Molecular modeling and dynamics studies of cytidylate kinase from Mycobacterium tuberculosis H37Rv.

abstract：:An electronic study of nimesulide was performed by using density functional theory calculations. The activities of the six different derivatives were related with electron donating or accepting capacities. All compounds which had nitro moiety had low electron donating and high electron accepting capacities. However, t...

journal_title：Journal of molecular modeling

authors： Borges RS,Oliveira JP,Matos RF,Chaves Neto AM,Carneiro AS,Monteiro MC

更新日期：2015-07-01 00:00:00

abstract：:Antihistamines are frequently used pharmaceuticals that treat the symptoms of allergic reactions. Loratadine (LOR) is an active component of the second generation of selective antihistaminic pharmaceutical usually known as Claritin. Frequent usage of this type of pharmaceuticals imposes the need for understanding thei...

journal_title：Journal of molecular modeling

authors： Armaković S,Armaković SJ,Abramović BF

更新日期：2016-10-01 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：:A comparative theoretical investigation into the change in strength of the trigger-bond upon formation of the Na(+), Mg(2+) and HF complexes involving the nitro group of RNO₂ (R = -CH₃, -NH₂, -OCH₃) or the C = C bond of (E)-O₂N-CH = CH-NO₂ was carried out using the B3LYP and MP2(full) methods with the 6-311++G**, 6-31...

journal_title：Journal of molecular modeling

authors： Zhang L,Ren FD,Cao DL,Wang JL,Gao JF

更新日期：2013-06-01 00:00:00

abstract：:A detailed investigation of the structure, electronic, spectroscopic, and optical properties of a series of transition metal-doped tetraphenylporphyrins (TM-TPP; TM = Fe, Co, Ni, Cu and Zn) is performed under density functional framework. The structure and stability of tetraphenylporphyrin (TPP) and TM-TPPs are unders...

journal_title：Journal of molecular modeling

authors： Shah EV,Kumar V,Sharma BK,Rajput K,Chaudhary VP,Roy DR

更新日期：2018-08-18 00:00:00

abstract：:The Z-DNA-binding domain of human double-stranded RNA adenosine deaminase I (hZαADAR1) can specifically recognize the left-handed Z-DNA which preferentially occurs at alternating purine-pyrimidine repeats, especially the CG-repeats. The interactions of hZαADAR1 and Z-DNAs in different sequence contexts can affect many...

journal_title：Journal of molecular modeling

authors： Wang Q,Li L,Wang X,Liu H,Yao X

更新日期：2014-11-01 00:00:00

abstract：:The reactivity of the 5-arylidenerhodanine and 5-arylideneisorhodanine derivatives in reactions with dimethyl maleate was computationally studied at the DFT(M06-2X)/6-311+G(d,p) theory level. Eight stereoisomers of the reaction products were considered. The effect of the solvent was taken into account by means of the ...

journal_title：Journal of molecular modeling

authors： Tejchman W,Michalski M,Zborowski KK,Berski S

更新日期：2019-06-14 00:00:00

abstract：:In the present study, DFT calculations are carried out on domestically designed 7-methyl-2-phenyl-5'H-spiro[chromene-4,2'-chromeno[3,4-e][1,3]oxazin]-5'-one spiropyran and merocyanine derivatives to recognize alkali and alkaline earth metal ions. Detection of these metal ions can be attained by exploiting the variatio...

journal_title：Journal of molecular modeling

authors： Arif AM,Yousaf A,Zhong RL,Akhtar M,Muhammad S,Xu HL,Su ZM

更新日期：2019-07-06 00:00:00

abstract：:The cold shock protein from the hyperthermophile Thermotoga maritima (Tm-Csp) exhibits significantly higher thermostability than its homologue from the thermophile Bacillus caldolyticus (Bc-Csp). Experimental studies have shown that the electrostatic interactions unique to Tm-Csp are responsible for improving its ther...

journal_title：Journal of molecular modeling

authors： Su JG,Han XM,Zhao SX,Hou YX,Li XY,Qi LS,Wang JH

更新日期：2016-04-01 00:00:00

abstract：:Here, we report theoretical research into the interaction of the drug tamoxifen drug with tripeptides found in the tumor environment-specifically, asparagine-glycine-arginine (NGR) and arginine-glycine-aspartic acid (RGD). Reactivity parameters of these tripeptides were calculated and their intrinsic reactivities and ...

journal_title：Journal of molecular modeling

authors： Landeros-Martínez LL,Glossman-Mitnik D,Flores-Holguín N

更新日期：2018-11-09 00:00:00

abstract：:The reaction mechanism of Ru-catalyzed cycloisomerization of 2-alkynylanilides to 3-substituted indole or 2-substituted indole was analyzed at the B3LYP level of density functional theory. The solvation effect of the system was also considered by SMD model. The calculation results show that the reaction system first f...

journal_title：Journal of molecular modeling

authors： Zhang X,Li S,Wei X,Lei Y

更新日期：2018-06-14 00:00:00

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：:Metallo-β-lactamases (MβLs) can hydrolyze and deactivate lactam-containing antibiotics, which are the major mechanism to cause drug resistance in the treatment of bacterial infections. This has become a global concern due to the lack of clinically approved inhibitors so far. SMB-1 from Serratia marcescents is a novel ...

journal_title：Journal of molecular modeling

authors： Mu X,Xu D

更新日期：2020-03-07 00:00:00

abstract：:Temperature dependences of the spontaneous polarization and the dielectric constant are calculated near the paraelectric-ferroelectric (cubic-tetragonal) transition in BaTiO3 using our mean field model. By expanding the free energy in terms of the spontaneous polarization (order parameter), expressions for the tempera...

journal_title：Journal of molecular modeling

authors： Yurtseven H,Kiraci A

更新日期：2013-09-01 00:00:00

abstract：:The effects of substituting nitrogen atoms on the stability of novel singlet (s) and triplet (t) forms of germylenes (1-20) are compared and contrasted, at B3LYP/AUG-cc-pVTZ level of theory. Every one of the 40 new divalents scrutinized appears as a minimum on its energy surface, for showing no negative force constant...

journal_title：Journal of molecular modeling

authors： Abedini N,Kassaee MZ

更新日期：2020-10-31 00:00:00

abstract：:In this study, the binding of Bovine serum albumin (BSA) with three flavonoids, kaempferol-3-O-a-L-rhamnopyranosyl-(1-3)-a-L-rhamnopyranosyl-(1-6)-b-D-galacto- pyranoside (drug 1),kaempfol-7-O-rhamnosyl-3-O-rutinoside (drug 2)andkaempferide-7-O-(4"-O-acetylrhamnosyl)-3-O-ruti- noside (drug 3) is investigated by molecu...

journal_title：Journal of molecular modeling

authors： Niu X,Gao X,Wang H,Wang X,Wang S

更新日期：2013-03-01 00:00:00

abstract：:Periodic first-principles calculations have been performed to study the effect of high pressure on the geometric, electronic, and absorption properties of 2,6-diamino-3,5-dinitropyrazine-1-oxide (LLM-105) under hydrostatic pressures of 0-50 GPa. Obvious irregular changes in lattice constants, unit-cell angles, bond le...

journal_title：Journal of molecular modeling

authors： Wu Q,Yang C,Pan Y,Xiang F,Liu Z,Zhu W,Xiao H

更新日期：2013-12-01 00:00:00

abstract：:The capture of N3-chains and N5-rings on the outer surface of C60 was studied using density functional calculations. For the neutral N5-ring, it was found that a N5-ring trapped by a C60 cage becomes more stable than an isolated N5-ring radical, and a C60-N5 compound with a C-N bond at an exohedral position of C60 is ...

journal_title：Journal of molecular modeling

authors： Liang Y,Gao X,Li N,Zhang X

更新日期：2015-10-01 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：:Natural hIFNγ is a glycoprotein with two N-glycosylation sites in each monomer chain, which are independently and differentially glycosylated. Although glycosylation is not necessary for the activity of the cytokine, it was proposed that it protects the cytokine from proteolytic degradation and thus extends its circul...

journal_title：Journal of molecular modeling

authors： Lilkova E,Petkov P,Ilieva N,Krachmarova E,Nacheva G,Litov L

更新日期：2019-04-25 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：:In this study, the newly synthesized non-centrosymmetric, 4-dimethylamino-3'-isothiocyanatochalcone (PKA) compound was presented. This compound belongs to the chalcone group, and its main purpose is to be used in biomedical imaging as a fluorescence dye. For this reason, the linear and nonlinear properties in solvents...

journal_title：Journal of molecular modeling

authors： Krawczyk P,Pietrzak M,Janek T,Jędrzejewska B,Cysewski P

更新日期：2016-06-01 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：:We use density functional theory-based calculations to study structural, electronic, and magnetic properties of two key reaction intermediates on a hematite, [Formula: see text]-Fe2O3, photoanode during the solar-driven water splitting reaction. Both intermediates contain an oxygen atom bonded to a surface iron atom. ...

journal_title：Journal of molecular modeling

authors： Poaty LT,Ulman K,Seriani N,M'Passi-Mabiala B,Gebauer R

更新日期：2018-09-18 00:00:00

abstract：:Comprehensive molecular dynamics simulations are conducted to identify material modifications which can improve strength and reduce hysteresis losses at the nanointerfaces formed between silica, silane coupling agent (SCA) and styrene-butadiene rubber (SBR), all of which are important ingredients of green tyres. Impro...

journal_title：Journal of molecular modeling

authors： Joseph E,Swaminathan N,Kannan K

更新日期：2020-08-17 00:00:00

abstract：:The ladder-type polyheterofluorenes were investigated theoretically by using density functional theory (DFT) to reveal their optical and electronic properties for applications in organic optoelectronic devices. The incorporation of heteroatoms (B, Si, Ge, N, P, O, and S) into the ladder-type highly fused polyfluorene ...

journal_title：Journal of molecular modeling

authors： Zheng C,Tao Y,Cao JZ,Chen RF,Zhao P,Wu XJ,Huang W

更新日期：2012-11-01 00:00:00

abstract：:The detailed decomposition mechanism of nitroglycerin (NG) in the gas phase was studied by examining reaction pathways using density functional theory (DFT) and canonical variational transition state theory combined with a small-curvature tunneling correction (CVT/SCT). The mechanism of NG autocatalytic decomposition ...

journal_title：Journal of molecular modeling

authors： Pei L,Dong K,Tang Y,Zhang B,Yu C,Li W

更新日期：2017-08-21 00:00:00

abstract：:The mechanism for the hydroxyl-radical-induced depolymerization of cellulose under alkaline conditions in air was investigated using density functional theory at the B3LYP/6-31+G(d,p) level as well as electron transfer theory. The pathway for the depolymerization of cellulose was obtained theoretically and H abstracti...

journal_title：Journal of molecular modeling

authors： Shao C,Shi K,Hua Q,Zhang L,Dai Y,You W,Liu Y,Li C,Zhang C

更新日期：2018-05-02 00:00:00

abstract：:A novel mechanism for switching a molecular junction based on a proton transfer reaction triggered by an external electrostatic field is proposed. As a specific example to demonstrate the feasibility of the mechanism, the tautomers [2,5-(4-hydroxypyridine)] and {2,5-[4(1H)-pyridone]} are considered. Employing a combin...

journal_title：Journal of molecular modeling

authors： Hofmeister C,Härtle R,Rubio-Pons O,Coto PB,Sobolewski AL,Thoss M

更新日期：2014-04-01 00:00:00

abstract：:The potential energy surfaces in gas phase and in aqueous solution for the nitration of benzene, chlorobenzene, and phenol have been elucidated with density functional theory at the M06-2X/6-311G(d,p) level combined with the polarizable continuum solvent model (PCM). Three reaction intermediates have been identified a...

journal_title：Journal of molecular modeling

authors： Liljenberg M,Stenlid JH,Brinck T

更新日期：2017-12-18 00:00:00