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1.
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
2.
As a follow-up study to our study on tetrazane (N4H6), we present computed thermodynamic properties of triazane (N3H5). Calculated properties include optimized geometries, infrared vibrations, enthalpy of formation, enthalpy of combustion,
and proton affinities. We have also mapped the potential energy surface as the molecule is rotated about the N-N bond. We
have predicted a specific enthalpy of combustion for triazane of about -20 kJ g−1.
Figure Schematic diagram of the dielectric barrier discharge (left) and typical temporal profiles of voltage and current, as obtained
from the simulations (right) 相似文献
3.
Twelve H-bonded supersystems constructed between the adenine tautomers and methanol, ethanol, and i-propanol were studied
at the B3LYP and MP2 levels of theory using 6-311G(d,p) and 6-311++G(d,p) basis functions. The thermodynamic parameters of
the complex formations were calculated in order to estimate the exact stability of the supersystems. It was proven that the
calculated energy barriers of the alcohol-assisted proton transfers are about 60% lower than those of the intramolecular proton
transfers in adenine found earlier (Gu and Leszczynski in J Phys Chem A 103:2744–2750, 1999).
Figure H-bonded complex between i-propanol and adenine 相似文献
4.
Realistic molecular models of one and two-centre catalytic active sites originating from the cleavage of a precursor material
known to give rise to an active double metal cyanide catalyst are described. Via periodic density functional calculations
the structure of the proposed catalytic sites are shown to be dependent on electrostatic and structural relaxation processes
occurring at the surfaces of the precursor material. It is shown how these effects may be adequately captured by small molecular
models of the active sites. The general methodology proposed should provide a computationally efficient basis for detailed
future studies into catalytic reactions over double metal cyanide materials.
Figure Reconstructed DMC [100]-surface: electrostatic potential mapped on charge density isosurface
This work has been originally presented on the Modelling and Design of Molecular Materials conference in Wrocław, Poland. 相似文献
5.
Following our recent study on triazane, we present a follow-up study on the thermodynamic properties of triazane’s unsaturated
analog, triazene. We predict optimized structural parameters, vibrational frequencies, enthalpies of formation, enthalpies
of combustion, specific enthalpies of combustion, and proton affinities. Our results indicate that the cis form of triazene
has a specific enthalpy of combustion of −15.2 kJ g−1 and the trans form has a specific enthalpy of combustion of −14.7 kJ g−1.
Figure Structures of cis- and trans-triazane, N3H3 相似文献
6.
Machado E Kaczmarski M Braida B Ordejón P Garg D Norman J Cheng H 《Journal of molecular modeling》2007,13(6-7):861-864
Processes for the deposition of copper films on transition metal barrier layers by means CVD using organometallic precursors
are often found to lead to poor adhesion characteristics of the grown film. By means of first-principles molecular dynamics
simulations, we show that the source of the problem is the strong reactivity of the surfaces toward the precursors, which
decompose spontaneously upon contact with the surface leading to contamination of the interface. Our simulations consider
Ti, Ta, and W as barrier layers, and Cu(hfac)-(tmvs) as precursor. In contrast, we show that surfaces of these metals properly
passivated with nitrogen, in such a way that only N atoms are exposed on the surface, are much less active and do not lead
to decomposition of the precursor. We propose this passivation procedure as a practical solution to the adhesion problem.
Figure CupraSelect on the WN (100) surface 相似文献
7.
Salcedo R 《Journal of molecular modeling》2007,13(9):1027-1031
A global electrophilicity parameter and the aromaticity of some heterocyclic polyaromatic hydrocarbons were evaluated on the
basis of DFT calculations. The substitution of carbon atoms by nitrogen atoms dramatically changes the global electrophilicity
of the molecules, with the fully substituted molecule being the most electrophilic with a reactivity very close to that of
fullerene.
Figure Fully substituted heterohexabenzocoronene
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
8.
Richard A. J. O’Hair Craig M. Williams Timothy Clark 《Journal of molecular modeling》2010,16(3):559-565
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
9.
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
10.
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
11.
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
12.
The tautomerization mechanism the isolated and monohydrated forms of two Schiff bases 1 and 2, and the effect of solvation
on the proton transfer from enol-imine form to the keto-enamine form have been investigated using the B3LYP hybrid density
functional method at the 6-31G** basis set level. The barrier heights for H2O-assisted reactions are significantly lower than that of unassisted tautomerization reaction in the gas phase. Nonspecific
solvent effects have also been taken into account by using the continuum model (IPCM) of four different solvent. The tautomerization
energies and the potential energy barriers are decreased by increasing solvent polarity.
Figure The tautomerization mechanism the isolated and monohydrated forms of two Schiff bases 1 and 2, and the effect of solvation
on the proton transfer from enol-imine form to the keto-enamine form have been investigated using the B3LYP hybrid density
functional method at the 6-31G** basis set level 相似文献
13.
On the basis of the experimental Gibbs free-energy barrier of the degenerate Cope arrangement in semibullvalene, B3P86 shows the best agreement, while B3LYP and MP2 underestimate and CCSD(T) overestimates the barrier. The substituent effect proposal by Hoffmann has been verified. In contrast to semibullvalenes with either localized energy-minimum structures or delocalized transition-state structures, perfluorosemibullvalene has both localized and delocalized energy-minimum structures that are very close in energy.
Localized and delocalized perfluorosemibullvalenes
Electronic supplementary material Supplementary material is available for this article at and is accessible for authorized users. 相似文献
14.
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
15.
A 3D-QSAR analysis has been carried out by comparative molecular field analysis (CoMFA) on a series of distamycin analogs
that bind to the DNA of drug-resistant bacterial strains MRSA, PRSP and VSEF. The structures of the molecules were derived
from the X-ray structure of distamycin bound to DNA and were aligned using the Database alignment method in Sybyl. Statistically significant CoMFA models for each activity were generated. The CoMFA contours throw light on the structure
activity relationship (SAR) and help to identify novel features that can be incorporated into the distamycin framework to
improve the activity. Common contours have been gleaned from the three models to construct a unified model that explains the
steric and electrostatic requirements for antimicrobial activity against the three resistant strains.
Figure A unified CoMFA model for broad-spectrum DNA minor-groove binders 相似文献
16.
Twelve binary and eight ternary supersystems between thymine and methanol, and water were investigated in the ground state
at the B3LYP and MP2 levels of theory using B3LYP/6-311 + + G(d,p) basis functions. The thermodynamics of complex formations
and the mechanisms of intermolecular proton transfers were clarified in order to find out the most stable H-boned system.
It was established that the energy barriers of the water/methanol-assisted proton transfers are several times lower than those
of the intramolecular proton transfers in the DNA/RNA bases. The X-ray powder spectra of thymine, and this precrystallized
from water and methanol showed that water molecules are incorporated in the crystal lattice of thymine forming H-bridges between
thymine molecules.
Figure Intermolecular H-bonding of thymine 相似文献
17.
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
18.
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
19.
Fifteen KSP inhibitors were docked into the receptor and the binding mode was analyzed for the first time. It was considered
that in addition to the main binding pocket all the inhibitors merged in, there exists a cooperative minor binding pocket,
which could be explored for significantly increased binding affinity. In addition, a good linear relationship between the
biological activities and the lowest binding free energies has also been found. This may help in predicting the binding affinity
of newly designed KSP inhibitors.
Figure Two binding pockets considered after the analysis. Seven docked ligands (compound 1–7) were overlapped at the binding site.
All inhibitors tested interacted with the main pocket, while CK0106023, interacted also with the cooperative minor pocket
mainly surrounded by Arg221 and Ala218. Coloring of the binding site surface are different ends of each amino acid residue:
blue represents amino group while red means carboxyl 相似文献
20.
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