy landscapes. It constructs a bias potential in a predefined collective variable (CV) space to overcome barriers between metastable states. In bias-exchange MTD (BE-MTD), multiple replicas approximate the CV space by exchanging bias potentials (replica conditions) with the Metropolis–Hastings (MH) algorithm. We demonstrate that the replica-exchange rates and the convergence of free energy estimates of BE-MTD are improved by introducing the infinite swapping (IS) or the Suwa-Todo (ST) algorithms. Conceptually, IS and ST perform transitions in a replica state space rather than exchanges in a replica condition space. To emphasize this, the proposed scheme is called the replica state exchange MTD (RSE-MTD). Benchmarks were performed with alanine polypeptides in vacuum and water. For the systems tested in this work, there is no significant performance difference between IS and ST. © 2015 Wiley Periodicals, Inc.

Metadynamics (MTD) is a powerful enhanced sampling method for systems with rugged energy landscapes. It constructs a bias potential in a collective variable (CV) space to overcome barriers between metastable states. In the bias-exchange MTD (BE-MTD), multiple replicas approximate the CV space by exchanging bias potentials (replica conditions). We propose the replica state exchange metadynamics (RSE-MTD), which use a more sophisticated replica-exchange scheme to improve the convergence of free energy for a given simulation time.

The mechanism of acetonitrile and methyl benzoate catalytic hydrogenation using pincer catalysts M(H)_{2}(CO)[NH(C_{2}H_{4}P*i*Pr_{2})_{2}] (**1M**) and M(H)(CO)[N(C_{2}H_{4}P*i*Pr_{2})_{2}] (**2M**) (M = Fe, Ru, Os) has been computed at various levels of density functional theory. The computed equilibrium between **1Fe** and **2Fe** agrees perfectly with the experimental observations. On the basis of the activation barriers and reaction energies, the best catalysts for acetonitrile hydrogenation are **1Fe/2Fe** and **1Ru/2Ru**, and the best catalysts for methyl benzoate hydrogenation are **1Ru/2Ru**. The best catalysts for the dehydrogenation of benzyl alcohol are **1Ru/2Ru**. It is to note that the current polarizable continuum model is not sufficient in modeling the solvation effect in the energetic properties of these catalysts as well as their catalytic properties in hydrogenation reaction, as no equilibrium could be established between **1Fe** and **2Fe**. Comparison with other methods and procedures has been made. © 2015 Wiley Periodicals, Inc.

DFT studies on the defined pincer-type catalysts M(H)_{2}(CO)[NH(C_{2}H_{4}P*i*Pr_{2})_{2}] (**1M**) and M(H)(CO)[N(C_{2}H_{4}P*i*Pr_{2})_{2}] (**2M**) (M = Fe, Ru, Os) reveal remarkable differences in electronic structures and hydrogenation reactivity of nitriles, ester, and ketones. For acetonitrile hydrogenation, Fe- and Ru-based catalysts are best. For methyl benzoate hydrogenation and dehydrogenation of benzyl alcohol, Ru-based catalysts are best. In contrast, Os-based catalysts are least active.

We present here a set of algorithms that completely rewrites the Hartree–Fock (HF) computations common to many legacy electronic structure packages (such as GAMESS-US, GAMESS-UK, and NWChem) into a massively parallel compute scheme that takes advantage of hardware accelerators such as Graphical Processing Units (GPUs). The HF compute algorithm is core to a library of routines that we name the Quantum Supercharger Library (QSL). We briefly evaluate the QSL's performance and report that it accelerates a HF 6-31G Self-Consistent Field (SCF) computation by up to 20 times for medium sized molecules (such as a buckyball) when compared with mature Central Processing Unit algorithms available in the legacy codes in regular use by researchers. It achieves this acceleration by massive parallelization of the one- and two-electron integrals and optimization of the SCF and Direct Inversion in the Iterative Subspace routines through the use of GPU linear algebra libraries. © 2015 Wiley Periodicals, Inc.

The Quantum Supercharger Library's Hartree–Fock module completely performed on a GPU hardware accelerator in double precision yields up to a 19× speed-up over the best performing GAMESS-UK CPU software.

This article describes an extension of the quantum supercharger library (QSL) to perform quantum mechanical (QM) gradient and optimization calculations as well as hybrid QM and molecular mechanical (QM/MM) molecular dynamics simulations. The integral derivatives are, after the two-electron integrals, the most computationally expensive part of the aforementioned calculations/simulations. Algorithms are presented for accelerating the one- and two-electron integral derivatives on a graphical processing unit (GPU). It is shown that a Hartree–Fock *ab initio* gradient calculation is up to 9.3X faster on a single GPU compared with a single central processing unit running an optimized serial version of GAMESS-UK, which uses the efficient Schlegel method for
- and
-orbitals. Benchmark QM and QM/MM molecular dynamics simulations are performed on cellobiose *in vacuo* and in a 39 Å water sphere (45 QM atoms and 24843 point charges, respectively) using the 6-31G basis set. The QSL can perform 9.7 ps/day of *ab initio* QM dynamics and 6.4 ps/day of QM/MM dynamics on a single GPU in full double precision. © 2015 Wiley Periodicals, Inc.

Complete parallelization of the one and two integral derivatives for GPU accelerators provides high speed *ab initio* QM/MM simulations of 10ps/day for single off-the-shelf GPU cards.

Combining classical force fields for the Hartree–Fock (HF) part and the method of increments for post-HF contributions, we calculate the cohesive energy of the ordered and randomly disordered nitrous oxide (N_{2}O) solid. At 0 K, ordered N_{2}O is most favorable with a cohesive energy of −27.7 kJ/mol. At temperatures above 60 K, more disordered structures become compatible and a phase transition to completely disordered N_{2}O is predicted. Comparison with experiment in literature suggests that experimentally prepared N_{2}O crystals are mainly disordered due to a prohibitively high activation energy of ordering processes. © 2015 Wiley Periodicals, Inc.

This study demonstrates a statistical approach to the calculation of temperature-dependent cohesive energies of randomly disordered molecular crystals such as nitrous oxide (N_{2}O) at sophisticated levels of post-Hartree-Fock theory.

Pteros is the high-performance open-source library for molecular modeling and analysis of molecular dynamics trajectories. Starting from version 2.0 Pteros is available for C++ and Python programming languages with very similar interfaces. This makes it suitable for writing complex reusable programs in C++ and simple interactive scripts in Python alike. New version improves the facilities for asynchronous trajectory reading and parallel execution of analysis tasks by introducing analysis plugins which could be written in either C++ or Python in completely uniform way. The high level of abstraction provided by analysis plugins greatly simplifies prototyping and implementation of complex analysis algorithms. Pteros is available for free under Artistic License from http://sourceforge.net/projects/pteros/. © 2015 Wiley Periodicals, Inc.

Pteros 2.0 is the high-performance open-source library for molecular modeling and analysis of molecular dynamics trajectories in C++ and Python languages. Pteros is suitable for writing complex reusable programs in C++ and simple interactive scripts in Python. The new version improves the facilities for asynchronous trajectory reading and parallel execution of analysis tasks by introducing analysis plug-ins, which could be written in either C++ or Python in a completely uniform way. The high level of abstraction provided by analysis plug-ins greatly simplifies prototyping and implementation of complex analysis algorithms.

The seven main crystal surfaces of forsterite (Mg_{2}SiO_{4}) were modeled using various Gaussian-type basis sets, and several formulations for the exchange-correlation functional within the density functional theory (DFT). The recently developed pob-TZVP basis set provides the best results for all properties that are strongly dependent on the accuracy of the wavefunction. Convergence on the structure and on the basis set superposition error-corrected surface energy can be reached also with poorer basis sets. The effect of adopting different DFT functionals was assessed. All functionals give the same stability order for the various surfaces. Surfaces do not exhibit any major structural differences when optimized with different functionals, except for higher energy orientations where major rearrangements occur around the Mg sites at the surface or subsurface. When dispersions are not accounted for, all functionals provide similar surface energies. The inclusion of empirical dispersions raises the energy of all surfaces by a nearly systematic value proportional to the scaling factor *s* of the dispersion formulation. An estimation for the surface energy is provided through adopting *C*_{6} coefficients that are more suitable than the standard ones to describe OO interactions in minerals. A 2 × 2 supercell of the most stable surface (010) was optimized. No surface reconstruction was observed. The resulting structure and surface energy show no difference with respect to those obtained when using the primitive cell. This result validates the (010) surface model here adopted, that will serve as a reference for future studies on adsorption and reactivity of water and carbon dioxide at this interface. © 2015 Wiley Periodicals, Inc.

This article presents an accurate assessment of methods for the study of forsterite surface properties and reactivity. The ability to build a realistic model for such system is essential to understand the fundamental interactions responsible for a variety of natural phenomena happening on Earth and in space.

This work is focused on the efficient evaluation of the Boys function located at the heart of Coulomb and exchange type electron integrals. Different evaluation strategies for individual orders and arguments of the Boys function are used to achieve a minimal number of floating-point operations. Based on previous work of other groups, two similar algorithms are derived that are compared based on both accuracy and efficiency: The first algorithm combines the work of Gill et al. (Int. J. Quantum Chem. 1991, 40, 745) and Kazuhiro Ishida (Int. J. Quantum Chem. 1996, 59, 209 and following work), amplifying the benefits of the two strategies. © 2015 Wiley Periodicals, Inc.

This work is focused on the efficient evaluation of the Boys function located at the heart of Coulomb and exchange type electron integrals. Different evaluation strategies for individual orders and arguments of the Boys function are used to achieve a minimal number of floating-point operations. Two similar algorithms are derived by amplifying the benefits of two strategies previously proposed by other groups (Gill et al., Int. J. Quantum Chem. 1991, 40, 745 and Ishida, Int. J. Quantum Chem. 1996, 59, 209).

Explicit treatment of electronic polarization in empirical force fields used for molecular dynamics simulations represents an important advancement in simulation methodology. A straightforward means of treating electronic polarization in these simulations is the inclusion of Drude oscillators, which are auxiliary, charge-carrying particles bonded to the cores of atoms in the system. The additional degrees of freedom make these simulations more computationally expensive relative to simulations using traditional fixed-charge (additive) force fields. Thus, efficient tools are needed for conducting these simulations. Here, we present the implementation of highly scalable algorithms in the GROMACS simulation package that allow for the simulation of polarizable systems using extended Lagrangian dynamics with a dual Nosé–Hoover thermostat as well as simulations using a full self-consistent field treatment of polarization. The performance of systems of varying size is evaluated, showing that the present code parallelizes efficiently and is the fastest implementation of the extended Lagrangian methods currently available for simulations using the Drude polarizable force field.

Polarizable force fields represent the new generation in biomolecular simulation. In the Drude oscillator model, additional particles are attached to atoms in the system to represent electronic degrees of freedom. These simulations are more expensive than those done with traditional force fields, and to this end the powerful GROMACS software package has been extended to include algorithms necessary to efficiently simulate polarizable systems, enabling long-scale simulations of increasingly informative and accurate biomolecular models.

Semiempirical quantum models are routinely used to study mechanisms of RNA catalysis and phosphoryl transfer reactions using combined quantum mechanical (QM)/molecular mechanical methods. Herein, we provide a broad assessment of the performance of existing semiempirical quantum models to describe nucleic acid structure and reactivity to quantify their limitations and guide the development of next-generation quantum models with improved accuracy. Neglect of diatomic differential overlap and self-consistent density-functional tight-binding semiempirical models are evaluated against high-level QM benchmark calculations for seven biologically important datasets. The datasets include: proton affinities, polarizabilities, nucleobase dimer interactions, dimethyl phosphate anion, nucleoside sugar and glycosidic torsion conformations, and RNA phosphoryl transfer model reactions. As an additional baseline, comparisons are made with several commonly used density-functional models, including M062X and B3LYP (in some cases with dispersion corrections). The results show that, among the semiempirical models examined, the AM1/d-PhoT model is the most robust at predicting proton affinities. AM1/d-PhoT and DFTB3-3ob/OPhyd reproduce the MP2 potential energy surfaces of 6 associative RNA phosphoryl transfer model reactions reasonably well. Further, a recently developed linear-scaling “modified divide-and-conquer” model exhibits the most accurate results for binding energies of both hydrogen bonded and stacked nucleobase dimers. The semiempirical models considered here are shown to underestimate the isotropic polarizabilities of neutral molecules by approximately 30%. The semiempirical models also fail to adequately describe torsion profiles for the dimethyl phosphate anion, the nucleoside sugar ring puckers, and the rotations about the nucleoside glycosidic bond. The modeling of pentavalent phosphorus, particularly with thio substitutions often used experimentally as mechanistic probes, was problematic for all of the models considered. Analysis of the strengths and weakness of the models suggests that the creation of robust next-generation models should emphasize the improvement of relative conformational energies and barriers, and nonbonded interactions. © 2015 Wiley Periodicals, Inc.

A series of semiempirical models have been tested against a wide range of datasets relevant to RNA catalysis, including: proton affinities and polarizabilities, nucleobase dimers, dimethyl phosphate anion conformations, nucleoside sugar and glycosidic torsion conformations, and RNA phosphoryl transfer model reactions through comparisons with high-level benchmark calculations. The assessment of semiempirical models provides guidelines for their range of application as well as insight for their improvement.

The positive electrostatic potentials (ESP) outside the σ-hole along the extension of OP bond in OPH_{3} and the negative ESP outside the nitrogen atom along the extension of the CN bond in NCX could form the Group V σ-hole interaction OPH_{3}⋯NCX. In this work, the complexes NCY⋯OPH_{3}⋯NCX and OPH_{3}⋯NCX⋯NCY (X, YF, Cl, Br) were designed to investigate the enhancing effects of Y⋯O and X⋯N halogen bonds on the P⋯N Group V σ-hole interaction. With the addition of Y⋯O halogen bond, the *V*_{S, max} values outside the σ-hole region of OPH_{3} becomes increasingly positive resulting in a stronger and more polarizable P⋯N interaction. With the addition of X⋯N halogen bond, the *V*_{S, min} values outside the nitrogen atom of NCX becomes increasingly negative, also resulting in a stronger and more polarizable P⋯N interaction. The Y⋯O halogen bonds affect the σ-hole region (decreased density region) outside the phosphorus atom more than the P⋯N internuclear region (increased density region outside the nitrogen atom), while it is contrary for the X⋯N halogen bonds. © 2015 Wiley Periodicals, Inc.

In this work, the complexes OPH_{3}⋯NCX, NCY⋯OPH_{3}⋯NCX, and OPH_{3}⋯NCX⋯NCY (X, YF, Cl, Br) were designed to investigate the enhancing effects of Y⋯O and X⋯N halogen bonds on the P⋯N Group V σ-hole interaction. The Y⋯O halogen bonds affect the σ-hole region (decreased density region) outside the phosphorus atom more than the P⋯N internuclear region (increased density region outside the nitrogen atom), while it is contrary for the X⋯N halogen bonds.

Weak inter- and intra- molecular C^{δ+}F^{δ−}···C^{δ+}O^{δ−} interactions were theoretically evaluated in 4 different sets of compounds at different theoretical levels. Intermolecular CH_{3}F···CO interactions were stabilizing by about 1 kcal mol^{−1} for various carbonyl containing functional groups. Intramolecular CF···CO interactions were also detected in aliphatic and fluorinated cyclohexane carbonyl derivatives. However, the stabilization provided by intramolecular CF···CO interactions was not enough to govern the conformational preferences of compounds **2–4**. © 2015 Wiley Periodicals, Inc.

Prototypical inter- and intramolecular CF···CO interactions are assessed computationally at the B3LYP-D3 level. The interactions are noticeable in intermolecular complexes **1**, where they can amount to stabilizations around about 1 kcal mol, however, they are not strong enough to dominate conformational preferences in organofluorine derivatives such as **2 - 4**.

The Gibbs energies of association between primary alkyl ammonium ions and crown ethers in solution are measured and calculated. Measurements are performed by isothermal titration calorimetry and revealed a strong solvent-dependent ion pair effect. Calculations are performed with density functional theory including Grimme's dispersion correction D3(BJ). The translational, rotational, and vibrational contributions to the Gibbs energy of association are taken into account by a rigid-rotor-harmonic-oscillator approximation with a free-rotor approximation for low lying vibrational modes. Solvation effects are taken into account by applying the continuum solvation model COSMO-RS. Our study aims at finding a suitable theoretical method for the evaluation of the host guest interaction in crown/ammonium complexes as well as the observed ion pair effects. A good agreement of theory and experiment is only achieved, when solvation and the effects of the counterions are explicitly taken into account.

Gibbs energies of association of monovalent crown/ammonium complexes in solution are calculated with DFT-D3(BJ) and the continuum solvation model COSMO-RS. For comparison, experimental data are obtained by isothermal titration calorimetry. Calculated and measured Gibbs energies of association in solution agree well.

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}.

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

To test force fields for intrinsically disordered systems, the machinery of statistical mechanics must be employed on each model. While many classical force fields model structured proteins well, it is important to understand how force fields affect structural properties when extended to modeling highly disordered polypeptides. To this end, Justin A. Drake and B. Montgomery Pettitt perform a comparative structural analysis of Gly_{3} and Gly_{10} in aqueous solution from all-atom, microsecond MD simulations using the CHARMM 27 (C27), CHARMM 36 (C36), and Amber ff12SB force fields on page 1275 (DOI: 10.1002/jcc.23934).

Molecular simulations can be used to study disordered polypeptide systems and to generate hypotheses on the underlying structural and thermodynamic mechanisms that govern their function. As the number of disordered protein systems investigated with simulations increase, it is important to understand how particular force fields affect the structural properties of disordered polypeptides in solution. To this end, we performed a comparative structural analysis of Gly_{3} and Gly_{10} in aqueous solution from all atom, microsecond molecular dynamics (MD) simulations using the CHARMM 27 (C27), CHARMM 36 (C36), and Amber ff12SB force fields. For each force field, Gly_{3} and Gly_{10} were simulated for at least 300 ns and 1 μs, respectively. Simulating oligoglycines of two different lengths allows us to evaluate how force field effects depend on polypeptide length. Using a variety of structural metrics (e.g., end-to-end distance, radius of gyration, dihedral angle distributions), we characterize the distribution of oligoglycine conformers for each force field and show that each sample conformation space differently, yielding considerably different structural tendencies of the same oligoglycine model in solution. Notably, we find that C36 samples more extended oligoglycine structures than both C27 and ff12SB. © 2015 Wiley Periodicals, Inc.

The number of disordered protein systems investigated with simulations continues to increase. While many classical force fields model structured proteins well, it is important to understand how force fields affect structural properties when extended to modeling highly disordered polypeptides. To this end, a comparative structural analysis of Gly_{3} and Gly_{10} in aqueous solution from all-atom, microsecond MD simulations using the CHARMM 27 (C27), CHARMM 36 (C36), and Amber ff12SB force fields was performed.

The accurate ground-state potential energy function of imidogen, NH, has been determined from *ab initio* calculations using the multireference averaged coupled-pair functional (MR-ACPF) method in conjunction with the correlation-consistent core-valence basis sets up to octuple-zeta quality. The importance of several effects, including electron correlation beyond the MR-ACPF level of approximation, the scalar relativistic, adiabatic, and nonadiabatic corrections were discussed. Along with the large one-particle basis set, all of these effects were found to be crucial to attain “spectroscopic” accuracy of the theoretical predictions of vibration-rotation energy levels of NH. © 2015 Wiley Periodicals, Inc.

The potential energy function and vibration-rotation constants of imidogen, NH, were predicted *ab initio* to near “spectroscopic” accuracy.

DFT investigations are carried out to explore the effective catalyst forms of DBU and H_{2}O and the mechanism for the formation of 2,3-dihydropyrido[2,3-*d*]-pyrimidin-4(1*H*)-ones. Three main pathways are disclosed under unassisted, water-catalyzed, DBU and water cocatalyzed conditions, which involves concerted nucleophilic addition and H-transfer, concerted intramolecular cyclization and H-transfer, and Dimroth rearrangement to form the product. The results indicated that the DBU and water cocatalyzed pathway is the most favored one as compared to the rest two pathways. The water donates one H to DBU and accepts H from 2-amino-nicotinonitrile (**1**), forming [DBU-H]^{+}-H_{2}O as effective catalyst form in the proton migration transition state rather than [DBU-H]^{+}-OH^{−}. The hydrogen bond between [DBU-H]^{+}···H_{2}O···**1**^{−} decreases the activation barrier of the rate-determining step. Our calculated results open a new insight for the green catalyst model of DBU-H_{2}O. © 2015 Wiley Periodicals, Inc.

DFT invesigations suggest that [DBU-H]^{+}-H_{2}O acts as a high efficency, green catalyst to facilitate the formation of 2,3-dihydropyrido[2,3-*d*]-pyrimidin-4(1*H*)-ones. The calculated results open a new insight for the green catalyst model of DBU-H_{2}O.

The prominence of endogenous peptide ligands targeted to receptors makes peptides with the desired binding activity good molecular scaffolds for drug development. Minor modifications to a peptide's primary sequence can significantly alter its binding properties with a receptor, and screening collections of peptide mutants is a useful technique for probing the receptor–ligand binding domain. Unfortunately, the combinatorial growth of such collections can limit the number of mutations which can be explored using structure-based molecular docking techniques. Genetic algorithm managed peptide mutant screening (GAMPMS) uses a genetic algorithm to conduct a heuristic search of the peptide's mutation space for peptides with optimal binding activity, significantly reducing the computational requirements of the virtual screening. The GAMPMS procedure was implemented and used to explore the binding domain of the nicotinic acetylcholine receptor (nAChR)
-isoform with a library of 64,000 *α*-conotoxin (*α*-CTx) MII peptide mutants. To assess GAMPMS's performance, it was compared with a virtual screening procedure that used AutoDock to predict the binding affinity of each of the *α*-CTx MII peptide mutants with the
-nAChR. The GAMPMS implementation performed AutoDock simulations for as few as 1140 of the 64,000 *α*-CTx MII peptide mutants and could consistently identify a set of 10 peptides with an aggregated binding energy that was at least 98% of the aggregated binding energy of the 10 top peptides from the exhaustive AutoDock screening. © 2015 Wiley Periodicals, Inc.

Genetic algorithm managed peptide mutant screening (GAMPMS) uses a genetic algorithm (GA) to perform a heuristic, structure-based virtual screening of a peptide mutant library. The GA uses a set of operators and a fitness evaluator (e.g., AutoDock) to iteratively identify groups of peptide mutants that are likely to have a relatively high binding affinity with the target receptor. GAMPMS is able to dramatically reduce the time and resources required for virtually screening peptide mutant libraries.

Force field parameters for polarizable coarse-grained (CG) supra-atomic models of liquid cyclohexane are proposed. Two different bead sizes were investigated, one representing two fine-grained (FG) CH_{2}r united atoms of the cyclohexane ring, and one representing three FG CH_{2}r united atoms. Electronic polarizability is represented by a massless charge-on-spring particle connected to each CG bead. The model parameters were calibrated against the experimental density and heat of vaporization of liquid cyclohexane, and the free energy of cyclohexane hydration. Both models show good agreement with thermodynamic properties of cyclohexane, yet overestimate the self-diffusion. The dielectric properties of the polarizable models agree very well with experiment. © 2015 Wiley Periodicals, Inc.

In this work, a polarizable coarse-grained (CG) force field for molecular dynamics simulations of liquid cyclohexane is reported. The polarizability of the compounds is introduced through the charge-on-spring or Drude's oscillator model. The model parameters were tested for structural, thermodynamic, dielectric, and dynamic properties. A good agreement with the experimental data for a large set of properties was obtained for two different CG models of cyclohexane.

Green systems able to capture or fix CO_{2} are becoming more important specially to reduce environmental impacts. In this work, the mechanism of insertion of CO_{2} into styrene oxide (STYO) both in the absence and presence of the catalyst 1-butyl-3-methyl-imidazolium bromide (BMIm Br) was investigated through calculations based on density functional theory in the *ω*B97X-D level. Two different routes were considered and it was shown they are energetically available and compete against each other. For both routes, the rate-determinant step is the ring opening of STYO resulting from the nucleophilic attack of the Br^{−} on the C atom from STYO and is associated mainly to the participation of the cation and the anion from the catalyst in the reaction. Reactive indices and noncovalent interaction analysis were used as a tool to investigate this reason. This work allowed a better comprehension of the underlying mechanism and the supplied data provide valuable support for the design of new more efficient ionic liquid catalyst. © 2015 Wiley Periodicals, Inc.

The catalyzed cycloaddition of CO_{2} into styrene oxide was addressed theoretically in the *ω*B97X-D level. Two possible routes were considered and the role of the cation and anion belonging to the catalyst in the ring opening of the epoxide was investigated. Reactive indices and noncovalent interaction analysis were performed to explain the reactivity and the attack position.

The electronic, bonding, and photophysical properties of one-dimensional [CuCN]* _{n}* (

A series of linear 1-D [CuCN]* _{n}* (