Journal of Computational Chemistry

The cover image shows the docking performance of a newly-developed docking program on a benchmark complex structure of 1hiv, as presented by Yu Liu, Lei Zhao, Wentao Li, Dongyu Zhao, Miao Song, and Yongliang Yang on page 67. The search algorithm of FIPSDock is based on the fully informed particle swarm (FIPS) optimization technique. The benchmark complex structure of 1hiv contains a highly flexible peptide-like inhibitor U-75875 with 23 rotatable bonds and represents a challenging problem for flexible docking. FIPSDock could obtain a significant improvement over other docking methods in term of ligand conformational sampling.

Conversion of biomass into useful aromatic chemicals in the aqueous phase requires an understanding of the fundamental catalytic chemistry of intermediate aromatic oxygenates on catalyst surfaces. As presented on page 60 by Jin Yang, Paul J. Dauenhauer, and Ashwin Ramasubramaniam, density functional theory calculations are used to elucidate the interaction between phloroglucinol and common hydrogenation catalysts, Pt and Pd. The importance of aqueous solvent effects on adsorption energies is quantified and shown to lead an to appreciable decrease in the binding between the molecule and the catalyst.

C_nv and D_n near-symmetries are commonly found in many molecules. The detailed derivation of symmetry measures for these multiple-operation point groups is described, and their application for the quantitative evaluation of the symmetry content of plenty of symmetry-distorted small molecules, complexes, and proteins is demonstrated. Useful correlations between symmetry and properties which depend on symmetry are envisaged.

Protein structure is determined by amino acid interactions and thus sequence specific. The 3D -fold of a protein gives rise to distance-dependent interactions of the amino acids. In this article, the full distance dependency is derived by formulating the underlying modeling problem as a linear program. Upon solving this optimization problem for the full or reduced amino acid alphabets, one obtains new insight into structure threading and protein evolution.

The standard hydrogen electrode potential is evaluated with a new computational procedure. The CCSD(T)/aug-cc-pVDZ calculation reproduces the IUPAC recommended value of 4.44 V, whereas DFT/HF calculations overestimate/underestimate this value. When the SHE potential obtained by the new scheme is applied, the calculated redox potential can reproduce the experimental value.

The scaling of several well-known as well as new approximation schemes for the vibrational CI-matrix is studied systematically for a few model molecules. A combination of approximations (“δ”) is shown to reduce the dimension of the VCI matrix as well as its buildup scaling considerably w.r.t. the generic case (“α”), without noticeable accuracy loss for its low-lying eigenstates which are relevant for many vibrational spectroscopy techniques.

A novel algorithm for the optimization of the VBSCF wave function for a complete active space, so-called VBSCF(CAS), was developed by using orthogonalized valence bond orbitals (OVBOs), and then transforming them to nonrothogonal VB orbitals (VBOs). The algorithm enables VBSCF to involve millions of VB structures. It is shown that the VBSCF(CAS) method shares the same computational scaling as CASSCF.

Pseudopotentials are extracted for hybridized atoms. This allows a reduction of the computational cost of calculations for chemical and spectroscopic applications. The focus is on the electronic properties of aromatic compound p systems. We show that the use of our potentials does not deteriorate results obtained with many ab initio methods.

Conversion of biomass into useful aromatic chemicals in the aqueous phase requires an understanding of the fundamental catalytic chemistry of intermediate aromatic oxygenates on catalyst surfaces. Density functional theory calculations are used to elucidate the interaction between phloroglucinol and common hydrogenation catalysts, Pt and Pd. The importance of aqueous solvent effects on adsorption energies is quantified and shown to lead an to appreciable decrease in the binding between the molecule and the catalyst.

A novel docking algorithm called FIPSDock is presented, which implements the fully informed particle swarm (FIPS) optimization method and adopts the newly developed scoring function of the AutoDock 4.20 suite. The search ability and docking accuracy of FIPSDock are evaluated by multiple cognate docking experiments and cross-docking experiments. FIPSDock outperforms a few state-of-the-art docking programs and the results reveal that the FIPS algorithm might be suitable in solving highly flexible docking problems.