Modeling studies on the uptake of hydrogen molecules by graphene.

Detailed ab initio molecular orbital calculations on the interactions of molecular hydrogen, H2, with various poly-aromatic hydrocarbons (PAHs) as a model system for graphene were carried out to accurately describe the physisorption phenomenon. The binding energies corrected for the basis set superposition error, ΔEbind(BSSE), were obtained using the optimized geometries at the MP2 level with a large basis set and were compared with the single point binding energies, denoted as ΔEbind(BSSE-s), using large basis sets on the geometries optimized at the small basis sets, such as SVP and TZVP. The calculations showed that the ΔEbind(BSSE-s) values were similar to those at the MP2 level with the large basis sets. The binding strength increased gradually with increasing size of the PAHs. The ΔEbind(BSSE-s) for an infinite graphene sheet was estimated to be -1.70 kcal mol(-1) using the non-linear curve fitting method. The present work could be expected to provide more useful and reliable information on H2 physisorption.

Comprehensive studies on the tautomerization of glycine: a theoretical study.

The tautomerization process of glycine between the neutral (NE) and zwitterionic (ZW) forms in aqueous solution was explored theoretically using the conductor-like polarizable continuum model (CPCM) by adopting the PAULING cavity model at the B3LYP, MP2 and CCSD levels with the 6-311+G(d,p) basis set. The tautomerization of glycine is unable to be predicted satisfactorily within the equilibrated framework of the CPCM method. Instead, in this study, three plausible non-equilibrated solvation situations were assumed: (S-1) one water molecule attached to the transferring proton in the ZW moves together with the transferring proton; (S-2) one water molecule attached to the transferring proton in the ZW remains motionless at a fixed position near the NH(2) fragment at the TS structure; and (S-3) proton transfer occurs without changing the position of the surrounding water molecules from their initial state, the ZW form, in the eight water clusters. Although the calculation of (S-3) failed, the Gibbs free energies of activation for tautomerization from the ZW to NE, ΔG(≠)(ZW → NE), was well consistent with the experimental findings in the hypothetical non-equilibrated solvation states of (S-1) and (S-2). This suggests that non-equilibrium solvation is essential to explain the observed experimental data.

Reexamination of the π-bond strengths within H2C=XHn systems: a theoretical study.

The accurate determination of π-bond energies, D(π), in doubly-bonded species has been an important issue in theoretical chemistry. The procedure using the divalent state stabilization energy defined by Walsh has been suggested, and the procedure seems to be conceptually reasonable and applicable to all kinds of doubly-bonded species. Therefore, the aim of this study was to examine whether the procedure could be a reliable methodology for estimating the D(π) values for a variety of H(2)C=XH(n) species. To achieve a higher accuracy, the D(π) values were estimated at QCISD(T)/6-311++G(3df,2p) level of theory combined with isogyric correction. The D(π) values estimated in this work were in excellent agreement with the extant literature values. On the other hand, in determining accurate D(π) values for doubly bonded species, especially in species with lone-pair electrons such as H(2)C=O, it has been found that consideration of highly sophisticated electron correlation effects could be important. However, sufficiently accurate D(π) values have been obtainable at QCISD(T) or CCSD(T) levels with a 6-311++G(3df,2p) basis set on geometries at relatively inferior correlated levels such as MP2 and B3LYP levels with a 6-31+G(d) basis set.

Comparative studies on the reactions of acetyl and thioacetyl halides with NH3 in the gas phase and in aqueous solution: a theoretical study.

The reactions of acetyl halides, CH3C(═ O)X and corresponding sulfur analogues, thioacetyl halides, CH3C(=S)X, where X = F and Cl, with NH3 nucleophile were studied theoretically, at the QCISD level of theory, in the gas phase and in aqueous solution. All reactions occurred via the tetrahedral species, and reactions through neutral intermediates both in the gas phase and in aqueous solution could be ruled out, except for the case of the gas-phase reaction of acetyl fluoride. The tetrahedral structure was a transition state (TS) in the reactions of acetyl chloride, while it was a stable intermediate in reactions of thioacetyl halides. These differences could be caused by the π-bond strength of C ═ O and C ═ S. In the case of acetyl fluoride, the T(±)-type species was neither a saddle point nor an energy minimum in the gas phase, but existed as a stable intermediate in aqueous solution due to solvation. Moreover, in reactions of thioacetyl chloride, the rate-limiting step changed from the first step in the gas phase to the second step in aqueous solution, since the zwitterionic intermediates become more stabilized in aqueous solution. However, lower activation energies (ΔG(‡)) in aqueous solution were not caused by the solvent effects, but smaller deformation effects, in going from reactants through the TS.

Effects of basis set superposition error on optimized geometries and complexation energies of organo-alkali metal cation complexes.

Theoretical studies were performed to study the binding of alkali metal cations, X(+) (X = Li, Na, K), to poly(ethylene oxide) (PEO, I), poly(ethylene amine) (PEA, II), and poly(ethylene N-methylamine) (PEMA, III) by the Hartree-Fock (HF) and B3LYP methods using the 6-31G(d) and 6-311+G(d,p) basis sets. Two types of complex were considered in this study: a singly coordinated system (SCS) and a doubly coordinated system (DCS). Complexation energies were calculated both without and with basis set superposition error (BSSE). Because of the strong charge-dipole interactions, the complexation energies were largely negative and decreased in the order Li(+) > Na(+) > K(+). Three possible counterpoise (CP) approaches were examined in detail. In the case of the function CP (fCP) correction, the complexation energies exhibited an unusual trend because of the deformation of the subunits. This problem was solved by including geometry relaxation in the CP-corrected (GCP) interaction energies. The effects on the structures and vibrational frequencies were small when the complexes were reoptimized on the CP-corrected potential energy surface (PES).

Prediction of densities for solid energetic molecules with molecular surface electrostatic potentials.

The densities of high energetic molecules in the solid state were calculated with a simplified scheme based on molecular surface electrostatic potentials (MSEP). The MSEP scheme for density estimation, originally developed by Politzer et al., was further modified to calculate electrostatic potential on a simpler van der Waals surface. Forty-one energetic molecules containing at least one nitro group were selected from among a variety of molecular types and density values, and were used to test the suitability of the MSEP scheme for predicting the densities of solid energetic molecules. For comparison purposes, we utilized the group additivity method (GAM) incorporating the parameter sets developed by Stine (Stine-81) and by Ammon (Ammon-98 and -00). The absolute average error in densities from our MSEP scheme was 0.039 g/cc. The results based on our MSEP scheme were slightly better than the GAM results. In addition, the errors in densities generated by the MSEP scheme were almost the same for various molecule types, while those predicted by GAM were somewhat dependent upon the molecule types.

Unusual pi-donating effects of pi-accepting substituents on the stabilities of benzylic cations: a theoretical study.

The pi-donating effects of pi-accepting X-substituents in substituted benzylic cations, X-C(6)H(5)-CHR(+) where R = CF(3), H and OCH(3), and X = p-NH(2), p-OCH(3), p-CH(3), H, p-F, p-Cl, p-CHO, m-CN, p-CN, m-NO(2) or p-NO(2), have been studied theoretically by using isodesmic hydride transfer reactions at various levels of theory. It might be difficult to determine the pi-donating effects of pi-acceptors using the simple Hammett-type linear equation, because it is not sensitive enough to include small pi-donating effects. Therefore, this effect was estimated using the NBO deletion energy (DeltaE(D)) of the second-order charge-transfer interaction (DeltaE(ct)) between the pi-orbitals (or lone pair orbitals) of the X-substituent and the pi-orbitals of phenyl ring. The extents of pi-donating effects increased in the order X = p-NO(2) < p-CHO < p-CN << p-Cl for both neutral and cationic species, and these effects were found to be more important for para- than for meta-substituents. Moreover, this could represent a general trend for pi-donation by pi-acceptors. On the other hand, the effects of R-substituents on this pi-donating effect were found to be in the order R = OCH(3) < H congruent with CF(3), as predicted by natural resonance theory (NRT) analyses.

DFT-PCM studies of solvent effects on the cross-interaction constants in benzhydryl cation and anion formation.

The Hammett rho+ and rho- values have been determined by varying substituent Y' for a given Y in the benzhydryl cation and anion formation (YH4C6-CH-C6H4Y' where C is a cationic or an anionic center) at the RHF/3-21G, RHF/6-31G, RHF/6-31+G, and B3LYP/6-31+G levels. The failure of RHF theory in accounting for the stabilization by delocalization leads to the smaller magnitudes of rho+ and rho- with electron-donating and -withdrawing substituents, Y, respectively, than the corresponding DFT values. The effects of solvent (benzene, dichloroethane, and acetonitrile) on the rho values were calculated by applying the conductor polarizable continuum model method to the DFT results. Finally, the cross-interaction constants (rho(YY)') and their variation with solvent were determined. As the polarity (dielectric constant, epsilon) of the solvent is increased, the magnitude of rho+ and rho- decreased, whereas that of rho(YY)' increased. Satisfactory correlations were obtained between rho values (rho+, rho- and rho(YY)') and the Kirkwood function f(k) (= epsilon - 1/2epsilon + 1). The rho(YY)' values are negative with a magnitude greater for the anionic (rho(YY)'-) than the cationic (rho(YY)'+) system.

Prediction of physicochemical properties of organic molecules using van der Waals surface electrostatic potentials.

The generalized interaction properties function (GIPF) methodology developed by Politzer and coworkers, which calculated molecular surface electrostatic potential (MSESP) on a density envelope surface, was modified by calculating the MSESP on a much simpler van der Waals (vdW) surface of a molecule. In this work, vdW molecular surfaces were obtained from the fully optimized structures confirmed by frequency calculations at B3LYP/6-31G(d) level of theory. Multiple linear regressions for normal boiling point, heats of vaporization, heats of sublimation, heats of fusion, liquid density, and solid density were performed using GIPF variables from vdW model surface. Results from our model are compared with those from Politzer and coworkers. The surface-dependent beta (and gamma) values are dependent on the surface models but the surface-independent alpha and regression coefficients (r) are constant when vdW surface and density surface with 0.001 a.u. contour value are compared. This interesting phenomenon is explained by linear dependencies of GIPF variables.

Transition-state variation in the nucleophilic substitution reactions of aryl bis(4-methoxyphenyl) phosphates with pyridines in acetonitrile.

The kinetics and mechanism of the reactions of Z-aryl bis(4-methoxyphenyl) phosphates, (4-MeOC(6)H(4)O)(2)P(=O)OC(6)H(4)Z, with pyridines (XC(5)H(4)N) are investigated in acetonitrile at 55.0 degrees C. In the case of more basic phenolate leaving groups (Z = 4-Cl, 3-CN), the magnitudes of beta(X) (beta(nuc)) and beta(Z) (beta(lg)) indicate that mechanism changes from a concerted process (beta(X) = 0.22-0.36, beta(Z) = -0.42 to -0.56) for the weakly basic pyridines (X = 3-Cl, 4-CN) to a stepwise process with rate-limiting formation of a trigonal bipyramidal pentacoordinate (TBP-5C) intermediate (beta(X) = 0.09-0.14, beta(Z) = -0.08 to -0.28) for the more basic pyridines (X = 4-NH(2), 3-CH(3)). This proposal is supported by a large negative cross-interaction constant (rho(XZ) = -1.98) for the former and a positive rho(XZ) (+0.97) for the latter processes. In the case of less basic phenolate leaving groups (Z = 3-CN, 4-NO(2)), the unusually small magnitude of beta(Z) values is indicative of a direct backside attack TBP-5C TS in which the two apical sites are occupied by the nucleophile and leaving group, ap(NX)-ap(LZ). The instability of the putative TBP-5C intermediate leading to a concerted displacement is considered to result from relatively strong proximate charge transfer interactions between the pi-lone pairs on the directly bonded equatorial oxygen atoms and the apical bond (n(O)(eq) - sigma(ap)). These are supported by the results of natural bond orbital (NBO) analyses at the NBO-HF/6-311+G//B3LYP/6-311+G level of theory.

Gas-phase identity nucleophilic substitution reactions of cyclopropenyl halides.

The gas-phase identity nucleophilic substitution reactions of halide anions (X = F, Cl, and Br) with cyclopropenyl halides, X(-) + (CH)(3)X <= => X(CH)(3) + X(-), are investigated theoretically at four levels of theory, B3LYP/6-311+G**, MP2/6-311+G**, G2(+)MP2//MP2/6-311+G**, and G2(+)//MP2/6-311+G**. Four types of reaction paths, the sigma-attack S(N)2, pi-attack S(N)2'-syn, and S(N)2'-anti and sigmatropic 1,2-shift, are possible for all the halides. In the fluoride anion reactions, two types of stable adducts, syn- and anti-1,2-difluorocyclopropyl anions, can exist on the triple-well-type potential energy surface of the identity substitution reactions with rearrangement of double bond (C=C), S(N)2'-syn, and S(N)2'-anti processes. The TSs for the sigma-attack S(N)2 paths have "open" (loose) structures so that the ring positive charges are high rendering strong aromatic cyclopropenyl (delocalized) cation-like character. In contrast, in the pi-attack S(N)2' paths, a lone pair is formed at the unsubstituted carbon (C3), which stabilizes the 1,2-dihalocyclopropyl (delocalized) anion-like TS by two strong n(C)-sigma*(C-F) vicinal charge-transfer delocalization interactions. The barrier height increases in the order S(N)2'-anti < sigma-attack S(N)2 < S(N)2'-syn for X = Cl and Br, whereas for X = F the order is changed to S(N)2'-anti < S(N)2'-syn < sigma-attack S(N)2 due to the stable difluoro adduct formation. The sigmatropic 1,2-shift (circumambulatory) reactions have high activation barriers and cannot interfere with the substitution reactions.