Role of electronic kinetic energy and resultant gradient information in chemical reactivity.

abstract：:The addition of C2 to HCN is of relevant interest in astrochemistry. We studied the pathways of this addition to produce CCCN and estimated its reaction rate using the Master Equation in the circumstellar environment. From the results of this study, it was possible to show that a different pathway in the Surface Poten...

journal_title：Journal of molecular modeling

authors： da Silva WB,Albernaz AF,Barreto PR,Correa E

更新日期：2017-04-01 00:00:00

abstract：:Although molecularly targeted therapy with imatinib has improved treatments of chronic myeloid leukemia (CML), clinical resistance gradually develops in patients with accelerated or blast phase CML. The inability of imatinib to cure CML suggests that inactivation of BCR-ABL kinase activity alone is not sufficient to c...

journal_title：Journal of molecular modeling

authors： Shao S,Yu R,Yu Y,Li Y

更新日期：2014-08-01 00:00:00

abstract：:The total energies, growth patterns, equilibrium geometries, relative stabilities, hardnesses, intramolecular charge transfer, and magnetic moments of HoSi n (n = 12-20) clusters have been reexamined theoretically using two different density functional schemes in combination with relativistic small-core Stuttgart effe...

journal_title：Journal of molecular modeling

authors： Hou L,Yang J,Liu Y

更新日期：2016-08-01 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 shuttling motion of a macrocycle in rotaxane-based molecular switching devices has been studied by computational density functional methods. In the test case, energy profiles corresponding to the dethreading process of different types of guest molecules in a cyclobis(paraquat-p-phenylene) host verified the experim...

journal_title：Journal of molecular modeling

authors： Hirva P,Haukka M,Pakkanen TA

更新日期：2008-10-01 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 interactions between the template molecule paclitaxel (PTX) and seven functional monomers containing methacrylic acid (MA), acrolein (AC), 4-vinylbenzoic acid (4VA), acrylonitrile (AN), 2-vinylpyridine (2VP), 2,6-bisacrylamide pyridine (BAP) and methyl methacrylate (MM) were systematically investigated adopting th...

journal_title：Journal of molecular modeling

authors： Wang L,Yang F,Zhao X,Li Y

更新日期：2020-01-11 00:00:00

abstract：:Molecular simulations were carried out to study the sodium dodecyl sulfate (SDS) surfactant with the interleukin 8 (IL8) protein as a model to investigate the influence of amphiphilic molecules on proteins. Simulations for an SDS micelle with an IL8 protein show that both aggregates, which were initially separated, ev...

journal_title：Journal of molecular modeling

authors： Dominguez H

更新日期：2017-07-01 00:00:00

abstract：:The contribution of folic acid (FA)-tryptophan interactions to FA-protein association was investigated in the context of using FA as a drug carrier in protein delivery systems. Bovine serum albumin (BSA) and indolicidin were used as model proteins in the study. The FA-BSA complex was characterized by using the Bradfor...

journal_title：Journal of molecular modeling

authors： Gupta R,Kalita P,Patil O,Mohanty S

更新日期：2015-12-01 00:00:00

abstract：:The effective dissolution of calcium oxalate, the main component of kidney stones, is important in the treatment of nephrolithisis. Polyphenol glycosides constitute compounds supporting dissolution and inhibition of formation of stones. These moieties possess oxygen atoms which can interact with calcium cations. Densi...

journal_title：Journal of molecular modeling

authors： Toczek D,Kubas K,Turek M,Roszak S,Gancarz R

更新日期：2013-10-01 00:00:00

abstract：:The nature of non-covalent interactions in self-assembling systems is a topic that has aroused great attention in literature. In this field, the 1,3,5-triazinane-2,4,6-trione or cyanuric acid (CA) is one of the most widely used molecules to formulate self-assembled materials or monolayers. In the present work, a varie...

journal_title：Journal of molecular modeling

authors： Petelski AN,Peruchena NM,Pamies SC,Sosa GL

更新日期：2017-08-14 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 work, we investigate the ground- and excited-state structures as well as the optical properties of a series of five formazanate dyes using state-of-the-art density-based and wavefunction-based methods. The present work is the first to evaluate the properties of formazanate-BF2 dyes with wavefunction-correlated...

journal_title：Journal of molecular modeling

authors： Laurent AD,Otten E,Le Guennic B,Jacquemin D

更新日期：2016-11-01 00:00:00

abstract：:A coarse-grained Brownian dynamics model was used to simulate two proteins of similar sizes inside model membrane pores of varying size and hydrophobicity. The two proteins, which have radii of gyration of approximately 9.5 Å in their native states, are a 36-residue hydrophilic villin head piece (HP-36) and a 40-resid...

journal_title：Journal of molecular modeling

authors： Zhang Y,Zhang Y,McCready MJ,Maginn EJ

更新日期：2019-04-25 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：:Recent ab initio investigations of some complexes formed between carbon dioxide and its analogues carbonyl sulfide, carbonyl selenide, carbon disulfide, and thiocarbonyl selenide and the common bases ammonia, water, phosphine, and hydrogen sulfide have revealed significant differences between the properties of those c...

journal_title：Journal of molecular modeling

authors： Ramasami P,Ford TA

更新日期：2015-02-01 00:00:00

abstract：:Carbon monoxide (CO) and oxygen (O2) catalyzed by small neutral iron oxide clusters (FeO(1-3)) was investigated at the density functional level of theory using the Becke-Perdew-Wang functional (BPW91). Three reaction pathways along with singlet, triplet and quintet states were calculated for ascertaining the presence ...

journal_title：Journal of molecular modeling

authors： Wang HJ,Wang YC

更新日期：2014-06-01 00:00:00

abstract：:We examine a short way to reach an exceptional point that corresponds to a coalescence of two resonance energies. The application concerns the photodissociation of the Na2 molecule exposed to a laser field. In this case, the resonances can be correlated with the field-free vibrational states of the diatomic species. T...

journal_title：Journal of molecular modeling

authors： Lefebvre R,Atabek O

更新日期：2013-05-01 00:00:00

abstract：:The average pull-out force and interaction energy of polyethylene (PE) cross-linked functionalized carbon nanotubes (cfCNTs) embedded in polymer matrices (PE-cfCNTs@polymers) was studied using molecular dynamics (MD) simulations. Accordingly, the pull-out process of PE-cfCNTs from inside polymer matrices, i.e., Aramid...

journal_title：Journal of molecular modeling

authors： Haghighi S,Ansari R,Ajori S

更新日期：2019-03-29 00:00:00

abstract：:The mechanism and origin of selectivity for [3 + 2]-cycloaddition (32CA) reactions between thioketone and carbohydrate-derived nitrones in THF were investigated by using the density functional theory (DFT) at the M06-2X/6-311+G(d,p)//M06-2X/6-31+G(d,p) level of theory combined with the solvation SMD model. The calcula...

journal_title：Journal of molecular modeling

authors： Yang J,Zhang Y,Yang Y,Xue Y

更新日期：2019-07-02 00:00:00

abstract：:In this work molecular modeling was applied to generate homology models of the pore region of the Na(v)1.2 and Na(v)1.8 isoforms of human voltage-gated sodium channels. The models represent the channels in the resting, open, and fast-inactivated states. The transmembrane portions of the channels were based on the equi...

journal_title：Journal of molecular modeling

authors： Scheib H,McLay I,Guex N,Clare JJ,Blaney FE,Dale TJ,Tate SN,Robertson GM

更新日期：2006-09-01 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：: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 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：:The work uses MD simulation to study effects of five water contents (3 %, 10 %, 20 %, 50 %, 100 % v/v) on the tetrahedral intermediate of chymotrypsin - trifluoromethyl ketone in polar acetonitrile and non-polar hexane media. The water content induced changes in the structure of the intermediate, solvent distribution ...

journal_title：Journal of molecular modeling

authors： Tian X,Jiang L,Yuan Y,Wang M,Guo Y,Zeng X,Li M,Pu X

更新日期：2013-06-01 00:00:00

abstract：:Clindamycin, a lincosamide antibiotic, binds to 23S ribosomal RNA and inhibits protein synthesis. The A2058G mutation in 23S RNA results in bacterial resistance to clindamycin. To understand the influence of this mutation on short-range interactions of clindamycin with 23S RNA, we carried out full-atom molecular dynam...

journal_title：Journal of molecular modeling

authors： Kulczycka-Mierzejewska K,Sadlej J,Trylska J

更新日期：2018-07-03 00:00:00

abstract：:BsoBI is a type II restriction endonuclease belonging to the EcoRI family. There is only one previously published X-ray structure for this endonuclease: it shows a homodimer of BsoBI completely encircling DNA in a tunnel. In this work, molecular dynamics simulations were employed to elucidate possible ways in which DN...

journal_title：Journal of molecular modeling

authors： Štěpán J,Kabelka I,Koča J,Kulhánek P

更新日期：2017-12-20 00:00:00

abstract：:This theoretical study presents a comparative analysis of the molecular properties of heterocyclic (C2H4O...HF and C2H5...HF) and homocyclic (C3H6...HF) hydrogen-bonded complexes. Initially, the equilibrium geometries of these complexes were analyzed in detail at the B3LYP/6-311++G(d,p) level of theory. Subsequently, ...

journal_title：Journal of molecular modeling

authors： Oliveira BG,Araújo RC,Carvalho AB,Ramos MN

更新日期：2009-02-01 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：: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