Molecular dynamics (MD) simulations have become an important tool to investigate biological systems. Free-energy calculations based on MD are playing increasingly role for computer-aided drug design and material discovery in recent years. differences between pairs of end-states can be estimated using well-established methods such as thermodynamic integration (TI) or Bennett’s acceptance ratio (...

Binding energies of negative sX−d and positive trions sX+d in quantum wires are studied for strong quantum confinement of carriers which results in a numerical exactly solvable model. The relative electron and hole confinement have a strong effect on the stability of trions. For equal hole and electron confinement, X+ is more stable but a small imbalance of the particle confinement towards a st...

Aspirin-aspirin and aspirin-leucine interactions are studied by the density functional theory (DFT) and high level ab initio calculations with second order Moller-Plesset perturbation theory (MP2). The rotational isomers of aspirin are identified by their relative stability both in gaseous phase and in water using the polarizable continuum method (PCM). Local minima of aspirin monomers in water...

We present a large-scale study of the temperature-dependence of structures, free energy differences and properties of polymorphic molecular organic crystals. Lattice-vibrational Gibbs free energy differences between 475 pairs of polymorphs of organic molecular crystals have been calculated at 0 K and at their respective melting points, using a highly accurate anisotropic multipole-based force f...

It is known that halogen bonding is supported by so-called sigma holes on halides that interact with bases, but what are the limits of that interaction? How does the interaction depend on the group to which the halogen atom is bonded? To answer these questions, complexes of the form MH3X---Y (where M=C, Si, Ge, Sn, Pb; X= F, Cl, Br, I and Y are Lewis bases) were optimized and their energetics a...

We present a large-scale study of the temperature-dependence of structures, free energy differences and properties of polymorphic molecular organic crystals. Lattice-vibrational Gibbs free energy differences between 475 pairs of polymorphs of organic molecular crystals have been calculated at 0 K and at their respective melting points, using a highly accurate anisotropic multipole-based force f...

Kinetics of solid state stability of seven derivatives of 3,5-disubstituted tetrahydro-2H-1,3,5-thiadiazine-2-thione (THTT) of glycine as a model for amino acids and peptide drugs were studied using differential scanning calorimetry (DSC). Each DSC curve for each derivative showed an endothermic peak followed by an exothermic one, which could be attributed to the melting and decomposition, resp...

We evaluate the ability of the embedded-atom method ~EAM! potentials and the tight-binding ~TB! method to predict reliably energies and stability of nonequilibrium structures by taking Cu as a model material. Two EAM potentials are used here. One is constructed in this work by using more fitting parameters than usual and including ab initio energies in the fitting database. The other potential ...