Accurate ab initio anharmonic force field and heat of formation for silane

From large basis set coupled cluster calculations and a minor empirical adjustment, an anharmonic force field for silane has been derived that is consistently of spectroscopic quality (±1 cm^?1 on vibrational fundamentals) for all isotopomers of silane studied. Inner-shell polarization functions have an appreciable effect on computed properties and even on anharmonic corrections. From large basis set coupled cluster calculations and extrapolations to the infinite-basis set limit, we obtain TAE₀ = 303.80 ± 0.18 kcal mol^?1, which includes an anharmonic zero-point energy (19.59 kcal mol^?1), inner-shell correlation (—0.36 kcal mol^?1), scalar relativistic corrections (— 0.70 kcal mol^?1) and atomic spin-orbit corrections (—0.43 kcal mol^?1). In combination with the recently revised ΔH ^o _{f, o}[Si(g)], we obtain ΔH ^o _f.o[SiH₄(g)] = 9.9 ± 0.4 kcal mol^?1 in between the two established experimental values.     

Time resolved measurements of methanol decomposition on Ni(100) utilizing laser induced desorption

A new method utilizing laser induced desorption (LID) is used to study the decomposition of methanol on Ni(100) in real time. The dependence of the rate of decompositition on surface coverage and on surface temperature is measured. The decomposition rate decreases during reaction in a manner characteristic of a self-poisoned reaction. The rate data are fit to a model in which the energy barrier to reaction increases in proportion to the coverage of the CH₃O product. The energy barrier obtained is 9 kcal mol^?1 plus 4 kcal mol^?1 monolayer^?1 of CH₃O. The frequency factor of 2 × 10⁹ s^?1 suggests there is significant entropy barrier to decomposition. Substitution of deuterium for the alcoholic hydrogen alters de decomposition rate appreciably and identifies the breaking of the OH bond as the rate determining step.     

Theoretical study of rearrangements in water dimer and trimer

The global minimum and transition states for the acceptor-tunnelling, donor-acceptor interchange and bifurcation tunnelling rearrangements of the water dimer, and the single-flip, bifurcation and concerted proton transfer processes in the water trimer have been reinvestigated. Our analysis of the tunnelling splittings and spectroscopy is based on ab initio calculations at the computational level of second-order M?ller-Plesset (MP2) theory with basis sets of aug-cc-pVXZ quality (X = D, T, Q for the dimer; X = D, T for the trimer). In both water dimer and trimer, the binding energy, barrier heights, intermonomer distances, and harmonic frequencies converge smoothly as the size of the basis set increases. In the water dimer, the binding energy was evaluated as 5.09kcal mol^?1, while the activation energies are 0.52 (acceptor-tunnelling) 0.79 (donor-acceptor interchange), and 1.94 kcal mol^?1 (bifurcation tunnelling) at the MP2/aug-cc-pVQZ level. In the water trimer, the binding energy was evaluated as 16.29 kcal mol^?1, while the activation energies are 0.28 (single-flip), 2.34 (bifurcation), and 26.36 (proton transfer) kcal mol^?1 at the MP2/aug-cc-pVTZ level.     

Theoretical investigation of an unusual substituent effect on the dienophilicity of >CP? functionality present in 2‐phosphaindolizines

Effect of the number and positions of the methoxycarbonyl substituents in 2‐phosphaindolizine on the feasibility of its Diels–Alder (DA) reaction with 1,3‐butadiene has been investigated theoretically at the density functional theory (DFT) level. Among the series of four differently substituted 2‐phosphaindolizines, 3‐methoxycarbonyl‐2‐phosphaindolizine does not undergo the DA reaction due to the highest activation barrier (29.49 kcal mol^?1) and endothermicity, whereas the activation barrier of the corresponding reaction of 1,3‐bis(methoxycarbonyl)‐2‐phosphaindolizine is lowest (22.43 kcal mol^?1) with exothermicity making it possible to occur. This reactivity trend is corroborated by FMO energy gaps as well as by global electrophilicity powers of the reactants. Copyright © 2008 John Wiley & Sons, Ltd.     

Solvent effects and potential of mean force study of the S_N2 reaction of CH_3F+CN~- in water

We used a combined quantum mechanics and molecular mechanics(QM/MM) method to investigate the solvent effects and potential of mean force of the CH_3F+CN~- reaction in water. Comparing to gas phase, the water solution substantially affects the structures of the stationary points along the reaction path. We quantitatively obtained the solvent effects' contributions to the reaction: 1.7 kcal/mol to the activation barrier and -26.0 kcal/mol to the reaction free energy.The potential mean of force calculated with the density functional theory/MM theory has a barrier height at 19.7 kcal/mol,consistent with the experimental result at 23.0 kcal/mol; the calculated reaction free energy at -43.5 kcal/mol is also consistent with the one estimated based on the gas-phase data at -39.7 kcal/mol.     

1,5‐electrocyclization versus 1,5‐proton shift in imidazolium allylides and 2‐phospha‐allylides: a DFT investigation

The competitive 1,5‐electrocyclization versus intramolecular 1,5‐proton shift in imidazolium allylides and imidazolium 2‐phosphaallylides has been investigated theoretically at the DFT (B3LYP/6‐311 + +G**//B3LYP/6‐31G**) level. 1,5‐Electrocyclization follows pericyclic mechanism and its activation barrier is lower than that for the pseudopericyclic mechanism by ～5–6 kcal mol^?1. The activation barriers for 1,5‐electrocyclization of imidazolium 2‐phosphaallylides are found to be smaller than those for their nonphosphorus analogues by ～3–5 kcal mol^?1. There appears to be a good correlation between the activation barrier for intramolecular 1,5‐proton shift and the density of the negative charge at C8, except for the ylides having fluorine substituent at this position ( 7b and 8b ). The presence of fluorine atom reduces the density of the negative charge at C8 (in 7b it becomes positively charged) and thus raises the activation barrier. The ylides 7f and 8f having CF₃ group at C8, in preference to the 1,5‐proton shift, follow an alternative route leading to different carbenes which is accompanied by the loss of HF. The carbenes Pr _{7 , 8b – e} resulting from intramolecular 1,5‐proton shift have a strong tendency to undergo intramolecular S_N2 type reaction, the activation barrier being 7–28 kcal mol^?1. Copyright © 2011 John Wiley & Sons, Ltd.     

A comparative coupled cluster and density functional theory study of the HOCI → HCIO transition state

The structural features of the HOCl → HClO isomerization mechanism, including all stationary points, and one saddle point, were examined by use of coupled cluster and the B3LYP density functional theory methodology. To improve the results a very large 6–311++G (3df, 3pd) Gaussian-type basis set was employed in the presented calculations. In addition, Gaussian-3 theory was tested against our coupled cluster (with single, double and triple excitations) results, and they were found to correlate closely with one another by around 1–2 kcal mol^?1. The energy change for this isomerization reaction is predicted to be 54.5 kcalmol^?1 and 52.5 kcalmol^?1 with the B3LYP and CCSD (T) methods, respectively, and the activation barrier is 76.1 kcal mol^?1 and 70.1 kcalmol^?1 with the same methods.     

QM/MM study of hydrolysis of arginine catalysed by arginase

ABSTRACT

In this paper, we have investigated the catalytic mechanism of rat liver arginase using a quantum mechanics/molecular mechanics (QM/MM) approach. The enzyme catalyses the hydrolysis of L-arginine (L-Arg) to generate L-ornithine and urea. The reaction mechanism proposed by the previous experimental studies is well reproduced by the QM/MM computations. The explicit treatment of the protein environment suggests that Glu277 fulfil its role in stabilising and orienting L-Arg before nucleophilic attack by the bridging hydroxide in the first step. We have also found that the proton transfer step involving a hydrogen bond switch is the rate-limiting step. The activation energy is computed to be 9.0 and 5.9 kcal/mol at the UB3LYP-D3/CHARMM22 and UBHandHLYP-D3/CHARMM22 levels, which are comparable to the observed activation barrier of 7.2 kcal/mol.     

Ab initio investigation of the gas phase reaction SO2 + H2O → SO2OH radical

High level ab initio calculations have been performed to investigate the reaction of the OH radical with SO₂. This reaction has been suggested as a possible first step in the atmospheric oxidation of SO₂. Results from both density functional theory (DFT) and second-order M?ller-Plesset calculations are reported. A small barrier has been located in the reaction channel and the structure of the corresponding transition state characterized. On the potential energy surface, the product, HOSO₂, occupies a double well potential that corresponds to a pair of equal energy rotamers separated by a barrier of ～12 kJ mol^?1 corresponding to a symmetric transition state.     

Computational studies on nonenzymatic pyroglutamylation mechanism of N-terminal glutamic acid residues in aqueous conditions*

Spontaneous cyclisation of glutamic acid (Glu) residues located at N-termini in peptides and proteins is called ‘pyroglutamylation’ and is assumed to be involved in several neurodegenerative diseases. Although it has long been believed that N-terminal Glu residues undergo pyroglutamylation enzymatically, it has recently been experimentally confirmed that nonenzymatic pyroglutamylation can proceed in some types of aqueous buffer. However, the detailed mechanism has not been proposed or investigated, and even whether some small-molecule catalysts are required for pyroglutamylation has not been clarified. Therefore, we investigated three types of pyroglutamylation mechanism of N-terminal Glu residues using quantum chemical calculations: in the absence of any catalysts, catalysed by one water molecule, and catalysed by two water molecules. All calculations were performed using N-terminal Glu residues capped with a methylamino group on the C-terminal as a model compound. Optimised energy minima and transition state geometries were obtained using the B3LYP density functional method. The pyroglutamylation mechanism is roughly divided into two steps: cyclisation and dehydration, and the calculated activation barrier was 108 and 107?kJ mol^?1 in the two- and three-water-assisted pathways, respectively. The results of computational analysis suggest that water molecules can act as catalysts for pyroglutamylation.

The calculated activation barrier of two-water-assisted pyroglutamylation was 108?kJ mol^?1, and the results of computational analysis indicate that water molecules can act as catalysts for pyroglutamylation.     

Combined multi-level quantum mechanics theories and molecular mechanics study of water-induced transition state of OH~- + CO_2 reaction in aqueous solution

The presence of a solvent interacting with a system brings about qualitative changes from the corresponding gasphase reactions. A solvent can not only change the energetics along the reaction pathway, but also radically alter the reaction mechanism. Here, we investigated the water-induced transition state of the OH~- + CO_2→ HCO_3~- reaction using a multi-level quantum mechanics and molecular mechanics method with an explicit water model. The solvent energy contribution along the reaction pathway has a maximum value which induces the highest energy point on the potential of mean force. The charge transfer from OH~- to CO_2 results in the breaking of the OH~- solvation shell and the forming of the CO_2 solvation shell. The loss of hydrogen bonds in the OH~-solvation shell without being compensated by the formation of hydrogen bonds in the CO_2 solvation shell induces the transition state in the aqueous solution. The calculated free energy reaction barrier at the CCSD(T)/MM level of theory, 11.8 kcal/mol, agrees very well with the experimental value, 12.1 kcal/mol.     

Isomerization of C3H3NO isomers: ab initio study

The structures and isomerization process of C₃H₃NO species have been explored at the MP2/6–311++G(d,p) level of theory of the ab initio method. Eleven minima and four interconversion transition states have been identified. The zero-point vibrational energy corrections were made to predict reliable energies. We predict a five-membered ring-like structure to be the lowest energy isomer, which is 177.73?kcal?mol^?1 more stable than the least stable isomer X found on the potential energy surface. The transition states and minima isomers were verified by frequency calculation. Intrinsic reaction coordinate (IRC) calculations have been performed to confirm that each transition state is linked by the desired reactants and products. The isomer stabilities have been studied using the relative energies, chemical hardness and chemical potential. The MHP principle could not predict the order of stability for C₃H₃NO isomers as arrived at with the relative energies. The role of intramolecular hydrogen bonds on the equilibrium structure has been discussed. The energy barrier and reaction enthalpy have been calculated during isomerization.     

The heats of formation of the haloacetylenes XCCY [X,Y = H,F, Cl]: basis set limit ab initio results and thermochemical analysis

The heats of formation of haloacetylenes are evaluated using the recent W1 and W2 ab initio computational thermochemistry methods. These calculations involve CCSD and CCSD(T) coupled cluster methods, basis sets of up to spdfgh quality, extrapolations to the one-particle basis set limit, and contributions of inner-shell correlation, scalar relativistic effects. and (where relevant) first-order spin-orbit coupling. The heats of formation determined using W2 theory are: δH₁ ²⁹⁸(HCCH) = 54.48 kcal mol^?1, δH_f ²⁹⁸(HCCH) = 25.15 kcal mol, δH_f ²⁹⁸(FCCF) = 1.38 kcal mol^?1, δH_f ²⁹⁸(HCCC1) = 54.83 kcal mol^?1, δH_f ²⁹⁸(CICCC1) = 56.21 kcal mol^?1, and δH_f ²⁹⁸(FCCC1) = 28.47 kcal mo1^?1. Enthalpies of hydrogenation and destabilization energies relative to acetylene were obtained at the WI level of theory. So doing we find the following destabilization order for acetylenes: FCCF > ClCCF > HCCF > ClCCCl > HCCCI > HCCH. By a combination of WI theory and isodesmic reactions. we show that the generally accepted heat of formation of 1,2-dichloroethane should be revised to ?31.8 ± 0.6 kcal mol^?1, in excellent agreement with a very recent critically evaluated review. The performance of compound thermochemistry schemes, such as G2, G3, G3X and CBS-QB3 theories, has been analysed.     

Anomeric effect plays a major role in the conformational isomerism of fluorinated pnictogen compounds

According to our theoretical studies, the anomeric effect, an stereoelectronic interaction between lone pair and a vicinal antibonding orbital, has shown to contribute decisively for the conformational isomerism of 1‐fluoro‐N,N‐dimethylmethanamine ( 1 ) and of its corresponding P, As and Sb analogues ( 2 – 4 ). C? X bonds in 2 – 4 are larger than in the parent compound 1 , thus providing a LP_X/C? F^* interaction progressively weaker on going from 1 to 4 . However, such hyperconjugation contributed by more than 1.3 kcal mol^?1 for the stabilization of anti conformer in 4 (θ_{LP? X? C? F} = 180°), increasing to 24.1 kcal mol^?1 in 1 . An isodesmic reaction model supported these findings. Copyright © 2008 John Wiley & Sons, Ltd.     

Characterization of aromatic-thiol π-type hydrogen bonding and phenylalanine-cysteine side chain interactions through ab initio calculations and protein database analyses

In this study, the aromatic-thiol π hydrogen bonding and phenylalanine-cysteine side chain interactions are characterized through both molecular orbital calculations on a C₆H₆-HSCH₃ model complex and database analyses of 609 X-ray protein structures. The aromatic-thiol π hydrogen bonding interaction can achieve a stabilization energy of 2.60 kcal mol^?1, and is stronger than the already documented aromatic-hydroxyl and aromatic-amino hydrogen bonds. However, the occurrence of the aromatic-thiol hydrogen bond is rather rare in proteins. This is because most of the thiol groups participate in the formation of either disulphide bonds or stronger S—H…O (or N) ‘normal’ hydrogen bonds in a protein environment. Interactions between the side chains of phenylalanine and cysteine residues are characterized as the phenyl(Phe)(HSCH₂-)(Cys) interaction. The bonding energy for such interactions is approximately 3.71 kcal mol-¹ and is achieved in a geometric arrangement with an optimal phenyl(Phe)-(HS-)(Cys) π-type hydrogen bonding interaction. The interaction is very sensitive to the orientation of the two lone electron pairs on the sulphur atom relative to the π electron cloud of the phenyl ring. Accordingly, the interaction configurations that can accomplish a significant bonding energy exist only within a narrow configurational space. The database analysis of 609 experimental X-ray protein structures demonstrates that only 268 of the 1620 cysteine residues involve such phenylalanine-cysteine side chain interactions. Most of these interactions occur in the form of π (aromatic)-lone pair(sulphur) attractions, and correspond to a bonding energy less than 1.5 kcal mol^?1. A few were identified as the aromatic-thiol hydrogen bond with a bonding energy of 2.0–3.6 kcal mol^?1.     

Theoretical investigation of the transition states leading to HCI elimination in 2-chloropropene

This paper describes ab initio electronic structure calculations on the planar transition states of 2-chloropropene leading to HCI elimination in the ground electronic state to form either propyne or allene as the cofragment. The calculations provide optimized geometries of the transition states for these two reaction channels, together with vibrational frequencies, barrier heights, and reaction endothermicities. The calculated barrier heights for the two distinct four-centre HCI elimination transition states, one leading to HCI and propyne and the other leading to HCI and allene, are 72.5kcalmol^?1 (77.8kcalmol^?1 without zero-point correction) and 73.2kcalmol^?1 (78.7kcalmol^?1) at the MP2/6-311G(d, p) level, 71.Okcalmol^?1 (76.3kcalmol^?1) and 70.5kcalmol^?1 (76.0kcalmol^?1) at the QCISD(T)/6-311 +G(d, p)//MP2/6-311G(d, p) level, and 66.9kcalmol^?1 (71.7kcalmol^?1) and 67.3kcalmol^?1 (72.1kcalmol¹) at the G3//B3LYP level of theory. Calculated harmonic vibrational frequencies at the B3LYP/6-31G(d) level along with transition state barrier heights from the G3//B3LYP level of theory are used to obtain RRKM reaction rate constants for each transition state, which determine the branching ratio between the two HCI elimination channels. Even at internal energies well above both HCI elimination barriers, the HCI elimination leading to propyne is strongly favoured. The smaller rate constant for the HCI elimination leading to allene can be attributed to the strong hindrance of the methyl rotor in the corresponding transition state.     

The 1,2-hydrogen shift reaction for monohalogenophosphanes PH2X and HPX (X = F,Cl)

The aim of the present study was to perform a quantum chemical investigation in the 1,2-hydrogen shift reaction for the PH₂X and HPX molecules (X = F,Cl). Several phosphorus–halogen-bearing molecules were studied, including PH₂F, PH₂Cl, HPF, HPCl, HPFH, HPClH, PFH and PClH. The energies of stationary and saddle points on the ground electronic potential energy surface were investigated with post-Hartree–Fock methods [CCSD(T), MP2, QCISD] and different DFT functionals. The PH₂F 1,2-hydrogen shift energy barrier was 75 kcal mol^?1 at the CCSD(T) level and only a small increase in this value was observed for the HPF isomerisation. In contrast, the HPCl 1,2-hydrogen shift barrier is higher than the PH₂Cl one, which presented a barrier height of 69 kcal mol^?1 among CCSD(T) and composite methods. The rate constants of these unimolecular rearrangements varied from 10^?44 to 10^?38 s^?1, and these isomerisation channels exhibited large half-lives. In addition, the heat of formation of each monohalogenophosphane was also calculated. The Quantum Theory of Atoms in Molecules (QTAIM) and Natural Bond Orbital (NBO) analysis were also employed to characterise the differences between the phosphorous–halogen bonds.     

A computational characterization of N2@C60

Recent observations of N₂@C₆₀ are supported computationally. The geometry is optimized at the B3LYP/3-21G and PW91/3-21G levels. The lowest-energy structure has the N₂ unit oriented towards a pair of parallel pentagons so that the complex exhibits D_5d symmetry. Single-point energy calculations are further carried out at the B3LYP/6-31G*, PW91/6-31G* and MP2?=?FC/6-31G* levels and corrected for the basis set superposition error (BSSE). The MP2?=?FC/6-31G* treatment with the BSSE correction gives a stabilization energy of -9.3?kcal?mol^?1, whereas DFT approaches mostly fail to produce a stabilization. The entropy term for the encapsulation is also evaluated and leads to a standard Gibbs energy change upon encapsulation at room temperature of -3.3?kcal?mol^?1. The computed structural and vibrational characteristics are also reported.     

Comparison of the Kinetics of the Exchange Mechanism of the Thallium Ion with 18C6 and with Pentaglyme in Acetonitrile Solutions

Abstract

In acetonitrile solutions, the exchange reaction is bimolecular in the Tl⁺ + 18C6 system, while in the Tl⁺ + pentaglyme system the associative-dissociative and the bimolecular mechanisms coexist at room temperature and the bimolecular exchange reaction dominates at 263° K. For the bimolecular mechanism in the case of Tl⁺ + 18C6 and the associative-dissociative mechanism in the case of Tl⁺ + pentaglyme, the activation energies of the exchange reactions change with temperature. At 298° K, in the Tl⁺ + 18C6 system the activation energy for the bimolecular exchange reaction is ≈ 2 kcal.mol^?1 and exchange rate constant (k₁) is (4.1 ± 0.1) × 10⁷ s^?1mol^?1; in the Tl⁺ + pentaglyme system, the activation energy for the associative-dissociative exchange reaction is ≈ 5 kcal mol^?1 and the decomplexation rate constant (k_?2) is (2.2 ± 0.4) X 10⁵ s^?1. The activation energy for the bimolecular exchange in the Tl⁺ + pentaglyme system was determined to be 3.00 ± 0.05 kcal.mol_?1 and the exchange rate constant (3.0 ± 0.1) X 10⁸ s^?1 mol^?1.