abstract：:Quantum chemical calculations have been performed to study the all-metal π halogen bonding in Al(4)(2-)···halohydrocarbon complexes. The result shows the existence of the all-metal π halogen bond in the complexes. There are three interaction modes (top, corner, and side) between Al(4)(2-) and halohydrocarbon. The inte...

journal_title：Journal of molecular modeling

authors： Li R,Li Q,Cheng J,Li W

更新日期：2012-06-01 00:00:00

abstract：:The Solanum lycopersicum aspartic protease inhibitor (SLAPI), which belongs to the STI-Kunitz family, is an effective inhibitor of the aspartic proteases human cathepsin D and Saccharomyces proteinase A. However, in contrast with the large number of studies on the inhibition mechanism of the serine proteases by the ST...

journal_title：Journal of molecular modeling

authors： Guerra Y,Valiente PA,Berry C,Pons T

更新日期：2012-06-01 00:00:00

abstract：:Theoretical and spectroscopic studies of a series of monomeric and dimeric complexes formed through the modification of a zirconium butoxide precursor with acetylacetone and subsequent hydrolysis and/or condensation have been performed by applying DFT/B3LYP/6-31++G(d) and highly accurate RI-ADC(2) methods as well as I...

journal_title：Journal of molecular modeling

authors： Georgieva I,Danchova N,Gutzov S,Trendafilova N

更新日期：2012-06-01 00:00:00

abstract：:Numerous studies suggest that two-phase morphology and thick interface are separately beneficial to the viscosity reduction and mechanical property maintainence of the matrix when normal molecular weight polymer (NMWP) is used for modification of ultrahigh molecular weight polyethylene (UHMWPE). Nevertheless, it is ve...

journal_title：Journal of molecular modeling

authors： Gai JG,Zuo Y

更新日期：2012-06-01 00:00:00

abstract：:In this paper, we theoretically studied the geometries, stabilities, and the electronic and thermodynamic properties of 4H-cyclopenta[2,1-b,3;4-b']dithiopene S-oxide derivatives (BTO-X, with X = BH(2), SiH(2), S, S=O, or O) using semi-empirical methods, ab initio methods, and density functional theory. The geometries ...

journal_title：Journal of molecular modeling

authors： Banjo S,Ayobami OO,Ajibade AI

更新日期：2012-06-01 00:00:00

abstract：: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 regio...

journal_title：Journal of molecular modeling

authors： Li D,Han JG,Chen H,Li L,Zhao RN,Liu G,Duan Y

更新日期：2012-05-01 00:00:00

abstract：:The virtual combinatorial chemistry approach as a methodology for generating chemical libraries of structurally-similar analogs in a virtual environment was employed for building a general mixed virtual combinatorial library with a total of 53.871 6-FQ structural analogs, introducing the real synthetic pathways of thr...

journal_title：Journal of molecular modeling

authors： Minovski N,Perdih A,Solmajer T

更新日期：2012-05-01 00:00:00

abstract：:Ab initio calculations have been performed using the complete basis set model (CBS-QB3) to study the reaction mechanism of butane radical (C(4)H(9)•) with oxygen (O(2)). On the calculated potential energy surface, the addition of O(2) to C(4)H(9)• forms three intermediates barrierlessly, which can undergo subsequent i...

journal_title：Journal of molecular modeling

authors： Du HC,Gong XD

更新日期：2012-05-01 00:00:00

abstract：:The present study analyzed binding of Cu(2+) to tetrapeptides in water solution at several levels of theoretical approximation. The methods used to study the energetic and structural properties of the complexes in question include semiempirical hamiltonians, density functional theory as well as ab initio approaches in...

journal_title：Journal of molecular modeling

authors： Czyżnikowska Z,Brasuń J

更新日期：2012-04-01 00:00:00

abstract：:ET(A) subtype selective antagonists constitute a novel and potentially important class of agents for the treatment of pulmonary hypertension, heart failure, and other pathological conditions. In this paper, 60 benzodiazepine derivatives displaying potent activities against ET(A) and ET(B) subtypes of endothelin recept...

journal_title：Journal of molecular modeling

authors： Xia J,Li J,Sun H

更新日期：2012-04-01 00:00:00

abstract：:Tautomerism in monomers/dimers and association of 2,5-dihydroxy-1,8-naphthyridine was studied at the DFT level recently recommended for studies of non-covalent interactions. Studied dimers are stabilized by double and triple hydrogen-bonding. In some associates the intermolecular proton transfer may take place. Transi...

journal_title：Journal of molecular modeling

authors： Ośmiałowski B

更新日期：2012-04-01 00:00:00

abstract：:Corynebacterium pseudotuberculosis is a facultatively intracellular Gram-positive bacterium that causes caseous lymphadenitis, principally in sheep and goats, though sometimes in other species of animals, leading to considerable economic losses. This pathogen has a TCS known as PhoPR, which consists of a sensory histi...

journal_title：Journal of molecular modeling

authors： Moraes G,Azevedo V,Costa M,Miyoshi A,Silva A,da Silva V,de Oliveira D,Teixeira MF,Lameira J,Alves CN

更新日期：2012-03-01 00:00:00

abstract：:DFT computations were carried out to characterize the (17)Oand (2)H electric field gradient, EFG, in various bisphosphonate derivatives. The computations were performed at the B3LYP level with 6-311++G (d,P) standard basis set. Calculated EFG tensors were used to determine the (17)O and (2)H nuclear quadrupole couplin...

journal_title：Journal of molecular modeling

authors： Aghabozorg H,Sohrabi B,Mashkouri S,Aghabozorg HR

更新日期：2012-03-01 00:00:00

abstract：:The biological toxicity of uranyl ion (UO (2) (2+) ) lies in interacting with proteins and disrupting their native functions. The structural and functional consequences of UO (2) (2+) interacting with cytochrome b (5) (cyt b (5)), a small membrane heme protein, and its heme axial ligand His39Ser variant, cyt b (5) H39...

journal_title：Journal of molecular modeling

authors： Wan D,Liao LF,Zhao MM,Wu ML,Wu YM,Lin YW

更新日期：2012-03-01 00:00:00

abstract：:Quantum chemical calculations of the structures and stabilities of the title series at the CCSD(T) theoretical level are performed. Laplacian, electron density deformation, electron localization function and reduced density gradient analysis are investigated to explore the nature of the interaction. The results show t...

journal_title：Journal of molecular modeling

authors： Li X

更新日期：2012-03-01 00:00:00

abstract：:The electron transport of the 4-(3-nitro-4-tetrafluorophenylthiolate-ethynyl, phenylethynyl) benzenethiolate (S-FNPPB-o) molecule assembled in two Au (111) electrodes, was studied using two approaches: in the first approximate approach an electric field was applied to the pure molecule attached to two thiolate ends fi...

journal_title：Journal of molecular modeling

authors： Serrato-Villegas L,Gallo M,Delgado-Ríos M,Romero MT,Glossman-Mitnik D

更新日期：2012-02-01 00:00:00

abstract：:ORF 3a of human severe acute respiratory syndrome corona virus (SARS-CoV) has been identified as a 274 amino acid membrane protein. When expressed in Xenopus oocytes the protein forms channels. Based on bioinformatics approaches the topology has been identified to include three transmembrane domains (TMDs). Since stru...

journal_title：Journal of molecular modeling

authors： Hsu HJ,Fischer WB

更新日期：2012-02-01 00:00:00

abstract：:The title compound, C(6)H(4)N(4)S(2)·C(3)H(7)NO, crystallizes in the monoclinic space group C 2/c with a = 26.673(5), b = 5.397(1), c = 16.522(3) Å, β = 95.49(3)°, Z = 8, R = 0.0461 for 1891 reflections with I > 2σ(I) and 174 parameters (4 restraints). Single pteridine-2,4(1 H,3 H)-dithione and dimethylformamide molec...

journal_title：Journal of molecular modeling

authors： Illán-Cabeza NA,Peña-Ruiz T,Moreno-Carretero MN

更新日期：2012-02-01 00:00:00

abstract：:This work is focused in three topical subjects: intermolecular interactions, metal ions, and aromaticity. A comprehensive MP2/6-31 + G and B3LYP/6-31 + G study of the influence of cation-π interactions on the aromatic character of phosphole was conducted. For this purpose, the structures of complexes were optimized at...

journal_title：Journal of molecular modeling

authors： Peña-Gallego A,Rodríguez-Otero J,Cabaleiro-Lago EM

更新日期：2012-02-01 00:00:00

abstract：:Multiple receptors conformation docking (MRCD) and clustering of dock poses allows seamless incorporation of receptor binding conformation of the molecules on wide range of ligands with varied structural scaffold. The accuracy of the approach was tested on a set of 120 cyclic urea molecules having HIV-1 protease inhib...

journal_title：Journal of molecular modeling

authors： Sivan SK,Manga V

更新日期：2012-02-01 00:00:00

abstract：:Human leukocyte antigen-related (PTP-LAR) is a receptor-like transmembrane phosphatase and a potential target for diabetes, obesity and cancer. In the present study, a sequence of in silico strategies (pharmacophore mapping, a 3D database searching, SADMET screening, and docking and toxicity studies) was performed to ...

journal_title：Journal of molecular modeling

authors： Ajay D,Sobhia ME

更新日期：2012-01-01 00:00:00

abstract：:Ab initio (MP2) and DFT (B3LYP) calculations, using the cc-pVTZ and aug-cc-pVTZ basis sets, have been performed to characterize some stationary points on the ground state potential energy surface of the title molecules. Several properties as, for instance, relative energies, the barriers for NO rotation around the NN ...

journal_title：Journal of molecular modeling

authors： do Monte SA,de Andrade RB,Ventura E,de Santana SR

更新日期：2012-01-01 00:00:00

abstract：:Ab initio and molecular simulation methods were used in calculations of the neutral individual betulin molecule, and molecular simulations were used to optimize the betulin molecule immersed in various amounts of water. Individual betulin was optimized in different force fields to find the one exhibiting best agreemen...

journal_title：Journal of molecular modeling

authors： Pospíšil M,Kovář P,Vácha R,Svoboda M

更新日期：2012-01-01 00:00:00

abstract：:To date, no suitable vaccine or specific antiviral drug is available to treat Chikungunya viral (CHIKV) fever. Hence, it is essential to identify drug candidates that could potentially impede CHIKV infection. Here, we present the development of a homology model of nsP2 protein based on the crystal structure of the nsP...

journal_title：Journal of molecular modeling

authors： Singh KhD,Kirubakaran P,Nagarajan S,Sakkiah S,Muthusamy K,Velmurgan D,Jeyakanthan J

更新日期：2012-01-01 00:00:00

abstract：:The present study reports the geometry, electronic structure and properties of neutral and anionic transition metal (TM = Ti, Zr and Hf)) doped germanium clusters containing 1 to 20 germanium atoms within the framework of linear combination of atomic orbitals density functional theory under spin polarized generalized ...

journal_title：Journal of molecular modeling

authors： Kumar M,Bhattacharyya N,Bandyopadhyay D

更新日期：2012-01-01 00:00:00

abstract：:Cystic fibrosis (CF), the most common lethal genetic disease among Caucasians, is caused by mutations in cystic fibrosis transmembrane conductance regulator (CFTR). CFTR's main role is to transport chloride ions across epithelial cell membranes. It also regulates many cell functions. However, the exact role of CFTR in...

journal_title：Journal of molecular modeling

authors： Siwiak M,Edelman A,Zielenkiewicz P

更新日期：2012-01-01 00:00:00

abstract：:In the past several years, halogen bonds have been shown to be relevant in crystal engineering and biomedical applications. One of the reasons for the utility of these types of noncovalent interactions in the development of, for example, pharmaceutical ligands is that their strengths and geometric properties are very ...

journal_title：Journal of molecular modeling

authors： Riley KE,Murray JS,Fanfrlík J,Rezáč J,Solá RJ,Concha MC,Ramos FM,Politzer P

更新日期：2011-12-01 00:00:00

abstract：:The three-dimensional (3D) structure of the substrate binding domain (SBD) of human ubiquitin ligase Siah2 (seven in absentia homolog) was constructed based on the homology modeling approach using the Modeller 9v7 program. The molecular dynamics method was utilized to refine the model and it was further assessed by Pr...

journal_title：Journal of molecular modeling

authors： Anupriya G,Roopa K,Basappa S,Chong YS,Annamalai L

更新日期：2011-12-01 00:00:00

abstract：:This paper investigates the thermodynamics of gas-phase CO(2) cascade uptake-reactions in the form of carbonate or monomethylcarbonate anions in the host cavity of various dinuclear octa-azacryptates of m-CH(2)C(6)H(4)CH(2) and 2,5-furano-spaced hosts, L (1) and L (2) cryptands, using density functional theory (DFT). ...

journal_title：Journal of molecular modeling

authors： El-Hendawy MM,English NJ,Mooney DA

更新日期：2011-12-01 00:00:00

abstract：:We report the parameterization of AM1 for the elements palladium and silver. The basis sets for both metals contain one set each of s-, p- and d-orbitals. AM1 parameters are now available for H, C, N, O and F (which use the original AM1 parameters), Al, Si, P, S, Cl, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Br, Zr, Mo, Pd, ...

journal_title：Journal of molecular modeling

authors： Kayi H,Clark T

更新日期：2011-10-01 00:00:00

abstract：:Eleven 1,4-naphthoquinone analogues with different amino substitutions at position 3 of the quinone ring earlier reported for macrofilaricidal activity were selected and screened against purified cytosolic GST isolated from the bovine filarial worm Setaria digitata and IC(50) values were determined. Of the 11 compound...

journal_title：Journal of molecular modeling

authors： Mathew N,Srinivasan L,Karunan T,Ayyanar E,Muthuswamy K

更新日期：2011-10-01 00:00:00

abstract：:The hydrogen bonding interactions between noradrenaline (NA) and DMSO were studied with density functional theory (DFT) regarding their geometries, energies, vibrational frequencies, and topological features of the electron density. The quantum theory of atoms in molecules (QTAIM) and the natural bond orbital (NBO) an...

journal_title：Journal of molecular modeling

authors： Huang Z,Dai Y,Yu L,Wang H

更新日期：2011-10-01 00:00:00

abstract：:This work focuses on the role of the dynamic hydrogen bonds (HB) formed in an aqueous solution of aspirin using molecular dynamics simulation. The statistics reveal the existence of internal HB that inhibit the rotational movements of the acetyl and the carboxylic acid groups, forcing the molecule to adopt a closed co...

journal_title：Journal of molecular modeling

authors： Donnamaria MC,de Xammar Oro JR

更新日期：2011-10-01 00:00:00

abstract：:Chemokine receptor 2 (CCR2) is a G-protein coupled receptor (GPCR) and a crucial target for various inflammatory and autoimmune diseases. The structure based antagonists design for many GPCRs, including CCR2, is restricted by the lack of an experimental three dimensional structure. Homology modeling is widely used for...

journal_title：Journal of molecular modeling

authors： Kim JH,Lim JW,Lee SW,Kim K,No KT

更新日期：2011-10-01 00:00:00

abstract：:Hydrogen dissociative chemisorption and desorption on small lowest energy Ni(n) clusters up to n=13 as a function of H coverage was studied using density functional theory. H adsorption on the clusters was found to be preferentially at edge sites followed by 3-fold hollow sites and on-top sites. The minimum energy pat...

journal_title：Journal of molecular modeling

authors： Zhou C,Yao S,Zhang Q,Wu J,Yang M,Forrey RC,Cheng H

更新日期：2011-09-01 00:00:00

abstract：:The binding of the reductase inhibitor drug fluvastatin, hydroxy-3-methylglutaryl coenzyme A, with the hydrophilic ι- or λ-carrageenan polymers, serving as potential controllers of the drug's release rate, have been studied at the density functional level of theory with the B3LYP exchange correlation functional. Three...

journal_title：Journal of molecular modeling

authors： Papadopoulos AG,Sigalas MP

更新日期：2011-07-01 00:00:00

abstract：:The quinolinol derivatives clioquinol (5-chloro-7-iodo-8-quinolinol, Quinoform) and cloxiquine (5-chloro-8-quinolinol) were studied experimentally in the solid state via ³⁵Cl NQR, ¹H-¹⁷O and ¹H-¹⁴N NQDR spectroscopies, and theoretically by density functional theory (DFT). The supramolecular synthon pattern of O-H···N ...

journal_title：Journal of molecular modeling

authors： Latosińska JN,Latosińska M,Tomczak MA,Seliger J,Zagar V

更新日期：2011-07-01 00:00:00

abstract：:Two important classes of organic molecules, perylene diimide (PDI) and pyrene derivatives have been found to possess relatively excellent photophysical and photochemical properties and especially high two-photon absorption cross sections (δ(T)(max)). Herein, one-photon absorption (OPA) and two-photon absorption (TPA) ...

journal_title：Journal of molecular modeling

authors： Liu XT,Zhao Y,Ren AM,Feng JK

更新日期：2011-06-01 00:00:00

abstract：:Theoretical studies on 1H-indole-3-acetic acid (IAA) were performed to investigate the conformational properties of dimeric species and vibrational spectra. Experimental infrared spectra at 100 K and 297 K and Raman spectrum at 297 K were analyzed and compared against calculations performed at B3LYP/6-31G** level. A e...

journal_title：Journal of molecular modeling

authors： Lobayan RM,Schmit MC,Jubert AH,Vitale A

更新日期：2011-06-01 00:00:00

abstract：:The electric field induced within a molecule by its electrons determines a whole series of important physical properties of the molecule. In particular, the values of the gradient of this field at the nuclei determine the interaction of their quadrupole moments with the electrons. Using unsymmetrical one-range additio...

journal_title：Journal of molecular modeling

authors： Guseinov II,Görgün NS

更新日期：2011-06-01 00:00:00