Conformational flexibility of pyrimidine rings of nucleic acid bases in polar environment: PCM study

The results of calculations of molecular structures of nucleic acid bases in polar environment using Polarized Continuum Model of solvent combined with the MP2/cc-pvdz level of ab initio theory demonstrate considerable polarization of thymine, cytosine, and guanine. This phenomenon can be related to considerable contribution of zwitter-ionic resonant forms into total structure of the studied species. It leads to significant increase (about 30%) of frequencies of the out-of-plane pyrimidine ring vibrations and is related to considerable decrease of conformational flexibility of heterocycle due to smaller out-of-plane deformability of pyrimidine ring in zwitter-ionic resonant forms. In the case of adenine, the presence of a polar environment results in an increase of conformational flexibility of pyrimidine ring.     

Novel type of mixed O–H···N/O–H···π hydrogen bonds: monohydrate of pyridine

Investigation of characteristics of hydrogen bonding between pyridine and water by MP2/aug-cc-pvdz method reveals that these two molecules may form three types of hydrogen bonds depending on nature of proton withdrawal site of pyridine. Change of orientation of water with respect to plane of aromatic ring leads to transformation of the O–H···N bond to O–H···π bond via wide region of the potential energy surface where both lone pair of the nitrogen atom and π-system make significant contribution into hydrogen bonding. Hydrogen bond in this intermediate region may be considered as mixed O–H···N/O–H···π bond representing new type of H bonds.     

Influence of microhydration on the ionization energy thresholds of thymine: comparisons of theoretical calculations with experimental values

In the present study the ionization energy thresholds (IETs) of thymine, and thymine keto-enol tautomers, have been calculated (with the B3LYP, and P3 levels of theory using the standard 6-31++G(d,p) basis set) with 1-3 water molecules placed in the first hydration shell. Calculations show there is a distinct effect of microhydration on the IET of thymine. The first water molecule is seen to decrease the IET by about 0.1 eV, whereas the second and third water molecules cause a further decrease of less than 0.1 eV each. The changes in IET calculated here for thymine with 1-3 waters of hydration are smaller than the experimental values determined by Kim et al. (J. Phys. Chem. 1996, 100, 7933). Therefore calculations have been performed on the microhydrated keto-enol tautomers of thymine. The calculated results on the keto-enol tautomers are seen to be in better agreement with the experimental results. However, the keto-enol thymine tautomers are considerably higher in energy than the canonical form of thymine, and there is presently no good evidence that these thymine tautomers are actually present in a supersonic jet-cooled experiment.     

Near-UV resonant two-photon ionization spectroscopy of gas phase guanine: evidence for the observation of three rare tautomers

In light of a recently published study on the IR spectroscopy of guanine in He droplets (Choi, M. Y.; Miller, R. E. J. Am. Chem. Soc. 2006, 128, 7320), the present letter proposes a new interpretation of the resonant two-photon ionization (R2PI) experiments on gas phase guanine, which is supported by quantum chemistry calculations. Whereas He droplet experiments detect the most stable forms, only one of these forms is observed (very marginally) in the R2PI spectrum, which is actually dominated by three less stable "rare" tautomers, whose stabilities lie in the 3-7 kcal/mol range. The absence of the most stable forms in the R2PI spectrum suggests that a tautomer-dependent ultrafast relaxation process takes place in the excited state of these stable tautomers. The present reinterpretation modifies qualitatively the picture of the excited state of guanine tautomers and should contribute to the understanding of the deactivation mechanisms taking place in the excited state of DNA bases.     

Maps of several variables of finite total variation. II. E. Helly-type pointwise selection principles

Given a=(a₁,…,an), b=(b₁,…,bn)∈Rn with a<b componentwise and a map f from the rectangle into a metric semigroup M=(M,d,+), denote by the Hildebrandt-Leonov total variation of f on , which has been recently studied in [V.V. Chistyakov, Yu.V. Tretyachenko, Maps of several variables of finite total variation. I, J. Math. Anal. Appl. (2010), submitted for publication]. The following Helly-type pointwise selection principle is proved: If a sequence{fj}_j∈Nof maps frominto M is such that the closure in M of the set{fj(x)}_j∈Nis compact for eachandis finite, then there exists a subsequence of{fj}_j∈N, which converges pointwise onto a map f such that. A variant of this result is established concerning the weak pointwise convergence when values of maps lie in a reflexive Banach space (M,‖⋅‖) with separable dual M^∗.     

On positive commutators

Let A and B be positive operators on a Banach lattice such that the commutator C = AB − BA is also positive. We study the size of the spectrum of C.     

Hydrogen bonding in dimers of tritolyl and tritosylurea derivatives of triphenylmethanes

The crystal structure of the homodimer formed by the tritolylurea 3a proves the existence of a belt of six bifurcated hydrogen bonds between both NH and the O=C groups of the adjacent urea residues. For the tritosylurea 3b, four additional three-center hydrogen bonds, also involving the SO2 oxygen, are found in the crystalline state. Molecular dynamics simulations in a chloroform box confirm these patterns of the hydrogen bonds and the resulting elongation of the dimer 3b. 3b in comparison to 3a x 3a. The calculated complexation energies for the three dimeric combinations are nearly identical in agreement with the simultaneous formation of heterodimer 3a x 3b in a mixture of 3a and 3b.     

Double-proton transfer in adenine-thymine and guanine-cytosine base pairs. A post-Hartree-Fock ab initio study

The results of a comprehensive study on the double-proton transfer in Adenine-Thymine (AT) and Guanine-Cytosine (GC) base pairs at room temperature in gas phase and with the inclusion of environmental effects are obtained. The double-proton-transfer process has been investigated in the AT and GC base pairs at the B3LYP/6-31G(d) and MP2/6-31G(d) levels of theory. It has been predicted that the hydrogen-bonded bases possess nonplanar geometries due to sp3 hybridization of nitrogen atoms and because of the soft intermolecular vibrations in the molecular complexes. An analysis of the energetic parameters of the local minima suggests that rare AT base pair conformation is not populated due to the shallowness of this minimum, which completely disappears from the Gibbs free energy surface. The stabilization of canonic or rare forms of the DNA bases by water molecules and metal cations has been predicted by calculating the optimal configuration of charges (using differential product/transition state stabilization approach) followed by calculations of the interactions between the base pair and a water/sodium cation.     

Chlorination of 4-methyl-8-methoxy-2,3-dihydro-1H,1,5-benzodiazepin-2-one

The results of the chlorination of 4-methyl-8-methoxy-2,3-dihydro-1H,1,5-benzodiazepin-2-ones are compared with the results of quantum-chemical calculations of 4-methyl-2,3-dihydro-1H-1,5-benzodiazepin-2-ones with various substituents in the benzene ring in the case of homolytic halogenation. The chlorination of 4-methyl-8-methoxy-2,3-dihydro-1H-1,5-benzodiazepin-2-one (I) with N-chlorosuccinimide leads to 3-chloro- and 3,3-dichloro-4-methyl-8-methoxy-2,3-dihydro-1H-1,5-benzodiazepin-2-ones, whereas chlorination with sulfuryl chloride leads to 4-chloromethyl and 3,3-dichloro-4-methyl derivatives. The IR, PMR, and mass spectra of the synthesized compounds are presented.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 9, pp. 1272–1274, September, 1981.