Conformational analysis of lignin models: a chemometric approach.

abstract：:The density functional theory method using the B3LYP/6-31G(d,p) level of theory was used to perform isoenergetic maps in order to determine the lower energy conformers of four disaccharides constituting alginic acids, which are based on β-D-mannuronic (M) and α-L-guluronic acid (G), called MM, GG, MG, and GM. The pref...

journal_title：Journal of molecular modeling

authors： Bekri L,Zouaoui-Rabah M,Springborg M,Rahal MS

更新日期：2018-10-10 00:00:00

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

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

更新日期：2014-03-01 00:00:00

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

authors： Li R,Li Q,Cheng J,Li W

更新日期：2012-06-01 00:00:00

abstract：:In the present study, we analyze the interactions of NAD+-dependent deacetylase (Sir2 homolog yeast Hst2) with carba-nicotinamide-adenine-dinucleotide (ADP-HPD). For the Sir2 homolog, a yeast Hst2 docking procedure was applied. The structure of the protein-ADP-HPD complex obtained during the docking procedure was used...

journal_title：Journal of molecular modeling

authors： Czeleń P,Czyżnikowska Ż

更新日期：2016-06-01 00:00:00

abstract：:DFT calculations were carried out on the homo- and hetero-bimetallic model wires [(η(5)-C5H5)(dpe)Fe-C≡C-C6H4-C≡C-Fe(dpe)(η(5)-C5H5)] (1'), [(η(7)-C7H7)(dpe)Mo-C≡C-C6H4-C≡C-Mo(dpe)(η(7)-C7H7)] (2'), and [(η(5)-C5H5)(dpe)Fe-C≡C-C6H4-C≡C-Mo(dpe)(η(7)-C7H7)] (3') used to tentatively mimic [(η(5)-C5Me5)(dppe)Fe-C≡C-C6H4-C...

journal_title：Journal of molecular modeling

authors： Ladjarafi A,Costuas K,Meghezzi H,Halet JF

更新日期：2015-04-01 00:00:00

abstract：:Mechanical properties of graphene- and carbon nanotube-reinforced Araldite LY 5052/Aradur HY 5052 epoxy resins were investigated by molecular dynamics simulations. The COMPASS II force field was implemented in the simulations. Mechanical properties of the reinforced araldite/aradur resin epoxy system with CNT reveal t...

journal_title：Journal of molecular modeling

authors： Faragi S,Hamedani A,Alahyarizadeh G,Minuchehr A,Aghaie M,Arab B

更新日期：2019-06-15 00:00:00

abstract：:3-phosphoinositide-dependent protein kinase-1 (PDK1) plays a crucial role in the signal transduction of massive growth-related protein kinases. In this work, a computational study has been performed to investigate the binding pose of the hydrolyzed product of SBF1 (SBF1-) with PDK1. The binding pose was predicted by V...

journal_title：Journal of molecular modeling

authors： Liu W,Li P,Mei Y

更新日期：2019-06-13 00:00:00

abstract：:The geometries of three isomers of the C2H4O...2HF tri-molecular heterocyclic hydrogen-bonded complex were examined through B3LYP/aug-cc-pVDZ calculations. Analysis of structural parameters, determination of CHELPG (charge electrostatic potential grid) intermolecular charge transfer, interpretation of infrared stretch...

journal_title：Journal of molecular modeling

authors： de Oliveira BG,Araújo RC,Chagas FF,Carvalho AB,Ramos MN

更新日期：2008-10-01 00:00:00

abstract：:In the past several years, halogen bonds have been shown to be relevant in crystal engineering and biomedical applications. One of the reasons for the utility of these types of noncovalent interactions in the development of, for example, pharmaceutical ligands is that their strengths and geometric properties are very ...

journal_title：Journal of molecular modeling

authors： Riley KE,Murray JS,Fanfrlík J,Rezáč J,Solá RJ,Concha MC,Ramos FM,Politzer P

更新日期：2011-12-01 00:00:00

abstract：:In the present work, C-F bond cleavage mediated by the super-reduced form of cobalamin (i.e., CoICbl) was theoretically studied at the ONIOM(BP86/6-311++G(d,p):PM6) + SMD level of theory. Dispersion effects were introduced by employing Grimme's empirical dispersion at the ONIOM(BP86-D/6-311++G(d,p):PM6) + SMD level. I...

journal_title：Journal of molecular modeling

authors： Cortés-Arriagada D,Toro-Labbe A,Mora JR,Rincón L,Mereau R,Torres FJ

更新日期：2017-08-17 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 structures of the N-(hydroxymethyl)acetamide (model molecule of ceramide) dimers have been fully optimized at B3LYP/6-311++G** level. The intermolecular hydrogen bonding interaction energies have been calculated using the B3LYP/6-311++G**, B3LYP/6-311++G(2df,2p), MP2(full)/6-311++G** and MP2(full)/6-311++G(2df,2p)...

journal_title：Journal of molecular modeling

authors： Tang HF,Zhong H,Zhang LL,Gong MX,Song SQ,Tian QP

更新日期：2018-05-31 00:00:00

abstract：:The concepts of polarization (induction), charge transfer and covalent bonding contributions are discussed in terms of weak interactions. They are shown to be different incarnations of the same phenomenon, so that using polarization to describe them is most consistent as it is the only real, measurable and uniquely de...

journal_title：Journal of molecular modeling

authors： Clark T

更新日期：2017-09-27 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：:We have used density-functional theory to investigate the neighboring-group stabilization of iodine, arsenic, and phosphorus-centered oxyanion moieties in species such as deprotonated 2-iodoxybenzoic acid (IBX) and its analogs. The magnitudes of different stabilizing effects and further candidates for analogous stabil...

journal_title：Journal of molecular modeling

authors： O'Hair RA,Williams CM,Clark T

更新日期：2010-03-01 00:00:00

abstract：:Hepatic fibrosis is a common complication of the infection by the parasite, Clonorchis sinensis. There is a high incidence of this disease in the Asian countries with an increased risk of conversion to cancer. A secretory phospholipase A(2) (PLA(2)) enzyme from the parasite is implicated in the pathology. This is an a...

journal_title：Journal of molecular modeling

authors： Hariprasad G,Kaur P,Srinivasan A,Singh TP,Kumar M

更新日期：2012-07-01 00:00:00

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

authors： Jeong K,Jeon Y,Kwon S

更新日期：2017-09-01 00:00:00

abstract：:The reaction pathways of several Friedel-Crafts acylations involving phenyl aromatic compounds were studied using density functional theory. The reactions were related to the Friedel-Crafts polycondensation of polyaryletherketones. In particular, the acylation of benzene with benzoyl chloride to form benzophenone and ...

journal_title：Journal of molecular modeling

authors： Melissen ST,Tognetti V,Dupas G,Jouanneau J,Lê G,Joubert L

更新日期：2013-11-01 00:00:00

abstract：:The structural and energetic properties of native and oxidized telomeric complexes were defined by means of molecular dynamic (MD) simulations. As a starting point, the experimental conformation of B-DNA d(GpTpTpApGpGpGpTpTpApGpGpG) oligomer bound to human protein telomeric repeat binding factor 1 (TRF1) was used. The...

journal_title：Journal of molecular modeling

authors： Czeleń P,Cysewski P

更新日期：2013-08-01 00:00:00

abstract：:The incidence of tuberculosis infections that are resistant to conventional drug therapy has risen steadily in the last decade. Several of the quinolone antibacterials have been examined as inhibitors of M. tuberculosis infection as well as other mycobacterial infections. However, not much has been done to examine spe...

journal_title：Journal of molecular modeling

authors： Bagchi MC,Mills D,Basak SC

更新日期：2007-01-01 00:00:00

abstract：:A practical mixed basis set was developed to facilitate accurate calculations of potential energy surfaces for π-stacking interactions. Correlation consistent basis sets (cc-PVXZ) were augmented by p-type Gaussian functions placed above and below the planes of C6 moieties. Møller-Plesset (MP2, SCS-MP2) and coupled clu...

journal_title：Journal of molecular modeling

authors： Yurtsever E

更新日期：2015-01-01 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：:The structures of non-ionic [Ag(Tu)(CN)] (1) and ionic [Ag(Dmtu)2]+[Ag(CN)2]- (2) and [Ag(Imt)2]+[Ag(CN)2]- (3) silver(I) complexes, where Tu = thiourea, Dmtu = N,N'-dimethylthiourea and Imt = imidazoline-2-thione), were modeled by periodic DFT/PAW-PBE calculations; results were in good agreement with experiments. The...

journal_title：Journal of molecular modeling

authors： Ahmad S,Georgieva I,Hanif M,Monim-Ul-Mehboob M,Munir S,Sohail A,Isab AA

更新日期：2019-03-08 00:00:00

abstract：:Quantum chemical calculations using density functional theory BP86/def2-TZVPP and ab initio methods at CCSD(T)/def2-TZVPP have been carried for the telluroketones H2A=Te (A = C, Si, Ge). DFT calculations have also been carried out for the ketones H2C=E (E = O, S, Se, Te) and for the complexes NHC → [H2A=Te] → B(C6F5)3...

journal_title：Journal of molecular modeling

authors： Jaufeerally NB,Ramasami P,Jerabek P,Frenking G

更新日期：2014-10-01 00:00:00

abstract：:Tautomerism in monomers/dimers and association of 2,5-dihydroxy-1,8-naphthyridine was studied at the DFT level recently recommended for studies of non-covalent interactions. Studied dimers are stabilized by double and triple hydrogen-bonding. In some associates the intermolecular proton transfer may take place. Transi...

journal_title：Journal of molecular modeling

authors： Ośmiałowski B

更新日期：2012-04-01 00:00:00

abstract：:The conformational analysis of polynorbornene (PNB) chains was investigated with the AM1, MM2, AMBER and OPLS methods taking into consideration the possibility of binding of norbornene monomers to each other at various positions, i.e. exo-exo, exo-endo, endo-endo. The chain that is formed by connecting exo-endo positi...

journal_title：Journal of molecular modeling

authors： Yilmaz SS,Abbasoğlu R,Hazer B

更新日期：2003-08-01 00:00:00

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

authors： Kandel DD,Raychaudhury C,Pal D

更新日期：2014-04-01 00:00:00

abstract：:A theoretical investigation is completed on the mechanism of electrical breakdown strength increment of polyethylene. It is shown that it is one of the most important factors for increasing electrical breakdown strength of polyethylene through keto-enol isomerization of acetophenone and its analogues at the ground sta...

journal_title：Journal of molecular modeling

authors： Zhang H,Shang Y,Zhao H,Han B,Li Z

更新日期：2013-10-01 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：:4'-substituted neutral/protonated furfurylidenanilines and trans-styrylfurans are able to exist in two different conformations related to the rotation around the furan ring-bridge double bond. In this work, the equilibrium geometry and the corresponding rotational barrier of the benzene ring for each furan derivative ...

journal_title：Journal of molecular modeling

authors： Santos-Carballal D,Suardíaz R,Crespo-Otero R,González L,Pérez CS

更新日期：2013-10-01 00:00:00