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1.
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
2.
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
3.
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.
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4.
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.
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
7.
Setzer WN 《Journal of molecular modeling》2008,14(10):967-973
A computational investigation of the sulfur-containing heterocyclic components (substituted thietanes and 1,2-dithiolanes)
of Mustela anal sac secretions has been carried out. A cluster analysis of the chemical compositions of Mustela anal sac volatiles reveals little similarity with established phylogenetic relationships between members of the genus. Ab initio calculations [MP2/6–311++G(2df,2p)//B3LYP/6–311++G**] show the lowest-energy C5H10S isomeric thietane to be 2,2-dimethylthietane, which is also the most abundant of the Mustela thietanes. Similarly, 3,3-dimethyl-1,2-dithiolane is the lowest-energy C5H10S2 compound. 2-n-Propylthietane is the highest-energy C6H12S compound, but the most abundant Mustela C6H12S compound produced, whereas cis-2-ethyl-4-methylthietane, the lowest-energy C6H12S thietane, has never been observed in Mustela anal sac secretions. A molecular docking analysis of the Mustela sulfur-containing heterocycles into both porcine and bovine odorant binding proteins reveals the interactions of the docked
ligands with the proteins to be largely hydrophobic, and have binding energies generally lower than typical odorant molecules
such as linalool or eugenol.
Figure Mustela anal sac volatile components, 2,2-dimethylthietane and cis-3,4-dimethyl–1,2-dithiolane. 相似文献
8.
The structure and stability of endohedral X@C20F20 complexes (X = H−, F−, Cl−, Br−, H, He) have been computed at the B3LYP level of theory. All complexes in I
h symmetry were found to be energy minimum structures. H−@C20F20 and F−@C20F20 complexes have negative inclusion energies, while other complexes have positive inclusion energies. Similarity between C20F20 and C20H20 has been found for X = H and He. On the basis of the computed nucleus independent chemical shift values at the cage center,
both C20F20 and C20F20 are aromatic.
Figure Endohedral X@C20F20 complexes 相似文献
9.
Setzer WN 《Journal of molecular modeling》2008,14(5):335-342
The energetics of the Cope rearrangement of 17 germacrane sesquiterpenoids to their respective elemane forms have been calculated
using both density functional theory (B3LYP/6-31G*) and post Hartee-Fock (MP2/6-31G**) ab initio methods. The calculations are in qualitative agreement with experimentally observed Cope rearrangements, but the two methods
give slightly different results. MP2 calculations generally show more favorable elemene energies compared to the respective
germacrenes (by around 3–4 kcal mol−1) and smaller activation energies (by 2–3 kcal mol−1). Additionally, neither method is accurate enough to consistently reproduce the germacrene/elemene equilibrium. Apparently,
the generally small energy differences between the two forms in these sesquiterpenoids cannot be adequately reproduced at
these levels of calculation.
Figure The Cope rearrangement of the germacrane sesquiterpenoid bacchascandon to the elemane shyobunone 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.
Abbasoglu R 《Journal of molecular modeling》2007,13(3):425-430
Full geometric optimization of endo,endo-tetracyclo[4.2.1.13,6.02,7]dodeca-4,9-diene (TTDD) has been carried out by ab initio and DFT/B3LYP methods and the structure of the molecule investigated. The double bonds of TTDD molecule are endo pyramidalized. The structure of π-orbitals and their mutual interactions for TTDD molecule were investigated. The cationic
intermediates and products obtained as a result of the addition reaction have been studied using the HF/6-311G(d), HF/6-311G(d,p)
and B3LYP/6-311G(d) methods. The bridged bromonium cation isomerized into the more stable N- and U-type cations and the difference
between the stability of these cations is small. The N- and U-type reaction products are obtained as a result of the reaction,
which takes place via the cations in question. The stability of exo, exo and exo, endo isomers of N-type product are nearly the same and the formation of both isomers is feasible. The U-type product basically
formed from the exo, exo-isomer. Although the U-type cation was 0.68 kcal mol−1 more stable than the N-type cation, the U-type product was 4.79 kcal mol−1 less stable than the N-type product.
Figure The energy diagram of TTDD–Br2 system (kcal mol−1)(MP2/6-311G*//HF/6-311G*) 相似文献
12.
Tezer N 《Journal of molecular modeling》2008,14(1):11-20
The protomeric tautomerizm and conformation of the 2-methyl-4-pyridin-2′-yl-1,5-benzodiazepine molecule were investigated,
and its three neutral tautomers (B1,B2,B3) and their rotamers (C1,C2,C3) were considered. Full geometry optimizations were carried out at the HF/6-31G* and B3LYP/6-31G* levels in gas phase and
in water. The tautomerization processes in water (ɛ = 78.54) were studied by using self-consistent reaction field theory.
The calculation showed that the boat conformation is dominant for the seven-membered diazepine ring in all of the structures,
even with different double bond positions. The calculated relative free energies (ΔG) showed that the tautomer C1 was the most stable structure, and its conformer B1 was the second most stable in the gas phase and in water.
Figure 2-Methyl-4-pyridin-2′-yl-1,5-benzodiazepine 相似文献
13.
14.
We present the results of simulations of a CCl4 monolayer adsorbed on a graphite surface. The CCl4 molecule was represented either by a shapeless superatom or by its atomic sites. The simulations were carried out over a
large range of temperatures, from 20 K up to 340 K. We address the following problems: (1) the influence of molecular shape
on the structure and stability of phases (particularly at low temperatures), and (2) the influence of the graphite corrugation
on layer stability and mechanism of phase transitions. In particular, we discuss the possibility and conditions of the appearance
of hexatic phase in the system.
Figure Temperature dependence of Φ6 order parameter for CCl4 monolayer adsorbed onsmooth and corrugated surfaces, in the spherical Lennard Jones (LJ) approximation.For comparison, the
order parameter calculated for MacDonald’s five-site potential is also presented 相似文献
15.
Ionization potential (IP), electron affinity (EA), dipole moment (μ) and electronic polarizability (α) of 1-, 3- and 6-nitrobenzo[a]pyrene isomers (1-NBaP, 3-NBaP, 6-NBaP) were determined by using density functional theory (DFT) and recent semiempirical PM6 methods. Calculated IP value remains
almost constant along the series of isomers, while EA value depends on the nitro group position, increasing by ca. 0.2 eV
on passing from 6- to 1-NBaP (or 3-NBaP) isomer. Stability, μ and α values decrease in the order 6-NBaP < 1-NBa ∼ 3-NBaP, the largest μ variation being predicted to be 1.5 D (30%) by DFT computations. The results obtained herein are consistent
with the observed greater mutagenic activity of 3- and 1-NBaP in comparison to 6-NBaP isomer, suggesting that both binding to enzyme, which depends on electric properties, and reduction process, which is related
to EA value may be crucial steps in the mutagenic mechanism of this series of isomers.
Figure Structure and dipole moment vector of nitrobenzo[a]pyrene isomers 相似文献
16.
Jacek C. Wojdeł 《Journal of molecular modeling》2009,15(6):567-572
Prussian Blue is a paradigmatic mixed valence material and a parent compound to a broad family of electronically, optically,
and magnetically active materials. Its exact composition varies greatly depending on the preparation route, leading to large
variations in its electronic properties. The influence of water molecules on the structural and electronic properties of Prussian
Blue were studied using state-of-the-art first principles calculations. Water-filled cavities were found to have a profound
influence on the band gap and density of states of this material while simultaneously leaving many of its properties largely
unchanged. The resulting model of an almost independent superimposition of dehydrated material and hydrated sites is briefly
discussed.
Unit cell of “insoluble” Prussian Blue used in calculations 相似文献
17.
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.
相似文献
18.
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
19.
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
20.
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