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1.
Glossman-Mitnik D 《Journal of molecular modeling》2007,13(1):43-46
Solanidine is the steroidal aglycon of some potato glycoalkaloids and a very important precursor for the synthesis of hormones and some pharmacologically active compounds. In this work, we make use of a new chemistry model within Density Functional Theory, called CHIH-DFT, to calculate the molecular structure of solanidine, as well to predict its infrared and ultraviolet spectra. The calculated values are compared with the experimental data available for this molecule as a means of validation of our proposed chemistry model.
Figure Molecular structure of solanidine calculated with the CHIH(small) model chemistry 相似文献
2.
William N. Setzer 《Journal of molecular modeling》2009,15(2):197-201
Quantum chemical calculations at the B3LYP/6-31G* level of theory have been carried out on 20 celastroid triterpenoids to
obtain a set of molecular electronic properties and to correlate these with cytotoxic activities. The cytotoxic activities
of these compounds can be roughly correlated with electronic effects related to nucleophilic addition to C(6) of the compounds:
The energies of the frontier molecular orbitals (E
HOMO and E
LUMO), the HOMO-LUMO energy gap, the dipole moment, the charge on C(6), and the electrophilicity on C(6).
Figure LUMO of Pristimerin. 相似文献
3.
Marek Doskocz Agnieszka Strupińska Szczepan Roszak Monika Prokopowicz Leo H. Koole Paweł Kafarski 《Journal of molecular modeling》2009,15(6):651-658
The study of spin-spin coupling constants across hydrogen bond provides useful information about configuration of complexes.
The interesting case of such interactions was observed as a coupling across an intramolecular hydrogen bond in 8-bromo-2′,3′-O-isopropylideneadenosine between the -CH2OH (at 5″ proton) group and the nitrogen atom of adenine. In this paper we report theoretical investigations on the 4h
J
NH coupling across the H″-C-O-H···N hydrogen bond in adenosine derivatives in various solvent models.
Figure Coupling constants in 8-bromo-2′,3′-O-isopropylideneadenosine
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
4.
The possibility that stable complexes may be formed between alpha particles (He2+) and small molecules is investigated using QCISD quantum mechanical calculations. Implications for their presence in the
terrestrial atmosphere and/or in interstellar space are discussed.
Figure Optimized structure of a stable H2OHe2+ complex 相似文献
5.
The enantioselective alkynylation of aldehyde catalyzed by chiral zinc(II)-complexes was studied by means of the density functional
theory (DFT). All the structures were optimized completely at the B3LYP/6-31G(d,p) level. To obtain more exact energies, single-point
energy calculations at B3LYP/6-31+G(d,p) level were carried out on the B3LYP/6-31G(d,p) geometries. As shown, this enantioselective
alkynylation was endothermic. The chirality-determining step for the alkynylation was the formation of the catalyst–ethanol
complexes and the transition states for this step involved a six-membered ring. The dominant products predicted theoretically
were of (R)-chirality, in good agreement with experiment.
相似文献
6.
Nitrile hydratase (NHase) is an enzyme containing non-corrin Co3+ in the non-standard active site. NHases from Pseudonocardia thermophila JCM 3095 catalyse hydration of nitriles to corresponding amides. The efficiency of the enzyme is 100 times higher for aliphatic
nitriles then aromatic ones. In order to understand better this selectivity dockings of a series of aliphatic and aromatic
nitriles and related amides into a model protein based on an X-ray structure were performed. Substantial differences in binding
modes were observed, showing better conformational freedom of aliphatic compounds. Distinct interactions with postranslationally
modified cysteines present in the active site of the enzyme were observed. Modeling shows that water molecule activated by
a metal ion may easily directly attack the docked acrylonitrile to transform this molecule into acryloamide. Thus docking
studies provide support for one of the reaction mechanisms discussed in the literature.
Figure Crystalographic structure of Pseudonocardia thermophila JCM 3095 nitrile hydratase (a) and the non-standard active site (b) 相似文献
7.
A series of [XN5]− (X=O, S, Se, Te) compounds has been examined with ab initio and Density Functional Theory (DFT) methods. The five-membered nitrogen ring series of structures are global minima and may exist or be characterized due to their significant dissociation barriers (29.7–32.7 kcal mol−1). Nucleus-independent chemical shifts (NICS) criteria and the presence of (4n+2) π-electrons confirmed that the five-membered nitrogen ring in their structures exhibits characteristics of aromaticity. Thus, the strong stability of the five-membered nitrogen ring structures may be attributed partially to their aromaticity.
相似文献
8.
3D-QSAR studies of Dipeptidyl peptidase IV inhibitors using a docking based alignment 总被引:1,自引:0,他引:1
Dipeptidyl peptidase IV (DPP-IV) deactivates the incretin hormones GLP-1 and GIP by cleaving the penultimate proline or alanine
from the N-terminal (P1-position) of the peptide. Inhibition of this enzyme will prevent the degradation of the incretin hormones
and maintain glucose homeostasis; this makes it an attractive target for the development of drugs for diabetes. This paper
reports 3D-QSAR analysis of several DPP-IV inhibitors, which were aligned by the receptor-based technique. The conformation
of the molecules in the active site was obtained through docking methods. The QSAR models were generated on two training sets
composed of 74 and 25 molecules which included phenylalanine, thiazolidine, and fluorinated pyrrolidine analogs. The 3D-QSAR
models are robust with statistically significant r2, q2, and values. The CoMFA and CoMSIA models were used to design some new inhibitors with several fold higher binding affinity.
Figure The CoMFA contours around molecule D1T155 (a) steric contours - favored (green); disfavored (yellow) (b) electrostatic contours
- electropositive (blue); electronegative (red) 相似文献
9.
The conformational stability of the extended antiparallel dimer structure of Met-enkephalin in water was analyzed by examining the hydration structure of enkephalin using molecular dynamics simulations. The result shows that, despite of the hydrophicility of the terminal atoms in the pentapeptide, the main contributor for the stability of the dimer in water is the four intermolecular hydrogen bonds between the Gly2 and Phe4 groups. The three-dimensional model of the δ-opioid pharmacophore for this dimer structure was also established. Such a model was demonstrated to match the δ-opioid pharmacophore query derived from the non-peptides SIOM, TAN-67, and OMI perfectly. This result thus strongly supports the assumption that the dimer structure of Met-enkephalin is a possible δ-receptor binding conformation.
Figure Schematic model of the extended antiparallel dimer structure of Met-enkephalin 相似文献
10.
The adsorption and primary oxidation step for the photodegradation of nitrobenzene (NB) have been studied computationally
using MSINDO SCF MO method. The method performs efficiently for extended surface models such as Ti36O90H36. Molecular dynamics simulations have revealed that NB is linked to TiO2 surface at the titanium ion via the oxygen atoms of NO2 group. In addition, the computed vibrational density of states for the adsorbed NB molecule is in reasonably good agreement
with the available experimental data and theoretical results. In order to identify the primary photochemical and photocatalytic
•OH initiated photooxidation intermediates, we have employed two different theoretical approaches, frontier orbital theory
and Wheland localization theory. It has been found that the meta- hydroxynitrocyclohexadienyl radical is energetically more favored than para- and ortho-hydroxynitrocyclohexadienyl radicals for the photochemical photolysis, whereas in the case of photocatalysis, the •OH radical attack is unselective and all three possible isomers have comparable stabilities.
Figure Minimum energy adsorption conformation of nitrobenzene onto TiO2 (100) surface 相似文献
11.
Coro J Alvarez-Puebla R Montero AL Suárez M Martin N Perez-Pineiro R 《Journal of molecular modeling》2008,14(7):641-647
Based on experimental evidence and DFT studies, a probable cyclization route to 1,3,5-thiadiazinanes-2-thiones in aqueous
medium is proposed. Experimental facts suggest the formation of a {[hydroxymethyl (substituted) carbamothioyl] sulfanyl}methanol
intermediate via reaction of dithiocarbamate (DTC) and formaldehyde. Nucleophilic addition of glycine to this intermediate
generates an adduct that undergoes intramolecular heterocyclization via an SN2 reaction. Computational calculations predict an active role of water in the reaction mechanism that promotes intramolecular
cyclization.
Figure Energy profile of the proposed reaction mechanism for the synthesis of thiadiazinane-2-thione ring 11 in aqueous medium from
a (hydroxymethylcarbamothioyl)sulfanylmethanol intermediate, 9 相似文献
12.
This work presents new developments of the moving-domain QM/MM (MoD-QM/MM) method for modeling protein electrostatic potentials.
The underlying goal of the method is to map the electronic density of a specific protein configuration into a point-charge
distribution. Important modifications of the general strategy of the MoD-QM/MM method involve new partitioning and fitting
schemes and the incorporation of dynamic effects via a single-step free energy perturbation approach (FEP). Selection of moderately
sized QM domains partitioned between and C (from C=O), with incorporation of delocalization of electrons over neighboring domains, results in a marked improvement
of the calculated molecular electrostatic potential (MEP). More importantly, we show that the evaluation of the electrostatic
potential can be carried out on a dynamic framework by evaluating the free energy difference between a non-polarized MEP and
a polarized MEP. A simplified form of the potassium ion channel protein Gramicidin-A from Bacillus brevis is used as the model system for the calculation of MEP.
Figure Schematic representation of the Moving Domain QM/MM method 相似文献
13.
Aminophosphine oxides and aminophosphonates are, in general, very stable compounds. However, following phosphorus–carbon bond
cleavage in aqueous acidic media these compounds sometimes decompose to phosphonic acids derivatives (PIII). Despite some controversy in the literature, careful analysis supported by theoretical studies leads to the conclusion that
decomposition to PIII derivatives proceeds via an elimination reaction.
Figure The decomposition of α-aminophosphine oxides to phosphonic acid derivatives (PIII) 相似文献
14.
To better understand the ligand-binding mechanism of protein Pir7b, important part in detoxification of a pathogen-derived
compound against Pyricularia oryzae, a 3D structure model of protein Pir7b was constructed based on the structure of the template SABP2. Three substrates were
docking to this protein, two of them were proved to be active, and some critical residues are identified, which had not been
confirmed by the experiments. His87 and Leu17 considered as ‘oxyanion hole’ contribute to initiating the Ser86 nucleophilic
attack. Gln187 and Asp139 can form hydrogen bonds with the anilid group to maintain the active binding orientation with the
substrates. The docking model can well interpret the specificity of protein Pir7b towards the anilid moiety of the substrates
and provide valuable structure information about the ligand binding to protein Pir7b.
Figure Ligand binding analysis based on the refined Pir7b model. Magenta dash line, hydrogen bond; Red dash line, distance label.
(a) Docking of 2-naphthol AS-acetate to Pir7b model. A 3D figure of 2-naphthol AS-acetate-Pir7b complex is also attached (b)
Docking of 2-naphthol AS-2-chlor-propionate to Pir7b model. (c) Docking of 2-naphthol-acetate to Pir7b model. 相似文献
15.
16.
Effective force fields for Ni-C interactions developed by Yamaguchi and Maruyama for the formation of metallofullerenes are
modified to simulate the catalyzed growth of single-wall carbon nanotubes on Nin clusters with n >20, and the reactive empirical bond order Brenner potential for C-C interactions is also revised to include the effect of
the metal atoms on such interactions.
Figure Force field parameters for carbon-metal interactions obtained from DFT calculations in small clusters. 相似文献
17.
Orvinols are potent analgesics that target opioid receptors. However, their analgesic mechanism remains unclear and no significant preference for subtype opioid receptor has been achieved. In order to find new orvinols that target the κ-receptor, comparative 3D–QSAR studies were performed on 26 orvinol analogs using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). The best predictions for the κ-receptor were obtained with the CoMFA standard model (q
2=0.686, r
2=0.947) and CoMSIA model combined steric, electrostatic, hydrophobic, and hydrogen bond donor/acceptor fields (q
2=0.678, r
2=0.914). The models built were further validated by a test set made up of seven compounds, leading to predictive r
2 values of 0.672 for CoMFA and 0.593 for CoMSIA. The study could be helpful for designing and prepare new category κ-agonists from orvinols.
相似文献
18.
Chun-Fang Huo Ralf Jackstell Matthias Beller Haijun Jiao 《Journal of molecular modeling》2010,16(3):431-436
The Pd-catalyzed telomerization in the presence of phosphine and carbene ligands has been computed. It is shown that the C–C
coupling of the less stable complex A with one trans- and one cis-butadiene in syn orientation forms the most stable intermediate B and is favorable both kinetically and thermodynamically. Protonation of B leads to equilibrium of the two most stable isomers of intermediate C. The overall regioselectivity is favored thermodynamically.
相似文献
19.
Martinez C Rivera JL Herrera R Rico JL Flores N Rutiaga JG López P 《Journal of molecular modeling》2008,14(2):77-81
The hydroxycinnamyl alcohols: p-coumarol, coniferol and sinapol are considered the basic units and precursors of lignins models. In this work, the specific
reactivity of these molecules was studied. We investigate their intrinsic chemical reactivity in terms of the Fukui function,
applying the principle of hard and soft acids and bases (HSAB) in the framework of the density functional theory (DFT). Comparisons
of their nucleophilic, electrophilic and free radical reactivity show their most probably sites to form linkages among them.
It is found that the most reactive sites, for reactions involving free radicals, are the carbons at the β-position in the p-coumarol and sinapol molecules, whilst the regions around the carbon-oxygen bond of the phenoxyl group are the most reactive
in coniferol.
Figure Isocontour plots for the free radical form of the Fukui function f
0
(r), showing the reactive sites toward electron-rich/poor reactants 相似文献
20.
Manhani KK Arcuri HA da Silveira NJ Uchôa HB de Azevedo WF Canduri F 《Journal of molecular modeling》2005,12(1):42-48
Cyclin-dependent kinases (CDKs) have been identified as potential targets for development of drugs, mainly against cancer. These studies generated a vast library of chemical inhibitors of CDKs, and some of these molecules can also inhibit kinases identified in the Plasmodium falciparum genome. Here we describe structural models for Protein Kinase 6 from P. falciparum (PfPK6) complexed with Roscovitine and Olomoucine. These models show clear structural evidence for differences observed in the inhibition, and may help designing inhibitors for PfPK6 generating new potential drugs against malaria.
Figure
Ribbon diagram of PfPK6 complexed with a roscovitine and b olomoucine 相似文献