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Planar H-bonded and stacked structures of guanine…cytosine (G…C), adeine…thymine (A…T), 9-methylguanine…1 -methylcytosine (mG…mC), and 9-methyladenine… 1 -methylthymine (mA…mT) were optimized at the Rl-MP2 level using the TZVPP ([5s3p2dlf/3s2pld]) basis set. Planar H-bonded structures of G…C, mG…mC, and A…T correspond to the Watson-Crick (WC) arrangement, in contrast to mA…mT for which the Hoogsteen (H) structure is found. Stabilization energies for all structures were determined as the sum of the complete basis set limit of MP2 energies and a (δE[supCC8D](T) - δ;E[supmp2]) correction term evaluated with the cc-pVDZ(0.25,0.15) basis set. The complete basis set limit of MP2 energies was determined by two-point extrapolation using the aug-cc-pVXZ basis sets for X = D and T and X = I and Q. This procedure is required since the convergency of the MP2 interaction energy for the present complexes is rather slow, and it is thus important to include the extrapolation to the complete basis set limit. For the MP2/aug-cc-pVQZ level of theory, stabilization energies for all complexes studied are already very close to the complete basis set limit. The much cheaper D→T extrapolation provided a complete basis set limit close (by less than 0.7 kcal/mol) to the more accurate T→Q term, and the D→T extrapolation can be recommended for evaluation of complete basis set limits of more extended complexes (e.g. larger motifs of DNA). The convergency of the (δE[CCSD(T)]-δ[supmp2]) term is known to be faster than that of the MP2 or CCSD(T) correlation energy itself, and the cc-pVDZ(0.25,O.15) basis set provides reasonable values for planar H-bonded as well as stacked structures. [ABSTRACT FROM AUTHOR]

We present a combined experimental and theoretical quantification of the adsorption enthalpies of seven organic molecules (acetone, acetonitrile, dichloromethane, ethanol, ethyl acetate, hexane, and toluene) on graphene. Adsorption enthalpies were measured by inverse gas chromatography and ranged from -5.9 kcal/mol for dichloromethane to -13.5 kcal/mol for toluene. The strength of interaction between graphene and the organic molecules was estimated by density functional theory (PBE, B97D, M06-2X, and optB88-vdW), wave function theory (MP2, SCS(MI)-MP2, MP2.5, MP2.X, and CCSD(T)), and empirical calculations (OPLS-AA) using two graphene models: coronene and infinite graphene. Symmetry-adapted perturbation theory calculations indicated that the interactions were governed by London dispersive forces (amounting to 60% of attractive interactions), even for the polar molecules. The results also showed that the adsorption enthalpies were largely controlled by the interaction energy. Adsorption enthalpies obtained from ab initio molecular dynamics employing non-local optB88-vdW functional were in excellent agreement with the experimental data, indicating that the functional can cover physical phenomena behind adsorption of organic molecules on graphene sufficiently well. [ABSTRACT FROM AUTHOR]

The complexation behavior of the distally substituted phosphonic acid and phosphonic ester 4-tert-butylcalix[4]arenes (hosts) with 1-chloro-4-(trifluoromethyl)benzene (guest) was examined in chloroform. The complex stability constants (Ks) and the thermodynamic parameters of the complexation were determined by a spectrofluorometric method using Job''s method and van''t Hoff theory, respectively. A strong dependence of the host–guest interaction on the extent of distortion in the conformation of calixarene host cavity was obtained. The ‘pinched cone’ conformer of 1,3-substituted calix[4]arenes seems to form a complex with electron-deficient neutral aromatics predominantly through π–π type interaction. [Copyright &y& Elsevier]

A systematic spectroscopic and computational study was conducted in order to probe the influence of base sequences on stacked (S) versus B-type (B) conformational heterogeneity induced by the major dG adduct derived from the model carcinogen 7-fluoro-2-aminofluorene (FAF). We prepared and characterized eight 12-mer DNA duplexes (-AG*N- series, d[CTTCTAG*NCCTC]; -CG*N- series, d[CTTCTCG*NCCTC]), in which the central guanines (G*) were site-specifically modified with FAF with varying flanking bases (N = G, A, C, T). S/B heterogeneity was examined by CD, UV, and dynamic 19F NMR spectroscopy. All the modified duplexes studied followed a typical dynamic exchange between the S and B conformers in a sequence dependent manner. Specifically, purine bases at the 3'-flanking site promoted the S conformation (G > A > C > T). Simulation analysis showed that the S/B energy barriers were in the 14-16 kcal/mol range. The correlation times (τ = I/K) were found to be in the millisecond range at 20 °C. The van der Waals energy force field calculations indicated the importance of the stacking interaction between the carcinogen and neighboring base pairs. Quantum mechanics calculations showed the existence of correlations between the total interaction energies (including electrostatic and solvation effects) and the S/B population ratios. The S/B equilibrium seems to modulate the efficiency of Escherichia coli UvrABC-based nucleotide excision repair in a conformation-specific manner: i.e., greater repair susceptibility for the S over B conformation and for the -AG*N- over the -CG*N- series. The results indicate a novel structure-function relationship, which provides insights into how bulky DNA adducts are accommodated by UvrABC proteins. [ABSTRACT FROM AUTHOR]