Influence of backbone conformations of human carbonic anhydrase II on carbon dioxide hydration: hydration pathways and binding of bicarbonate

In this study, the hydration of carbon dioxide and the formation of bicarbonate in human carbonic anhydrase II have been examined. From semiempirical QM/MM molecular dynamics studies, dominant conformations of the protein backbone, possibly contributing to the catalytic activity, have been isolated and further examined by means of density functional QM/MM methods. In agreement with experimental observations, a binding site for cyanate, which acts as an inhibitor, has been located, whereas for carbon dioxide, depending on the conformation of the protein environment, either a different binding site or no binding site has been found. In the latter case, carbon dioxide diffuses barrierless to the zinc-bound oxygen, and then a weakly bound bicarbonate complex is formed. The formed complex is characterized by a long C-O bond to the zinc-bound hydroxide. The nature of the calculated stationary points was verified by determination of vibrational frequencies. Finally, the dissociation of the formed bicarbonate from zinc has been considered. Therefore, a water molecule was included in the QM zone of the QM/MM hybrid potential, and minimization yielded a pentacoordinated intermediate. From a potential energy scan, an activation energy of 6.2 kcal/mol for dissociation of bicarbonate from Zn has been found.     

Acid-base chemistry of a carbenium ion in a zeolite under equilibrium conditions: verification of a theoretical explanation of carbenium ion stability

The 1,3-dimethylcyclopentenyl carbenium ion (C7H11(+)) was reproducibly prepared on zeolite HZSM-5 using a pulse-quench reactor, and then each of a number of bases was coadsorbed into the catalyst channels to either compete with the cation for protonation or to possibly react with it as a nucleophile. For seven bases with proton affinities (PA) between 142 and 212.1 kcal/mol, there was no reaction with C7H11(+). Coadsorption of smaller amounts of dimethylacetamide (PA = 217 kcal/mol) also produced no reaction, but with a higher loading, a proton was transferred from the carbenium ion to the base to leave 1,3-dimethylcyclopenta-1,3-diene in the zeolite as a neutral olefin. Deprotonation was the primary reaction with coadsorption of either pyridine (PA = 222 kcal/mol) or trimethylphosphine (PA = 229.2 kcal/mol). The estimated experimental deprotonation enthalpy for C7H11(+), approximately 217 kcal/mol in the zeolite, is in excellent agreement with MP4/6-311G gas-phase value of 215.6 kcal/mol. Coadsorption of either NH3 (PA = 204.0 kcal/mol) or PH3 (PA = 188 kcal/mol) does not deprotonate the carbenium ion, but these species do react as nucleophiles to form onium ion derivatives of C7H11(+). Analogous onium complexes with pyridine or trimethylphosphine formed in lower yields due to steric constraints in the zeolite channels. The essential experimental observations were all predicted and explained by density functional calculations (B3LYP/6-311G) and extensions of our recently developed theory of carbenium ion stability in zeolites. In addition, we report theoretical geometries for several complexes which contain unusual C-H- - -X hydrogen bonds.     

Theoretical studies of proton-transfer reactions of 2-hydroxypyridine--(H2O)n (n = 0-2) in the ground and excited states

The potential energy profiles for proton-transfer reactions of 2-hydroxypyridine and its complexes with water were determined by MP2, CASSCF and MR-CI calculations with the 6-31G** basis set. The tautomerization reaction between 2-hydroxypyridine (2HP) and 2-pyridone (2PY) does not take place at room temperature because of a barrier of approximately 35 kcal/mol for the ground-state pathway. The water-catalyzed enol-keto tautomerization reactions in the ground state proceed easily through the concerted proton transfer, especially for the two-water complex. The S1 tautomerization between the 2HP and 2PY monomers has a barrier of 18.4 kcal/mol, which is reduced to 5.6 kcal/mol for the one-water complex and 6.4 kcal/mol for the two-water complex. The results reported here predict that the photoinduced tautomerization reaction between the enol and keto forms involves a cyclic transition state having one or two water molecules as a bridge.     

Ab initio study of hydrogen-bond formation between aliphatic and phenolic hydroxy groups and selected amino acid side chains

Hydrogen bonding was studied in 24 pairs of isopropyl alcohol and phenol as one partner, and water and amino-acid mimics (methanol, acetamide, neutral and protonated imidazole, protonated methylalamine, methyl-guanidium cation, and acetate anion) as the other partner. MP2/6-31+G* and MP2/aug-cc-pvtz calculations were conducted in the gas phase and in a model continuum dielectric environment with dielectric constant of 15.0. Structures were optimized in the gas phase with both basis sets, and zero-point energies were calculated at the MP2/6-31+G* level. At the MP2/aug-cc-pvtz level, the BSSE values from the Boys-Bernardi counterpoise calculations amount to 10-20 and 5-10% of the uncorrected binding energies of the neutral and ionic complexes, respectively. The geometry distortion energy upon hydrogen-bond formation is up to 2 kcal/mol, with the exception of the most strongly bound complexes. The BSSE-corrected MP2/aug-cc-pvtz binding energy of -27.56 kcal/mol for the gas-phase acetate...phenol system has been classified as a short and strong hydrogen bond (SSHB). The CH3NH3+...isopropyl alcohol complex with binding energy of -22.54 kcal/mol approaches this classification. The complete basis set limit (CBS) for the binding energy was calculated for twelve and six complexes on the basis of standard and counterpoise-corrected geometry optimizations, respectively. The X...Y distances of the X-H...Y bridges differ by up to 0.03 A as calculated by the two methods, whereas the corresponding CBS energy values differ by up to 0.03 kcal/mol. Uncorrected MP2/aug-cc-pvtz hydrogen-bonding energies are more negative by up to 0.35 kcal/mol than the MP2/CBS values, and overestimate the CCSD(T)/CBS binding energies generally by up to 5% for the eight studied complexes in the gas phase. The uncorrected MP2/aug-cc-pvtz binding energies decreased (in absolute value) by 11-18 kcal/mol for the ionic species and by up to 5 kcal/mol for the neutral complexes when the electrostatic effect of a polarizable model environment was considered. The DeltaECCSD(T) - DeltaEMP2 corrections still remained close to their gas-phase values for four complexes with 0, +/-1 net charges. Good correlations (R2 = 0.918-0.958) for the in-environment MP2/aug-cc-pvtz and MP2/6-31+G* hydrogen-bonding energies facilitate the high-level prediction of these energies on the basis of relatively simple MP2/6-31+G* calculations.     

Ab initio studies on the mechanism of the size-dependent hydrogen-loss reaction in Mg+(H2O)n

The mechanism of size-dependent intracluster hydrogen loss in the cluster ions Mg(+)(H(2)O)(n), which is switched on around n=6, and off around n=14, was studied by ab initio calculations at the MP2/6-31G* and MP2/6-31G** levels for n=1-6. The reaction proceeds by Mg(+)-assisted breaking of an H-O bond in one of the H(2)O molecules. The reaction barrier is dependent on both the cluster size and the solvation structure. As n increases from 1 to 6, there is a dramatic drop in the reaction barrier, from greater than 70 kcal mol(-1) for n=1 to less than 10 kcal mol(-1) for n=6. In the transition structures, the Mg atom is close to the oxidation state of +2, and H(2)O molecules in the first solvation shell are much more effective in stabilizing the transition structures and lowering the reaction barriers than H(2)O molecules in the other solvation shells. While the reaction barrier for trimer core structures with only three H(2)O molecules in the first shell is greater than 24 kcal mol(-1), even for Mg(+)(H(2)O)(6), it drops considerably for clusters with four-six H(2)O molecules in the first shell. The more highly coordinated complexes have comparable or slightly higher energy than the trimer core structures, and the presence of such high coordination number complexes is the underlying kinetic factor for the switching on of the hydrogen-loss reaction around n=6. For clusters with trimer core structures, the hydrogen loss reaction is much easier when it is preceded by an isomerization step that increases the coordination number around Mg(+). Delocalization of the electron on the singly occupied molecular orbital (SOMO) away from the Mg(+) ion is observed for the hexamer core structure, while at the same time this isomer is the most reactive for the hydrogen-loss reaction, with an energy barrier of only 2.7 kcal mol(-1) at the MP2/6-31G** level.     

Corannulene as a Lewis base: computational modeling of protonation and lithium cation binding.

A computational modeling of the protonation of corannulene at B3LYP/6-311G(d,p)//B3LYP/6-311G(d,p) and of the binding of lithium cations to corannulene at B3LYP/6-311G(d,p)//B3LYP/6-31G(d,p) has been performed. A proton attaches preferentially to one carbon atom, forming a sigma-complex. The isomer protonated at the innermost (hub) carbon has the best total energy. Protonation at the outermost (rim) carbon and at the intermediate (bridgehead rim) carbon is less favorable by ca. 2 and 14 kcal mol(-)(1), respectively. Hydrogen-bridged isomers are transition states between the sigma-complexes; the corresponding activation energies vary from 10 to 26 kcal mol(-)(1). With an empirical correction obtained from calculations on benzene, naphthalene, and azulene, the best estimate for the proton affinity of corannulene is 203 kcal mol(-)(1). The lithium cation positions itself preferentially over a ring. There is a small energetic preference for the 6-ring over the 5-ring binding (up to 2 kcal mol(-)(1)) and of the convex face over the concave face (3-5 kcal mol(-)(1)). The Li-bridged complexes are transition states between the pi-face complexes. Movement of the Li(+) cation over either face is facile, and the activation energy does not exceed 6 kcal mol(-)(1) on the convex face and 2.2 kcal mol(-)(1) on the concave face. In contrast, the transition of Li(+) around the corannulene edge involves a high activation barrier (24 kcal mol(-)(1) with respect to the lowest energy pi-face complex). An easier concave/convex transformation and vice versa is the bowl-to-bowl inversion with an activation energy of 7-12 kcal mol(-)(1). The computed binding energy of Li(+) to corannulene is 44 kcal mol(-)(1). Calculations of the (7)Li NMR chemical shifts and nuclear independent chemical shifts (NICS) have been performed to analyze the aromaticity of the corannulene rings and its changes upon protonation.     

Interaction of adenine adducts with thymine: a computational study

The existence of DNA adducts bring the danger of carcinogenesis because of mispairing with normal DNA bases. 1,N6-ethenoadenine adducts (epsilonA) and 1,N6-ethanoadenine adducts (EA) have been considered as DNA adducts to study the interaction with thymine, as DNA base. Several different stable conformers for each type of adenine adduct with thymine, [epsilonA(1)-T(I), epsilonA(2)-T(I), epsilonA(3)-T(I) and EA(1)-T(I), EA(2)-T(I), EA(3)-T(I)] and [epsilonA(1)-T(II), epsilonA(2)-T(II), epsilonA(3)-T(II) and EA(1)-T(II), EA(2)-T(II), EA(3)-T(II)], have been considered with regard to their interactions. The differences in their geometrical structures, energetic properties, and hydrogen-bonding strengths have also been compared with Watson-Crick adenine-thymine base pair (A-T). Single-point energy calculations at MP2/6-311++G** levels on B3LYP/6-31+G* optimized geometries have also been carried out to better estimate the hydrogen-bonding strengths. The basis set superposition error corrected hydrogen-bonding strength sequence at MP2/6-311++G**//B3LYP/6-31+G* for the most stable complexes is found to be EA(2)-T(I) (15.30 kcal/mol) > EA(1)-T(II) (14.98 kcal/mol) > EA(3)-T(II) (14.68 kcal/mol) > epsilonA(2)-T(I) (14.54 kcal/mol) > epsilonA(3)-T(II) (14.22 kcal/mol) > epsilonA(3)-T(II) (13.64 kcal/mol) > A-T (13.62 kcal/mol). The calculated reaction enthalpy value for epsilonA(2)-T(I) is 10.05 kcal/mol, which is the highest among the etheno adduct-thymine complexes and about 1.55 kcal/mol more than those obtained for Watson-Crick A-T base pair and the reaction enthalpy value for EA(1)- T(II) is 10.22 kcal/mol, which is highest among the ethano addcut-thymine complexes and about 1.72 kcal/mol more than those obtained for Watson-Crick A-T base pair. The aim of this research is to provide fundamental understanding of adenine adduct and thymine interaction at the molecular level and to aid in future experimental studies toward finding the possible cause of DNA damage.     

New model for a theoretical density functional theory investigation of the mechanism of the carbonic anhydrase: how does the internal bicarbonate rearrangement occur?

A theoretical density functional theory (DFT, B3LYP) investigation has been carried out on the catalytic cycle of the carbonic anhydrase. A model system including the Glu106 and Thr199 residues and the "deep" water molecule has been used. It has been found that the nucleophilic attack of the zinc-bound OH on the CO(2) molecule has a negligible barrier (only 1.2 kcal mol(-1)). This small value is due to a hydrogen-bond network involving Glu106, Thr199, and the deep water molecule. The two usually proposed mechanisms for the internal bicarbonate rearrangement have been carefully examined. In the presence of the two Glu106 and Thr199 residues, the direct proton transfer (Lipscomb mechanism) is a two-step process, which proceeds via a proton relay network characterized by two activation barriers of 4.4 and 9.0 kcal mol(-1). This pathway can effectively compete with a rotational mechanism (Lindskog mechanism), which has a barrier of 13.2 kcal mol(-1). The fast proton transfer found here is basically due to the effect of the Glu106 residue, which stabilizes an intermediate situation where the Glu106 fragment is protonated. In the absence of Glu106, the barrier for the proton transfer is much larger (32.3 kcal mol(-1)) and the Lindskog mechanism becomes favored.     

Quantum mechanical study of the potential energy surface of the ClO + NO2 reaction

In the study of the reaction pathways of the ClO + NO2 reaction including reliable structures of the reactants, products, intermediates, and transition states as well as energies the MP2/6-311G(d), B3LYP/6-311G(d), and G2(MP2) methods have been employed. Chlorine nitrate, ClONO2, is formed by N-O association without an entrance barrier and is stabilized by 29.8 kcal mol(-1). It can undergo either a direct 1,3 migration of Cl or OCl rotation to yield an indistinguishable isomer. The corresponding barriers are 45.8 and 7.1 kcal mol(-1), respectively. ClONO2 can further decompose into NO3 + Cl with an endothermicity of 46.4 kcal mol(-1). The overall endothermicity of the NO2 + ClO --> NO3 + Cl reaction is calculated to be 16.6 kcal mol(-1). The formation of cis-perp and trans-perp conformer of chlorine preoxynitrite, ClOONO(cp) and ClOONO(tp), are exothermic by 5.4 and 3.8 kcal mol(-1), respectively. Calculations on the possible reaction pathways for the isomerization of ClOONO to ClONO2 showed that the activation barriers are too high to account for appreciable nitrate formation from peroxynitrite isomerization. All quoted relative energies are related to G2(MP2) calculations.     

Thermodynamic and ab initio analysis of the controversial enthalpy of formation of formaldehyde.

There are two values, -26.0 and -27.7 kcal mol(-1), that are routinely reported in literature evaluations for the standard enthalpy of formation, Delta(f) H(o)(298), of formaldehyde (CH(2)=O), where error limits are less than the difference in values. In this study, we summarize the reported literature for formaldehyde enthalpy values based on evaluated measurements and on computational studies. Using experimental reaction enthalpies for a series of reactions involving formaldehyde, in conjunction with known enthalpies of formation, its enthalpy is determined to be -26.05+/-0.42 kcal mol(-1), which we believe is the most accurate enthalpy currently available. For the same reaction series, the reaction enthalpies are evaluated using six computational methods: CBS-Q, CBS-Q//B3, CBS-APNO, G2, G3, and G3B3 yield Delta(f) H(o)(298)=-25.90+/-1.17 kcal mol(-1), which is in good agreement to our experimentally derived result. Furthermore, the computational chemistry methods G3, G3MP2B3, CCSD/6-311+G(2df,p)//B3LYP/6-31G(d), CCSD(T)/6-311+G(2df,p)//B3LYP/6-31G(d), and CBS-APNO in conjunction with isodesmic and homodesmic reactions are used to determine Delta(f) H(o)(298). Results from a series of five work reactions at the higher levels of calculation are -26.30+/-0.39 kcal mol(-1) with G3, -26.45+/-0.38 kcal mol(-1) with G3MP2B3, -26.09+/-0.37 kcal mol(-1) with CBS-APNO, -26.19+/-0.48 kcal mol(-1) with CCSD, and -26.16+/-0.58 kcal mol(-1) with CCSD(T). Results from heat of atomization calculations using seven accurate ab initio methods yields an enthalpy value of -26.82+/-0.99 kcal mol(-1). The results using isodesmic reactions are found to give enthalpies more accurate than both other computational approaches and are of similar accuracy to atomization enthalpy calculations derived from computationally intensive W1 and CBS-APNO methods. Overall, our most accurate calculations provide an enthalpy of formation in the range of -26.2 to -26.7 kcal mol(-1), which is within computational error of the suggested experimental value. The relative merits of each of the three computational methods are discussed and depend upon the accuracy of experimental enthalpies of formation required in the calculations and the importance of systematic computational errors in the work reaction. Our results also calculate Delta(f) H(o)(298) for the formyl anion (HCO(-)) as 1.28+/-0.43 kcal mol(-1).     

Transition state stabilization and substrate strain in enzyme catalysis: ab initio QM/MM modelling of the chorismate mutase reaction

To investigate fundamental features of enzyme catalysis, there is a need for high-level calculations capable of modelling crucial, unstable species such as transition states as they are formed within enzymes. We have modelled an important model enzyme reaction, the Claisen rearrangement of chorismate to prephenate in chorismate mutase, by combined ab initio quantum mechanics/molecular mechanics (QM/MM) methods. The best estimates of the potential energy barrier in the enzyme are 7.4-11.0 kcal mol(-1)(MP2/6-31+G(d)//6-31G(d)/CHARMM22) and 12.7-16.1 kcal mol(-1)(B3LYP/6-311+G(2d,p)//6-31G(d)/CHARMM22), comparable to the experimental estimate of Delta H(++)= 12.7 +/- 0.4 kcal mol(-1). The results provide unequivocal evidence of transition state (TS) stabilization by the enzyme, with contributions from residues Arg90, Arg7, and Arg63. Glu78 stabilizes the prephenate product (relative to substrate), and can also stabilize the TS. Examination of the same pathway in solution (with a variety of continuum models), at the same ab initio levels, allows comparison of the catalyzed and uncatalyzed reactions. Calculated barriers in solution are 28.0 kcal mol(-1)(MP2/6-31+G(d)/PCM) and 24.6 kcal mol(-1)(B3LYP/6-311+G(2d,p)/PCM), comparable to the experimental finding of Delta G(++)= 25.4 kcal mol(-1) and consistent with the experimentally-deduced 10(6)-fold rate acceleration by the enzyme. The substrate is found to be significantly distorted in the enzyme, adopting a structure closer to the transition state, although the degree of compression is less than predicted by lower-level calculations. This apparent substrate strain, or compression, is potentially also catalytically relevant. Solution calculations, however, suggest that the catalytic contribution of this compression may be relatively small. Consideration of the same reaction pathway in solution and in the enzyme, involving reaction from a 'near-attack conformer' of the substrate, indicates that adoption of this conformation is not in itself a major contribution to catalysis. Transition state stabilization (by electrostatic interactions, including hydrogen bonds) is found to be central to catalysis by the enzyme. Several hydrogen bonds are observed to shorten at the TS. The active site is clearly complementary to the transition state for the reaction, stabilizing it more than the substrate, so reducing the barrier to reaction.     

DFT studies on the copolymerization of alpha-olefins with polar monomers: ethylene-methyl acrylate copolymerization catalyzed by a Pd-based diimine catalyst.

Gradient-corrected density functional theory has been used to study the elementary reactions for the copolymerization of ethylene with methyl acrylate catalyzed by Pd-based diimine catalysts, modeled by the generic complex N(wedge)N-Pd(n-C(3)H(7))(+), with N(wedge)N = -NHCHCHNH-. The steric effects in the real systems are discussed on the basis of the calculations for the catalyst with N(wedge)N = -NArCRCRNAr-, R = CH(3), and Ar = C(6)H(3)(i-Pr(2)) and the previous calculations on ethylene/propylene polymerization. Considerations have been given to the different possible acrylate complexes, as well as the transition states and the products (agostic complexes and the alternative chelates) for two acrylate insertion paths (1,2 and 2,1). The chelate-opening reactions have also been studied. The results revealed a strong electronic preference for the 2,1-insertion paths, with a barrier that is 4.5 kcal/mol lower than any other studied insertion pathway. In the real systems the 2,1-insertion of acrylate is preferred by 0.5 kcal/mol. The 2,1-insertion barrier calculated for the real system of 12.4 kcal/mol is in very good agreement with the experimental value of 12.1 kcal/mol. The six-member chelate is the most stable insertion product with an energy that is 21 kcal/mol lower than the kinetic insertion product. The reactions of the chelate opening by ethylene that start from the lowest energy complexes have the lowest barrier for the four-member ring (23 kcal/mol) and the highest for the six-member structure (30.4 kcal/mol). The high barrier for the opening of the six-member chelate suggests the possibility of a two-step chelate-opening mechanism. The internal barriers for the chelate-opening reactions starting from the higher energy complexes are lower then the one-step reaction that starts from the preferred complex and comparable to those of the ethylene insertion into the Pd-alkyl bond. While the chelate opening by a subsequent acrylate insertion seems to be facile for the generic catalyst, steric effects in the real catalyst are likely to decrease the acrylate pi-complexation energies and increase the insertion barriers to the extent where such a reaction becomes unfeasible.     

Terminal vanadium-neopentylidyne complexes and intramolecular cross-metathesis reactions to generate azametalacyclohexatrienes

Four-coordinate vanadium complexes containing a terminal neopentylidyne functionality have been prepared by two consecutive alpha-hydrogen abstraction reactions both of which were induced by one-electron oxidations. Among these vanadium-alkylidyne complexes are the neutral and the cation (Nacnac)VCtBu(OTf) and [(Nacnac)VCtBu(THF)]+, respectively (Nacnac- = [Ar]NC(CH3)CHC(CH3)N[Ar], Ar = 2,6-(CHMe2)2C6H3). The vanadium-alkylidynes have been characterized by 1H, 13C, 51V NMR spectroscopy and single-crystal X-ray diffraction and are consistent with a short VC bond. These alkylidynes were found to transform to azametalacyclohexatriene systems via an intramolecular cross-metathesis reaction. Kinetic studies of the transformation of (Nacnac)VCtBu(OTf) in C7D8 reveal the formation of the azametalacyclohexatriene to be independent of solvent (toluene vs THF) and the reaction to be first order in vanadium (k = 3.30(5) x 10-5 s-1 at 80 degrees C, with activation parameters DeltaH= 25.4(3) kcal/mol, DeltaS = -6(3) cal/molK). High-level DFT calculations on the full model suggest an intramolecular mechanism invoking only one transition state. The overall thermodynamic driving force for the reaction (DeltaG) in solution phase was estimated to be -21.3 kcal/mol.     

Polarization Effects for Hydrogen-Bonded Complexes of Substituted Phenols with Water and Chloride Ion

Variations in hydrogen-bond strengths are investigated for complexes of nine para-substituted phenols (XPhOH) with a water molecule and chloride ion. Results from ab initio HF/6-311+G(d, p) and MP2/6-311+G(d, p)//HF/6-311+G(d, p) calculations are compared with those from the OPLS-AA and OPLS/CM1A force fields. In the OPLS-AA model, the partial charges on the hydroxyl group of phenol are not affected by the choice of para substituent, while the use of CM1A charges in the OPLS/CM1A approach does provide charge redistribution. The ab initio calculations reveal a 2.0-kcal/mol range in hydrogen-bond strengths for the XPhOH?OH(2) complexes in the order X = NO(2) > CN > CF(3) > Cl > F > H >OH >CH(3) > NH(2). The pattern is not well-reproduced with OPLS-AA, which also compresses the variation to 0.7 kcal/mol. However, the OPLS/CM1A results are in good accord with the ab initio findings for both the ordering and range, 2.3 kcal/mol. The hydrogen bonding is, of course, weaker with XPhOH as acceptor, the order for X is largely inverted, and the range is reduced to ca. 1.0 kcal/mol. The substituent effects are found to be much greater for the chloride ion complexes with a range of 11 kcal/mol. For quantitative treatment of such strong ion-molecule interactions the need for fully polarizable force fields is demonstrated.     

Stabilisation energy of C(6)H(6)...C(6)X(6) (X = F, Cl, Br, I, CN) complexes: complete basis set limit calculations at MP2 and CCSD(T) levels

Stabilisation energies of stacked structures of C(6)H(6)...C(6)X(6) (X = F, Cl, Br, CN) complexes were determined at the CCSD(T) complete basis set (CBS) limit level. These energies were constructed from MP2/CBS stabilisation energies and a CCSD(T) correction term determined with a medium basis set (6-31G**). The former energies were extrapolated using the two-point formula of Helgaker et al. from aug-cc-pVDZ and aug-cc-pVTZ Hartree-Fock energies and MP2 correlation energies. The CCSD(T) correction term is systematically repulsive. The final CCSD(T)/CBS stabilisation energies are large, considerably larger than previously calculated and increase in the series as follows: hexafluorobenzene (6.3 kcal mol(-1)), hexachlorobenzene (8.8 kcal mol(-1)), hexabromobenzene (8.1 kcal mol(-1)) and hexacyanobenzene (11.0 kcal mol(-1)). MP2/SDD** relativistic calculations performed for all complexes mentioned and also for benzene[dot dot dot]hexaiodobenzene have clearly shown that due to relativistic effects the stabilisation energy of the hexaiodobenzene complex is lower than that of hexabromobenzene complex. The decomposition of the total interaction energy to physically defined energy components was made by using the symmetry adapted perturbation treatment (SAPT). The main stabilisation contribution for all complexes investigated is due to London dispersion energy, with the induction term being smaller. Electrostatic and induction terms which are attractive are compensated by their exchange counterparts. The stacked motif in the complexes studied is very stable and might thus be valuable as a supramolecular synthon.     

The reaction of tricarbon with acetylene: an ab initio/RRKM study of the potential energy surface and product branching ratios

Ab initio calculations of the potential energy surface for the C3(1Sigmag+)+C2H2(1Sigmag+) reaction have been performed at the RCCSD(T)/cc-pVQZ//B3LYP/6-311G(d,p) + ZPE[B3LYP/6-311G(d,p)] level with extrapolation to the complete basis set limit for key intermediates and products. These calculations have been followed by statistical calculations of reaction rate constants and product branching ratios. The results show the reaction to begin with the formation of the 3-(didehydrovinylidene)cyclopropene intermediate i1 or five-member ring isomer i7 with the entrance barriers of 7.6 and 13.8 kcal/mol, respectively. i1 rearranges to the other C5H2 isomers, including ethynylpropadienylidene i2, singlet pentadiynylidene i3, pentatetraenylidene i4, ethynylcyclopropenylidene i5, and four- and five-member ring structures i6, i7, and i8 by ring-closure and ring-opening processes and hydrogen migrations. i2, i3, and i4 lose a hydrogen atom to produce the most stable linear isomer of C5H with the overall reaction endothermicity of approximately 24 kcal/mol. H elimination from i5 leads to the formation of the cyclic C5H isomer, HC2C3, +H, 27 kcal/ mol above C3+C2H2. 1,1-H2 loss from i4 results in the linear pentacarbon C5+H2 products endothermic by 4 kcal/mol. The H elimination pathways occur without exit barriers, whereas the H2 loss from i4 proceeds via a tight transition state 26.4 kcal/mol above the reactants. The characteristic energy threshold for the reaction under single collision conditions is predicted be in the range of approximately 24 kcal/mol. Product branching ratios obtained by solving kinetic equations with individual rate constants calculated using RRKM and VTST theories for collision energies between 25 and 35 kcal/mol show that l-C5H+H are the dominant reaction products, whereas HC2C3+H and l-C5+H2 are minor products with branching ratios not exceeding 2.5% and 0.7%, respectively. The ethynylcyclopropenylidene isomer i5 is calculated to be the most stable C5H2 species, more favorable than triplet pentadiynylidene i3t by approximately 2 kcal/mol.     

Addition of alkyl radicals to transition-metal-coordinated CO: calculation of the reaction of [Ru(CO)5] and related complexes and relevance to alkane carbonylation

Electronic structure methods have been used to study the transition state and products of the reaction between alkyl radicals and CO coordinated in transition-metal complexes. At the B3LYP DFT level, methyl addition to a carbonyl of [Ru(CO)5] or [Ru(CO)3(dmpe)] is calculated to be about 6 kcal/mol more exothermic than addition to free CO. In contrast, methyl addition to [Mo(CO)6] is 12 kcal/mol less exothermic than addition to CO, while the reaction enthalpy of methyl addition to [Pd(CO)4] is comparable to that of free CO. Related results are obtained at the CCSD-T level and for the reactions of the cyclohexyl radical. The transition state for these reactions is characterized by significant distortion of the geometry of the reactant complex, which include lengthening and bending of the M-CO bond, but with negligible C-C bond formation. Accordingly, the activation energy for addition to coordinated carbonyls is 2-10 kcal/mol greater than that of addition to free CO. Additional calculations were also carried out on representative unsaturated metal carbonyls. The calculated results afford an understanding of the mechanism of previously reported photochemical alkane carbonylation systems utilizing d(8)-ML5 metal carbonyls as cocatalysts. In particular, it is strongly indicated that such systems operate via direct attack by an alkyl radical at a CO ligand, a reaction that has not previously been proposed.     

Disproportionation of Gold(II) complexes. A density functional study of ligand and solvent effects

A computational study of gold(II) disproportionation is presented for the atomic ion as well as complexes with chloride and neutral ligands. The Au2+ atomic ion is stable to disproportionation, but the barrier is more than halved to 119 kcal/mol in an aqueous environment vs 283 kcal/mol in the gas phase. For dissociative disproportionation of chloride complexes, the loss of chlorine, either as an atom (Delta G(aq) = +20 kcal/mol) or as an anion (Delta G(aq) = +15 kcal/mol) represents the largest calculated barrier. The calculated transition state for associative disproportionation is only 9 kcal/mol above separated Au(II)Cl3(-) anions. For the disproportionation of Au(II)L3 complexes with neutral ligands, disproportionation is highly endergonic in the gas phase. Calculations imply that for synthesis of a monometallic Au(II) complex, a nonpolar solvent is preferred. With the exception of [Au(CO)3]2+, disproportionation of Au(II)L3 complexes to Au(I)L and Au(III)L3 is exergonic in solution phase for the ligands investigated. The driving force is provided by the very favorable solvation free energy of the trivalent gold complex. The solvation free energy contribution to the reaction (Delta G(solv)) is very large for small and polar ligands such as ammonia and water. Furthermore, calculations imply that choosing ligands that would yield neutral species upon disproportionation may provide an effective route to thwart this decomposition pathway for Au(II) complexes. Likewise, bulkier ligands that yield larger, more weakly solvated complex ions would appear to be desirable.     

Formaldehyde encapsulated in lithium-decorated metal-organic frameworks: a density functional theory study

The stability of monomeric formaldehyde encapsulated in the lithium-decorated metal-organic framework Li-MOF-5 was investigated by means of density functional calculations with the M06-L functional and the 6-31G(d,p) basis set. To assess the efficiency of Li-MOF-5 for formaldehyde preservation, we consider the reaction kinetics and the thermodynamic equilibrium between formaldehyde and its trimerized product, 1,3,5-trioxane. We propose that trimerization of encapsulated formaldehyde takes place in a single reaction step with an activation energy of 34.5 kcal mol(-1). This is 17.2 kcal mol(-1) higher than the corresponding activation energy in the bare system. In addition, the reaction energy of the system studied herein is endothermic by 6.1 kcal mol(-1) and the Gibbs free energy (ΔG) of the reaction becomes positive (11.0 kcal mol(-1)). Consequently, the predicted reverse rate for the trimerization reaction in the Li-MOF-5 is significantly faster than the forward rate. The calculations show that the oligomerization of formaldehyde in Li-MOF-5 is a reversible reaction, suggesting that such a zeolite might be a good candidate material for preserving formaldehyde in its monomeric form.     

Heat of hydrogenation of 1,5-dehydroquadricyclane. A computational and experimental study of a highly pyramidalized alkene

The radical anion of the highly pyramidalized alkene 1,5-dehydroquadricyclane (1) was generated in the gas phase from the Squires reaction of 1,5-bis(trimethylsilyl)quadricyclane with F-/F2. The electron binding energy and proton affinity of 1*- were determined by bracketing experiments to be 0.6 +/- 0.1 eV and 386 +/- 5 kcal/mol, respectively. These values are in good agreement with values predicted by density functional theory (B3LYP/6-31+G*) and ab initio (CASPT2/6-31+G*) calculations. The experimental heat of hydrogenation of 1, obtained from a thermochemical cycle, was found to be 91 +/- 9 kcal/mol. This value of deltaH(H2) leads to values of 67 +/- 9 kcal/mol for the olefin strain energy (OSE) of 1, 172 +/- 9 kcal/mol for its heat of formation, and 23 +/- 9 kcal/mol for its pi bond dissociation enthalpy. Since the retro-Diels-Alder reaction of neutral 1 is computed to be highly exothermic, the finding that 1*- apparently does not undergo a retro-Diels-Alder reaction is of particular interest. The B3LYP/6-31+G* optimized geometry of 1 suggests that the bonding in this alkene is partially delocalized, presumably because the highly pyramidalized double bond in 1 interacts with the distal cyclopropane bonds in a manner that eventually leads to a retro-Diels-Alder reaction. The good agreement of the B3LYP and (2/2)CASPT2 values for the heat of hydrogenation and OSE of 1 with the experimentally derived values provides indirect evidence for the correctness of the B3LYP prediction that the equilibrium geometry of 1 lies part way along the reaction coordinate to the transition structure for the retro-Diels-Alder reaction.