Accuracy of intermolecular interaction energies, particularly those of hetero-atom containing molecules obtained by DFT calculations with Grimme's D2, D3 and D3BJ dispersion corrections.

Intermolecular interaction potentials for benzene, propane, perfluoromethane, furan, thiophene, selenophene, pyridine, phosphorine dimers and benzene-methane, benzene-chlorobenzene, benzene-bromobenzene complexes were calculated using the BLYP, B97 (B98), BP86, BPBE, PBE, PW91, B3LYP, B3PW91, BMK, PBE1PBE, APF, ωB97 (ωB97X), CAM-B3LYP, LC-ωPBE, B2PLYP, mPW2PLYP, TPSS, M06L, M05, M052X, M06, M062X and M06HF functionals with Grimme's dispersion correction methods of D2, D3 and D3BJ versions. The calculated potentials were compared with the CCSD(T) level potentials to evaluate the accuracy of the dispersion corrected DFT methods for calculating the intermolecular interaction energies of hydrocarbon molecules and molecules including heteroatoms (N, P, O, S, Se, F, Cl and Br). The performance of the calculations depends strongly on the choice of the functional and the dispersion correction method. None of the combinations of the functionals and the dispersion correction methods can reproduce well the CCSD(T) level interaction potentials of all the complexes. The improvement of the functionals from GGA to hybrid GGA, meta GGA or meta hybrid GGA is not essential for improving the performance. The significant functional dependence suggests that the scaling factors, which were determined for each functional by fitting, are the cause of the dependence. The performance of the calculations of hydrocarbon molecules is much better than that of the molecules including heteroatoms. A smaller number of molecules including heteroatoms were used for the reference data of the fitting compared with hydrocarbon molecules, which might be one of the causes of the worse performance of the calculations of molecules including heteroatoms.

Thermal stabilities and conformational behaviors of isocyanurates and cyclotrimerization energies of isocyanates: a computational study.

Isocyanurates are cyclic trimers of isocyanate molecules. They are generally known as highly thermostable compounds. However, it is interesting how the thermal stabilities of the isocyanurate molecules will be altered depending on the substituents of their three nitrogen atoms. We performed computational investigations on the thermochemical behaviors of isocyanurate molecules with various alkyl and phenyl substituents. The cyclotrimerization processes of isocyanates are highly exothermic. Our best estimate of the enthalpy change for the cyclotrimerization of methyl isocyanate into trimethyl isocyanurate was -66.4 kcal mol-1. Additional negative cyclotrimerization enthalpy changes were observed for n-alkyl-substituted isocyanates. This trend was enhanced with an extension of n-alkyl chains. Conversely, low negative cyclotrimerization enthalpy changes were shown for secondary and tertiary alkyl-substituted isocyanates. The n-alkyl-substituted isocyanurates were shown to be stabilized due to attractive dispersion interactions between the substituents. Meanwhile, the branched alkyl-substituted isocyanurates were destabilized due to the deformation of their isocyanurate rings. For various alkyl-substituted isocyanates, the sum of the deformation energy of the isocyanurate ring and the intramolecular inter-substituent nonbonding interaction energies was found to be linearly correlated with their cyclotrimerization energies. The cyclotrimerization energy for phenyl isocyanate was shown to have significantly deviated from the linear relationship observed for the alkyl-substituted isocyanurates. This is probably attributable to a remarkable change in the orbital resonance interactions during the cyclotrimerization of phenyl isocyanate to triphenyl isocyanurate.

Rate Constants for the Reactions of OH Radicals with the ( E)/( Z) Isomers of CFCl=CFCl and ( E)-CHF=CHF.

The rate constants for the OH radical reactions with halogenated ethenes were investigated experimentally and computationally. The rate constants for the reactions of OH radicals with ( E)-CFCl=CFCl ( k1), ( Z)-CFCl=CFCl ( k2), and ( E)-CHF=CHF ( k3) were measured using flash and laser photolysis methods. The temporal profile of the OH radical was monitored by a laser-induced fluorescence technique. Kinetic measurements were carried out over the temperature range of 250-430 K. Arrhenius rate constants were determined to be k1 = (1.67 ± 0.06) × 10-12·exp[(140 ± 10) K/ T], k2 = (1.75 ± 0.04) × 10-12·exp[(140 ± 10) K/ T], and k3 = (3.99 ± 0.15) × 10-12·exp[(260 ± 10) K/ T] cm3 molecule-1 s-1. The quoted uncertainties are 95% confidence levels and do not include systematic errors. Infrared absorption spectra were measured at room temperature. The atmospheric lifetimes and the global warming potentials of ( E)-CFCl=CFCl, ( Z)-CFCl=CFCl, and ( E)-CHF=CHF were estimated to be 4.3, 4.2, and 1.2 days and 0.035, 0.036, and 0.0056, respectively. The ozone depletion potentials of ( E)-CFCl=CFCl and ( Z)-CFCl=CFCl were determined to be 0.00011 and 0.00010, respectively. The photochemical ozone creation potentials of the halogenated ethenes were less than 1/4 that of ethene. In addition, the ( E)/( Z) differences in the energy and IR spectra of the CFCl=CFCl and CHF=CHF molecules were computationally examined. The reactivities of these halogenated ethenes toward OH radicals were investigated through the combination of DFT and ab initio computations. The rate constants calculated for the OH radical reactions of these halogenated ethenes showed reasonable agreement with the experimentally determined values. Our computational results for the CFCl=CFCl and CHF=CHF ( E)/( Z) isomeric pairs indicated that the rate constants toward OH radicals are larger for the higher-energy geometrical isomers than for the lower-energy counterparts.

Rate Constants for the Reactions of OH Radical with the ( E)/( Z) Isomers of CF3CF═CHCl and CHF2CF═CHCl.

The rate constants for the reactions of OH radical with ( E)- and ( Z)-isomers of CF3CF═CHCl and CHF2CF═CHCl have been measured over the temperature range of 250-430 K. Kinetic measurements have been performed using flash and laser photolysis methods combined with laser-induced fluorescence. Arrhenius rate constants have been determined as k(( E)-CF3CF═CHCl) = (1.09 ± 0.03) × 10-12 · exp[(50 ± 10)K/ T], k(( Z)-CF3CF═CHCl) = (8.02 ± 0.19) × 10-13 · exp[-(100 ± 10)K/ T], k(( E)-CHF2CF═CHCl) = (1.50 ± 0.03) × 10-12 · exp[(160 ± 10)K/ T], and k(( Z)-CHF2CF═CHCl) = (1.36 ± 0.03) × 10-12 · exp[(360 ± 10)K/ T] cm3 molecule-1 s-1. Infrared absorption spectra have also been measured at room temperature. The atmospheric lifetimes of ( E)-CF3CF═CHCl, ( Z)-CF3CF═CHCl, ( E)-CHF2CF═CHCl, and ( Z)-CHF2CF═CHCl have been estimated as 8.9, 20, 4.6, and 2.6 days, respectively, and their global warming potentials and ozone depletion potentials were determined as 0.23, 0.88, 0.060, and 0.016 and 0.00010, 0.00023, 0.000057, and 0.000030, respectively. Additionally, the rate constants for OH radical addition and IR spectra of these compounds were determined computationally. Consistent with experiment, our calculations indicate that the reactivity toward OH radical addition is reduced as ( Z)-CHF2CF═CHCl > ( E)-CHF2CF═CHCl > ( E)-CF3CF═CHCl > ( Z)-CF3CF═CHCl, where the ( E)/( Z) reactivity is reversed for CF3CF═CHCl and CHF2CF═CHCl. The calculations reproduced the observed temperature dependencies of the rate constants for the OH radical reactions, which is slightly positive for ( Z)-CF3CF═CHCl but negative for the other compounds.

Origin of attraction in p-benzoquinone complexes with benzene and p-hydroquinone.

The origin of the attraction in charge-transfer complexes (a p-hydroquinone-p-benzoquinone complex and benzene complexes with benzoquinone, tetracyanoethylene and Br2) was analyzed using distributed multipole analysis and symmetry-adapted perturbation theory. Both methods show that the dispersion interactions are the primary source of the attraction in these charge-transfer complexes followed by the electrostatic interactions. The natures of the intermolecular interactions in these complexes are close to the π/π interactions of neutral aromatic molecules. The electrostatic interactions play important roles in determining the magnitude of the attraction. The contribution of charge-transfer interactions to the attraction is not large compared with the dispersion interactions in these complexes.

Magnitude and Directionality of Halogen Bond of Benzene with C6F5X, C6H5X, and CF3X (X = I, Br, Cl, and F).

Geometries of benzene complexes with C6F5X, C6H5X, and CF3X (X is I, Br, Cl, and F) were optimized, and their interaction energies were evaluated. The CCSD(T) interaction energies at the basis set limit (Eint) of C6F5X (X is I, Br, Cl, and F) with benzene were -3.24, -2.88, -2.31, and -0.92 kcal mol(-1). Eint of C6H5X (X is I, Br, and Cl) with benzene were -2.31, -1.97, and -1.48 kcal mol(-1). The fluorination of halobenzenes slightly enhances the attraction. Eint of CF3X (X is I, Br, Cl, and F) with benzene (-3.11, -2.74, -2.22, and -0.71 kcal mol(-1)) were very close to Eint of corresponding C6F5X with benzene. In contrast to the halogen bond of iodine and bromine with pyridine (n-type halogen bond acceptor) where the main cause of the attraction is the electrostatic interactions, that of halogen bond with benzene (p-type acceptor) is dispersion interaction. In the halogen bonds with p-type acceptors (halogen-π interactions), the electrostatic interactions and induction interactions are small. The overall orbital-orbital interactions are repulsive. The directionality of halogen bonds with p-type acceptors is very weak, owing to the weak electrostatic interactions, in contrast to the strong directionality of the halogen bonds with n-type acceptors and hydrogen bonds.

Two Reaction Mechanisms via Iminium Ion Intermediates: The Different Reactivities of Diphenylprolinol Silyl Ether and Trifluoromethyl-Substituted Diarylprolinol Silyl Ether.

The reactions of α,ß-unsaturated aldehydes with cyclopentadiene in the presence of diarylprolinol silyl ethers as catalyst proceed via iminium cations as intermediates, and can be divided into two types; one involving a Michael-type reaction (type A) and one involving a cycloaddition (type B). Diphenylprolinol silyl ethers and trifluoromethyl-substituted diarylprolinol silyl ethers, which are widely used proline-type organocatalysts, have been investigated in this study. As the LUMO of the iminium ion derived from trifluoromethyl-substituted diarylprolinol silyl ether is lower in energy than that derived from diphenylprolinol silyl ether, as supported by ab initio calculations, the trifluoromethyl-substituted catalyst is more reactive in a type B reaction. The iminium ion from an α,ß-unsaturated aldehyde is generated more quickly with diphenylprolinol silyl ether than with the trifluoromethyl-substituted diarylprolinol silyl ether. When the generation of the iminium ion is the rate-determining step, the diphenylprolinol silyl ether catalyst is the more reactive. Because acid accelerates the generation of iminium ions and reduces the generation of anionic nucleophiles in the Michael-type reaction (type A), it is necessary to select the appropriate acid for specific reactions. In general, diphenylprolinol silyl ether is a superior catalyst for type A reactions, whereas the trifluoromethyl-substituted diarylprolinol silyl ether catalyst is preferred for type B reactions.

A theoretical and experimental study of the effects of silyl substituents in enantioselective reactions catalyzed by diphenylprolinol silyl ether.

The effect of silyl substituents in diphenylprolinol silyl ether catalysts was investigated. Mechanistically, reactions catalyzed by diphenylprolinol silyl ether can be categorized into three types: two that involve an iminium ion intermediate, such as for the Michael-type reaction (type A) and the cycloaddition reaction (type B), and one that proceeds via an enamine intermediate (type C). In the Michael-type reaction via iminium ions (type A), excellent enantioselectivity is realized when the catalyst with a bulky silyl moiety is employed, in which efficient shielding of a diastereotopic face of the iminium ion is directed by the bulky silyl moiety. In the cycloaddition reaction of iminium ions (type B) and reactions via enamines (type C), excellent enantioselectivity is obtained even when the silyl group is less bulky and, in this case, too much bulk reduces the reaction rate. In other cases, the yield increases when diphenylprolinol silyl ethers with bulky substituents are employed, presumably by suppressing side reactions between the nucleophilic catalyst and the reagent. The conformational behaviors of the iminium and enamine species have been determined by theoretical calculations. These data explain the effect of the bulkiness of the silyl substituent on the enantioselectivity and reactivity of the catalysts.

Equatorenes: synthesis and properties of chiral naphthalene, phenanthrene, chrysene, and pyrene possessing bis(1-adamantyl) groups at the peri-position.

Chiral polycyclic aromatic hydrocarbons containing bis(1-adamantyl) groups at the peri-positions, named equatorenes, were synthesized in optically pure form starting from optically pure 4,5-bis(1-adamantyl)-8-methoxy-1-naphthol. A sequential Diels-Alder reaction of furan and arynes generated from 1,2-bromotriflates provided tricyclic and tetracyclic epoxides, and acid-catalyzed aromatization gave phenanthrol and chrysenol. Deoxygenation reactions involving the hydrogenolysis of triflates gave 1,8-bis(1-adamantyl)naphthalene, 1,10-bis(1-adamantyl)phenanthrene, and 1,12-bis(1-adamantyl)chrysene. 3,4-Bis(1-adamantyl)pyrene was synthesized from phenanthrol by Sonogashira coupling and Pt-catalyzed cyclization. Essentially no racemization occurred during the synthesis. X-ray analysis indicated the distorted naphthalene moiety possessing the peri-diadamantyl groups and the flat structure of the other benzene rings. UV-vis analysis of the equatorenes showed considerable redshifts compared with that of the corresponding achiral arenes. Electrochemical analysis of the naphthalene and pyrene indicated that the distortion decreased the highest occupied molecular orbital stability with no marked effect on the lowest unoccupied molecular orbital energy level, and the origin was discussed on the basis of calculation results.

CCSD(T) level interaction energy for halogen bond between pyridine and substituted iodobenzenes: origin and additivity of substituent effects.

The CCSD(T) level interaction energies at the basis set limit (E(int)) were calculated for 33 halogen bonded pyridine complexes with substituted iodobenzenes. The CCSD(T) level electron correlation correction substantially decreases the magnitude of attraction in comparison with the MP2. The E(int) for the pyridine complexes with mono substituted iodobenzenes varies from -3.14 to -4.42 kcal mol(-1), depending on the substituent. The electron-withdrawing substituents such as NO2 enhance the attraction, while the effects of electron-donating substituents reduce. The additivity of the substituent effects is observed for the E(int) of the pyridine complexes with multiple substituted iodobenzenes. The electrostatic interactions are mainly responsible for the substituent effects on the magnitude of the attraction in the halogen-bonded complexes. The electrostatic energy depends significantly on the substituent. They have a strong correlation with the E(int). On the other hand the effects of the substituent on the dispersion energy are small, however the dispersion does contribute greatly to the attraction.

Organocatalytic, enantioselective intramolecular [6+2] cycloaddition reaction for the formation of tricyclopentanoids and insight on its mechanism from a computational study.

Diphenylprolinol silyl ether was found to be an effective organocatalyst for promoting the asymmetric, catalytic, intramolecular [6 + 2] cycloaddition reactions of fulvenes substituted at the exocyclic 6-position with a δ-formylalkyl group to afford synthetically useful linear triquinane derivatives in good yields and excellent enantioselectivities. The cis-fused triquinane derivatives were obtained exclusively; the trans-fused isomers were not detected among the reaction products. The intramolecular [6 + 2] cycloaddition occurs between the fulvene functionality (6π) and the enamine double bond (2π) generated from the formyl group in the substrates and the diphenylprolinol silyl ether. The absolute configuration of the reaction products was determined by vibrational circular dichroism. The reaction mechanism was investigated using molecular orbital calculations, B3LYP and MP2 geometry optimizations, and subsequent single-point energy evaluations on model reaction sequences. These calculations revealed the following: (i) The intermolecular [6 + 2] cycloaddition of a fulvene and an enamine double bond proceeds in a stepwise mechanism via a zwitterionic intermediate. (ii) On the other hand, the intramolecular [6 + 2] cycloaddition leading to the cis-fused triquinane skeleton proceeds in a concerted mechanism via a highly asynchronous transition state. (iii) The fulvene functionality and the enamine double bond adopt the gauche-syn conformation during the C-C bond formation processes in the [6 + 2] cycloaddition. (iv) The energy profiles calculated for the intramolecular reaction explain the observed exclusive formation of the cis-fused triquinane derivatives in the [6 + 2] cycloaddition reactions. The reasons for the enantioselectivity seen in these [6 + 2] cycloaddition reactions are also discussed.

Magnitude and nature of carbohydrate-aromatic interactions in fucose-phenol and fucose-indole complexes: CCSD(T) level interaction energy calculations.

The CH/π contact structures of the fucose-phenol and fucose-indole complexes and the stabilization energies by formation of the complexes (E(form)) were studied by ab initio molecular orbital calculations. The three types of interactions (CH/π and OH/π interactions and OH/O hydrogen bonds) were compared and evaluated in a single molecular system and at the same level of theory. The E(form) calculated for the most stable CH/π contact structure of the fucose-phenol complex at the CCSD(T) level (-4.9 kcal/mol) is close to that for the most stable CH/π contact structure of the fucose-benzene complex (-4.5 kcal/mol). On the other hand the most stable CH/π contact structure of the fucose-indole complex has substantially larger E(form) (-6.5 kcal/mol). The dispersion interaction is the major source of the attraction in the CH/π contact structures of the fucose-phenol and fucose-indole complexes as in the case of the fucose-benzene complex. The electrostatic interactions in the CH/π contact structures are small (less than 1.5 kcal/mol). The nature of the interactions between the nonpolar surface of the carbohydrate and aromatic rings is completely different from that of the conventional hydrogen bonds where the electrostatic interaction is the major source of the attraction. The distributed multipole analysis and DFT-SATP analysis show that the dispersion interactions in the CH/π contact structure of fucose-indole complex are substantially larger than those in the CH/π contact structures of fucose-benzene and fucose-phenol complexes. The large dispersion interactions are responsible for the large E(form) for the fucose-indole complex.

High-yielding synthesis of the anti-influenza neuraminidase inhibitor (-)-oseltamivir by two "one-pot" sequences.

The efficient asymmetric total synthesis of (-)-oseltamivir, an antiviral reagent, has been accomplished by using two "one-pot" reaction sequences, with excellent overall yield (60 %) and only one required purification by column chromatography. The first one-pot reaction sequence consists of a diphenylprolinol silyl ether mediated asymmetric Michael reaction, a domino Michael reaction/Horner-Wadsworth-Emmons reaction combined with retro-aldol/Horner-Wadsworth-Emmons reaction and retro Michael reactions, a thiol Michael reaction, and a base-catalyzed isomerization. Six reactions can be successfully conducted in the second one-pot reaction sequence; these are deprotection of a tert-butyl ester and its conversion into an acyl chloride then an acyl azide, Curtius rearrangement, amide formation, reduction of a nitro group into an amine, and a retro Michael reaction of a thiol moiety. A column-free synthesis of (-)-oseltamivir has also been established.

Mechanism of orientational isomerism of unsymmetrical guests in a heterodimeric capsule: analysis by ab initio molecular orbital calculations.

The geometries and interaction energies of the heterodimeric capsule [tetrakis(4-hydroxyhphenyl)-cavitand 1 and tetra(4-pyridyl)-cavitand 2] complexes with methyl p-acetoxybenzoate 3, methyl p-ethoxybenzeoate 4, and p-ethoxyiodobenzene 5 were studied by ab initio molecular orbital calculations. The optimized structures and charge distributions of the complexes suggest that the electrostatic interactions of oxygen atoms in the guest molecules with the hydrogen atoms of aromatic rings and methylene-bridge rim in the heterodimeric capsule stabilize the complexes. The calculated relative energies of the two orientational isomers of the complexes well reproduce the experimentally observed orientational selectivity of the guest molecules. The calculated stabilization energies for the major orientational isomers of the heterodimeric capsule (1.2) complexes with guest molecules (3, 4, and 5) are -21.6, -19.6, and -19.4 kcal/mol, respectively. Those for the minor orientational isomers are 1.5, 3.5, and 3.7 kcal/mol smaller (less negative), respectively. The magnitude of the calculated energy differences agrees well with the order of the experimental population of the major orientational isomer (3 < 4 approximately 5). The large electron correlation contributions to the attraction (-27.0 to -31.8 kcal/mol) show that the dispersion interactions are the major source of the attraction in the complexes, while the electrostatic interactions (-4.9 to -12.5 kcal/mol) are also an important source of the attraction. Although the electrostatic interactions are weaker than the dispersion interactions, the highly orientation dependent electrostatic interactions mainly determine the orientation of the unsymmetrical guest molecules in the complexes. The electrostatic interactions in the major orientational isomer are 2.6-3.9 kcal/mol larger (more negative) than those in the minor orientational isomer, while the differences of other energy terms are small (less than 1.1 kcal/mol). The interaction energies calculated for model complexes show that the CH/pi interactions are not playing important roles in controlling the orientation of the guest molecules in the complexes.

Magnitude and nature of carbohydrate-aromatic interactions: ab initio calculations of fucose-benzene complex.

The stable geometries of fucose-benzene complex and the stabilization energies by formation of the complex (E(form)) were studied by ab initio molecular orbital calculations. The benzene ring has close contact with an O-H or C-H bond of fucose in the optimized geometries (OH/pi hydrogen-bonded structures and CH/pi contact structures). The E(form) calculated for the most stable OH/pi hydrogen-bonded structure was -5.1 kcal/mol. The E(form) calculated for the most stable CH/pi contact structure was -4.5 kcal/mol, which shows that significant attraction exists between the nonpolar surface of fucose and a benzene. The E(form) is close to the interaction energies in typical hydrogen-bonded complexes. A few nearly isoenergetic CH/pi contact structures were found by the calculations, which suggests that the directionality of the carbohydrate-aromatic interaction is weak. The dispersion interaction is the major source of the attraction in the complex. The electrostatic contributions to the attraction are relatively small. Although the size of the interaction energy is not largely different from that of typical hydrogen bonds, the nature of the carbohydrate-aromatic interaction, which is sometimes denoted as a CH/pi hydrogen bond, is completely different from that of typical hydrogen bonds, which have strong directionality due to the strong electrostatic interactions.

CH/pi interactions in methane clusters with polycyclic aromatic hydrocarbons.

Geometries and interaction energies for methane clusters with naphthalene and pyrene were studied. Estimated CCSD(T) interaction energies for the clusters at the basis set limit were -1.92 and -2.50 kcal mol(-1), respectively. Dispersion is mainly responsible for the attraction. Electrostatic interaction is very small. Although the benzene-methane cluster prefers a monodentate structure, in which a C-H bond of the methane points toward the benzene, the methane clusters with the polycyclic aromatic hydrocarbons do not prefer monodentate structures. In the benzene-methane cluster, the weak electrostatic interaction stabilizes the monodentate structure. On the other hand the dispersion interaction controls the orientation of methane in the naphthalene and pyrene clusters. The dispersion interactions in these clusters are significantly larger than those in the benzene-methane cluster. The methane prefers the orientation which is suitable for stabilization by dispersion. Hydrogen atoms of the methane locate above the centers of hexagonal rings of the polycyclic aromatic hydrocarbons in the stable structures. The structures have a small steric repulsion and this positions them only a short distance from the aromatic plane. The large dispersion contribution to the attraction shows that interactions between carbon atoms are mainly responsible for the attraction, and that hydrogen atoms are not important for the attraction. This shows that the interactions between the methane and polycyclic aromatic hydrocarbons are not pi-hydrogen bonds.

Direct asymmetric alpha-amination of cyclic ketones catalyzed by siloxyproline.

trans-tert-Butyldimethylsiloxy-L-proline displays greater catalytic activity and affords higher enantioselectivity than the parent proline in the alpha-amination reaction of carbonyl compounds with azodicarboxylate. A quantum mechanical calculation reveals the structure of the transition state. In the presence of a catalytic amount of siloxyproline and water (3-9 equiv), alpha-amino carbonyl derivatives, which are important synthetic intermediates, are obtained in good yield and with excellent enantioselectivity.