Computer-based design of novel HIV-1 entry inhibitors: neomycin conjugated to arginine peptides at two specific sites.

abstract：:Insulin-like growth factor-binding proteins (IGFBPs) control bioactivity and distribution of insulin-like growth factors (IGFs) through high-affinity complex of IGFBP and IGF. To get more insight into the binding interaction of IGF system, the site-directed mutagenesis and force-driving desorption methods were employe...

journal_title：Journal of molecular modeling

authors： Chen X,Zhu S,Duan D,Wu T,Wang Q

更新日期：2013-12-01 00:00:00

abstract：:The interaction between tetramethylcucurbit[6]uril (host) and 5,5'-dimethyl-2,2'-bipyridyl hydrochloride (guest) was studied by 1H NMR, X-ray crystallography, electronic absorption spectroscopy, fluorescence emission spectra and quantum chemistry calculations. This experimental-computational study that indicated the h...

journal_title：Journal of molecular modeling

authors： Cong H,Zhao YJ,Xue SF,Tao Z,Zhu QJ

更新日期：2007-12-01 00:00:00

abstract：:The formation of selenium species in some biological processes involves the generation of ionic and radical intermediates such as RSe●, RSe-, RSeO●, and RSeO-, among others. We performed a theoretical study of the possible mechanisms for the reaction of the two simplest Se radicals-the hydroselenyl (HSe●) and seleneni...

journal_title：Journal of molecular modeling

authors： Vega-Teijido MA,Kieninger M,Ventura ON

更新日期：2017-12-05 00:00:00

abstract：:Thermotropic polyurethanes with mesogenic groups in side chains were prepared from two diisocyanates and four diols with stoichiometric ratios of reactive isocyanate (NCO) and hydroxy (OH) groups. Their thermal behavior was determined by differential scanning calorimetry. The effect of structure modifications of the d...

journal_title：Journal of molecular modeling

authors： Repáková J,Capková P,Studenovský M,Ilavský M

更新日期：2004-08-01 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：:We here report a combined quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) study on the binding interactions between the α(V)β₃ integrin and eight cyclic arginine-glycine-aspartate (RGD) containing peptides. The initial conformation of each peptide within the binding site of the integrin was det...

journal_title：Journal of molecular modeling

authors： Xiang M,Lin Y,He G,Chen L,Yang M,Yang S,Mo Y

更新日期：2012-11-01 00:00:00

abstract：:The halogen bonding interactions between C6F5I and a series of transition metal monohalides trans-[M(X)(2-C5NF4)-(PR3)2] (M = Ni, Pd, Pt; X = F, Cl, Br; R = Me, Cy) have been studied with quantum chemical calculations. Optimized geometries of the halogen bonding complexes indicate that angles C1-I···X are basically li...

journal_title：Journal of molecular modeling

authors： Cheng N,Liu Y,Zhang C,Liu C

更新日期：2013-09-01 00:00:00

abstract：:We investigated the dynamics of an electron subjected to a uniform electric field in the scope of a tight-binding electron-phonon interacting approach. We aimed at describing the transport in a one-dimensional lattice in which the on-site energies are distributed according to a Fibonacci sequence. Within this physical...

journal_title：Journal of molecular modeling

authors： de Brito PE,Enders BG,Ribeiro LA Jr,Nazareno HN

更新日期：2019-03-28 00:00:00

abstract：:Modulation of γ-aminobutyric acid (GABA) levels has been required in various disorders. GABA itself cannot be directly introduced into central nervous system (CNS) because of the blood brain barrier; inhibition of GABA aminotransferase (GABA-AT), which degrades GABA in CNS, has been the target for the modulation of GA...

journal_title：Journal of molecular modeling

authors： Park JY,Lee Y,Lee HJ,Kwon YS,Chun W

更新日期：2020-08-11 00:00:00

abstract：:Fully atomistic molecular dynamics simulation studies of thermotropic bilayers were performed using a set of glycosides namely n-octyl-β-D-glucopyranoside (β-C8Glc), n-octyl-α-D-glucopyranoside (α-C8Glc), n-octyl-β-D-galactopyranoside (β-C8Gal), and n-octyl-α-D-galactopyranoside (α-C8Gal) to investigate the stereochem...

journal_title：Journal of molecular modeling

authors： Ahmadi S,Manickam Achari V,Nguan H,Hashim R

更新日期：2014-03-01 00:00:00

abstract：:The ONIOM2 (B3LYP/6-31G (d, p): PM3) and B3LYP/6-31G (d, p) methods were applied to investigate the interaction between STI-571 and abelson tyrosine kinase binding site. The complex of N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)- phenyl]-benzamide (part of STI-571) and related 16 amino acid residues were found ...

journal_title：Journal of molecular modeling

authors： Xiong YZ,Chen PY

更新日期：2008-11-01 00:00:00

abstract：:The aim of the present work entitled electronic structure of PVA-PEG-Y2O3 (54 atom) is to present a theoretical study based on the hybrid function of three parameters Lee-Yang-Parr B3LYP of the density functional theory "DFT" quantum mechanical approach together with LanL2DZ basis sets for optoelectronics applications...

journal_title：Journal of molecular modeling

authors： Ahmed H,Hashim A

更新日期：2020-07-20 00:00:00

abstract：:Density functional theory (DFT) has been applied to understand the influence of various linkages on the energetic properties and stability of the polynitro-biphenyl compounds. Structures were optimized using the B3PW91/6-31G(d,p) level, and the heats of formation (HOFs) were computed by employing the selected isodesmi...

journal_title：Journal of molecular modeling

authors： Nirwan A,Devi A,Ghule VD

更新日期：2019-09-15 00:00:00

abstract：:It is well-known that properties of poly(vinyl alcohol) (PVA) in the pure and solution states depend largely on the hydrogen bonding networks formed. In the context of molecular simulation, such networks are handled through the Coulombic interactions. Therefore, a good set of partial atom charges (PACs) for simulation...

journal_title：Journal of molecular modeling

authors： Noorjahan A,Choi P

更新日期：2015-03-01 00:00:00

abstract：:We present a critical discussion related to the recent definition of the intrinsic reactivity index, IRI, (Tetrahedron Lett. 2013, 54, 339-342; Tetrahedron 2013, 69, 4247-4258) formulated to describe both, electrophilicity (charge acceptance) and nucleophilicity (charge donation) reactivities. We here stress that such...

journal_title：Journal of molecular modeling

authors： Chamorro E,Melin J

更新日期：2015-03-01 00:00:00

abstract：:Periplasmic binding proteins are the initial receptors for the transport of various substrates over the inner membrane of gram-negative bacteria. The binding proteins are composed of two domains, and the substrate is entrapped between these domains. For several of the binding proteins it has been established that a cl...

journal_title：Journal of molecular modeling

authors： Siuda I,Thøgersen L

更新日期：2013-11-01 00:00:00

abstract：:We investigate the conformational properties of a potent inhibitor of neuropilin-1, a protein involved in cancer processes and macular degeneration. This inhibitor consists of four aromatic/conjugated fragments: a benzimidazole, a methylbenzene, a carboxythiourea, and a benzene-linker dioxane, and these fragments are ...

journal_title：Journal of molecular modeling

authors： Goldwaser E,de Courcy B,Demange L,Garbay C,Raynaud F,Hadj-Slimane R,Piquemal JP,Gresh N

更新日期：2014-11-01 00:00:00

abstract：:Four clusters of ZnO, O-Zn-SR (-SR = ligand) and doping ZnO structures (with Cr, Cu, Al atoms) were investigated using density functional theory at theB3LYP/Lanl2dz level. The characteristics of Zn(3)O(3) and Zn(4)O(4) structures, which are the units of experimental wurtzite and zinc blende structures, were found to b...

journal_title：Journal of molecular modeling

authors： Wang C,Xu S,Ye L,Lei W,Cui Y

更新日期：2011-05-01 00:00:00

abstract：:In this work a molecular modeling study was carried out based on a series of organotin(IV) derivatives which were complexed with ONO-Donor type Schiff base ligands to build up a statistical data pool for researchers. For this purpose, various properties of the selected complexes such as energies, band gaps, chemical r...

journal_title：Journal of molecular modeling

authors： Şirikci G,Ancın NA,Öztaş SG

更新日期：2015-09-01 00:00:00

abstract：:The geometries of three isomers of the C2H4O...2HF tri-molecular heterocyclic hydrogen-bonded complex were examined through B3LYP/aug-cc-pVDZ calculations. Analysis of structural parameters, determination of CHELPG (charge electrostatic potential grid) intermolecular charge transfer, interpretation of infrared stretch...

journal_title：Journal of molecular modeling

authors： de Oliveira BG,Araújo RC,Chagas FF,Carvalho AB,Ramos MN

更新日期：2008-10-01 00:00:00

abstract：:4-hydroxybenzoate oligoprenyltransferase of E. coli, encoded in the gene ubiA, is an important key enzyme in the biosynthetic pathway to ubiquinone. It catalyzes the prenylation of 4-hydroxybenzoic acid in position 3 using an oligoprenyl diphosphate as a second substrate. Up to now, no X-ray structure of this oligopre...

journal_title：Journal of molecular modeling

authors： Bräuer L,Brandt W,Wessjohann LA

更新日期：2004-12-01 00:00:00

abstract：:Density functional theory (DFT) was used to investigate cobalt(0)-catalyzed intramolecular hydroacylation of 4-pentenal. The calculated results indicated the involvement of five possible reaction pathways: the formation of cyclopentanone, cyclobutanone, butylenes, cyclobutane, and cyclopropane, respectively. The forme...

journal_title：Journal of molecular modeling

authors： Meng Q,Wang F,Li M

更新日期：2013-06-01 00:00:00

abstract：:Molecular-dynamics simulations have been used to study the diffusion of a short single model carbonic chain on the graphite (001) surface. The calculated diffusion coefficient (D) first increases, then decreases with increasing chain length (N). This abnormal behavior is similar to polymer lateral diffusion at the sol...

journal_title：Journal of molecular modeling

authors： Yang H,Lu ZY,Li ZS,Sun CC

更新日期：2006-03-01 00:00:00

abstract：:Nitriles are important chemical species in organic transformations, material chemistry, and environmental sciences. Nitriles are used as cyanating reagents in many organic reactions, where the C-CN bond dissociation has an important role. The reactivity of nitriles can be better understood by studying the bond dissoci...

journal_title：Journal of molecular modeling

authors： Kosar N,Ayub K,Gilani MA,Mahmood T

更新日期：2019-01-28 00:00:00

abstract：:Leishmaniasis is an endemic disease caused by infection with one of several different species of protozoan parasite Leishmania. Oligopeptidase B (OPB) is a serine peptidase which plays a vital role in survival of the Leishmania parasite in the host (human) macrophage and help in attaining complete virulence. Inhibitio...

journal_title：Journal of molecular modeling

authors： Goyal S,Grover S,Dhanjal JK,Goyal M,Tyagi C,Chacko S,Grover A

更新日期：2014-03-01 00:00:00

abstract：:Through the B3LYP/6-311++G(d,p) calculations, theoretical studies of structural parameters, electronic properties, infrared vibration modes, and charge density topologies on the C2H4O∙∙∙HX and C2H5N∙∙∙HX (X = F or O-F) heterocylic hydrogen complexes are presented. The H-bond distances and high energies point out stron...

journal_title：Journal of molecular modeling

authors： Oliveira BG

更新日期：2015-11-01 00:00:00

abstract：:The treatment of neuropathic pain is very complex and there are few drugs approved for this purpose. Among the studied compounds in the literature, sigma-1 receptor antagonists have shown to be promising. In order to develop QSAR studies applied to the compounds of 1-arylpyrazole derivatives, multivariate analyses hav...

journal_title：Journal of molecular modeling

authors： Oliveira AA,Lipinski CF,Pereira EB,Honorio KM,Oliveira PR,Weber KC,Romero RAF,de Sousa AG,da Silva ABF

更新日期：2017-10-02 00:00:00

abstract：:The adsorption behavior of sulfur-based toxic gases (H2S and SO2) on armchair silicene nanoribbons (ASiNRs) was investigated using first-principles density functional theory (DFT). Being a zero band gap material, application of bulk silicene is limited in nanoelectronics, despite its high carrier mobility. By restrict...

journal_title：Journal of molecular modeling

authors： Walia GK,Randhawa DKK

更新日期：2018-03-16 00:00:00

abstract：:Meta-hybrid density functional theory calculations using M06-2X/6-31+G(d,p) and M06-2X/6-311+G(d,p) levels of theory have been performed to understand the strength of C-H(…)π interactions of two possible types for benzene-acetylene, 1,3,5-trifluorobenzene-acetylene and coronene-acetylene complexes. Our study reveals t...

journal_title：Journal of molecular modeling

authors： Dinadayalane TC,Paytakov G,Leszczynski J

更新日期：2013-07-01 00:00:00

abstract：:The structural characteristics involving thermal stabilities of liquid nitromethane (NM)—one of the simplest energetic materials—confined within a graphene (GRA) bilayer were investigated by means of all-atom molecular dynamics simulations and density functional theory calculations. The results show that ordered and l...

journal_title：Journal of molecular modeling

authors： Liu Y,Yu T,Lai W,Kang Y,Ge Z

更新日期：2015-03-01 00:00:00