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Access to accurate force-field parameters for small molecules is crucial for computational studies of their interactions with proteins. Although a number of general force fields for small molecules exist, e.g., CGenFF, GAFF, and OPLS, they do not cover all common chemical groups and their combinations. The Force Field Toolkit (ffTK) provides a comprehensive graphical interface that streamlines the development of classical parameters for small molecules directly from quantum mechanical (QM) calculations, allowing for force-field generation for almost any chemical group and validation of the fit relative to the target data. ffTK relies on supported external software for the QM calculations, but it can generate the necessary QM input files and parse and analyze the QM output. In previous ffTK versions, support for Gaussian and ORCA QM packages was implemented. Here, we add support for Psi4, an open-source QM package free for all users, thereby broadening user access to ffTK. We also compare the parameter sets obtained with the new ffTK version using Gaussian, ORCA, and Psi4 for three molecules: pyrrolidine, n-propylammonium cation, and chlorobenzene. Despite minor differences between the resulting parameter sets for each compound, most prominently in the dihedral and improper terms, we show that conformational distributions sampled in molecular dynamics simulations using these parameter sets are quite comparable. [ABSTRACT FROM AUTHOR]

The effects of a gate potential on the conductance of two members of the EMAC family, Ru3(dpa)4(NCS)2 and its asymmetric analogue, [Ru3(npa)4(NCS)2]+, are explored with a density functional approach combined with non-equilibrium Green's functions. From a computational perspective, the inclusion of an electrochemical gate potential represents a significant challenge because the periodic treatment of the electrode surface resists the formation of charged species. However, it is possible to mimic the effects of the electrochemical gate by including a very electropositive or electronegative atom in the unit cell that will effectively reduce or oxidize the molecule under study. In this contribution we compare this approach to the more conventional application of a solid-state gate potential, and show that both generate broadly comparable results. For two extended metal atom chain (EMAC) compounds, Ru3(dpa)4(NCS)2 and [Ru3(npa)4(NCS)2], we show that the presence of a gate potential shifts the molecular energy levels in a predictable way relative to the Fermi level, with distinct peaks in the conductance trace emerging as these levels enter the bias window. [ABSTRACT FROM AUTHOR]

Multiconfigurational electronic structure theory calculations including spin-orbit coupling effects were performed on four uranium-based single-molecule-magnets. Several quartet and doublet states were computed and the energy gaps between spin-orbit states were then used to determine magnetic susceptibility curves. Trends in experimental magnetic susceptibility curves were well reproduced by the calculations, and key factors affecting performance were identified. [ABSTRACT FROM AUTHOR]

Both density functional theory and multi-configurational ab initio (CASPT2) calculations are used to explore the potential energy surface of the hexagonal prismatic cluster [Mn@Si12]+. Unlike isoelectronic Cr@Si12, the ground state is a biradical, with triplet and open-shell singlet states lying very close in energy. The results are discussed in the context of recent experimental studies using infra-red multiple photon dissociation spectroscopy and X-ray MCD spectroscopy. [ABSTRACT FROM AUTHOR]

The magnetic coupling in transition metal compounds with more than one unpaired electron per magnetic center has been studied with multiconfigurational perturbation theory. The usual shortcomings of these methodologies (severe underestimation of the magnetic coupling) have been overcome by describing the Slater determinants with a set of molecular orbitals that maximally resemble the natural orbitals of a high-level multiconfigurational reference configuration interaction calculation. These orbitals have significant delocalization tails onto the bridging ligands and largely increase the coupling strengths in the perturbative calculation. © 2014 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Modeling and simulation of small molecules such as drugs and biological cofactors have been both a major focus of computational chemistry for decades and a growing need among computational biophysicists who seek to investigate the interaction of different types of ligands with biomolecules. Of particular interest in this regard are quantum mechanical (QM) calculations that are used to more accurately describe such small molecules, which can be of heterogeneous structures and chemistry, either in purely QM calculations or in hybrid QM/molecular mechanics (MM) simulations. QM programs are also used to develop MM force field parameters for small molecules to be used along with established force fields for biomolecules in classical simulations. With this growing need in mind, here we report a set of software tools developed and closely integrated within the broadly used molecular visualization/analysis program, VMD, that allow the user to construct, modify, and parametrize small molecules and prepare them for QM, hybrid QM/MM, or classical simulations. The tools also provide interactive analysis and visualization capabilities in an easy-to-use and integrated environment. In this paper, we briefly report on these tools and their major features and capabilities, along with examples of how they can facilitate molecular research in computational biophysics that might be otherwise prohibitively complex.

The effects of a gate potential on the conductance of two members of the EMAC family, Ru3(dpa)4(NCS)2 and its asymmetric analogue, [Ru3(npa)4(NCS)2]+, are explored with a density functional approach combined with non-equilibrium Green's functions. From a computational perspective, the inclusion of an electrochemical gate potential represents a significant challenge because the periodic treatment of the electrode surface resists the formation of charged species. However, it is possible to mimic the effects of the electrochemical gate by including a very electropositive or electronegative atom in the unit cell that will effectively reduce or oxidize the molecule under study. In this contribution we compare this approach to the more conventional application of a solid-state gate potential, and show that both generate broadly comparable results. For two extended metal atom chain (EMAC) compounds, Ru3(dpa)4(NCS)2 and [Ru3(npa)4(NCS)2], we show that the presence of a gate potential shifts the molecular energy levels in a predictable way relative to the Fermi level, with distinct peaks in the conductance trace emerging as these levels enter the bias window.

Extended metal atom chains constitute an interesting class of molecules from both theoretical and applied points of view. In the chromium-based series Cr 2 M(dpa) 4 X 2 (with M = Zn, Ni, Fe, Mn, Cr), the direct metal-metal interactions span a wide range of possibilities and so do their associated properties. The multiplicity and symmetry components of the metal-metal bond are herein analyzed via the effective bond order (EBO) concept using complete active space self-consistent field wave functions and compared with similar bimetallic Cr 2 L 4 X 2 systems. The bond multiplicity follows a trend dominated by the Cr-Cr distance which, in turn, depends on the nature of the axial ligand (X). Cr 2 M compounds present asymmetric structures with virtually no interaction between the Cr 2 unit and M, whereas fully symmetric structures with delocalized bonding among the three metals are also possible in Cr 3 complexes. In such cases, a strategy that involves localization of the molecular orbitals into each Cr-Cr pair is applied to quantify the contribution of each pair to the overall metal-metal bond multiplicity.

Both density functional theory and multi-configurational ab initio (CASPT2) calculations are used to explore the potential energy surface of the hexagonal prismatic cluster [Mn@Si12](+). Unlike isoelectronic Cr@Si12, the ground state is a biradical, with triplet and open-shell singlet states lying very close in energy. The results are discussed in the context of recent experimental studies using infra-red multiple photon dissociation spectroscopy and X-ray MCD spectroscopy.