Journal Of Computational Chemistry
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- Wiley from 1980
Binding affinity of substituted ureido-benzenesulfonamide ligands to the carbonic anhydrase receptor: A theoretical study of enzyme inhibiti...
The binding properties of a series of benzenesulfonamide inhibitors (4-substituted-ureido-benzenesulfonamides, UBSAs) of human carbonic anhydrase II (hCA II) enzyme with active site residues have been studied using a hybrid quantum mechanical/molecular mechanical (QM/MM) model. To account for the im...
Analytic derivatives for the XYG3 type of doubly hybrid density functionals: Theory, implementation, and assessment.
We present a theoretical development of the equations required to perform an analytic geometry optimization of a molecular system using the XYG3 type of doubly hybrid (xDH) functionals. In contrast to the well-established B2PLYP type of DH functionals, the energy expressions in the xDH functionals a...
First principles study of gallium cleaning for hydrogen-contaminated α-Al2O3(0001) surfaces.
The use of gallium for cleaning hydrogen-contaminated Al2O3 surfaces is explored by performing first principles density functional calculations of gallium adsorption on a hydrogen-contaminated Al-terminated α-Al2O3(0001) surface. Both physisorbed and chemisorbed H-contaminated α-Al2O3(0001) surfaces...
Hardness potential derivatives and their relation to Fukui indices.
A simple as well as easy to compute formalism of hardness potential (originally defined by Parr and Gazquez, J. Phys. Chem., 1993, 97, 3939) is presented. Use of hardness potential formally resolves the N-dependence problem of local hardness. However, the hardness potential cannot describe the intra...
Inside cover, volume 34, issue 11.
TargetATPsite, a new method based on residue evolution image sparse representation and classifier ensemble, is developed for predicting ATP-binding sites from primary sequences, as presented by Dong-Jun Yu, Jun Hu, Yan Huang, Hong-Bin Shen, Yong Qi, Zhen-Min Tang, and Jing-Yu Yang on...
Water PMF for predicting the properties of water molecules in protein binding site.
We constructed a water PMF (wPMF) based on 3946 non-redundant high resolution crystal structures. The extracted wPMF potential was first used to investigate the structure pattern of water and analyze the residue hydrophilicity. Then, the relationship between wPMF score and the B factor value of crys...
Relations frequency hypermatrices in mutual, conditional and joint entropy-based information indices.
We have introduced a novel matrix representation, named the duplex relations frequency matrix, F, derived from the generalization of an incidence matrix whose row entries are connected subgraphs of a given molecular graph G. Using this matrix, a series of information indices (IFIs) were proposed. In...
Pseudopotentials for hybridized carbon atoms.
Pseudopotentials for hybridized atoms are extracted and combined. The study focuses on sp(2) carbon atoms and their combination to give rise to a π electronic system. As electrons of interest are treated explicitly, any ab initio method can be used, thus, configuration interaction methods and time-d...
Prediction of hydrocarbon enthalpies of formation by various thermochemical schemes.
The correlation consistent composite approach (ccCA) has been used to compute the enthalpies of formation (ΔH(f)'s) for 60 closed-shell, neutral hydrocarbon molecules selected from an established set (Cioslowski et al., J. Chem. Phys. 2000, 113, 9377). This set of thermodynamic values includes ΔH(f)...
Computational study on hydrolysis of cefotaxime in gas phase and in aqueous solution.
We are presenting a theoretical study of the hydrolysis of a β-lactam antibiotic in gas phase and in aqueous solution by means of hybrid quantum mechanics/molecular mechanics potentials. After exploring the potential energy surfaces at semiempirical and density functional theory (DFT) level, potent...