Effect of the aminoacid composition of model α-helical peptides on the physical properties of lipid bilayers and peptide conformation: a molecular dynamics simulation.

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：:Following our recent studies of the thermodynamic properties of azaspiropentane and borospiropentane, in consideration of their usefulness as new potential high energy materials, we follow up with ab initio calculations on the thermodynamic properties of azaborospiropentanes. Properties reported in this study include ...

journal_title：Journal of molecular modeling

authors： Richard RM,Ball DW

更新日期：2008-09-01 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：:Ab initio calculations were performed to study the quantum chemistry reactions mechanisms among Hg(0), elemental halogen and O3. The geometry of reactions, transition states (TS), intermediates (M) and products were optimized using the MP2 method at the SDD basis function level for Hg, and using 6-311++G (3df, 3pd) fo...

journal_title：Journal of molecular modeling

authors： Gao Z,Lv S,Yang W,Yang P,Ji S,Meng X

更新日期：2015-06-01 00:00:00

abstract：:Since the human body for many reasons can adapt and become resistant to drugs, it is important to develop and validate computer aided drug design (CADD) methods that could help predict binding affinity changes that can result from these resistant enzymes. The free energy perturbation (FEP) methodology is the most accu...

journal_title：Journal of molecular modeling

authors： Reddy RN,Mutyala RR,Aparoy P,Reddanna P,Reddy MR

更新日期：2010-02-01 00:00:00

abstract：:The hydration free energies, structures, and dynamics of open- and closed-shell trivalent lanthanide and actinide metal cations are studied using molecular dynamics simulations (MD) based on a polarizable force field. Parameters for the metal cations are derived from an ab initio bottom-up strategy. MD simulations of ...

journal_title：Journal of molecular modeling

authors： Marjolin A,Gourlaouen C,Clavaguéra C,Ren PY,Piquemal JP,Dognon JP

更新日期：2014-10-01 00:00:00

abstract：:The adsorption of the molecules CO, CO2, and H2 on several ceria and zinc oxide surfaces was studied by means of periodical DFT calculations and compared with infrared frequency data. The stable CeO2(111), CeO2(331), and ZnO(0001) perfect faces were the first substrates considered. Afterwards, the same surfaces with o...

journal_title：Journal of molecular modeling

authors： Reimers WG,Baltanás MA,Branda MM

更新日期：2014-06-01 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

abstract：:An azo bridge (-N=N-) can not only desensitize explosives but also dramatically increase their heats of formation and explosive properties. Amino and nitro are two important high energy density functional groups. Here, we present calculations on 1-nitro-1-triazene (NH2-N=N-NO2). Thermal stability and detonation parame...

journal_title：Journal of molecular modeling

authors： Chi W,Yan T,Li B

更新日期：2014-08-01 00:00:00

abstract：:Iridium (III) 2-phenylpyridine (ppy) complexes with two suitable monodentate L ligands [Ir(ppy)₂(L)₂]⁺ (ppy = 2-phenylpyridine, py = pyridine, L = 4-pyCN 1, 4-pyCHO 2, 4-pyCl 3, py 4, 4-pyNH₂ 5) were studied by density functional theory (DFT) and time-dependent DFT methods. The influences of ligands L on the electroni...

journal_title：Journal of molecular modeling

authors： Zhang TT,Qi XX,Jia J,Wu HS

更新日期：2012-10-01 00:00:00

abstract：:Antiamoebin I (AAM-I) and zervamicin II (Zrv-IIB) are peptaibols that exert antibiotic activity through the insertion/disruption of cell membranes. In this study, we investigated how the folding of these peptaibols are affected when some of their native residues are replaced with proline analogues and asymmetrical D-α...

journal_title：Journal of molecular modeling

authors： Castro TG,Micaêlo NM,Melle-Franco M

更新日期：2017-10-16 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：:In this work, hybrid functional and G4 methods were employed in the rational design of carbonitrile-carboxaldehyde receptor models for cation recognition. Electron-sharing and ionic interactions between the models and the cations were analyzed utilizing the concepts of overlap population, atomic valence, electrostatic...

journal_title：Journal of molecular modeling

authors： Rosli AN,Abu Bakar MA,Lee VS,Zain SM,Ahmad MR,Abdul Manan NS,Alias Y,Woi PM

更新日期：2014-09-01 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：: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：:The first and second moment operators are used to define the origin invariant shape and size of a molecule or functional group, as well as expressions for the distance between two electrons and the distance between an electron and a nucleus. The measure of molecular size correlates quite well with an existing theoreti...

journal_title：Journal of molecular modeling

authors： Hollett JW,Poirier RA

更新日期：2009-06-01 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：:In this theoretical study we used density functional theory to calculate the molecular and crystalline structures of sodium selenite. Our structural results were compared with experimental data. From the molecular structure we determined the ionization potential, electronic affinity, and global reactivity parameters l...

journal_title：Journal of molecular modeling

authors： Barraza-Jiménez D,Flores-Hidalgo MA,Galvan DH,Sánchez E,Glossman-Mitnik D

更新日期：2011-04-01 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：:Six nitramines (N1-6) were designed with all possible arrangements of N-NO2 groups on a cyclic skeleton and structural optimization was performed using the density functional theory (DFT). We observed that all nitramines have high positive heats of formation proportionate to the number of N-NO2 groups in their molecul...

journal_title：Journal of molecular modeling

authors： Devi A,Deswal S,Dharavath S,Ghule VD

更新日期：2015-11-01 00:00:00

abstract：:Molecular modeling of the La(III) complex of 3,3'-(benzylidene)bis(4-hydroxycoumarin) (PhDC) was performed using density functional theory (DFT) methods at B3LYP/6-31G(d) and BP86/TZP levels. Both Stuttgart-Dresden effective core potential and ZORA approximation were applied to the La(III) center. The electron density...

journal_title：Journal of molecular modeling

authors： Mihaylov T,Trendafilova N,Georgieva I

更新日期：2008-05-01 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：:Thermodynamic integration (TI) molecular dynamics (MD) simulations for the binding of a pair of a reference ("ref") ligand and an analogous ("analog") ligand to either tagged (with six extra residues at the N-terminus) or untagged p38 kinase proteins were carried out in order to probe how the binding affinity is influ...

journal_title：Journal of molecular modeling

authors： Sun YC,Hsu WC,Hsu CJ,Chang CM,Cheng KH

更新日期：2015-11-01 00:00:00

abstract：:Faced with the worldwide spread of multidrug-resistant (MDR) bacterial strains, together with a lack of any appropriate treatment, urgent steps to combat infectious diseases should be taken. Usually, bacterial components are studied to understand, by analogy, the functioning of human proteins. However, molecular data ...

journal_title：Journal of molecular modeling

authors： Wiczew D,Borowska A,Szkaradek K,Biegus T,Wozniak K,Pyclik M,Sitarska M,Jaszewski L,Radosinski L,Hanus-Lorenz B,Kraszewski S

更新日期：2019-06-11 00:00:00

abstract：:In this work, a computational framework is proposed by utilizing molecular dynamics simulation to explore the existing relation between molecular structure and ionic conductivity of the electrolyte system [LiPF6+(EC+DMC 1:1)] consisting of a mixture of cyclic ethylene carbonate (EC) and acyclic dimethyl carbonate (DMC...

journal_title：Journal of molecular modeling

authors： Haghkhah H,Ghalami Choobar B,Amjad-Iranagh S

更新日期：2020-08-01 00:00:00

abstract：:The triplet-triplet absorption spectra of three newly synthesized N-substituted 4,5,6,7-tetrachlorophthalimides (TCP) were measured experimentally and calculated with density functional theory. The heavy atom effect increases the intersystem crossing rate, and the transient triplet absorbance could be measured. Fluore...

journal_title：Journal of molecular modeling

authors： Kelterer AM,Mansha A,Iftikhar FJ,Zhang Y,Wang W,Xu JH,Grampp G

更新日期：2014-07-01 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：:In order to introduce effectively the external electric fields into the explosive systems, the change trends of the strengths of trigger linkages, nitro group charges, and explosive sensitivities of 1,4-dinitroimidazole-N-oxide (1,4-DNIO) were investigated in the external electric fields at the B3LYP/6-311++G(2d,p) an...

journal_title：Journal of molecular modeling

authors： Wang BG,Ren FD,Wang Y

更新日期：2019-11-28 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：:The structural characteristics involving thermal stabilities of liquid nitromethane (NM)—one of the simplest energetic materials—confined within a graphene (GRA) bilayer were investigated by means of all-atom molecular dynamics simulations and density functional theory calculations. The results show that ordered and l...

journal_title：Journal of molecular modeling

authors： Liu Y,Yu T,Lai W,Kang Y,Ge Z

更新日期：2015-03-01 00:00:00