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1.
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.
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2.
Computational studies of retinal protonated Schiff base (PSB) isomers show that a twisted curl-shaped conformation of the
retinyl chain is a new low-lying minimum on the ground-state potential energy surface. The curl-shaped isomer has a twisted
structure in the vicinity of the C11=C12 double bond where the 11-cis retinal PSB isomerizes in the rhodopsin photoreaction. The twisted configuration is a trapped structure between the 11-cis and all-trans isomers. Rotation around the C10–C11 single bond towards the 11-cis structure is prevented by steric interactions of the two methyl groups on the retinyl chain and by the torsion barrier of
the C10–C11 bond in the other direction. Calculations of spectroscopic properties of the 11-cis, all-trans, and curl-shaped isomers provide useful data for future identification of the new retinal PSB isomer. Circular dichroism
(CD) spectroscopy might be used to distinguish between the retinal PSB isomers. The potential energy surface for the orientation
of the β-ionone ring of the 11-cis retinal PSB reveals three minima depending on the torsion angle of the β-ionone ring. Two of the minima correspond to 6-s-cis configurations and one has the β-ionone ring in 6-s-trans position. The calculated CD spectra for the two 6-s-cis configurations differ significantly indicating that the sign of the β-ionone ring torsion angle could be determined using CD spectroscopy. Calculations of the CD spectra suggest that a flip of
the β-ionone ring might occur during the first 1 ps of the photoreaction. Rhodopsin has a negative torsion angle for the β-ionone ring, whereas the change in the sign of the first peak in the experimental CD spectrum for bathorhodopsin could suggest
that it has a positive torsion angle for the β-ionone ring. Calculated nuclear magnetic resonance (NMR) shielding constants and infrared (IR) spectra are also reported
for the retinal PSB isomers.
Figure The figure shows the optimized molecular structure of the curl-shaped retinal isomer.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
3.
4.
Quinoline alkaloids are abundant in the Rutaceae, and many have exhibited cytotoxic activity. Because structurally related
antitumor alkaloids such as camptothecin and fagaronine are known to function as intercalative topoisomerase poisons, it is
hypothesized that cytotoxic Stauranthus alkaloids may also serve as intercalative topoisomerase inhibitors. To test this hypothesis theoretically, ten Stauranthus quinoline alkaloids were examined for potential intercalation into DNA using a molecular docking approach. Four of the alkaloids
(stauranthine, skimmianine, 3′,6′-dihydroxy-3′,6′-dihydrostauranthine, and trans-3′,4′-dihydroxy-3′,4′-dihydrostauranthine) were able to intercalatively dock consistently into DNA. In order to probe the
intermolecular interactions that may be responsible for intercalation of these quinoline alkaloids, density functional calculations
have been carried out using both the B3LYP and M06 functionals. M06 calculations indicated favorable π–π interactions between
either skimmianine or stauranthine and the guanine–cytosine base pair. Furthermore, the lowest-energy face-to-face orientation
of stauranthine with guanine is consistent with favorable dipole–dipole orientations, favorable electrostatic interactions,
and favorable frontier molecular orbital interactions. Likewise, the lowest-energy face-to-face orientation of stauranthine
with the guanine–cytosine base pair reveals favorable electrostatic interactions as well as frontier molecular orbital interactions.
Thus, not only can quinoline alkaloids dock intercalatively into DNA, but the docked orientations are also electronically
favorable.
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5.
The ONIOM2 (B3LYP/6–31G (d, p): PM3) and B3LYP/6–31G (d, p) methods were applied to investigate the interaction between STI-571 and abelson tyrosine kinase binding site. The complex of N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)- phenyl]-benzamide (part of STI-571) and related 16 amino acid residues were found at B3LYP/6–31G (d, p) level to have hydrogen bonds and π....π stacking interaction,
their binding energy via HAF optimization was −20.4 kcal mol−1. The results derived from this study agreed well with the reported observation.
Figure Optimized structure of STI-571 and Thr315 in abelson tyrosine kinase based on ONIOM2 method 相似文献
6.
7.
The mechanism of the enantioselective deprotonation of cyclohexene oxide with isopinocampheyl-based chiral lithium amide was studied by quantum chemical calculations. The transition states of eight molecules were fully optimized at the ab initio HF/3-21G and density functional B3LYP/3-21G levels with Gaussian 98. The activation energies were calculated at the B3LYP/6-31+G(3df,2p)//B3LYP/3-21G level. We found the theoretical evaluation to be consistent with the experimental data. At the best case, an enantiomeric excess of up to 95% for (R)-2-scyclohexen-1-ol was achieved with (−)-N, N-diisopinocampheyl lithium amide.
Enantioselective deprotonation of cyclohexene oxide
Electronic Supplementary Material Supplementary material is available for this article at
Dedicated to Professor Dr. Paul von Ragué Schleyer on the occasion of his 75th birthday. 相似文献
8.
Haripal PK Raval HK Raval MK Rawal RM Biswal B Biswal UC 《Journal of molecular modeling》2006,12(6):847-853
A three-dimensional model of the PsbS protein was built with the help of homology-modeling methods. This protein is also known as CP22 and is associated with the protection of photosystem II of thylakoid from excess quanta of light energy absorbed by the photosynthetic apparatus. PsbS is reported to bind two molecules of zeaxanthin at low pH (<5.0) and is believed to be essential for rapid nonphotochemical quenching (qE) of chlorophyll a fluorescence in photosystem II. An attempt was made to explain the pH modulation of the conformation of protein through salt-bridges Glu−(122)-Lys+(113) and Glu−(226)-Lys+(217). Binding of two molecules of zeaxanthin in the three-dimensional model of PsbS is postulated. The molecular mechanism of photoprotection by PsbS is explained through the model.
1 Backbone structure of the PsbS protein with two molecules of all trans zeaxanthin (ZEX). Residues Glu 90, 122, 194, 226 and Lys 113, 217 are shown. The figure is drawn with RASMOL (Molecular Visualization Program, RasMol V2.6, Roger Sayle, Glaxo Wellcome Research and Development, Stevenage, Hertfordshire, UK)
Electronic Supplementary Material Supplementary material is available for this article at 相似文献
9.
Ab initio molecular dynamics (MD) calculations have been performed to study the photoisomerization of a 3-double-bond retinal model chromophore, the all-trans-4, 6-dimethylpenta-3, 5-dieniminium cation, and the possible influence of non-planar distortions on the product distribution. In total, 171 trajectories have been generated for four different conformations of the structure, a planar one and three in which the C4–C5 and the C5=C6 bonds were increasingly twisted out of plane. Starting geometries randomly distributed about the equilibrium geometry were generated by zero-point energy sampling; trajectories were calculated using CASSCF-BOMD methodology and were followed until the photoproduct and its configuration could be assigned. For the latter, two different approaches were applied, one involving the CASSCF configuration vectors, the other an analysis of the MD at the first possible hopping event. Isomerization was found to occur almost exclusively about the central C3=C4 double bond in the case of the planar model compound. Twisting the conjugated π-system shifts the isomerization site from the central double bond to the terminal C5=C6 double bond. With both the C4–C5 and the C5=C6 bonds twisted by 20°, about 35% of the trajectories lead to the configurationally inverted 5-cis product. The results are discussed with reference to the highly selective and efficient photo-induced isomerization of the retinal chromophore in rhodopsin.
Figure Product distribution in the MD simulations of models 1–4. The percentage of trajectories that lead to either C3=C4 or C5=C6 rotation is given beside the bar graphs. The green and the red portions of the bars represent the productive and the unproductive events, respectively, with respect to that particular rotation estimated from the torsion angles at the first close approach of the energy surfaces
Dedicated to Professor Dr. Paul von Ragué Schleyer on the occasion of his 75th birthday. 相似文献
10.
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
11.
Frans T. I. Marx Johan H. L. Jordaan Hermanus C. M. Vosloo 《Journal of molecular modeling》2009,15(11):1371-1381
The productive self-metathesis reaction of 1-octene in the presence of the Phobcat precatalyst [RuCl2(Phoban-Cy)2(=CHPh)] using density functional theory was investigated and compared to the Grubbs 1 precatalyst [RuCl2(PCy3)2(=CHPh)]. At the GGA-PW91/DNP level, the geometry optimization of all the participating species and the PES scans of the various
activation and catalytic cycles in the dissociative mechanism were performed. The formation of the catalytically active heptylidene
species is kinetically and thermodynamically favored, while the formation of trans-tetradecene is thermodynamically favored.
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12.
The microphase separation dynamics of the triblock copolymer surfactant P103 [(ethylene oxide)17(propylene oxide)60(ethylene oxide)17] was investigated by a dynamic variant of mean-field density functional theory. Different self-assembled aggregates, spherical
micelles, micellar clusters and disk-like micelles, are explored in the solution. The spherical micelle above critical micelle
concentration (CMC) is a dense core consisting mainly of PPO and a hydrated PEO swollen corona, and is in good agreement with
the experimental results concerning their structures. At a concentration of 10–15%, micellar clusters with a larger PPO core
form as a result of coalescence among spherical micelles. At concentrations above 16% by volume, a series of disk-like micelles
come into being. The order parameters show that spherical micelles are easily formed, while the micellar clusters or disk-like
micelles need a longer time to reach steady equilibrium. The results show that mesoscopic simulation can augment experimental
results on amphiphilic polymers, and provide some mesoscopic information at the mesoscale level.
Figure Coalescence of Micelles with time evolution for 15% vol system. □ represents spherical micelle that coalesce. (a) 180 μs, (b) 190 μs, (c)225 μs, and (d) 250 μs 相似文献
13.
Nongnit Morakot Wandee Rakrai Somchai Keawwangchai Chatthai Kaewtong Banchob Wanno 《Journal of molecular modeling》2010,16(1):129-136
The thiourea based receptor containing naphthalene groups (1), has been successfully designed and synthesized for application as an oxalate receptor. A density functional theory at B3LYP/6-31G(d,p)
level of theory has been applied to predict the binding ability between 1 and selected anions, i.e., oxalate, malonate, succinate, glutarate, dihydrogen phosphate, and hydrogen sulphate. Calculation results point out that
receptor 1 shows the strongest interaction to oxalate ion with the binding free energy of 172.48 kcal mol−1. The recognition ability of 1 to the selected anions has been also investigated by means of the absorption and emission techniques. Experimental results
are in excellent agreement with the calculation data in which receptor 1 shows highly selective for oxalate ion over the other anions with logβ of 3.82 (0.02) M−1 by means of the size of binding cavity.
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14.
Halogen bonding (XB) is a type of noncovalent interaction between a halogen atom X in one molecule and a negative site in another. X can be chlorine, bromine or iodine. The strength of the interaction increases in the order Cl<Br<I. After a brief review
of experimental evidence relating to halogen bonding, we present an explanation for its occurrence in terms of a region of
positive electrostatic potential that is present on the outermost portions of some covalently-bonded halogen atoms. The existence
and magnitude of this positive region, which we call the σ-hole, depends upon the relative electron-attracting powers of X
and the remainder of its molecule, as well as the degree of sp hybridization of the s unshared electrons of X. The high electronegativity of fluorine and its tendency to undergo significant sp hybridization account for its failure to halogen bond. Some computed XB interaction energies are presented and discussed.
Mention is also made of the importance of halogen bonding in biological systems and processes, and in crystal engineering.
Figure The computed B3PW91/6-31G(d,p) electrostatic potential, in kcal mol−1, on the 0.001 electrons/bohr3 surface of NC–C≡C–Cl. The chlorine atom is at the right. The color ranges are: red, more positive than 15; yellow between 7 and 15; green, between 0 and 7; blue, between −10 and 0; purple, more positive than −10.
Proceedings of “Modeling Interactions in Biomolecules II”, Prague, September 5th–9th, 2005. 相似文献
15.
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
16.
Vuk Micovic Milovan D. Ivanovic Ljiljana Dosen-Micovic 《Journal of molecular modeling》2009,15(3):267-280
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
17.
We have carried out B3PW91 and MP2-FC computational studies of dimethyl sulfoxide, (CH3)2SO, and dimethyl sulfone, (CH3)2SO2. The objective was to establish quantitatively the basis for their high polarities and boiling points, and their strong solvent
powers for a variety of solutes. Natural bond order analyses show that the sulfur–oxygen linkages are not double bonds, as
widely believed, but rather are coordinate covalent single S+→O− bonds. The calculated electrostatic potentials on the molecular surfaces reveal several strongly positive and negative sites
(the former including σ-holes on the sulfurs) through which a variety of simultaneous intermolecular electrostatic interactions
can occur. A series of examples is given. In terms of these features the striking properties of dimethyl sulfoxide and dimethyl
sulfone, their large dipole moments and dielectric constants, their high boiling points and why they are such good solvents,
can readily be understood.
Figure Dimers of dimethyl sulfoxide (DMSO; left) and dimethyl sulfone (DMSO2; right) showing O S—O -hole bonding and C H—O hydrogen bonding. Sulfur atoms are yellow, oxygens are red, carbons are gray and hydrogens are white 相似文献
18.
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
19.
Zaleśny R Matczyszyn K Kaczmarek A Bartkowiak W Cysewski P 《Journal of molecular modeling》2007,13(6-7):785-791
The UV-Vis spectra of series of polymethylmethacrylate (PMMA) copolymers with attached trans-azobenzene derivatives were measured
in 1,1,2-trichloroethane. In order to gain some insight into the recorded spectra, the quantum chemical calculations were
performed for the substituted azobenzenes using both configuration interaction with single excitations method (CIS) as well
as density functional theory (DFT) with B3LYP and PBE0 functionals. The calculations were performed in solvent. In particular,
we found that the PBE0 excitation energies are in very good agreement with the experimental data.
Figure The plots of orbital contour surfaces for molecule II. The molecular orbitals were calculated at the PBE0/6-311++G(d,p) level of theory. The upper plot presents contour surface of HOMO and the lower presents contour surface of LUMO. Shown are the contour surfaces of orbital amplitude 0.04 (red) and -0.04 (blue) 相似文献
20.
Seshasayee AS Raghunathan K Sivaraman K Pennathur G 《Journal of molecular modeling》2006,12(2):197-204
β-Hairpins are the simplest form of β-sheets which, due to the presence of long-range interactions, can be considered as tertiary
structures. Molecular dynamics simulation is a powerful tool that can unravel whole pathways of protein folding/unfolding
at atomic resolution. We have performed several molecular dynamics simulations, to a total of over 250 ns, of a β-hairpin
peptide in water using GROMACS. We show that hydrophobic interactions are necessary for initiating the folding of the peptide.
Once formed, the peptide is stabilized by hydrogen bonds and disruption of hydrophobic interactions in the folded peptide
does not denature the structure. In the absence of hydrophobic interactions, the peptide fails to fold. However, the introduction
of a salt-bridge compensates for the loss of hydrophobic interactions to a certain extent.
Figure Model of b-hairpin folding: Folding is initiated by hydrophobic interactions (Brown circles). The folded structure, once formed, is stabilized by hydrogen bonds (red lines) and is unaffected by loss of hydrophobic contacts 相似文献