Evaluation of intermolecular distance and binding energy (BE) of van der Waals complex/cluster at ab initio level of theory is computationally demanding when many monomers are involved. Starting from MP2 energy, we reached a two-step evaluation method of BE of van der Waals complex/cluster through reasonable approximations; BE = BE(HF) + sum Mi> Mj{BE (Mi- Mj)(MP2 or MP2.5) - BE(Mi-Mj)(HF)} whe...

We analyze the effects of Zeeman degeneracies on the long-range interactions between like Rydberg atoms, with particular emphasis on applications to quantum-information processing using the van der Waals blockade. We present a general analysis of how degeneracies affect the primary error sources in blockade experiments, emphasizing that blockade errors are sensitive primarily to the weakest pos...

We present faster sequential and parallel algorithms for computing the solvent accessible surface area (ASA) of protein molecules. The ASA is computed by finding the exposed surface areas of the spheres obtained by increasing the van der Waals’ radii of the atoms with the van der Waals’ radius of the solvent. Using domain specific knowledge, we show that the number of sphere intersections is on...

A comparative study of 36 molecular descriptors derived from the topological distance matrix and van der Waals space is carried out within this paper. They are partitioned into 16 generalized topological distance matrix indices, 11 topological distance indices known in the literature (seven obtained from eigenvalues/eigenvectors of distance matrix), and 9 van der Waals molecular descriptors. Th...

Reaction mechanism among indoline-2,3-dione, pyrrolidine-2-carboxylic acid and (Z)-2-(1-(2-hydroxynaphthalen-1-yl)ethylidene)hydroxycarboxamide to form 1’-((((aminooxy)carbonyl)amino)methyl)-2’-(1-hydroxynaphthalen-2-yl)-2’-methyl-1’,2’,5’,6’,7’,7a’-hexahydrospiro[indoline-3,3’-pyrrolo[1,2-a]imidazole-2-one was investigated using density functional theory (DFT) at B3LYP basis theory. The three-...

Stability of self-similar solutions for van der Waals driven thin film rupture.

Motivated by recent drop-drying experiments of Au nanoparticle (NP) island self-assembly, we investigate the structure, diffusion, and binding of dodecanethiol-coated Au NPs adsorbed at the toluene-vapor interface using molecular dynamics (MD) simulations as well as analytical calculations. For a 6 nm core diameter NP our results indicate the existence of significant intermixing between the lig...