当前位置： SCI文献检索 > JOURNAL OF MOLECULAR MODELING期刊下所有文献 > DFT study of glucose based glycolipid crown ethers and their complexes with alkali metal cations Na(+) and K(+).

DFT study of glucose based glycolipid crown ethers and their complexes with alkali metal cations Na(+) and K(+).

Abstract：

:A theoretical study of a series of five glucose based glycolipid crown ethers and their complexes with Na(+) and K(+) was performed using the density functional theory with B3LYP/6-31 G* to obtain the optimized geometrical structures and electronic properties. The local nucleophilicity of the five molecules was investigated using Fukui function, while the global nucleophilicity was calculated from the ionization potential and electron affinity. The structures and coordination of the complexes were studied to identify the best match of the glycolipid crown ethers with cations. In general, it was found that the oxygen atoms pairs O2 and O3 (or O4 and O6) on the sugar ring are constrained from moving toward the cation, which results in a weaker O-cation coordination strength for the oxygen pair compared to the other oxygen atoms in the crown ether ring. The thermodynamic properties of the binding of the complexes and the exchange reaction in gas phase were evaluated. The cation selectivity pattern among the five molecules was in good agreement with the experiment.

journal_name

J Mol Model

journal_title

Journal of molecular modeling

authors

Nguan H,Ahmadi S,Hashim R

doi

10.1007/s00894-012-1497-x

subject

Has Abstract

pub_date

2012-12-01 00:00:00

pages

5041-50

issue

12

eissn

1610-2940

issn

0948-5023

journal_volume

18

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR MODELING文献大全
  • Molecular modeling of the effects of glycosylation on the structure and dynamics of human interferon-gamma.

    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

    pub_type： 杂志文章

    doi：10.1007/s00894-019-4013-8

    authors： Lilkova E,Petkov P,Ilieva N,Krachmarova E,Nacheva G,Litov L

    更新日期：2019-04-25 00:00:00

  • Functional role of R462 in the degradation of hyaluronan catalyzed by hyaluronate lyase from Streptococcus pneumoniae.

    abstract：:Hyaluronan lyase from Streptococcus pneumoniae can degrade hyaluronic acid, which is one of the major components in the extracellular matrix. Hyaluronan can regulate water balance, osmotic pressure, and act as an ion exchange resin. Followed by our recent work on the catalytic reaction mechanism and substrate binding ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-015-2724-z

    authors： Li F,Xu D

    更新日期：2015-08-01 00:00:00

  • First principles calculations on the influence of water-filled cavities on the electronic structure of Prussian Blue.

    abstract：:Prussian Blue is a paradigmatic mixed valence material and a parent compound to a broad family of electronically, optically, and magnetically active materials. Its exact composition varies greatly depending on the preparation route, leading to large variations in its electronic properties. The influence of water molec...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-008-0425-6

    authors： Wojdeł JC

    更新日期：2009-06-01 00:00:00

  • Reaction mechanism of CH3M≡MCH 3 (M=C, Si, Ge) with C2H4: [2+1] or [2+2] cycloaddition?

    abstract：:The mechanism of the cycloaddition reaction CH3M≡MCH3 (M=C, Si, Ge) with C2H4 has been studied at the CCSD(T)/6-311++G(d,p)//MP2/6-311++G(d,p) level. Vibrational analysis and intrinsic reaction coordinate (IRC), calculated at the same level, have been applied to validate the connection of the stationary points. The br...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-013-1882-0

    authors： Huo S,Li X,Zeng Y,Zheng S,Meng L

    更新日期：2013-09-01 00:00:00

  • Assessment of various DFT, DFT-D, and MP2 methods for studying FOX-7 detonation properties.

    abstract：:B3LYP, PBE, M06-2X, B2PLYP, BN2PLYP-D, ωB97X-D, and MP2 levels of theory, in combination with the 6-311++G(d,p) and cc-pVTZ basis sets were comprehensively assessed for their ability to reproduce experimental FOX-7 structural and detonation data. ωB97X-D/cc-pVTZ, B3LYP/cc-pVTZ, and M06-2X/cc-pVTZ provided highly accur...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-017-3427-4

    authors： Jeong K,Jeon Y,Kwon S

    更新日期：2017-09-01 00:00:00

  • Molecular modeling and dynamics studies of cytidylate kinase from Mycobacterium tuberculosis H37Rv.

    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

    pub_type： 杂志文章

    doi：10.1007/s00894-008-0291-2

    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

  • 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 stereochem...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-014-2165-0

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

    更新日期：2014-03-01 00:00:00

  • Behavior of BsoBI endonuclease in the presence and absence of DNA.

    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

    pub_type： 杂志文章

    doi：10.1007/s00894-017-3557-8

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

    更新日期：2017-12-20 00:00:00

  • Interaction of a Ti-doped semi-fullerene (TiC30) with molecules of CO and CO2.

    abstract：:Using density functional theory (DFT) and molecular dynamics (MD), we studied the interaction of a titanium atom with a half of a C60 fullerene (i.e., C30), formed from the corannulene structure with a pentagonal base. We considered atmospheric pressure and 300 K. We found that the most stable adsorption of the titani...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-016-3086-x

    authors： Canales M,Ramírez-de-Arellano JM,Magana LF

    更新日期：2016-09-01 00:00:00

  • Relationship between mutation of serine residue at 315th position in M. tuberculosis catalase-peroxidase enzyme and Isoniazid susceptibility: an in silico analysis.

    abstract：:Remarkable advances have been made in the drug therapy of tuberculosis. However much remains to be learned about the molecular and structural basis of drug resistance in Mycobacterium tuberculosis. It is known that, activation of Isoniazid (INH) is mediated by Mycobacterium tuberculosis catalase-peroxidase (MtBKatG) a...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-010-0785-6

    authors： Purohit R,Rajendran V,Sethumadhavan R

    更新日期：2011-04-01 00:00:00

  • Closing loop base pairs in RNA loop-loop complexes: structural behavior, interaction energy and solvation analysis through molecular dynamics simulations.

    abstract：:Nanosecond molecular dynamics using the Ewald summation method have been performed to elucidate the structural and energetic role of the closing base pair in loop-loop RNA duplexes neutralized by Mg2+ counterions in aqueous phases. Mismatches GA, CU and Watson-Crick GC base pairs have been considered for closing the l...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-004-0216-7

    authors： Golebiowski J,Antonczak S,Fernandez-Carmona J,Condom R,Cabrol-Bass D

    更新日期：2004-12-01 00:00:00

  • Ab initio study of MKr(n)²⁺(M = Cu, Ag, and Au, n = 1-6) clusters.

    abstract：:Quantum chemical calculations of the structures and stabilities of the title series at the CCSD(T) theoretical level are performed. Laplacian, electron density deformation, electron localization function and reduced density gradient analysis are investigated to explore the nature of the interaction. The results show t...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-011-1138-9

    authors： Li X

    更新日期：2012-03-01 00:00:00

  • A theoretical thermodynamic investigation of cascade reactions in dinuclear octa-azacryptates involving carbon dioxide.

    abstract：:This paper investigates the thermodynamics of gas-phase CO(2) cascade uptake-reactions in the form of carbonate or monomethylcarbonate anions in the host cavity of various dinuclear octa-azacryptates of m-CH(2)C(6)H(4)CH(2) and 2,5-furano-spaced hosts, L (1) and L (2) cryptands, using density functional theory (DFT). ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-011-0965-z

    authors： El-Hendawy MM,English NJ,Mooney DA

    更新日期：2011-12-01 00:00:00

  • Importance of amino acids Leu135 and Tyr236 for the interaction between EhCFIm25 and RNA: a molecular dynamics simulation study.

    abstract：:The CFIm25 subunit of the heterotetrameric cleavage factor Im (CFIm) is a critical factor in the formation of the poly(A) tail at mRNA 3' end, regulating the recruitment of polyadenylation factors, poly(A) site selection, and cleavage/polyadenylation reactions. We previously reported the homologous protein (EhCFIm25) ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-018-3729-1

    authors： Ospina-Villa JD,García-Contreras J,Rosas-Trigueros JL,Ramírez-Moreno E,López-Camarillo C,Zamora-López B,Marchat LA,Zamorano-Carrillo A

    更新日期：2018-07-12 00:00:00

  • Computational study of Th(4+) and Np(4+) hydration and hydrolysis of Th(4+) from first principles.

    abstract：:The aqueous solvation of Th and Np in the IV oxidation state was examined using cluster models generated by Monte Carlo simulations and density functional theory embedded within the COSMO continuum model to approximate the effect of bulk water. Our results suggest that the coordination number (CN) for both Th(IV) and ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-017-3252-9

    authors： Amador DH,Sambrano JR,Gargano R,de Macedo LG

    更新日期：2017-03-01 00:00:00

  • DFT-based molecular modeling and vibrational study of the La(III) complex of 3,3'-(benzylidene)bis(4-hydroxycoumarin).

    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

    pub_type： 杂志文章

    doi：10.1007/s00894-008-0277-0

    authors： Mihaylov T,Trendafilova N,Georgieva I

    更新日期：2008-05-01 00:00:00

  • Molecular modeling study on chemically diverse series of cyclooxygenase-2 selective inhibitors: generation of predictive pharmacophore model using catalyst.

    abstract：:Cyclooxygenase (COX) enzymes catalyse the biosynthesis of prostaglandins and thromboxane from arachidonic acid (AA). We summarize in this paper, the development of pharmacophores of a dataset of inhibitors for COX-2 by using the Catalyst/Hypogen module using six chemically diverse series of compounds. Training set con...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-008-0350-8

    authors： Chopra M,Gupta R,Gupta S,Saluja D

    更新日期：2008-11-01 00:00:00

  • Mechanistic insights into small molecule activation induced by ligand cooperativity in PCcarbeneP nickel pincer complexes: a quantum chemistry study.

    abstract：:Mechanisms for the activation of water, ammonia, and other small molecules by the PCcarbeneP nickel pincer complex were studied computationally with the aid of density functional theory. The calculation results indicate that the strongly donating, nucleophilic carbene center can engage in a variety of heterolytic spli...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-015-2792-0

    authors： Liu CC,Liu QL,Wu ZY,Chen YC,Xie HJ,Lei QF,Fang WJ

    更新日期：2015-09-01 00:00:00

  • Unsaturated trinuclear iron fluoroborylene complexes.

    abstract：:The unsaturated trinuclear iron fluoroborylene complexes Fe3(BF)3(CO) n (n = 7, 6) have been studied using density functional theory (DFT). Relatively complicated potential energy surfaces are found with nine and eight structures within 15 kcal mol-1 of the lowest energy structures for the Fe3(BF)3(CO)7 and Fe3(BF)3(C...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-017-3301-4

    authors： Xu L,Li QS,King RB

    更新日期：2017-04-01 00:00:00

  • Influence of polyethylene cross-linked functionalization on the interfacial properties of carbon nanotube-reinforced polymer nanocomposites: a molecular dynamics study.

    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

    pub_type： 杂志文章

    doi：10.1007/s00894-019-3983-x

    authors： Haghighi S,Ansari R,Ajori S

    更新日期：2019-03-29 00:00:00

  • Cyano or o-nitrophenyl? Which is the optimal electron-withdrawing group for the acrylic acid acceptor of D-π-A sensitizers in DSSCs? A density functional evaluation.

    abstract：:We report a DFT, TDDFT and DFTB investigation of the performance of two donor-π-acceptor (D-π-A)-type organic dyes bearing different electron-withdrawing groups (EWG) for dye-sensitized solar cells (DSSCs) to evaluate which EWG is better for an acrylic acid acceptor, i.e., Cyano (-CN) or o-nitrophenyl (o-NO2-Ph). A se...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-012-1719-2

    authors： Zhang J,Kan YH,Li HB,Geng Y,Wu Y,Duan YA,Su ZM

    更新日期：2013-04-01 00:00:00

  • An accurate comparative theoretical study of the interaction of furan, pyrrole, and thiophene with various gaseous analytes.

    abstract：:An accurate comparison of the interaction of furan, pyrrole, and thiophene with different gaseous analytes is vital not only for understanding the sensing mechanism of corresponding polymers but also for rational design of new materials. In the present study, DFT calculations at (M05-2X/Aug-cc-PVDZ) have been performe...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-017-3458-x

    authors： Sajid H,Mahmood T,Ayub K

    更新日期：2017-09-26 00:00:00

  • Stability of rolled-up GaAs nanotubes.

    abstract：:This work presents a theoretical study of gallium arsenide (GaAs) nanotubes obtained from the (100), (110) and (111) crystal planes of zincblende structure in order to evaluate the electronic properties. The DFT/B3LYP/6-31G method was used to predict structures and stabilities. It was found that nanotubes from the (11...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-017-3371-3

    authors： Silva JCF,Dos Santos JD,Taft CA,Martins JBL,Longo E

    更新日期：2017-07-01 00:00:00

  • Steered molecular dynamics simulation of the binding of the β2 and β3 regions in domain-swapped human cystatin C dimer.

    abstract：:The crystal structure of the human cystatin C (hCC) dimer revealed that a stable twofold-symmetric dimer was formed via 3D domain swapping. Domain swapping with the need for near-complete unfolding has been proposed as a possible route for amyloid fibril initiation. Thus, the interesting interactions that occur betwee...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-012-1609-7

    authors： He J,Xu L,Zhang S,Guan J,Shen M,Li H,Song Y

    更新日期：2013-02-01 00:00:00

  • Pharmacophore and molecular dynamics based activity profiling of natural products for kinases involved in lung cancer.

    abstract：:To determine the kinase inhibitory potential of natural products that could be utilized in lung cancer therapy in the near future, a pharmacophore-based activity profiling protocol using parallel pharmacophore-based virtual screening of ZINC-a natural product database-was employed. The work presented here is based on ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-018-3849-7

    authors： Singh PK,Silakari O

    更新日期：2018-10-20 00:00:00

  • Theoretical study of absorption of 2,2,6,6-tetramethylpiperidine-1-oxoammonium cation (TEMPO) on TiO₂(110) rutile surface.

    abstract：:We present a theoretical study of the adsorption of 2,2,6,6-tetramethylpiperidine-1-oxoammonium cation (TEMPO) onto the TiO₂(110) surface rutile, investigating its bonding nature, electron properties and structural stability. Based on the results obtained with the PBE0/def2-SVP method, natural bond orbital (NBO) analy...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-014-2149-0

    authors： Nieto-López I,Hernández-García L,Bonilla-Cruz J,Sanchez M

    更新日期：2014-03-01 00:00:00

  • Adsorption and dissociation of sulfur-based toxic gas molecules on silicene nanoribbons: a quest for high-performance gas sensors and catalysts.

    abstract：:The adsorption behavior of sulfur-based toxic gases (H2S and SO2) on armchair silicene nanoribbons (ASiNRs) was investigated using first-principles density functional theory (DFT). Being a zero band gap material, application of bulk silicene is limited in nanoelectronics, despite its high carrier mobility. By restrict...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-018-3631-x

    authors： Walia GK,Randhawa DKK

    更新日期：2018-03-16 00:00:00

  • A new interaction mechanism of LiNH2 with MgH2: magnesium bond.

    abstract：:Quantum chemical calculations were performed for LiNH2-HMgX (X=H, F, Cl, Br, CH3, OH, and NH2) complexes to propose a new interaction mechanism between them. This theoretical survey showed that the complexes are stabilized through the combinative interaction of magnesium and lithium bonds. The binding energies are in ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-012-1538-5

    authors： Yang X,Li Q,Cheng J,Li W

    更新日期：2013-01-01 00:00:00

  • Periodic density functional theory study of the high-pressure behavior of energetic crystalline 1,4-dinitrofurazano[3, 4-b]piperazine.

    abstract：:A detailed study of the structural, electronic, and optical absorption properties of crystalline 1,4-dinitrofurazano[3,4-b]piperazine (DNFP) under hydrostatic pressures of 0-100 GPa was performed using periodic density functional theory. As the pressure increases, the lattice constants and cell volumes calculated by L...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-012-1547-4

    authors： Wang W,Zhu W,Li J,Cheng B,Xiao H

    更新日期：2013-01-01 00:00:00

  • The first intermediates in the bromination of bicyclo[3.3.1]nonylidenebicyclo[3.3.1]nonane, combination of experiments and theoretical results.

    abstract：:Bicyclo[3.3.1]nonylidenebicyclo[3.3.1]nonane (1) and adamantylideneadamantane (Ad=Ad) are two caged olefins with closely related structures at the double bond. Both compounds react instantaneously with Br2 in chlorinated hydrocarbon solvents to give mixtures of olefin-Br2 aggregates identified as the 1:1 pi-complex an...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-005-0038-2

    authors： Chiappe C,Pomelli CS,Lenoir D,Wattenbach C

    更新日期：2006-07-01 00:00:00