当前位置： SCI文献检索 > JOURNAL OF MOLECULAR MODELING期刊下所有文献 > Atomistic simulation studies of the α/β-glucoside and galactoside in anhydrous bilayers: effect of the anomeric and epimeric configurations.

Atomistic simulation studies of the α/β-glucoside and galactoside in anhydrous bilayers: effect of the anomeric and epimeric configurations.

Abstract：

:Fully atomistic molecular dynamics simulation studies of thermotropic bilayers were performed using a set of glycosides namely n-octyl-β-D-glucopyranoside (β-C8Glc), n-octyl-α-D-glucopyranoside (α-C8Glc), n-octyl-β-D-galactopyranoside (β-C8Gal), and n-octyl-α-D-galactopyranoside (α-C8Gal) to investigate the stereochemical relationship of the epimeric/anomeric quartet liner glycolipids with the same octyl chain group. The results showed that, the anomeric stereochemistry or the axial/equatorial orientation of C1-O1 (α/β) is an important factor controlling the area and d-spacing of glycolipid bilayer systems in the thermotropic phase. The head group tilt angle and the chain ordering properties are affected by the anomeric effect. In addition, the L(C) phase of β-C8Gal, is tilting less compared to those in the fluid L(α). The stereochemistry of the C4-epimeric (axial/equatorial) and anomeric (α/β) centers simultaneously influence the inter-molecular hydrogen bond. Thus, the trend in the values of the hydrogen bond for these glycosides is β-C8Gal > α-C8Glc > β-C8Glc > α-C8Gal. The four bilayer systems showed anomalous diffusion behavior with an observed trend for the diffusion coefficients; and this trend is β-C8Gal > β-C8Glc > α-C8Gal > α-C8Glc. The "bent" configuration of the α-anomer results in an increase of the hydrophobic area, chain vibration and chain disorganization. Since thermal energy is dispensed more entropically for the chain region, the overall molecular diffusion decreases.

journal_name

J Mol Model

journal_title

Journal of molecular modeling

authors

Ahmadi S,Manickam Achari V,Nguan H,Hashim R

doi

10.1007/s00894-014-2165-0

subject

Has Abstract

pub_date

2014-03-01 00:00:00

pages

2165

issue

3

eissn

1610-2940

issn

0948-5023

journal_volume

20

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR MODELING文献大全
  • Influence of C-terminal tail deletion on structure and stability of hyperthermophile Sulfolobus tokodaii RNase HI.

    abstract：:The C-terminus tail (G144-T149) of the hyperthermophile Sulfolobus tokodaii (Sto-RNase HI) plays an important role in this protein's hyperstabilization and may therefore be a good protein stability tag. Detailed understanding of the structural and dynamic effects of C-terminus tail deletion is required for gaining ins...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-013-1816-x

    authors： Chen L,Zhang JL,Zheng QC,Chu WT,Xue Q,Zhang HX,Sun CC

    更新日期：2013-06-01 00:00:00

  • New molecular scaffolds for the design of Mycobacterium tuberculosis type II dehydroquinase inhibitors identified using ligand and receptor based virtual screening.

    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

    pub_type： 杂志文章

    doi：10.1007/s00894-009-0595-x

    authors： Kumar A,Siddiqi MI,Miertus S

    更新日期：2010-04-01 00:00:00

  • Metastable region of phase diagram: optimum parameter range for processing ultrahigh molecular weight polyethylene blends.

    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

    pub_type： 杂志文章

    doi：10.1007/s00894-011-1268-0

    authors： Gai JG,Zuo Y

    更新日期：2012-06-01 00:00:00

  • Unveiling the mechanism and selectivity of [3+2] cycloaddition reactions of benzonitrile oxide to ethyl trans-cinnamate, ethyl crotonate and trans-2-penten-1-ol through DFT analysis.

    abstract：:The mechanism and regioselectivity of [3+2] cycloaddition (32CA) reactions of benzonitrile oxide with ethyl trans-cinnamate, ethyl crotonate and trans-2-penten-1-ol has been studied in gas phase and in acetonitrile, ethyl acetate and tetrahydrofuran using the B3LYP functional in connection with 6-31G(d) basis set. The...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-020-04547-6

    authors： Abbiche K,Acharjee N,Salah M,Hilali M,Laknifli A,Komiha N,Marakchi K

    更新日期：2020-09-22 00:00:00

  • Correlation between biological activity and binding energy in systems of integrin with cyclic RGD-containing binders: a QM/MM molecular dynamics study.

    abstract：:We here report a combined quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) study on the binding interactions between the α(V)β₃ integrin and eight cyclic arginine-glycine-aspartate (RGD) containing peptides. The initial conformation of each peptide within the binding site of the integrin was det...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-012-1487-z

    authors： Xiang M,Lin Y,He G,Chen L,Yang M,Yang S,Mo Y

    更新日期：2012-11-01 00:00:00

  • Calculation of multicenter electric field gradient integrals over Slater-type orbitals using unsymmetrical one-range addition theorems.

    abstract：:The electric field induced within a molecule by its electrons determines a whole series of important physical properties of the molecule. In particular, the values of the gradient of this field at the nuclei determine the interaction of their quadrupole moments with the electrons. Using unsymmetrical one-range additio...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-010-0851-0

    authors： Guseinov II,Görgün NS

    更新日期：2011-06-01 00:00:00

  • dockYard--a repository to assist modeling of protein-protein docking.

    abstract：:In the absence of interlogs, building docking models is a time intensive task, involving generation of a large pool of docking decoys followed by refinement and screening to identify near native docking solutions. This limits the researcher interested in building docking methods with the choice of benchmarking only a ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-010-0758-9

    authors： Mitra P,Pal D

    更新日期：2011-03-01 00:00:00

  • The structure, properties, and nature of unconventional π halogen bond in the complexes of Al4(2-) and halohydrocarbons.

    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

    pub_type： 杂志文章

    doi：10.1007/s00894-011-1252-8

    authors： Li R,Li Q,Cheng J,Li W

    更新日期：2012-06-01 00:00:00

  • Studies on filarial GST as a target for antifilarial drug development-in silico and in vitro inhibition of filarial GST by substituted 1,4-naphthoquinones.

    abstract：:Eleven 1,4-naphthoquinone analogues with different amino substitutions at position 3 of the quinone ring earlier reported for macrofilaricidal activity were selected and screened against purified cytosolic GST isolated from the bovine filarial worm Setaria digitata and IC(50) values were determined. Of the 11 compound...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-010-0952-9

    authors： Mathew N,Srinivasan L,Karunan T,Ayyanar E,Muthuswamy K

    更新日期：2011-10-01 00:00:00

  • Predicting the efficiencies of 2-mercaptobenzothiazole collectors used as chelating agents in flotation processes: a density-functional study.

    abstract：:In recent years, several new chelating reagents have been synthesized and tested for their collecting power in sulfide and non-sulfide minerals flotation. Many researchers have indicated that chelating reagents have the advantage of offering better selectivity and specificity as flotation collectors. Therefore, densit...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-005-0092-9

    authors： Yekeler H,Yekeler M

    更新日期：2006-09-01 00:00:00

  • Theoretical study of interactions between electron-deficient arenes and coinage metal anions.

    abstract：:The binding behavior of coinage metal anions with some electron-deficient arenes has been investigated by MP2 calculations, and the character of interactions in these complexes has been examined by NBO analysis. The results indicate that coinage metal anions can interact with electron-deficient arenes to form anion-π,...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-015-2584-6

    authors： Chen Y,Wang F

    更新日期：2015-03-01 00:00:00

  • Buckling analysis of defective cross-linked functionalized single- and double-walled carbon nanotubes with polyethylene chains using molecular dynamics simulations.

    abstract：:Functionalized carbon nanotubes (CNTs) can be used for improving the mechanical properties and load transfer in nanocomposites. In this research, the buckling behavior of perfect and defective cross-linked functionalized CNTs with polyethylene (PE) chains is studied employing molecular dynamics (MD) simulations. Two d...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-016-3157-z

    authors： Ajori S,Ansari R,Parsapour H

    更新日期：2016-12-01 00:00:00

  • The quantum chemical study of the electronic states of S2Cl and its monovalent ions.

    abstract：:High-level quantum chemical techniques have been utilized to accurately describe the geometrical parameters, vibrational frequencies and dissociation pathways of the X (2)A″, 1 (2)A', 2 (2)A', 2 (2)A″ states of S(2)Cl; X (1)A', 1 (3)A″, 1 (1)A″, 1 (3)A' states of S(2)Cl(+); X (1)A', 1 (3)A', (1)A″ states of S(2)Cl(-),...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-012-1422-3

    authors： Czernek J,Zivný O

    更新日期：2012-09-01 00:00:00

  • Molecular dynamics and QM/MM-based 3D interaction analyses of cyclin-E inhibitors.

    abstract：:Abnormal expression of cyclin-dependent kinase 2 (CDK2)/cyclin-E is detected in colorectal, ovarian, breast and prostate cancers. The study of CDK2 with a bound inhibitor revealed CDK2 as a potential therapeutic target for several proliferative diseases. Several highly selective inhibitors of CDK2 are currently underg...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-012-1620-z

    authors： Pasha FA,Neaz MM

    更新日期：2013-02-01 00:00:00

  • G2, G3, and complete basis set calculations of the thermodynamic properties of cis- and trans-triazene.

    abstract：:Following our recent study on triazane, we present a follow-up study on the thermodynamic properties of triazane's unsaturated analog, triazene. We predict optimized structural parameters, vibrational frequencies, enthalpies of formation, enthalpies of combustion, specific enthalpies of combustion, and proton affiniti...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-007-0248-x

    authors： Richard RM,Ball DW

    更新日期：2008-01-01 00:00:00

  • Theoretical study of CO oxidation on cationic, neutral, and anionic AuM dimers (M = Pd and Ag).

    abstract：:The CO and O2 adsorption as well as CO oxidation on cationic, neutral, and anionic AuM dimers (M = Pd, Ag) are studied by density functional calculations. Our results show that CO and O2 are adsorbed more stably on AuPd dimers than on AuAg dimers with corresponding charge state. O2 is favorable to be adsorbed on Pd at...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-014-2313-6

    authors： Chen X,Lu RF,Kan EJ,Liu YZ,Xiao CY,Deng KM

    更新日期：2014-06-01 00:00:00

  • Importance of oligomerisation on Pseudomonas aeruginosaLectin-II binding affinity. In silico and in vitro mutagenesis.

    abstract：:The effect of terminal GLY114* deletion on the binding affinity of the PA-IIL lectin toward L: -fucose was investigated. Both experimental (isothermal titration calorimetry) and computational (molecular dynamics simulations) methods have shown that the deletion mutation decreases the L-fucose affinity. It implies that...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-009-0464-7

    authors： Wimmerová M,Mishra NK,Pokorná M,Koca J

    更新日期：2009-06-01 00:00:00

  • Insights into amprenavir resistance in E35D HIV-1 protease mutation from molecular dynamics and binding free-energy calculations.

    abstract：:Drug resistance is a very important factor contributing to the failure of current HIV therapies. The ability to understand the resistance mechanism of HIV-protease mutants may be useful in developing more effective and longer lasting treatment regimens. In this paper, we report the first computational study of the cli...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-006-0121-3

    authors： Meiselbach H,Horn AH,Harrer T,Sticht H

    更新日期：2007-02-01 00:00:00

  • Density functional theory studies on a non-covalent interaction system: hydrogen-bonded dimers of zoledronate.

    abstract：:A computational study was carried out to characterize the hydrogen-bonded dimers of Zoledronate (ZOL), which is used widely in treating skeletal diseases. The stable conformations, hydrogen bonding interactions, IR spectra, thermodynamic properties, and electronic characteristics of nine possible ZOL dimers were studi...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-018-3826-1

    authors： Liu Q,Li K,Lv G,Li X,Peng Y,Lin J,Qiu L

    更新日期：2018-10-09 00:00:00

  • Self-consistent field convergence for proteins: a comparison of full and localized-molecular-orbital schemes.

    abstract：:Proteins in the gas phase present an extreme (and unrealistic) challenge for self-consistent-field iteration schemes because their ionized groups are very strong electron donors or acceptors, depending on their formal charge. This means that gas-phase proteins have a very small band gap but that their frontier orbital...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-014-2159-y

    authors： Wick CR,Hennemann M,Stewart JJ,Clark T

    更新日期：2014-03-01 00:00:00

  • Computational characterization of sodium selenite using density functional theory.

    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

    pub_type： 杂志文章

    doi：10.1007/s00894-010-0766-9

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

    更新日期：2011-04-01 00:00:00

  • Two new atom centered fragment descriptors and scoring function enhance classification of antibacterial activity.

    abstract：:Classification of pharmacologic activity of a chemical compound is an essential step in any drug discovery process. We develop two new atom-centered fragment descriptors (vertex indices)--one based solely on topological considerations without discriminating atom or bond types, and another based on topological and elec...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-014-2164-1

    authors： Kandel DD,Raychaudhury C,Pal D

    更新日期：2014-04-01 00:00:00

  • Chemical carcinogens in non-enzymatic cytosine deamination: 3-isocyanatoacrylonitrile.

    abstract：:Uracil has long been known as the main product of nitrosative cytosine deamination in aqueous solution. Recent mechanistic studies of cytosinediazonium ion suggest that the cation formed by its dediazoniation can ring-open to N-protonated (Z,s-cis)-3-isocyanatoacrylonitrile 7. Stereochemical preferences are discussed ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-005-0048-0

    authors： Glaser R,Wu H,von Saint Paul F

    更新日期：2006-07-01 00:00:00

  • Structure-based discovery of small molecule APC-Asef interaction inhibitors: In silico approaches and molecular dynamics simulations.

    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

    pub_type： 杂志文章

    doi：10.1007/s00894-020-04467-5

    authors： Jadav SS,Macalino SJY,Alluri R

    更新日期：2020-07-16 00:00:00

  • Simple and accurate correlation of experimental redox potentials and DFT-calculated HOMO/LUMO energies of polycyclic aromatic hydrocarbons.

    abstract：:The ability to accurately predict the oxidation and reduction potentials of molecules is very useful in various fields and applications. Quantum mechanical calculations can be used to access this information, yet sometimes the usefulness of these calculations can be limited because of the computational requirements fo...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-012-1694-7

    authors： Méndez-Hernández DD,Tarakeshwar P,Gust D,Moore TA,Moore AL,Mujica V

    更新日期：2013-07-01 00:00:00

  • Molecular design of modified polyacrylamide for the salt tolerance.

    abstract：:In our work, three kinds of functional monomers were selected to modify polyacrylamide (PAM) or partially hydrolyzed polyacrylamide (HPAM) by molecular dynamics simulation so as to achieve the stronger salt-tolerance of modified HM-HPAM. The radius of gyration (R (g)), the hydrodynamic radius (...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-012-1447-7

    authors： Yao L,Chen P,Ding B,Luo J,Jiang B,Zhou G

    更新日期：2012-09-01 00:00:00

  • Density functional study of closed-shell attraction on X(ML)3 + (X = O, S, Se; M = Au, Ag, Cu) systems.

    abstract：:With the help of quantum mechanical calculations, we have examined the series of central system X(ML)(3) (+)(X = O, S, Se; M = Au, Ag, Cu). Using a scalar-relativistic density functional approach, we studied the geometry structures, Mulliken populations and charges of the systems. Structure parameters of the experimen...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-006-0156-5

    authors： Fang H,Wang SG

    更新日期：2007-01-01 00:00:00

  • Theoretical study of the reactions of the hydroselenyl radical (HSe●) with the selenenic radical (HSeO●).

    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

    pub_type： 杂志文章

    doi：10.1007/s00894-017-3535-1

    authors： Vega-Teijido MA,Kieninger M,Ventura ON

    更新日期：2017-12-05 00:00:00

  • Investigation of differences in the binding affinities of two analogous ligands for untagged and tagged p38 kinase using thermodynamic integration MD simulation.

    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

    pub_type： 杂志文章

    doi：10.1007/s00894-015-2825-8

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

    更新日期：2015-11-01 00:00:00

  • A genetic algorithm survey on closed-shell atomic nitrogen clusters employing a quantum chemical approach.

    abstract：:The DFT potential energy hypersurfaces of closed-shell nitrogen clusters up to ten atoms are explored via a genetic algorithm (GA). An atom-atom distance threshold parameter, controlled by the user, and an "operator manager" were added to the standard evolutionary procedure. Both B3LYP and PBE exchange-correlation fun...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-018-3724-6

    authors： Silva MX,Silva FT,Galvão BRL,Braga JP,Belchior JC

    更新日期：2018-07-07 00:00:00