DFT/TDDFT investigation on the chemical reactivities, aromatic properties, and UV-Vis absorption spectra of 1-butoxy-4-methoxybenzenepillar[5]arene constitutional isomers.

abstract：:Monoamine oxidase (MAO) is an enzyme of major importance in neurochemistry, because it catalyzes the inactivation pathway for the catecholamine neurotransmitters, noradrenaline, adrenaline and dopamine. In the last decade it was demonstrated that imidazoline derivatives were able to inhibit MAO activity. Furthermore, ...

journal_title：Journal of molecular modeling

authors： Moraes FP,de Azevedo WF Jr

更新日期：2012-08-01 00:00:00

abstract：:Ergothioneine (2-mercaptohistidine trimethylbetaine) is a very stable natural compound largely present in cells and tissues of plants and mammals. The biological role of ET is still incompletely understood but its antioxidant properties are well assessed experimentally. However, no theoretical study had been performed...

journal_title：Journal of molecular modeling

authors： Lespade L

更新日期：2019-10-26 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：:Survivin, the smallest inhibitor of apoptosis protein (IAP), is a valid target for cancer research. It mediates both the apoptosis pathway and the cell cycle and has been proposed to form a complex with the cyclin-dependent kinase protein CDK4. The resulting complex transports CDK4 from the cytosol to the nucleus, whe...

journal_title：Journal of molecular modeling

authors： Selent J,Kaczor AA,Guixà-González R,Carrió P,Pastor M,Obiol-Pardo C

更新日期：2013-04-01 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：: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：:Contact sites between amino acids characterize important structural features of a protein. We investigated characteristics of contact sites in a representative set of proteins and their relations between protein class or topology. For this purpose, we used a non-redundant set of 5872 protein domains, identically categ...

journal_title：Journal of molecular modeling

authors： Wozniak PP,Kotulska M

更新日期：2014-11-01 00:00:00

abstract：:Bacterial cytidylate kinase or cytidine monophosphate kinase (CMP kinase) catalyses the phosphoryl transfer from ATP to CMP and dCMP, resulting in the formation nucleoside diphosphates. In eukaryotes, CMP/UMP kinase catalyses the conversion of UMP and CMP to, respectively, UDP and CDP with high efficiency. This work d...

journal_title：Journal of molecular modeling

authors： Caceres RA,Macedo Timmers LF,Vivan AL,Schneider CZ,Basso LA,De Azevedo WF Jr,Santos DS

更新日期：2008-05-01 00:00:00

abstract：:Using addition theorems for complete orthonormal sets of exponential type orbitals in the momentum representation introduced by the author, the addition theorems are established for Slater type orbitals in momentum space. With the help of these addition theorems, the general series expansion formulae in terms of the p...

journal_title：Journal of molecular modeling

authors： Guseinov II

更新日期：2005-03-01 00:00:00

abstract：:The original version of this article unfortunately contained a mistake. Schemes I and II were missing. These important components are given below. ...

journal_title：Journal of molecular modeling

authors： Roy RS,Mondal A,Nandi PK

更新日期：2017-11-01 00:00:00

abstract：:The mechanism of C-H bond activation of ethane was catalyzed by palladium halide cations (PdX+ (X = F, Cl, Br, H, and CH3)), which was investigated using density functional theory (DFT) at B3LYP level. The reaction mechanism was taken into account in triplet and singlet spin state potential energy surfaces. For PdF+, ...

journal_title：Journal of molecular modeling

authors： Nie YX,Zhang XX,Yuan YN,Lu F,Geng ZY

更新日期：2020-04-03 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：:A series of oligo(thienylenevinylene) derivatives with 1,4-dihydropyrrolo[3,2-b]pyrrole as core has been investigated at the PBE0/6-31G(d) and the TD-PBE0/6-31+G(d,p) levels to design materials with high performances such as broad absorption spectra and higher balance transfer property. The results show that position ...

journal_title：Journal of molecular modeling

authors： Tang S,Tang B,Liang D,Chen G,Jin R

更新日期：2013-09-01 00:00:00

abstract：:A high-throughput screen against Aurora A kinase revealed several promising submicromolar pyrimidine-aniline leads. The bioactive conformation found by docking these leads into the Aurora A ATP-binding site had a semicircular shape. Macrocycle formation was proposed to achieve novelty and selectivity via ring-closing ...

journal_title：Journal of molecular modeling

authors： Poulsen A,William A,Blanchard S,Nagaraj H,Williams M,Wang H,Lee A,Sun E,Teo EL,Tan E,Goh KC,Dymock B

更新日期：2013-01-01 00:00:00

abstract：:Multi-tetrazole derivatives with conjugated structures were designed and investigated in this study. Using quantum chemistry methods, the crystal structures, electrostatic potentials (ESPs), multicenter bond orders, HOMO-LUMO energy gaps, and detonation properties of the derivatives were calculated. As expected, these...

journal_title：Journal of molecular modeling

authors： Sun S,Lu M

更新日期：2018-06-23 00:00:00

abstract：:Human dihydrofolate reductase-like 1 (DHFRL1) has been identified as a second human dihydrofolate reductase (DHFR) enzyme. Although DHFRL1 have high sequence homology with human DHFR, dihydrofolate (DHF) exhibits a lowered binding affinity to DHFRL1 and the corresponding molecular mechanism is still unknown. To addres...

journal_title：Journal of molecular modeling

authors： Gao J,Cui W,Du Y,Ji M

更新日期：2013-12-01 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：:1,3-Dimethylimidazolium dimethylphosphate ([C1mim][DMP]) was observed experimentally to be able to eliminate the atmospheric azeotropic point of acetone and methanol, which is an important azeotrope generally encountered in furfural production and the Fischer-Tropsch process. Here, we employed ab initio calculation to...

journal_title：Journal of molecular modeling

authors： Yu G,Liu X,Zhang X,Chen X,Liu Z,Abdeltawab AA

更新日期：2017-03-01 00:00:00

abstract：:A 3D QSAR analysis has been performed on a series of 67 benzodiazepine analogues reported as gamma-secretase inhibitors using molecular field analysis (MFA), with G/PLS to predict steric and electrostatic molecular field interaction for the activity. The MFA study was carried out using a training set of 54 compounds. ...

journal_title：Journal of molecular modeling

authors： Sammi T,Silakari O,Ravikumar M

更新日期：2009-04-01 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：:In this work, the low-lying states of several isomers of ScSi n-/0 (n = 4-6) were investigated with the B3LYP functional and CASPT2 method. The ground states of the anionic clusters were predicted to be the singlet states of the trigonal bipyramid ScSi4- (A-ScSi4-), the face-capped trigonal bipyramid ScSi5- (A-ScSi5-)...

journal_title：Journal of molecular modeling

authors： Nguyen MT,Tran QT,Tran VT

更新日期：2017-09-20 00:00:00

abstract：:The functionalization of pristine and Stone-Wales defected BC3 nanosheets with a pyrene molecule was investigated using density functional theory. Frontier molecular analysis shows that the main interaction is π-π stacking, releasing energies in the range of 143.6 to 169.1 kJ mol(-1). We predicted that after the funct...

journal_title：Journal of molecular modeling

authors： Peyghan AA,Noei M,Bagheri Z

更新日期：2014-12-01 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：:The B3LYP/6-31G (d) method of density functional theory (DFT) was used to study molecular geometry, electronic structure, infrared spectrum (IR) and thermodynamic properties. The heat of formation (HOF) and calculated density were estimated to evaluate the detonation properties using Kamlet-Jacobs equations. Thermal s...

journal_title：Journal of molecular modeling

authors： Zhao GZ,Lu M

更新日期：2013-01-01 00:00:00

abstract：:The mechanism of the copper(I)-catalyzed cyclopropanation reaction for methyl diazoacetate with both (Z)- and (E)-but-2-ene stereoisomers has been studied using the 6-311++G(d,p) basis set by means of M06-2X and O3LYP functionals. According to both methods, the rate-limiting step is the formation of a copper-carbene i...

journal_title：Journal of molecular modeling

authors： Angulo B,Herrerías CI,Hormigón Z,Mayoral JA,Salvatella L

更新日期：2018-07-05 00:00:00

abstract：:Prion diseases are associated with misfolding and aggregation of prion protein (PrP). Cellular prion protein contains a disulfide bond linking Cys residues at positions 179 and 214. It has been proposed that this disulfide bond plays an important role in the conversion between cellular (PrP(C)) and the scrapie form of...

journal_title：Journal of molecular modeling

authors： Ning L,Guo J,Jin N,Liu H,Yao X

更新日期：2014-02-01 00:00:00

abstract：:We present an ab initio based molecular mechanics model for prominent additives used in lubricants to moderate oil-steel interfaces. The force field is created for zinc dialkyldithiophosphate and calcium sulfonate charge neutral ligand-ion-ligand complexes and benchmarked to the widely spread generalized amber force f...

journal_title：Journal of molecular modeling

authors： Ectors P,Zahn D

更新日期：2019-03-25 00:00:00

abstract：:D222G mutation of the hemagglutinin (HA) is of special interest because of its close association with the enhanced virulence of 2009 pandemic influenza A (H1N1) virus through the increased binding affinity to α2,3-linked sialylated glycan receptors. However, there is still a lack of detailed understanding about the mo...

journal_title：Journal of molecular modeling

authors： Pan D,Xue W,Wang X,Guo J,Liu H,Yao X

更新日期：2012-09-01 00:00:00

abstract：:The structures and stabilities of eleven N13+ and N13- isomers have been investigated with second-order Moller-Plesset (MP2) and density functional theory (DFT) methods. Five N13+ isomers and six N13- isomers are all reasonable local minima on their potential energy hypersurfaces. The most stable N13+ cation is struct...

journal_title：Journal of molecular modeling

authors： Yin PG,Li QS

更新日期：2004-02-01 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