The role of hydrogen bonds in an aqueous solution of acetylsalicylic acid: a molecular dynamics simulation study.

abstract：:Given the increasing complexity of simulated molecular systems, and the fact that simulation times have now reached milliseconds to seconds, immense amounts of data (in the gigabyte to terabyte range) are produced in current molecular dynamics simulations. Manual analysis of these data is a very time-consuming task, a...

journal_title：Journal of molecular modeling

authors： Victor Paul Raj FR,Exner TE

更新日期：2014-04-01 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：:A theoretical study of the chemisorption and dissociation pathways of water on the Al₁₃ cluster was performed using the hybrid density functional B3LYP method with the 6-311+G(d, p) basis set. The activation energies, reaction enthalpies, and Gibbs free energy of activation for the reaction were determined. Calculatio...

journal_title：Journal of molecular modeling

authors： Zhao JY,Zhao FQ,Gao HX,Ju XH

更新日期：2013-04-01 00:00:00

abstract：:The USFDA has approved pramlintide, commercially named Symlin (sIAPP), as adjunctive therapy for type 2 diabetes (T2D). This analogue of the human amylin peptide (hIAPP) has triple proline substitutions typical of the rat isoform (rIAPP). Recently, it was proposed that pramlintide solubility and aggregation resistance...

journal_title：Journal of molecular modeling

authors： Alves NA,Dias LG,Frigori RB

更新日期：2019-08-19 00:00:00

abstract：:Fruit softening is associated to cell wall modifications produced by a set of hydrolytic enzymes and proteins. Expansins are proteins with no catalytic activity, which have been associated with several processes during plant growth and development. A role for expansins has been proposed during softening of fruits, and...

journal_title：Journal of molecular modeling

authors： Gaete-Eastman C,Morales-Quintana L,Herrera R,Moya-León MA

更新日期：2015-05-01 00:00:00

abstract：:The increase of multidrug-resistant strains of bacteria to known classes of antibiotics present a severe challenge for modern medicine. The most promising strategy to combat pathogenic bacteria is to discover new drug targets. In this regard, aminoacyl-tRNA synthetases are particularly well suited to develop novel dru...

journal_title：Journal of molecular modeling

authors： Hoffmann M,Torchala M

更新日期：2009-06-01 00:00:00

abstract：:The effect of crystal modifier 2,2',4,4',6,6'-hexanitrostillbene(HNS) on the reinforcement of crystalline 1,3,5-trinitrotoluene (TNT) was investigated by molecular simulation. The intermolecular interactions between HNS and TNT were revealed by quantum chemistry calculations in detail, strong attractive forces were fo...

journal_title：Journal of molecular modeling

authors： Qian W,Shu Y,Li H,Ma Q

更新日期：2014-10-01 00:00:00

abstract：:We perform density functional theory studies to investigate structural and electronic properties of the (5,5) boron nitride nanotubes (BNNTs) with surfaces and ends functionalized by thiol (SH) and hydroxyl (OH) groups. The exchange-correlation energies are treated according to the functional of Hamprecht-Cohen-Tozer-...

journal_title：Journal of molecular modeling

authors： Chigo Anota E,Cocoletzi GH

更新日期：2013-06-01 00:00:00

abstract：:Matrix metalloproteinase-8 (MMP-8) is the key mediator in initiating type I collagen degradation and is associated with rheumatoid arthritis. In the present study, a pharmacophore hypothesis was developed based on selective non zinc binding inhibitors of MMP-8. The pharmacophore hypothesis was refined manually and val...

journal_title：Journal of molecular modeling

authors： Kalva S,Vinod D,Saleena LM

更新日期：2014-05-01 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：: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 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：: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：:Checkpoint kinase 1 (Chk1), a member of the serine/threonine kinase family, is an attractive therapeutic target for anticancer combination therapy. A structure-based modeling approach complemented with shape components was pursued to develop a reliable pharmacophore model for ATP-competitive Chk1 inhibitors. Common ch...

journal_title：Journal of molecular modeling

authors： Chen XM,Lu T,Lu S,Li HF,Yuan HL,Ran T,Liu HC,Chen YD

更新日期：2010-07-01 00:00:00

abstract：:Studying the electrochemical characteristics is an important step for determining interactions between molecules and the chemical environment. Moreover, the electrochemical evaluation of dyes is highly needed to establish the behavior of electro-active chemical species inside dye-sensitized solar cells (DSSCs). Four c...

journal_title：Journal of molecular modeling

authors： Ortega E,Bernède JC,Ramírez AMR,Louarn G,Díaz FR,Cattin L,Del Valle MA

更新日期：2019-02-27 00:00:00

abstract：:Colorectal cancer, which is considered one of the leading causes of mortality worldwide, develops through the formation of benign polyps on the inner colon or rectum wall. Truncations in adenomatous polyposis coli (APC) gene lead to the spread of the disease in the entire colon region when combined with the guanine nu...

journal_title：Journal of molecular modeling

authors： Jadav SS,Macalino SJY,Alluri R

更新日期：2020-07-16 00:00:00

abstract：:Density functional calculations have been used to investigate the interactions of 1-(2-hydroxyethyl)-3-methylimidazolium ([C2OHmim](+))-based ionic liquids (hydroxyl ILs) with water (H2O), methanol (CH3OH), and dimethyl sulfoxide (DMSO). It was found that the cosolvent molecules interact with the anion and cation of e...

journal_title：Journal of molecular modeling

authors： Zhao S,Tian X,Ren Y,Wang J,Liu J,Ren Y

更新日期：2016-08-01 00:00:00

abstract：:A density functional theory augmented by the long-range corrected hybrid density functional ωB97XD and 6-31G(d,p) basis set has been applied to generate sandwich structures consist of nanocomposites between graphene oxide and polyvinyl alcohol. We predicted the interaction energies and discuss the contribution of elec...

journal_title：Journal of molecular modeling

authors： Gorb L,Ilchenko M,Leszczynski J

更新日期：2020-06-25 00:00:00

abstract：:This article analyzes the interplay between X···N and X···X halogen bonds interactions in NCX···NCX···XCH3 complexes, where X=Cl and Br. To better understand the properties of these systems, the corresponding dyads were also studied. These effects are studied theoretically in terms of geometric and energetic features ...

journal_title：Journal of molecular modeling

authors： Esrafili MD,Vakili M,Solimannejad M

更新日期：2014-02-01 00:00:00

abstract：:We have recently shown that the anti-HIV activities of reverse transcriptase inhibitors can be related quantitatively to properties of the electrostatic potentials on their molecular surfaces. We now introduce the technique of using only segments of the drug molecules in developing such expressions. If an improved cor...

journal_title：Journal of molecular modeling

authors： Brinck T,Jin P,Ma Y,Murray JS,Politzer P

更新日期：2003-04-01 00:00:00

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：:Noncovalent interactions in XCN···YO2H (X = F, Cl, Br, I; Y = P, As, Sb) complexes were investigated using ab initio calculations at the MP2/aug-cc-pVDZ level of theory. There are four different configurations of these complexes, and the complexes are formed via hydrogen bonds, halogen bonds, π-hole interactions, or d...

journal_title：Journal of molecular modeling

authors： Zhao Q

更新日期：2017-06-01 00:00:00

abstract：:The internal rotation in ammonia borane (AB) was studied on the basis of natural orbitals for chemical valence (NOCV) and eigenvectors for Pauli repulsion (NOPR). We found that the total hyperconjugation stabilization (ca. 5 kcal mol(-1)), based on the charge transfer from the occupied σ (B-H) orbitals into the empty ...

journal_title：Journal of molecular modeling

authors： Parafiniuk M,Mitoraj MP

更新日期：2014-06-01 00:00:00

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：: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：:The equilibrium structures, spectroscopic and thermodynamic parameters [entropy (S), internal energy (E), heat capacity (C p)] of U₂, U₂O, U₂O₂ and U₂O₄ uranium oxide molecules were investigated systematically using density functional theory (DFT). Our computations indicated that the ground electronic state of U₂ is t...

journal_title：Journal of molecular modeling

authors： Li P,Niu WX,Gao T,Wang F,Jia TT,Meng DQ,Li G

更新日期：2013-12-01 00:00:00

abstract：:Vertical ionization energies (VIEs) of medazepam, nordazepam and their molecular subunits have been calculated using the electron propagator method in the P3/CEP-31G* approximation. Vertical electron affinities (VEAs) have been obtained with a ∆SCF procedure at the DFT-B3LYP/6-31+G* level of theory. Excellent correlat...

journal_title：Journal of molecular modeling

authors： Millefiori S,Alparone A

更新日期：2011-02-01 00:00:00

abstract：:The quinolinol derivatives clioquinol (5-chloro-7-iodo-8-quinolinol, Quinoform) and cloxiquine (5-chloro-8-quinolinol) were studied experimentally in the solid state via ³⁵Cl NQR, ¹H-¹⁷O and ¹H-¹⁴N NQDR spectroscopies, and theoretically by density functional theory (DFT). The supramolecular synthon pattern of O-H···N ...

journal_title：Journal of molecular modeling

authors： Latosińska JN,Latosińska M,Tomczak MA,Seliger J,Zagar V

更新日期：2011-07-01 00:00:00

abstract：:To date, no suitable vaccine or specific antiviral drug is available to treat Chikungunya viral (CHIKV) fever. Hence, it is essential to identify drug candidates that could potentially impede CHIKV infection. Here, we present the development of a homology model of nsP2 protein based on the crystal structure of the nsP...

journal_title：Journal of molecular modeling

authors： Singh KhD,Kirubakaran P,Nagarajan S,Sakkiah S,Muthusamy K,Velmurgan D,Jeyakanthan J

更新日期：2012-01-01 00:00:00

abstract：:Three-dimensional pharmacophore models of human adenosine receptor A(₂A) antagonists were developed based on 23 diverse compounds selected from a large number of A(₂A) antagonists. The best pharmacophore model, Hypo1, contained five features: one hydrogen bond donor , three hydrophobic points and one ring aromatic. It...

journal_title：Journal of molecular modeling

authors： Xu Z,Cheng F,Da C,Liu G,Tang Y

更新日期：2010-12-01 00:00:00