Correction: A theoretical study of the geometries, and electronic and surface properties of sphere-like (SiB) (n = 6-27, 30) functional nanomaterials.

Correction for 'A theoretical study of the geometries, and electronic and surface properties of sphere-like (SiB)2n (n = 6-27, 30) functional nanomaterials' by Run-Ning Zhao et al., Phys. Chem.

A theoretical study of the geometries, and electronic and surface properties of sphere-like (SiB) (n = 6-27, 30) functional nanomaterials.

The geometries and electronic properties of (SiB) (n = 6-27, 30) clusters are systematically investigated based on the gradient corrected Perdew-Burke-Ernzerhof exchange-correlation functional. In particular, the (SiB) cage is identified as the most stable nanocluster and (SiB) (n = 6-27, 30) nanocages prefer to have sphere-like geometries. By increasing the (SiB) (n = 6-27, 30) nanocage size, the calculated energy gaps of (SiB) (n = 6-27, 30) nanocages generally decrease and absorption wavelengths of the spectra of (SiB) (n = 6-27, 30) nanoclusters are elongated.

Molecular dynamics study of segment peptides of Bax, Bim, and Mcl-1 BH3 domain of the apoptosis-regulating proteins bound to the anti-apoptotic Mcl-1 protein.

Mcl-1 has emerged as a potential therapeutic target in the treatment of several malignancies. Peptides representing BH3 region of pro-apoptotic proteins have been shown to bind the hydrophobic cleft of anti-apoptotic Mcl-1 and this segment is responsible for modulating the apoptotic pathways in living cells. Understanding the molecular basis of protein-peptide interaction is required to develop potent inhibitors specific for Mcl-1.

Investigation on the mechanism for the binding and drug resistance of wild type and mutations of G86 residue in HIV-1 protease complexed with Darunavir by molecular dynamic simulation and free energy calculation.

Residue Gly86 is considered as the highly conversed residue in the HIV-1 protease. In our work, the detailed binding free energies for the wild-type (WT) and mutated proteases binding to the TMC-114 are estimated to investigate the protein-inhibitor binding and drug resistance mechanism by molecule dynamic simulations and molecular mechanics Poisson Boltzmann surface area (MM-PBSA) method. The binding affinities between the mutants and inhibitor are different than that in the wild-type complex and the major resistance to Darunavir (DRV) of G86A and G86S originate from the electrostatic energy and entropy, respectively.

The investigations on HIV-1 gp120 bound with BMS-488043 by using docking and molecular dynamics simulations.

BMS-488043, like its predecessor BMS-378806, is a small molecule that can block the interactions between gp120 and CD4, and has shown good clinical efficacy. However, the crystal structure of drug-gp120 complexes or the full-length gp120 free of bound ligand is unpublished until now. Docking combined with molecular dynamics simulation is used to investigate the binding mode between BMS-488043 and gp120.

Insights into the structural function of the complex of HIV-1 protease with TMC-126: molecular dynamics simulations and free-energy calculations.

The binding properties of the protein-inhibitor complex of human immunodeficiency virus type 1 (HIV-1) protease with the inhibitor TMC-126 are investigated by combining computational alanine scanning (CAS) mutagenesis with binding free-energy decomposition (BFED). The calculated results demonstrate that the flap region (residues 38-58) and the active site region (residues 23-32) in HIV-1 protease contribute 63.72% of the protease to the binding of the inhibitor.

Does the incoming oxygen atom influence the geometries and the electronic and magnetic structures of Co(n) clusters?

The small-sized Co(n)O (n = 1-5) clusters with different spin states have been systematically investigated by using the density-functional approach. The total energies, equilibrium geometries, and magnetic properties are discussed. Equilibrium geometries and the relative stabilities in terms of the calculated fragmentation energies are discussed, manifesting that the remarkable stable small-sized cluster corresponds to the Co(2)O isomer, and that the O atom prefers the surface-capped pattern on Co(n) (n > 2) clusters and bonds with three Co atoms simultaneously.

Geometries and stabilities of the carbon clusters with the rhodium impurity: a computational investigation.

A density functional study of the RhCn(n = 1-6) clusters with different spin states has been carried out systematically by using the B3LYP/Lan2DZ method. The equilibrium geometries associated with total energies and natural populations of RhCn (n = 1-6) clusters are calculated and presented. Stabilities and electronic properties are discussed in detail.

Geometries, stabilities, and growth patterns of the bimetal Mo2-doped Sin (n=9-16) clusters: a density functional investigation.

The behaviors of the bimetal Mo-Mo doped cagelike silicon clusters Mo2Sin at the size of n=9-16 have been investigated systematically with the density functional approach. The growth-pattern behaviors, relative stabilities, and charge-transfer of these clusters are presented and discussed. The optimized geometries reveal that the dominant growth patterns of the bimetal Mo-Mo doped on opened cagelike silicon clusters (n=9-13) are based on pentagon prism MoSi10 and hexagonal prism MoSi12 clusters, while the Mo2 encapsulated Sin(n=14-16) frames are dominant growth behaviors for the large-sized clusters.

Geometries and magnetisms of the Zr(n) (n=2-8) clusters: the density functional investigations.

The geometries, stabilities, and electronic and magnetic properties of small-sized Zr(n) (n=2-8) clusters with different spin configurations were systematically investigated by using density functional approach. Emphasis is placed on studies that focus on the total energies, equilibrium geometries, growth-pattern behaviors, fragmentation energies, and magnetic characteristics of zirconium clusters. The optimized geometries show that the large-sized low-lying Zr(n) (n=5-8) clusters become three-dimensional structures.

Geometries and electronic properties of the neutral and charged rare earth Yb-doped Si(n) (n = 1-6) clusters: a relativistic density functional investigation.

The neutral and charged YbSi(n) (n = 1-6) clusters considering different spin configurations have been systematically investigated by using the relativistic density functional theory with generalized gradient approximation. The total bonding energies, equilibrium geometries, Mulliken populations (MP), Hirshfeld charges (HC), fragmentation energies, and highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) gaps are calculated and discussed. The optimized geometries indicate that the most stable YbSi(n) (n = 1-6) clusters keep basically the analogous frameworks as the low-lying Si(n)(+1) clusters, while the charged species deviate from their neutral counterparts, and that the doped Yb tends to occupy the substitutional site of the neutral and charged YbSi(n) isomers.