Exploration on Electronic Properties of Self-Assembled Indium Nitrogen Nanosheets and Nanowires by a Density Functional Method.

Equilibrium geometries and properties of self-assembled (InN) (n = 1-9) nanoclusters (nanowires and nanosheets) are studied using the GGA-PBE (general gradient approximation with Perdew-Burke-Ernzerh) method. The relative stabilities and growth patterns of semiconductor (InN) nanoclusters are investigated. The odd-numbered nano-size (InN) (n is odd) have weaker stabilities compared with the neighboring even-numbered (InN) (n is even) ones.

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.

An all-atom molecular dynamics study of the anti-interferon signaling of Ebola virus: interaction mechanisms of EBOV VP24 binding to Karyopherin alpha5.

Ebola virus (EBOV) is highly lethal due to virally encoded immune antagonists, and the combination of EBOV VP24 with karyopherin alpha (KPNA) will trigger anti-interferon (IFN) signaling. The crystal structure of VP24-KPNA5 has been proposed in recent studies, but the precise binding mechanisms are still unclear. In order to explore the VP24-KPNA5 protein binding micro-mechanisms, Molecular Dynamic (MD) simulations and Molecular Mechanics Generalized Born Surface Area (MM-GB/SA) energy calculation are performed.

A simulation investigation on interaction mechanism between Ebola nucleoprotein and VP35 peptide.

Ebola viruses (EBOV) will induce acute hemorrhagic fever, which is fatal to humans and nonhuman primates. The combination of EBOV VP35 peptide with nucleoprotein N-terminal (NPNTD) is proposed based on static crystal structures in recent studies, but VP35 binding mechanism and conformational dynamics are still unclear. This investigation, using Molecular Dynamic (MD) simulation and Molecular Mechanics Generalized Born Surface Area (MM-GB/SA) energy calculation, more convincingly proves the greater roles of the protein binding mechanisms than do hints from the static crystal structure observations.

Exploration micromechanism of VP35 IID interaction and recognition dsRNA: A molecular dynamics simulation.

Multifunctional viral protein (VP35) encoded by the highly pathogenic Ebola viruses (EBOVs) can antagonize host double-stranded RNA (dsRNA) sensors and immune response because of the simultaneous recognition of dsRNA backbone and blunt ends. Mutation of select hydrophobic conserved basic residues within the VP35 inhibitory domain (IID) abrogates its dsRNA-binding activity, and impairs VP35-mediated interferon (IFN) antagonism. Herein the detailed binding mechanism between dsRNA and WT, single mutant, and double mutant were investigated by all-atom molecular dynamics (MD) simulation and binding energy calculation.

Molecular dynamics exploration of the binding mechanism and properties of single-walled carbon nanotube to WT and mutant VP35 FBP region of Ebola virus.

VP35 of Ebola viruses (EBOVs) is an attractive potential target because of its multifunction. All-atom molecular dynamics (MD) simulations and Molecular Mechanics Generalized Born surface area (MM/GBSA) energy calculations are performed to investigate the single-walled carbon nanotube (SWCNT) as an inhibitor in wild-type (WT) VP35 as well as in three primary mutants (K248A, I295A, and K248A/I295A) through docking the SWCNT in the first basic patch (FBP) of VP35. The SWCNTs of all the four systems effectively bind to the FBP.

Insights into resistance mechanism of the macrolide biosensor protein MphR(A) binding to macrolide antibiotic erythromycin by molecular dynamics simulation.

Macrolide biosensor protein MphR(A) has been known as a key regulatory protein in metabolite sensing and genetic expression regulating. MphR(A) protein binds to macrolide antibiotic erythromycin (Ery) and releases the gene operon, thus activates expression of the mphA gene and initiates Ery resistance. The two mutant amino acid residues (V66L and V126L) might potentially disrupt Ery binding to MphR(A).

Exploring interaction mechanisms of the inhibitor binding to the VP35 IID region of Ebola virus by all atom molecular dynamics simulation method.

Ebola viruses (EBOVs) cause an acute and serious illness which is often fatal if untreated, and there is no effective vaccine until now. Multifunctional VP35 is critical for viral replication, RNA silencing suppression and nucleocapsid formation, and it is considered as a future target for the molecular biology technique. In the present work, the binding of inhibitor pyrrole-based compounds (GA017) to wild-type (WT), single (K248A, K251A, and I295A), and double (K248A/I295A) mutant VP35 were investigated by all-atom molecular dynamic (MD) simulations and Molecular Mechanics Generalized Born surface area (MM/GBSA) energy calculation.

The binding mechanism of a novel nicotinamide isostere inhibiting with TNKSs: a molecular dynamic simulation and binding free energy calculation.

Tankyrases (TNKSs), a member of human poly (ADP-ribose) polymerase (PARP) protein superfamily, plays a key role in regulation of cell proliferation. Among the representative proteins of the PARPs family, it is found that the inhibitors have high selectivity for Tankyrase1 (TNKS1). The specific binding modes are investigated between the TNKS1 protein and nicotinamide isostere (ISX) which functions as an inhibitor of TNKS1.

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.

Insight into the binding modes of Lassa nucleoprotein complexed with ssRNA by molecular dynamic simulations and free energy calculations.

Lassa virus (LASV), an arenavirus known to be responsible for a severe hemorrhagic fever, causes thousands of deaths annually and there is no effective vaccine for it so far. The nucleoprotein (NP) of LASV plays an essential role in the replication and transcription of the viral genome. Recent research shows that viral RNA binds in a deep crevice located within the N-terminal domain of NP and suggests a gating mechanism in which NP transforms from a "closed" position to an "open" position to bind RNA.

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.

Studies on the binding modes of Lassa nucleoprotein complexed with m7GpppG and dTTP by molecular dynamic simulations and free energy calculations.

Lassa virus can cause dreadful human hemorrhagic disease, for which there is no effective therapy. A recent study points out that the amino (N)-terminal domain of Lassa virus nucleoprotein (NP) plays an important role in viral RNA synthesis and firstly solved the X-ray crystal structures of NP complexed with the capped Deoxythymidine triphosphate (dTTP) analog, but the binding mode of m7GpppG to the N domain of NP, which is required for viral RNA transcription, has not been studied. In this study, molecular dynamics (MD) simulations have been carried out to investigate the characters of dTTP binding to two forms of NP, i.

Probing ligand-binding modes and binding mechanisms of benzoxazole-based amide inhibitors with soluble epoxide hydrolase by molecular docking and molecular dynamics simulation.

Soluble epoxide hydrolase (sEH) has become a new therapeutic target for treating a variety of human diseases. The inhibition of human sEH hydrolase activity was studied by molecular docking and molecular dynamics (MD) simulation techniques. A set of six benzoxazole-based amide inhibitors binding to sEH has been studied through molecular docking, MD simulation, free energy calculations, and energy decomposition analysis.

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.

Photoionization study of L-valine in the gas phase by vacuum ultraviolet synchrotron radiation.

The photoionization and photodissociation of L-valine are studied by tunable synchrotron vacuum ultraviolet photoionization mass spectrometry at the photon energy of 13 eV. The ionization energy of L-valine and the appearance energies of major fragments are measured by the photoionization efficiency spectrum in the photon energy range of 8-11 eV. Possible formation pathways of the major fragments, NH(2)CHC(OH)(2)(+) (m/z=75), NH(2)(CH(3))(2)(CH)(2)(+) (m/z=72) and NH(2)CHCO(+) (m/z=57), are discussed in detail with the theoretical calculations at the B3LYP/6-31++G (d, p) level.

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 vibrational properties of bimetallic Mo2-doped Gen (n = 9-15) clusters: a density functional investigation.

Geometries of the bimetallic Mo2Gen (n = 9-15) clusters have been investigated systematically with the density functional approach. The relative stabilities and charge-transfer and vibrational properties of these clusters are presented and discussed. The dominant geometries of Mo2Gen (n = 9-12) clusters can be described as one Mo atom inside a Ge cage and another Mo atom on the surface at smaller sizes with n = 9-12.

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 electronic properties of the tungsten-doped germanium clusters: WGen (n = 1-17).

Geometries associated with relative stabilities, energy gaps, and polarities of W-doped germanium clusters have been investigated systematically by using density functional theory. The threshold size for the endohedral coordination and the critical size of W-encapsulated Gen structures emerge as, respectively, n = 8 and n = 12, while the fullerene-like W@Ge(n) clusters appears at n = 14. The evaluated relative stabilities in term of the calculated fragmentation energies reveal that the fullerene-like W@Ge(14) and W@Ge(16) structures as well as the hexagonal prism WGe(12) have enhanced stabilities over their neighboring clusters.

Relativistic computational investigation: the geometries and electronic properties of TaSi(n)+ (n = 1-13, 16) clusters.

The equilibrium geometries, stabilities, and electronic properties of the TaSi(n)+ (n = 1-13, 16) clusters are investigated systematically by using the relativistic density functional method with generalized gradient approximation. The small-sized TaSi(n)+ clusters with slight geometrical adjustments basically keep the frameworks that are analogous to the neutrals while the medium-sized charged clusters significantly deform the neutral geometries, which are confirmed by the calculated AIP and VIP values. Furthermore, the optimized geometries of the charged clusters agree with the experimental results of Hiura and co-workers (Hiura, H.

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.