排序方式: 共有15条查询结果,搜索用时 15 毫秒
1.
Lakshmipathi Senthilkumar Palanivel Umadevi Kumaranathapuram Natarajan Sweety Nithya Ponmalai Kolandaivel 《Journal of molecular modeling》2013,19(8):3411-3425
Twenty cocaine–water complexes were studied using density functional theory (DFT) B3LYP/6-311++G** level to understand their geometries, energies, vibrational frequencies, charge transfer and topological parameters. Among the 20 complexes, 12 are neutral and eight are protonated in the cocaine-water complexes. Based on the interaction energy, the protonated complexes are more stable than the neutral complexes. In both complexes, the most stable structure involves the hydrogen bond with water at nitrogen atom in the tropane ring and C?=?O groups in methyl ester. Carbonyl groups in benzoyl and methyl ester is the most reactive site in both forms and it is responsible for the stability order. The calculated topological results show that the interactions involved in the hydrogen bond are electrostatic dominant. Natural bond orbital (NBO) analysis confirms the presence of hydrogen bond and it supports the stability order. Atoms in molecules (AIM) and NBO analysis confirms the C-H?·?·?·?O hydrogen bonds formed between the cocaine-water complexes are blue shifted in nature. 相似文献
2.
Intermolecular hydrogen-bond interactions in the monohydrated complexes of formamide, N-methylacetamide and glycylglycine have been studied using ab initio and DFT methods. The geometries were optimized using second-order Møller–Plesset perturbation theory and the B3LYP DFT functional with the 6-311++G** basis set. It is observed that hydrogen-bond interactions at the carbonyl group of the peptide moiety are stronger than those at the amino group of the formamide and N-methylacetamide molecules. Because of the presence of cyclic hydrogen-bonding interactions in glycylglycine, the interaction at the amino group is higher than at the carbonyl. The 13C and 15N NMR shielding values were calculated for the non-hydrated and monohydrated complexes. Condensed Fukui functions have also been calculated for non-hydrated formamide, N-methylacetamide and glycylglycine molecules at the B3LYP/6-311++G** level of theory, and the results are discussed.Figure Structure of hydrated glycylglycine dipeptide 相似文献
3.
The switching propensity and maximum probability of occurrence of the side chain imidazole group in the dipeptide cyclo(His–Pro)
(CHP) were studied by applying molecular dynamics simulations and density functional theory. The atomistic behaviour of CHP
with the neurotoxins glutamate (E) and paraquat (Pq) were also explored; E and Pq engage in hydrogen bond formation with the
diketopiperazine (DKP) ring of the dipeptide, with which E shows a profound interaction, as confirmed further by NH and CO
stretching vibrational frequencies. The effect of CHP was found to be greater on E than on Pq neurotoxin. A ring puckering
study indicated a twist boat conformation for the six-membered DKP ring. Molecular electrostatic potential (MESP) mapping
was also used to explore the hydrogen bond interactions prevailing between the neurotoxins and the DKP ring. The results of
this study reveal that the DKP ring of the dipeptide CHP can be expected to play a significant role in reducing effects such
as oxidative stress and cell death caused by neurotoxins. 相似文献
4.
The quantum chemical and molecular dynamics studies have been performed to infer the structural changes of all-trans and all-cis
forms of cyclo[(1R,3S)-3-aminocyclohexanecarboxylicacid(γ-Acc)-α-Glycine(Gly)]3 hexapeptide. The backbone conformations of the above peptide have been analyzed using the valence and peptide deformation
angles applying B3LYP/6–311G** level of theory. The conformational preference of the backbone of all-trans and all-cis cyclo[(1R,3S)-γ-Acc-Gly]3 hexapeptides is found to depend on the puckering of cyclohexane rings. The non-uniform distribution of water inside the cavity
is observed, where sometimes water molecules formed a chain like conformation through hydrogen bond networks while traversing
the pore of all-cis cyclo[(1R,3S)-γ-Acc-Gly]3 peptide. Larger relaxation times of the order of a hundred to two hundred pico seconds for active site…water hydrogen bond
interactions were noticed. The hydrophobic nature of the cavity of all-trans cyclo[(1R,3S)-γ-Acc-Gly]3 due to the presence of cyclohexane moiety has been analyzed. Further this investigation emphasized on the non-transport of
molecules through the pore of all-trans cyclo[(1R,3S)-γ-Acc-Gly]3 peptide due to the obstruction produced by cyclohexane groups. 相似文献
5.
6.
R. Radhika S. Vijayakumar P. Kolandaivel 《Journal of biomolecular structure & dynamics》2018,36(6):1369-1401
The theoretical studies on DNA with the anticancer drug 6-Mercaptopurine (6-MP) are investigated using theoretical methods to shed light on drug designing. Among the DNA base pairs considered, 6-MP is stacked with GC with the highest interaction energy of –46.19 kcal/mol. Structural parameters revealed that structure of the DNA base pairs is deviated from the planarity of the equilibrium position due to the formation of hydrogen bonds and stacking interactions with 6-MP. These deviations are verified through the systematic comparison between X–H bond contraction and elongation and the associated blue shift and red shift values by both NBO analysis and vibrational analysis. Bent’s rule is verified for the C–H bond contraction in the 6-MP interacted base pairs. The AIM results disclose that the higher values of electron density (ρ) and Laplacian of electron density (?2ρ) indicate the increased overlap between the orbitals that represent the strong interaction and positive values of the total electron density show the closed-shell interaction. The relative sensitivity of the chemical shift values for the DNA base pairs with 6-MP is investigated to confirm the hydrogen bond strength. Molecular dynamics simulation studies of G-quadruplex DNA d(TGGGGT)4 with 6-MP revealed that the incorporation of 6-MP appears to cause local distortions and destabilize the G-quadruplex DNA. 相似文献
7.
A theoretical investigation on the interaction of myristic fatty acid (M) with Acutohaemolysin and Piratoxin-II of PLA2 family
is performed using two layered ONIOM (B3LYP/6-31G*: UFF) method. The results predict that though proteins show revulsion to
incoming fatty acid, the interaction of the phenyl ring of Phenylalanine restricts the passage of M through the channel. To
unveil the nature of interaction of M, quantum chemical studies are carried out on the palindromic tripeptides Alanine-Phenylalanine-Alanine
(AFA) and Alanine-Valine-Alanine (AVA) present in Acutohaemolysin and Piratoxin-II at B3LYP/6-311G** level of theory. The
mode of interaction of the fatty acid with protein is electrostatic, confirmed further through molecular electrostatic potential
(MEP) maps. The AFA shows stronger interaction than AVA, validating the impact of mutation on catalytic activity. Further
such strong interaction and hence the higher probability of prohibition for catalytic activity exists only when the fatty
acid interacts at the center of phenyl ring than at its edges. The preferred secondary structural configuration and conformational
properties of AVA and AFA also validate the strong interaction of fatty acid with Phenylalanine. In general, this theoretical
investigation shows that the loss of catalytic activity would take place only when fatty acid interacts at the center of phenyl
ring. 相似文献
8.
The relative stabilities of Guanine-Cytosine (G-C) DNA bare base pairs, its tautomeric forms and microhydrated base pairs are theoretically investigated with a focus on the keto-enol tautomerism as well as on the cis-trans isomerism using ab initio and density functional theory methods. The stabilities of the G-C bare base pairs, its tautomeric forms and microhydrated base pairs were affected by various factors including keto-enol tautomerization, cis-trans enol isomerization, and steric hindrance between the base pair and water molecules. The Atoms in Molecules theory (AIM) is employed to investigate H-bonding patterns both in bare and microhydrated base pairs. From the above topological results, an excellent linear correlation is shown between electron density [rho(r)], and its Laplacian [V2rho(r)] at the bond critical points. NBO analysis has been carried out to study the charge transfer between proton acceptor to the antibonding orbital of the X-H bond both in bare and microhydrated base pairs. 相似文献
9.
The hydrogen bonds formed by the interaction of nitriles with water, hydrogen fluoride, ammonia and hydrogen sulphide have been studied using B3LYP and second-order Møller–Plesset perturbation (MP2) methods and 6-311+ + G(d,p) basis set. The energies and structures of 80 hydrogen-bonded complexes between nitriles and small molecules were examined systematically using B3LYP and MP2 procedure. Categorisation of the hydrogen bonds involved in the various complexes led to an ordering of hydrogen bond donor and acceptor abilities for some functional groups. The interaction energies have been corrected for the basis set superposition error using Boy's counterpoise correction method. The Morokuma energy decomposition analysis reveals that the strong interactions are due to the attractive contributions from the electrostatic (ES), polarisation (PL) and charge transfer (CT) components. The topological parameters, electron density and Laplacian of electron density show excellent correlation with the hydrogen bond length. Natural bond orbital (NBO) analysis has also been performed to study the CT from proton acceptor to the antibonding orbital of the H–Y bond in the proton donor part of complexes. The frequency analysis of C–H…Y bond in the complexes indicates the blue-shifting nature largely in case of sp2 hybridised carbon atom. 相似文献
10.
The conformational dependence of nonplanarity of the peptide bond of formylglycinamide has been studied using ab initio and density functional theory methods. Hartree-Fock self-consistent field theory (HF), M?ller-Plesset perturbation theory (MP2) of ab initio and B3LYP level of theory of dft method have been used employing 6-31++G** basis set. The MP2 method predicts better results than HF and B3LYP levels of theory for conformational stability dependence of nonplanarity. Systematic dependence of planarity deviation has been observed in MP2 theory. The chemical hardness values successfully predict the conformational region, but fail to obey maximum hardness principle. It is concluded that the most reliable dft method could not successfully predict the planarity of peptide bond in comparison with electron correlated method of ab initio method. 相似文献