Adsorption of paracresol and water into the silicalite-1 (MFI) zeolite has been investigated using canonical and grand-canonical
Monte Carlo simulations. The most stable sites of adsorption of paracresol are found to be located at the channel intersections.
Grand-canonical simulations have shown that at low loading, water molecules adsorb preferably at the vicinity of paracresol
molecules, whereas they are also located in the sinusoidal channels as the loading increases. In order to explain the experimental
adsorption isotherm observed for the coadsorption of water and paracresol in the MFI zeolite we propose a new concept of apparent
adsorption enthalpy that varies with the concentration of the solution. The mathematical expression for the apparent enthalpy
is introduced in an adsorption isotherm model. We shall refer to this theoretical isotherm as a non-langmuirian isotherm.
The non-linear expression for the apparent adsorption enthalpy accounts for a variable accessibility of the sites of adsorption
with respect to the concentration of the solution.
Figure Co-adsorption of paracresol and water in silicalite-1 zeolite and comparison between experimental and modelled adsorption
isotherms. 相似文献
Eight H-bonded complexes between serotonin (5-hydroxy-tryptamine) and water/hydrogen peroxide were studied at the B3LYP and
HF levels of theory, using the 6-31+G(d) basis set. A thermodynamic analysis was performed in order to find the most stable
complex. The calculated bonding parameters showed that the most stable H-bonded complex is formed between serotonin and hydrogen
peroxide by means of the intermolecular H-bond –H2N...H–OOH.
Fig. a Theoretical study of the hydrogen-bonded supersystems serotonin-water/hydrogen peroxide 相似文献
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
The geometric and electronic structure of tetracyanoethylene (TCNE)-aniline (donor-acceptor type) complex has been investigated
in gas phase using ab initio and time dependent density functional theory calculations. Both the above calculations predict a composed structure for the
complex, in which the interacting site is a C≡N and C=C bond center in the TCNE and, –NH2 and π-electrons of aniline. The N atom of aniline is oriented toward the TCNE molecule. The charge transfer transition energy,
estimated by calculating the ground-to-excited state transition electric dipole moments of the complex, agree well with the
reported experimental value in chloroform medium.
TCNE-aniline at ground state. TCNE-aniline at excited state 相似文献
Cytochrome P-450 is a group of enzymes involved in the biotransformation of many substances, including drugs. These enzymes
possess a heme group (1) that when it is properly modified induces several important physicochemical changes that affect their enzymatic activity.
In this work, the five structurally modified heme derivatives 2–6 and the native heme 1 were docked on CYP2B4, (an isoform of P450), in order to determine whether such modifications alter their binding form and
binding affinity for CYP2B4 apoprotein. In addition, docking calculations were used to evaluate the affinity of CYP2B4 apoprotein-heme
complexes for aniline (A) and N-methyl-aniline (NMA). Results showing the CYP2B4 heme 4- and heme 6-apoprotein complexes to be most energetically stable indicate that either hindrance effects or electronic properties are
the most important factors with respect to the binding of heme derivatives at the heme-binding site. Furthermore, although
all heme-apoprotein complexes demonstrated high affinity for both A and NMA, the CYP2B4 apoprotein-5 complex had higher affinity for A, and the heme 6 complex had higher affinity for NMA. Finally, surface electronic properties (SEP) were calculated in order to explain why
certain arginine residues of CYP2B4 apoprotein interact with polarizable functionalities, such as ester groups or sp2 carbons, present in some heme derivates. The main physicochemical parameter involved in the recognition process of the heme
derivatives, the CYP2B4 apoprotein and A or NMA, are reported.
Figure Scheme of steps to be followed for obtaining five new CYP2B4 apoprotein-heme complexes by docking 相似文献
Hydrogen molecule adsorption on frameworks consisting of alkaline earth metal atoms (Be, Mg, or Ca) in LTL zeolite was investigated via density functional theory. A 24T zeolite cluster model was used in this study. HOMO and LUMO energy, chemical potential, chemical hardness, electronegativity, adsorption energy, and adsorption enthalpy values were calculated. The Mg-LTL and Ca-LTL clusters were found to have much lower chemical potentials and adsorption energies than those of the Be-LTL cluster. Additionally, the calculations indicated that the Mg-LTL and Ca-LTL clusters are softer (considering their lower chemical hardness values) and more chemically reactive than the Be-LTL cluster. The calculated hydrogen adsorption enthalpies were ?14.7 and ?9.4 kJ/mol for the Mg-LTL and Ca-LTL clusters, respectively, which are significantly larger than the enthalpy of liquefaction for the hydrogen molecule. These results imply that the Mg-LTL and Ca-LTL zeolite structures are promising cryoadsorbents for hydrogen storage.
Graphical abstract Hydrogen adsorption was theoretically investigated on Be-, Ca- and Mg-LTL clusters. Ca- and Mg-LTL zeolites are potential cryoadsorbent materials for hydrogen storage.
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 stabilization are analyzed.
相似文献
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 4hJNH 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
Virulent H5N1 strains of influenza virus often harbor a D92E point mutation in the nonstructural protein NS1. This crucial
mutation has been correlated with increased virulence and/or cytokine resistance, but the structural implications of such
a change are still unclear. Furthermore, NS1 protein could also be a potential target for the development of novel antiviral
agents against H5N1 strains. Therefore, a reasonable 3D model of H5N1 NS1 is important for the understanding of the molecular
basis of increased virulence and the design of novel antiviral agents. Based on the crystal structure of a non-H5N1 NS1 protein,
a model of H5N1 NS1 was developed by homology modeling, molecular mechanics and molecular dynamics simulations. It was found
that the D92E mutation could result in weakened interactions of the carboxylate side chain with other phosphorylated residues,
thereby activating phosphorylation of NS1.
Figure Superposition of snapshots picked from the two molecular dynamic (MD) trajectories: a H5N1 NS1 homology model and b non-H5N1 NS1 crystal structure after 0 (green ribbon), 5 (blue ribbon) and 10 ns (pink ribbon) MD simulation 相似文献
The adsorption processes of elemental lead on carbonaceous surfaces which adsorbed CO/CO2/NO flue gases were investigated to understand the effects of CO/CO2/NO on elemental lead adsorption on carbonaceous surfaces with density functional theory. All calculations including optimizations, energies, and frequencies were conducted at B3PW91 density functional theory level, utilizing SDD basis set for lead and 6-31G(d) Pople basis set for other atoms. The results indicate that CO, CO2, and NO can promote the adsorption of elemental lead on the carbonaceous surface, but probably compete for adsorption sites with elemental lead. The promotion effects on adsorption can be attributed to active sites on the carbonaceous surface rather than flue gas adsorption on the carbonaceous surface. In addition, the adsorption order of three kinds of flue gas on the carbonaceous surface is CO2?>?NO?>?CO?>?Pb on average. Furthermore, the enhancement order of three kinds of flue gas on the elemental lead adsorption on carbonaceous surfaces is CO-CS?>?CO2-CS?>?NO-CS?>?CS in general. In particular, atomic charge and adsorption energy have good linear relationship in the process of elemental lead adsorption.
An automated docking procedure was used to study binding of a series of δ-selective ligands to three models of the δ-opioid
receptor. These models are thought to represent the three ligand-specific receptor conformations. Docking results are in agreement
with point mutation studies and suggest that different ligands—agonists and antagonists—may bind to the same binding site
under different receptor conformations. Docking to different receptor models (conformations) also suggests that by changing
to a receptor-specific conformation, the receptor may open or close different binding sites to other ligands.
Figure Ligands 5 (green) and 6 (orange) in bindingpocket BP1 of the R1 δ-opioid receptor model 相似文献
This article describes in a sequential fashion how ab initio quantum mechanical methods can be applied to study the pharmacophoric
features of drugs. It also describes how accurate drug–receptor interaction calculations can guide the careful design of balanced
dual inhibitors, which form an important class of second generation drugs. As an example, the authors have chosen balanced
inhibitors of angiotensin converting enzyme/neutral endopeptidase (ACE/NEP) as modern antihypertensive drugs. A unified, accurate,
in silico design approach is presented, encompassing all steps from pharmacophore derivation to complete understanding of
mechanistic aspects leading to drug design.
相似文献
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
A computational study of hydrogen-bonded complexes between the oxo-/hydroxo-amino N7/9H tautomers of guanine and water, methanol,
and hydrogen peroxide has been performed at the B3LYP/6-31+G(d) level of theory. The mechanisms of the water-, methanol-,
and hydrogen peroxide-assisted proton transfers in guanine were studied and compared with the intramolecular proton transfer
in guanine in the gas phase. It was found that the assisted proton transfers pass through about three times lower energy barriers
than those found for isolated guanine tautomers.
Figure DFT study of the gas phase proton transfer in guanine assisted by water, methanol and hydrogen peroxide 相似文献
A 3D QSAR analysis has been performed on a series of 67 benzodiazepine analogues reported as γ-secretase inhibitors using
molecular field analysis (MFA), with G/PLS to predict steric and electrostatic molecular field interaction for the activity.
The MFA study was carried out using a training set of 54 compounds. The predictive ability of model developed was assessed
using a test set of 13 compounds ( as high as 0.729). The analyzed MFA model has demonstrated a good fit, having r2 value of 0.858 and cross validated coefficient, value as 0.790. The analysis of the best MFA model provided insight into possible modification of the molecules for better
activity.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
The three-dimensional (3D) structure of the catalytic domain of Gas1p, a protein belonging to the only family of β-(1,3)-glucan
transferases so far identified in yeasts and some pathogenic fungi (family GH-72), has been predicted by combining results
derived from threading methods, multiple sequence alignments and secondary-structure predictions. The 3D model has allowed
the identification of several residues that are predicted to play a crucial role in structural integrity, substrate recognition
and catalysis. In particular, the model of the catalytic domain can be useful for designing site-directed mutagenesis experiments
and for developing inhibitors of Gas1p enzymatic activity.
Figure Three-dimensional models of the Gas1p catalytic domain as predicted using as template 7A3H (PDB code) protein
Electronic Supplementary Material Supplementary material is available for this article at 相似文献
Structure-based 3D-QSAR studies were performed on 20 thiazoles against their binding affinities to the 5-HT3 receptor with comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). The thiazoles were initially docked into the binding pocket of a human 5-HT3A receptor homology model, constructed on the basis of the crystal structure of the snail acetylcholine binding protein (AChBP), using the GOLD program. The docked conformations were then extracted and used to build the 3D-QSAR models, with cross-validated values 0.785 and 0.744 for CoMFA and CoMSIA, respectively. An additional five molecules were used to validate the models further, giving satisfactory predictive values of 0.582 and 0.804 for CoMFA and CoMSIA, respectively. The results would be helpful for the discovery of new potent and selective 5-HT3 receptor antagonists.
相似文献
Cyclin-dependent kinases (Cdks) play important roles in the regulation of the cell cycle. Their inhibitors have entered clinical
trials to treat cancer. Very recently, Davis et al. (Nat Struct Biol 9:745–749, 2002) have found a ligand NU6102, which has
a high affinity with cyclin-dependent kinase 2 (Ki=6 nM) but a low affinity with cyclin-dependent kinase 4 (Ki=1,600 nM). To understand the selectivity, we use homology modeling, molecular docking, molecular dynamics and free-energy
calculations to analyze the interactions. A rational 3D model of the Cdk4–NU6102 complex is built. Asp86 is a key residue
that recognizes NU6102 more effectively with Cdk2 rather than Cdk4. Good binding free energies are obtained. Energetic analysis
reveals that van der Waals interaction and nonpolar contributions to solvent are favorable in the formation of complexes and
the sulfonamide group of the ligand plays a crucial role for binding selectivity between Cdk2 and Cdk4.
Figure Two-dimensional representative for the interacting model of NU6102 complexed with the Cdk4 from a predicted structure by
LIGPLOT.
相似文献
In this study, we performed a molecular docking and dynamics simulation for a benzoxazinone–human oxytocin receptor system to determine the possible hydrophobic and electrostatic interaction points in the dynamic complex. After the homology modeling, the ligand was docked into the putative active using AutoDock 3.05. After the application of energetic and structural filters, the complexes obtained were further refined with a simulated annealing protocol (AMBER8) to remove steric clashes. Three complexes were selected for subjection to the molecular dynamics simulation (5 ns), and the results on the occurrence of average anchor points showed a stable complex between the benzoxazinone derivative and the receptor. The complex could be used as a good starting point for further analysis with site-directed mutagenesis, or further computational research.
Figure The location of the ligands (complex B – blue; complex E – red; and complex F –
green) in the transmembrane regions (TM1 – red; TM2 – blue; TM3 – yellow; TM4
– purple; TM5 – orange; TM6 – cyan; TM7 – pink) of the hOTR. For clarity, the EC
and IC loops are not shown
Electronic Supplementary Material Supplementary material is available at 相似文献