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In this work, we exploit a new formulation of the potential energy and of the related computational procedures, which embodies the coupling between the intra and intermolecular components, to characterize possible propensities of the collision dynamics in energy transfer processes of interest for simulation and control of phenomena occurring in a variety of equilibrium and nonequilibrium environments. The investigation reported in the paper focuses on the prototype CO2-N2 system, whose intramolecular component of the interaction is modeled in terms of a many body expansion while the intermolecular component is modeled in terms of a recently developed bonds-as-interacting-molecular-centers' approach. The main advantage of this formulation of the potential energy surface is that of being (a) truly full dimensional (i.e., all the variations of the coordinates associated with the molecular vibrations and rotations on the geometrical and electronic structure of the monomers, are explicitly taken into account without freezing any bonds or angles), (b) more flexible than other usual formulations of the interaction and (c) well suited for fitting procedures better adhering to accurate ab initio data and sensitive to experimental arrangement dependent information. Specific attention has been given to the fact that a variation of vibrational and rotational energy has a higher (both qualitative and quantitative) impact on the energy transfer when a more accurate formulation of the intermolecular interaction (with respect to that obtained when using rigid monomers) is adopted. This makes the potential energy surface better suited for the kinetic modeling of gaseous mixtures in plasma, combustion and atmospheric chemistry computational applications. © 2016 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

This paper reports density functional theory study of the structural and mechanical properties of tobermorite mineral (9 Å phase) as one of the main component of cementitious materials in a concrete chemistry. Calculated bulk modulus and elastic constants reflect a relatively high resistance of the tobermorite structure with respect to external isostatic compression. Moreover, the elastic constants proved the anisotropic character of the tobermorite structure. The directions parallel to the ax b plane are more resistant to the compression than the perpendicular direction. The largest contribution to this resistance comes from the 'dreierketten' silicate chains. The bonding analysis linked macroscopic mechanical properties and the atomic structure of the tobermorite. It was found that polar covalent SiO bonds are stiffer than iono-covalent CaO bonds. The SiO tetrahedra are resistant with respect to the compression and the effect of external pressure is reflected by the large mutual tilting of these tetrahedra as it is shown by changes of the SiOSi bridging angles. Polyhedra with the seven-fold coordinated Ca cations undergo large structural changes. Especially, axial CaO bonds perpendicular to the ax b plane are significantly shortened. Besides, it was shown that structural parameters, more or less in parallel orientation to the ax b plane, are mainly responsible for the high resistance of the tobermorite structure to external pressure. The main mechanism of a dissipation of energy entered to the structure through the compression is proceeded by the tilting of the tetrahedra of the silicate chains and by large shortening of the axial CaO distances. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011 [ABSTRACT FROM AUTHOR]

An update to the computational framework CONDON, introducing the ability to model and predict the magnetic and electronic properties of polynuclear exchanged‐coupled actinide systems, such as homonuclear and heteronuclear coordination clusters of 5f ions, is presented. The program can intuitively fit experimental magnetic and spectroscopic data from multiple sources simultaneously, under consideration of a "full model" ligand field theory Hamiltonian. CONDON accounts simultaneously for all aspects relevant to the magnetic characteristics: interelectronic repulsion, ligand field potential, spin‐orbit coupling, interatomic exchange interactions, and applied magnetic field. As exemplified by several examples, CONDON represents the first program package able to accurately describe single‐ion effect in exchange‐coupled actinide systems, limited only by available computational resources. © 2018 Wiley Periodicals, Inc. The magnetochemical computation framework CONDON has been updated to provide comprehensive analysis of the magnetic characteristics of homopolynuclear and heteropolynuclear exchange‐coupled actinide systems. Implementing both effective and "full" models, CONDON offers simulation and fitting methods, the latter simultaneously for different experimental datasets. [ABSTRACT FROM AUTHOR]

Protein-nucleic acid complexes are important for many cellular processes including the most essential functions such as transcription and translation. For many protein-nucleic acid complexes, flexibility of both macromolecules has been shown to be critical for specificity and/or function. The flexibility-rigidity index (FRI) has been proposed as an accurate and efficient approach for protein flexibility analysis. In this article, we introduce FRI for the flexibility analysis of protein-nucleic acid complexes. We demonstrate that a multiscale strategy, which incorporates multiple kernels to capture various length scales in biomolecular collective motions, is able to significantly improve the state of art in the flexibility analysis of protein-nucleic acid complexes. We take the advantage of the high accuracy and O( N) computational complexity of our multiscale FRI method to investigate the flexibility of ribosomal subunits, which are difficult to analyze by alternative approaches. An anisotropic FRI approach, which involves localized Hessian matrices, is utilized to study the translocation dynamics in an RNA polymerase. © 2016 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Halogenated compounds are gaining an increasing importance in medicinal chemistry and materials science. Ab initio quantum chemistry (QC) has unraveled the existence of a 'sigma hole' along the CX (X = F, Cl, Br, I) bond, namely, a depletion of electronic density prolonging the bond, concomitant with a build-up on its sides, both of which are enhanced along the F < Cl < Br < I series. We have evaluated whether these features were intrinsically built-in in an anisotropic, polarizable molecular mechanics (APMM) procedure such as SIBFA (sum of interactions between fragments ab initio computed). For that purpose, we have computed the interaction energies of fluoro-, chloro-, and bromobenzene with two probes: a divalent cation, Mg(II), and water approaching X through either one H or its O atom. This was done by parallel QC energy-decomposition analyses (EDA) and SIBFA computations. With both probes, the leading QC contribution responsible for the existence of the sigma hole is the Coulomb contribution Ec. For all three halogenated compounds, and with both probes, the in- and out-of-plane angular features of Ec were closely mirrored by the SIBFA electrostatic multipolar contribution ( EMTP). Resorting to such a contribution thus dispenses with empirically-fitted 'extra', off-centered partial atomic charges as in classical molecular mechanics/dynamics. © 2013 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

We present a stochastic model for the kinetics of photoinduced anisotropy in a sample of molecular chromophores that may undergo photoisomerization. It is assumed that the chromo-phores do not interact among them, but are embedded in a medium that slows down the rotational diffusion. The model makes use of data about the photoinduced reorientation of the single chromophore, its photoisomerization and its rotational diffusion, that are made available by molecular dynamics simulations. For the first time such molecular scale processes are computationally connected to the development of anisotropy in a large sample and on a long time scale. A test on azobenzene shows the potentiality of the method and the interplay between photoinduced anisotropy and photoisomerization. © 2012 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Dimers are the smallest chemical objects that show magnetic anisotropy. We focus on 3d and 4d transition metal dimers that have magnetic ground states in most cases. Some of these magnetic dimers have a considerable barrier against re-orientation of their magnetization, the so-called magnetic anisotropy energy, MAE. The height of this barrier is important for technological applications, as it determines, e.g., the stability of information stored in magnetic memory devices. It can be estimated by means of relativistic density functional calculations. Our approach is based on a full-potential local-orbital method (FPLO) in a four-component Dirac-Kohn-Sham implementation. Orbital polarization corrections to the local density approximation are employed. They are discussed in the broader context of orbital dependent density functionals. Ground state properties (spin multiplicity, bond length, harmonic vibrational frequency, spin- and orbital magnetic moment, and MAE) of the 3d and 4d transition metal dimers are evaluated and compared with available experimental and theoretical data. We find exceptionally high values of MAE, close to 0.2 eV, for four particular dimers: Fe2, Co2, Ni2, and Rh2. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008 [ABSTRACT FROM AUTHOR]