Theoretical study of noncovalent interactions in XCN···YO2H (X = F, Cl, Br, I; Y = P, As, Sb) complexes.

abstract：:The unsaturated trinuclear iron fluoroborylene complexes Fe3(BF)3(CO) n (n = 7, 6) have been studied using density functional theory (DFT). Relatively complicated potential energy surfaces are found with nine and eight structures within 15 kcal mol-1 of the lowest energy structures for the Fe3(BF)3(CO)7 and Fe3(BF)3(C...

journal_title：Journal of molecular modeling

authors： Xu L,Li QS,King RB

更新日期：2017-04-01 00:00:00

abstract：:Hepatic fibrosis is a common complication of the infection by the parasite, Clonorchis sinensis. There is a high incidence of this disease in the Asian countries with an increased risk of conversion to cancer. A secretory phospholipase A(2) (PLA(2)) enzyme from the parasite is implicated in the pathology. This is an a...

journal_title：Journal of molecular modeling

authors： Hariprasad G,Kaur P,Srinivasan A,Singh TP,Kumar M

更新日期：2012-07-01 00:00:00

abstract：:The effect of terminal GLY114* deletion on the binding affinity of the PA-IIL lectin toward L: -fucose was investigated. Both experimental (isothermal titration calorimetry) and computational (molecular dynamics simulations) methods have shown that the deletion mutation decreases the L-fucose affinity. It implies that...

journal_title：Journal of molecular modeling

authors： Wimmerová M,Mishra NK,Pokorná M,Koca J

更新日期：2009-06-01 00:00:00

abstract：:The fractional derivative concept to treat non-isothermal solid state thermal decomposition was employed in this work. Simulated data were compared with the exact solutions for the method validation. Calculated fractional kinetics data for four heating rates were initially considered and the Kissinger-Akahira-Sunose (...

journal_title：Journal of molecular modeling

authors： Carvalho FS,Braga JP,Marques MBF,Sebastião RCO

更新日期：2020-06-10 00:00:00

abstract：:We present a theoretical investigation of the electric properties of two kinds of one-dimensional lithium bonded chains: (NC-Li)n and (NC-CC-Li)n (n = 1-8). The resulting (NC-Li)n and (NC-CC-Li)n were found to exhibit enhanced first hyperpolarizabilities (β 0) with increasing n, and a slight change in the absorption m...

journal_title：Journal of molecular modeling

authors： Ma F,Bai D,Xu H

更新日期：2014-12-01 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 distinguishing property of Sm protein associations is very high stability. In order to understand this property, we analyzed the interfaces and compared the properties of Sm protein interfaces with those of a test set, the Binding Interface Database (BID). The comparison revealed that the main differences between ...

journal_title：Journal of molecular modeling

authors： Stojanović SD,Zarić BL,Zarić SD

更新日期：2010-11-01 00:00:00

abstract：:We report a study of the structure of (+)-catechin, which belongs to the family of the flavan-3-ols-one of the five most widely distributed phenolic groups. The biological activities and pharmaceutical utility of these compounds are related to antioxidant activity due to their ability to scavenge free radicals. A brea...

journal_title：Journal of molecular modeling

authors： Bentz EN,Pomilio AB,Lobayan RM

更新日期：2014-02-01 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：:A density functional theory investigation of adsorption of monomer, dimer and trimer forms of pyrrole on the outer surface of zigzag (7,0) single-walled carbon nanotube (SWCNT) has been reported. Geometries of the complexes were optimized using the M06-2X functional and the 6-31G(d,p) basis set. Moreover, 6-311G(d,p),...

journal_title：Journal of molecular modeling

authors： Shukla MK,Boddu V,Hill F

更新日期：2014-09-01 00:00:00

abstract：:Human immunodeficiency virus (HIV) infections continue to exert an enormous impact on global human health. This led experts to emphasize the importance of new measures for preventing HIV infections, including the development of vaccines and novel drugs. In this context, a promising approach involves the use of lectins...

journal_title：Journal of molecular modeling

authors： Conceição de Souza R,de Medeiros Muniz G,Siqueira AS,de Melo Lima A,da Silva AP,Gonçalves EC,da Silva Gonçalves Vianez Júnior JL

更新日期：2016-11-01 00:00:00

abstract：:Membranolytic anticancer peptides (ACPs) are drawing increasing attention as potential future therapeutics against cancer, due to their ability to hinder the development of cellular resistance and their potential to overcome common hurdles of chemotherapy, e.g., side effects and cytotoxicity. In this work, we present ...

journal_title：Journal of molecular modeling

authors： Grisoni F,Neuhaus CS,Hishinuma M,Gabernet G,Hiss JA,Kotera M,Schneider G

更新日期：2019-04-05 00:00:00

abstract：:B3LYP, PBE, M06-2X, B2PLYP, BN2PLYP-D, ωB97X-D, and MP2 levels of theory, in combination with the 6-311++G(d,p) and cc-pVTZ basis sets were comprehensively assessed for their ability to reproduce experimental FOX-7 structural and detonation data. ωB97X-D/cc-pVTZ, B3LYP/cc-pVTZ, and M06-2X/cc-pVTZ provided highly accur...

journal_title：Journal of molecular modeling

authors： Jeong K,Jeon Y,Kwon S

更新日期：2017-09-01 00:00:00

abstract：:The structural features, spectroscopic properties, and interaction energies of the linear proton-bound complexes of OCH(+) and its sulfur analog SCH(+) with N2 were investigated using the high-level ab initio methods MP2 and CCSD(T) as well as density functional theory with the aug-cc-pVXZ (X = D, T) basis sets. The r...

journal_title：Journal of molecular modeling

authors： Begum S,Subramanian R

更新日期：2016-01-01 00:00:00

abstract：:Recently inulinase has regained interest due to its usage in the production of fructooligosaccharides, biofuels, and in pharmaceutical industries. Inulinases properties are experimentally reported by nomerous studies but their characteristics are just partially explained by only a few computational investigations. In ...

journal_title：Journal of molecular modeling

authors： Singh PK,Joseph J,Goyal S,Grover A,Shukla P

更新日期：2016-04-01 00:00:00

abstract：:The interaction of a model Lys flanked α-helical peptides K2-X24-K2, (X = A,I,L,L+A,V) with lipid bilayers composed of dimyristoylphosphatidylcholine (DMPC) and dipalmitoylphosphatidylcholine (DPPC) both, in a gel and in a liquid-crystalline state, has been studied by molecular dynamics simulations. It has been shown ...

journal_title：Journal of molecular modeling

authors： Melicherčík M,Holúbeková A,Hianik T,Urban J

更新日期：2013-11-01 00:00:00

abstract：:Ab initio computations are performed to study the structural, elastic, electronic, and vibrational characteristics of the cubic antiperovskite compound PbNCa3 under pressure up to 50 GPa. By using the generalized gradient approximation (GGA), the equilibrium structural parameters, energy band structure, density of sta...

journal_title：Journal of molecular modeling

authors： Ciftci YO,Evecen M,Alp İO

更新日期：2021-01-03 00:00:00

abstract：:In recent years, it has become clear that the neuronal nicotinic acetylcholine receptor (nAChR) is a valid target in the treatment of a variety of diseases, including Alzheimer's disease, anxiety, and nicotine addiction. As with most membrane proteins, information on the three-dimensional (3D) structure of nAChR is li...

journal_title：Journal of molecular modeling

authors： Bisson WH,Westera G,Schubiger PA,Scapozza L

更新日期：2008-10-01 00:00:00

abstract：:The theoretical three-dimensional structure of a novel δ-endotoxin Cry1Id (81 kDa) belonging to Cry1I class, toxic to many of the lepidopteran pests has been investigated through comparative modeling. Molecular dynamics (MD) simulations was carried out to characterize its structural and dynamical features at 10 ns in ...

journal_title：Journal of molecular modeling

authors： Dehury B,Sahu M,Sahu J,Sarma K,Sen P,Modi MK,Barooah M,Choudhury MD

更新日期：2013-12-01 00:00:00

abstract：:Fifteen KSP inhibitors were docked into the receptor and the binding mode was analyzed for the first time. It was considered that in addition to the main binding pocket all the inhibitors merged in, there exists a cooperative minor binding pocket, which could be explored for significantly increased binding affinity. I...

journal_title：Journal of molecular modeling

authors： Jiang C,Chen Y,Wang X,You Q

更新日期：2007-09-01 00:00:00

abstract：:Intramolecular and intermolecular hydrogen bonding in electronic excited states of calixarene building blocks bis(2-hydroxyphenyl)methane (2HDPM) monomer and hydrogen-bonded 2HDPM-H₂O complex were studied theoretically using the time-dependent density functional theory (TDDFT). Twenty-four stable conformations (12 pai...

journal_title：Journal of molecular modeling

authors： Wang S,Hao C,Gao Z,Chen J,Qiu J

更新日期：2013-04-01 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：:Using ligand and receptor based virtual screening approaches we have identified potential virtual screening hits targeting type II dehydroquinase from Mycobacterium tuberculosis, an effective and validated anti-mycobacterial target. Initially, we applied a virtual screening workflow based on a combination of 2D struct...

journal_title：Journal of molecular modeling

authors： Kumar A,Siddiqi MI,Miertus S

更新日期：2010-04-01 00:00:00

abstract：:Molecular and quantum mechanics calculations were carried out in a series of tripeptides (GXG, where X = D, N and C) as models of the unfolded states of proteins. The selected central amino acids, especially aspartic acid (D) and asparagine (N) are known to present significant average conformations in partially allowe...

journal_title：Journal of molecular modeling

authors： Ramos J,Cruz VL

更新日期：2016-11-01 00:00:00

abstract：:The Fbw7-Skp1 complex is an essential component in the formation and development of the mammalian cardiovascular system; the complex interaction is mediated through binding of Skp1 C-terminal peptide (qGlu-peptide) to the F-box domain of Fbw7. By visually examining the crystal structure, we identified a typical cation...

journal_title：Journal of molecular modeling

authors： Zhou J,Wang YS

更新日期：2017-09-26 00:00:00

abstract：:Drug resistance is a very important factor contributing to the failure of current HIV therapies. The ability to understand the resistance mechanism of HIV-protease mutants may be useful in developing more effective and longer lasting treatment regimens. In this paper, we report the first computational study of the cli...

journal_title：Journal of molecular modeling

authors： Meiselbach H,Horn AH,Harrer T,Sticht H

更新日期：2007-02-01 00:00:00

abstract：:In recent years, several new chelating reagents have been synthesized and tested for their collecting power in sulfide and non-sulfide minerals flotation. Many researchers have indicated that chelating reagents have the advantage of offering better selectivity and specificity as flotation collectors. Therefore, densit...

journal_title：Journal of molecular modeling

authors： Yekeler H,Yekeler M

更新日期：2006-09-01 00:00:00

abstract：:A good understanding of the inhibition mechanism of enzymes exhibiting high levels of similarity is the first step to the discovery of new drugs with selective potential. Examples of such proteins include glycogen synthase kinase-3 (GSK-3β) and cyclin-dependent kinase 2 (CDK-2). This article reports the mechanism of s...

journal_title：Journal of molecular modeling

authors： Czeleń P

更新日期：2017-08-01 00:00:00

abstract：:The ion-pair S(N)2 reaction LiNCS + CH3F with two mechanisms, inversion and retention, was investigated at the MP2(full)/6-311+G**//HF/6-311+G** level in the gas phase and in acetone solution. All HF-optimized structures were confirmed by vibrational frequency analysis. Based on IRC analyses, eight possible reaction p...

journal_title：Journal of molecular modeling

authors： Ren Y,Li M,Wong NB,Chu SY

更新日期：2006-01-01 00:00:00

abstract：:Odorant binding proteins (OBPs) are important in insect olfactory recognition. These proteins bind specifically to insect semiochemicals and induce their seeking, mating, and alarm behaviors. Molecular docking and molecular dynamics simulations were performed to provide computational insight into the interaction mode ...

journal_title：Journal of molecular modeling

authors： Wang S,Sun Y,Du S,Qin Y,Duan H,Yang X

更新日期：2016-06-01 00:00:00