Broadening access to small-molecule parameterization with the force field toolkit.

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.

From complex data to clear insights: visualizing molecular dynamics trajectories.

Advances in simulations, combined with technological developments in high-performance computing, have made it possible to produce a physically accurate dynamic representation of complex biological systems involving millions to billions of atoms over increasingly long simulation times. The analysis of these computed simulations is crucial, involving the interpretation of structural and dynamic data to gain insights into the underlying biological processes. However, this analysis becomes increasingly challenging due to the complexity of the generated systems with a large number of individual runs, ranging from hundreds to thousands of trajectories.

VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical Simulations.

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.

Gating the conductance of extended metal atom chains: a computational analysis of Ru(dpa)(NCS) and [Ru(npa)(NCS)].

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.

Trends in the Bond Multiplicity of Cr, Cr, and CrM (M = Zn, Ni, Fe, Mn) Complexes Extracted from Multiconfigurational Wave Functions.

Extended metal atom chains constitute an interesting class of molecules from both theoretical and applied points of view. In the chromium-based series CrM(dpa)X (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 CrLX systems.

Quantum Chemical Characterization of Single Molecule Magnets Based on Uranium.

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.

Biradical character in the ground state of [Mn@Si12](+): a DFT and CASPT2 study.

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.

Improving the calculation of magnetic coupling constants in MRPT methods.

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.