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
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
Effects of explicit consideration of charges displaced from atomic sites due to atomic orbital hybridization called hybridization-displaced
charges (HDC) on dipole moments and surface molecular electrostatic potentials of certain radicals and their complexes with
closed-shell molecules have been studied. HDC were computed for several radicals and their complexes at the B3LYP/6–31G**
level of theory. At this level, HDC consist of three point charges associated with hydrogen atoms and seven point charges
associated with heavy atoms belonging to the second row of the periodic table. HDC are so calculated that the contribution
of each atom to the component of molecular dipole moment arising due to atomic orbital hybridization is preserved. It is found
that dipole moments and electrostatic potentials of the systems studied here can be obtained with a significantly improved
accuracy using a combination of Mulliken charges and HDC over that obtained by Mulliken charges only.
Figure Surface MEP map of H2O-HO· radical complex obtained using Mulliken charges combined with HDC 相似文献
Quantum chemical (Hartree-Fock) calculations were performed on neutral and protonated saxitoxin in order to obtain optimum
geometries, rotational energy barriers for the guanidinium ions and proton affinities. For comparison purposes, as model compounds,
guanidinium systems in five and six membered rings were also investigated. In addition, DFT (B3LYP) calculations with the
6-31G** basis set were performed and the sodium affinities of the guanidinium groups in saxitoxin were obtained. It was concluded
that the inhibition of the sodium channels by the saxitoxin is due to the interaction of the guanidinium group with carboxylate
groups from the wall of the channel and not to the binding of the sodium ions.
Figure Calculated structure of Compound 1, neutral saxitoxin.
a Calculated structure of Compound 1a, saxitoxin protonated on the guanidine of the five-membered ring.
b Calculated structure of Compound 1b, saxitoxin protonated on the guanidine of the six-membered ring 相似文献
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
Schiff bases have many chemical and biological applications in medicine and pharmaceuticals due to the presence of an imine group (?C=N?). These bases are used in many different fields of technology, and in photochemistry because of their photochromic properties. Here, the structural and electronic properties of the Schiff base formed by tacrine and saccharin (TacSac) were explored using density functional theory with the B3LYP, M06-2X, M06L, and ωB97XD functionals in combination with the 6-311++G(d,p) basis set. The time-dependent formalism was used at the B3LYP/6-311++G(d,p) level to obtain electronic transitions. The calculations were repeated in an implicit solvent model mimicking water, using the polarizable continuum model in conjunction with a solvation model based on a density approach. The results indicate that TacSac cannot form spontaneously, but can be obtained in mild reactions. However, the resulting Schiff base displays different characteristics to its monomers. It also has the potential for use in photochemical intramolecular charge-transfer systems.
Quantum chemical calculations at the B3LYP/6-31G* level of theory have been carried out on 20 celastroid triterpenoids to
obtain a set of molecular electronic properties and to correlate these with cytotoxic activities. The cytotoxic activities
of these compounds can be roughly correlated with electronic effects related to nucleophilic addition to C(6) of the compounds:
The energies of the frontier molecular orbitals (EHOMO and ELUMO), the HOMO-LUMO energy gap, the dipole moment, the charge on C(6), and the electrophilicity on C(6).
Figure LUMO of Pristimerin. 相似文献
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
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
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
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.
相似文献
The mechanism of the spontaneous initiation of the polymerization of methyl methacrylate (MMA) was investigated theoretically.
The six minimum energy paths (MEP) of the possible reactions were calculated using the density functional theory (DFT) in
conjunction with the B3LYP functional and 6-31G* basis set. The Diels-Alder initiation mechanism (path (I) and path (II))
with remarkably high energy barriers is not applicable to MMA. Four favorable paths were found (path (III), path (IV), path
(V) and path (VI)), which are supporting the Flory mechanism. Path (V) has the lowest active energy. Therefore this path is
considered as the main path for the spontaneous polymerization of MMA.
Figure The mechanism of the spontaneous initiation of the polymerization of methyl methacrylate (MMA) was investigated theoretically.
The six minimum energy paths (MEP) of the possible reactions were calculated using the density functional theory (DFT) in
conjunction with the B3LYP functional and 6-31G* basis set. 相似文献
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
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
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
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
The molecular geometries, normal mode frequencies, intensities and corresponding infrared assignments of monomeric and dimeric
2,3-dimethylpyridine, 2,4-dimethylpyridine, 3,4-dimethylpyridine, 3,5-dimethylpyridine and monomeric 2,6-dimethylpyridine
in the ground state were investigated at the density functional theory (DFT)-B3LYP level using the 6-311+G(d, p) basis set.
The vibrational frequencies and geometric parameters of C–H stretching and bending in the fundamental region were calculated
and compared to the Fourier transform infrared (FT-IR) data obtained. In the studied monomeric and dimeric dimethyl substituted
pyridine derivatives, the C–H stretching and bending frequency shifts that occur between the dimer and the monomer may be
diagnostic of the magnitude of dimerization energy. As supported by data in the literature, the most stable dimeric form was
obtained for the 3,4-dimethylpyridine molecule.
Figure Molecular model and numbering scheme of the studied dimeric dimethylpyridinederivatives 相似文献
The structural and electronic properties of a three-state molecular switch—an active device in a nano-electronic circuit—were
studied using the B3LYP/6-31G* method. Due to its chemical stability, high conductivity upon doping, and non-linear optical
properties, polythiophene is among the most widely studied conjugated organic polymers, both experimentally and theoretically.
The aim of the present work was to theoretically study a very complex case: a three-state switch synthesized and experimentally
investigated by Nishida et al. (Org Lett 6:2523–2526, 2004). An initial set of test calculations showed B3LYP level of theory
and 6-31G* basis set to be the most appropriate for our purpose, i.e., the study of the structure, charge and spin distributions,
as well as electrical characteristics such as electric polarizability, HOMO-LUMO gap (HLG) and electric dipole moment, for
one of the 1,2-dithienylcyclopentene derivatives. Also, natural bond orbital analyses were performed to calculate local charges
and charge transfers in order to study the capability of the molecule as a molecular switch. The results reported here are
of general significance, and demonstrate that it is possible to use certain structural and electrical properties to understand
and design electro-photochromic compounds showing a switching function in cases where stable forms can be exchanged by light
or electron transfer.
Figure Model of a thiophene wire incorporating a redox active unit 相似文献
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