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1.
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
2.
Semiempirical molecular orbital theory has been used for a systematic scan of the binding positions for a Mg2+ ion with 5a,6–anhydrotetracycline taking both conformational flexibility and possible different tautomeric forms into account. The magnesium ion has been calculated alone and with four or five complexed water molecules in order to simulate the experimental situation more closely. The results are analyzed by comparing the behavior of the title compound with that of tetracycline itself and possible causes for the stronger induction of the Tetracycline Receptor (TetR) by 5a,6–anhydrotetracycline than by tetracycline are considered.
Energetically favored 3D -structure of the zwitteranionic 5a,6-anhydrotetracycline magnesium complex in solution
Electronic Supplementary Material Supplementary material is available for this article at 相似文献
3.
Molecular-dynamics simulations have been used to study the diffusion of a short single model carbonic chain on the graphite
(001) surface. The calculated diffusion coefficient (D) first increases, then decreases with increasing chain length (N). This abnormal behavior is similar to polymer lateral diffusion at the solid–liquid interface. Furthermore, we have studied
the relation between the mean-square gyration radius and N.
Figure Log–log plot of the self-diffusion coefficient D versus the chain length N. The error bars are the standard deviation measured in three repeated simulations 相似文献
4.
49Ti chemical shifts for a total of 20 titanium complexes are reported, and several levels of theory are evaluated in order to identify a reliable approach for the calculation of titanium NMR data. The popular B3LYP/6–31G(d)//B3LYP/6–31G(d) proves to give very good agreement with experimental data over a range from 1,400 to −1,300 ppm. The MP2/6–31G(d)//MP2/6–31G(d) level computes even smaller average deviations but fails for TiI4. This behavior together with its huge demand for computational resources requires careful handling of this theoretical level. In addition, NMR data for five titanium fulvene (or related) complexes are given.
Dedicated to Professor Dr. Paul von Ragué Schleyer on the occasion of his 75th birthday 相似文献
5.
The structures and stabilities of square–hexagon alternant boron nitrides (B
x
N
x
, x=12–36) vs their tube isomers containing octagons, decagons and dodecagons have been computed at the B3LYP density functional level of theory with the correlation-consistent cc-pVDZ basis set of Dunning. It is found that octagonal B20N20 and B24N24 tube structures are more stable than their square–hexagon alternants by 18.6 and 2.4 kcal mol−1, respectively, while the square–hexagon alternants of other cages are more stable. Trends in stability as a function of cluster size are discussed.Figure The octagonal B20N20 and B24N24 tube structures are more stable than their square-hexagon alternant cagesDedicated to Professor Dr. Paul von Ragué Schleyer on the occasion of his 75th birthday 相似文献
6.
Eight H-bonded complexes between isocytosine (isoC) tautomeric forms and R/S-lactic acid (LA) have been studied at the B3LYP and HF levels of theory using 6–31+G(d) basis set. The energy barriers of the intermolecular proton transfers were also estimated as the results showed that they are several times lower than those of the intramolecular proton transfers of isoC in the gas phase. Furthermore, the energy barriers of the tautomerizations in which the carboxylic H-atom takes part are several times lower than those in which the LA OH group assists the proton transfer.
Figure 相似文献
7.
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.
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8.
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
9.
Rotational strengths in the far-UV of TEM-1 β-lactamase have been investigated with two theoretical models based on the matrix
method. The first model excludes, and a second includes, effects of the local electrostatic interactions on the chromophore
energies. Special attention is given to the contributions of the aromatic side-chain chromophores, and the mechanisms of generation
of rotational strengths are analyzed. The sensitivity of the computational models with respect to the structural changes of
the protein are discussed.
Figure Structure of TEM-1 β-lactamase. Both domains—α and αβ, the secondary structural elements and the aromatic and disulfide chromophores
are shown 相似文献
10.
Umpolung catalysis is studied by a sequence of model reactions (CPCM in THF, B3LYP/6-31G*) with different aldehydes and catalysts. We involved addition of the catalyst to the aldehyde and 1,2-H-migration to form a carbanionic d1-species, which is the crucial intermediate according to the Lapworth- and Breslow-mechanisms. Cyanide, N-methylthiazol-2-ylidene, and a glycol-based phosphite perform as umpolung catalysts, formaldehyde, acetaldehyde, benzaldehyde, and acrolein are substrates in this study. In these aldehyde substrates, alkyl-substitution disfavors but π-conjugation favors formation of the carbanionic d1-intermediate. The nucleophilic carbene, N-methylthiazol-2-ylidene, is the strongest umpolung catalyst, while the phosphite is about as active as cyanide.
Figure Transitions structure for the umpolung of formaldehyde with a glycol phosphinite catalyst
Dedicated to Professor Dr. Paul von Ragué Schleyer on the occasion of his 75th birthday 相似文献
11.
A theoretical analysis of the nature of the interactions in dibenzo[24]crown-8 (DB24C8)-n-dibutylammonium (DBM)—pseudorotaxane complex at the MP2 and DFT levels shows that the main contribution to the binding energy is the electrostatic interaction with moderate (20–25%) correlation stabilization. The total binding energy in the DB24C8-DBM complex represents a sum of the binding energies of two NH–O and one CH–O hydrogen bonds and the latter constitutes about 25% of the total interaction energy, giving the total binding energy of −41.2 kcal mol−1 at the BHandHLYP/6-311++G** level. Deprotonation of the DB24C8-DBM complex reduces the binding energy by some 50 kcal mol−1, giving metastable complexes DB24C8-DBA-1 or DB24C8-DBA-2, which will dissociate to give free crown ether and n-dibutylamine because of the strong exchange repulsion that prevails in neutral complexes.
Figure
Formation of DB24C8-DBM pseudorotoxane complex 相似文献
12.
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
13.
Streitwieser A 《Journal of molecular modeling》2006,12(5):673-680
Two methods have been developed for determining the aggregation equilibrium constants of lithium enolates based on the change in UV-vis spectrum with concentration and the effect of aggregation on proton-transfer equilibria. Dimers and tetramers are common. Substitution α to the carbonyl group generally reduces aggregation. Kinetic studies show that SN2 alkylations generally occur with the monomers, even in the presence of large amounts of aggregate. The qualitative chemistry is well modeled by ab initio computations at the HF level with modest basis sets; in these studies solvation is modeled by a combination of coordination of lithium cation with an ether oxygen and the electrostatic interaction of the resulting dipoles and quadrupoles with the solvent dielectric continuum.
This review is based on the fifth annual Paul vR Schleyer Lecture presented at Professor Schleyer's 75th birthday symposium, Athens GA, Feb 26, 2005. Carbon Acidity 123. For no. 122 see Streitwieser A, Kaufman MJ, Bors DA, MacArthur CA, Murphy JT, Guibe F, Arkivoc (2005) (vi) 200–210Dedicated to Professor Dr. Paul von Ragué Schleyer on the occasion of his 75th birthday 相似文献
14.
Muñoz-Muriedas J Barril X López JM Orozco M Luque FJ 《Journal of molecular modeling》2007,13(2):357-365
We investigate the changes in the solvation properties of the natural nucleic acid bases due to the formation of the canonical
Watson–Crick hydrogen-bonded complexes. To this end, the changes in the free energy of solvation of the bases induced upon
hydrogen-bonded dimerization are analyzed by means of the hydrophobic similarity index, which relies on the atomic contributions
to the free energy of solvation determined by the partitioning method implemented in the framework of the MST continuum model.
Such an index is also used to examine the hydrophobic similarity between the canonical nucleic acid bases and a series of
highly apolar analogues, which have been designed as potential candidates to expand the genetic alphabet. The ability of these
analogues to be incorporated into modified DNA duplexes can be related to the large reduction in the hydrophilicity of the
natural bases upon formation of the canonical hydrogen-bonded dimers. The results illustrate the suitability of the hydrophobic
similarity index to rationalize the role played by solvation in molecular recognition.
Proceedings of “Modeling Interactions in Biomolecules II”, Prague, September 5th–9th, 2005. 相似文献
15.
Semi-empirical quantum mechanics calculations using AM1 (Austin Method 1) were carried out for various host-guest combinations of α-cyclodextrin and mono-halogen benzoic acids. The energetically favorable inclusion structures were identified. The AM1 results show that α-cyclodextrin complexes with mono-halogen benzoic acid acids (where the halogen is chlorine, bromide, iodine) as guest compounds are more stable in the “head first” position than in the “tail-first” position for meta and para isomers while ortho mono-halogen benzoic acids complexes with α-cyclodextrin are more stable in “tail-first” position. The calculated structures were found to be in good agreement with those obtained from crystalographic databases.
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16.
The potential of various organic species to catalyze epoxidation of ethene by hydrogen peroxide is explored with B3LYP/6-31G* DFT calculations.
Electronic Supplementary Materials Supplementary material is available for this article at http://dx.doi.org/10.1007/s00894-005-0044-4.Dedicated to Professor Dr. Paul von Ragué Schleyer on the occasion of his 75th birthday 相似文献
17.
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 (K
i
=6 nM) but a low affinity with cyclin-dependent kinase 4 (K
i
=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
18.
Jin H Zheng S Wang Z Luo C Shen J Jiang H Zhang L Zhang L 《Journal of molecular modeling》2006,12(6):781-791
Some structural insights into the conformations of the isonucleosides containing duplexes have been provided. Unrestrained molecular-dynamics simulations on 18-mer duplexes with isonucleosides incorporated at the 3'-end or in the center of one strand have been carried out with explicit solvent under periodic boundary conditions using the AMBER force field and the particle mesh Ewald method. The Watson–Crick hydrogen-bonding patterns of the duplexes studied remained intact throughout the simulation. For the modified duplexes, the changes observed in the inter-base pair parameters and backbone torsional angles were primarily localized at the isonucleoside-inserted area. All five structures studied remained in the B-form family. The decreased stacking abilities indicated by the large changes in inter-base pair parameters and the large changes in backbones made the modified duplexes show a minor thermal destabilization in comparison with native DNA. The MM_PBSA method for estimating binding free energies on two complementary strands was used. The results showed that the binding free energies of isonucleoside-incorporated DNA duplexes were lower than the native DNA duplex, which is in good agreement with experimental observations.
相似文献
19.
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
20.
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