A protein energy surface is constructed. Validation is through applications of global energy minimization to surface loops of protein crystal structures. For 9 of 10 predictions, the native backbone conformation is identified correctly. Electrostatic energy is modeled as a pairwise sum of interactions between anisotropic atomic charge densities. Model repulsion energy has a softness similar to ...

We report six-dimensional quantum dynamical calculations of dissociative adsorption and associative desorption of the system H2/Pd(100) using an ab initio potential energy surface. We focus on rotational effects in the steering mechanism, which is responsible for the initial decrease of the sticking probability with kinetic energy. In addition, steric effects are briefly discussed. Typeset usin...

The low-temperature cation-ordered superstructure of anhydrous sodium sodalite, a zeolite with composition Na 6 ͓AlSiO 4 ] 6 , has been determined through the use of both density functional theory ͑DFT͒ and classical force-field lattice energy minimizations. The charge-balancing Na ϩ cations are assumed to occupy their characteristic locations within the cubic alumino–silicate framework near the c...

We review our methodology for producing physically accurate potential energy functions, particularly relevant in the context of Lifson's goal of including frequency agreement as one of the criteria of a self-consistent force field. Our spectroscopically determined force field (SDFF) procedure guarantees such agreement by imposing it as an initial constraint on parameter optimization, and accomp...

Tight-binding molecular dynamics simulations of the adsorption of O2/Pt(111) have been performed based on an ab initio potential energy surface. We demonstrate that, contrary to common belief, in this system the whole adsorption probability as a function of the kinetic energy can be understood in terms of trapping into chemisorbed molecular precursor states. This provides a novel unified pictur...

The effective fragment potential (EFP) method is an ab initio based polarizable classical method in which the intermolecular interaction parameters are obtained from preparative ab initio calculations on isolated molecules. The polarization energy in the EFP method is modeled with asymmetric anisotropic dipole polarizability tensors located at the centroids of localized bond and lone pair orbit...

An effective Hamiltonian mixed molecular orbital and valence bond (EH-MOVB) method is described to obtain an accurate potential energy surface for chemical reactions. Building upon previous results on the construction of diabatic and adiabatic potential surfaces using ab initio MOVB theory, we introduce a diabatic-coupling scaling factor to uniformly scale the ab initio off-diagonal matrix elem...

a computational study of the electronic structure and stability of complexes formed between zeolite y and boric acid was carried out at the hf and b3lyp levels using 6-31g* basis set. five structures located as local minimum in pes of complex (structures d, e, f, g, and h). the most stable structure is formed due to hydrogen bonding between two hydroxyl of boric acid and both oxygen of ...