Double proton transfer and one-electron oxidation behavior in double H-bonded glycinamide-glycine complex in the gas phase

The behaviors of double proton transfer (DPT) occurring in a representative glycinamide-glycine complex have been investigated employing the B3LYP/6-311++G** level of theory. Thermodynamic and especially kinetic parameters, such as tautomerization energy, equilibrium constant, and barrier heights have been discussed, respectively. The relevant quantities involved in the DPT process including geometrical changes, interaction energies, and deformation energies have also been studied. Analogous to that of tautomeric process assisted with a formic acid molecule, the participation of a glycine molecule favors the proceeding of the proton transfer (PT) for glycinamide compared with that without mediator-assisted case. The DPT process proceeds with a concerted mechanism rather than a stepwise one because no zwitterionic complexes have been located during the DPT process. The barrier heights are 12.14 and 0.83 kcal/mol for the forward and reverse directions, respectively. However, both of them have been reduced by 3.10 and 2.66 kcal/mol to 9.04 and -1.83 kcal/mol with further inclusion of zero-point vibrational energy (ZPVE) corrections, where the disappearance of the reverse barrier height implies that the reverse reaction should proceed with barrierless spontaneously, analogous to those of DPTs occurring between glycinamide and formic acid (or formamide). Additionally, the oxidation process for the double H-bonded glycinamide-glycine complex has also been investigated. The oxidated product is characterized by a distonic radical cation due to the fact that one-electron oxidation takes place on glycine fragment and a proton has been transferred from glycine to glycinamide fragment spontaneously. As a result, the vertical and adiabatic ionization potentials for the neutral complex have been determined to be about 8.71 and 7.85 eV, respectively, where both of them have been reduced by about 0.54 (1.11) and 0.75 (1.13) eV relative to those of isolated glycinamide (glycine) due to the formation of the intermolecular H-bond.     

2-hydroxypyridine <--> 2-pyridone tautomerization: catalytic influence of formic acid

A 1:1 hydrogen-bonded complex between 2-pyridone and formic acid has been characterized using laser-induced-fluorescence excitation and dispersed fluorescence spectroscopy in a supersonic jet expansion. Under the same expansion condition, the fluorescence signal of the tautomeric form of the complex (2-hydroxypyridine...formic acid) is absent, although both the bare tautomeric molecules exhibit well-resolved laser-induced-fluorescence spectra. Quantum chemistry calculation at the DFT/B3LYP/6-311++G** level predicts that in the ground electronic state the activation barrier for tautomerization from hydroxy to keto form in bare molecules is very large (approximately 34 kcal/mol). However, the process turns out to be nearly barrierless when assisted by formic acid, and double proton transfer occurs via a concerted mechanism.     

New insight into the gas-phase bimolecular self-reaction of the HOO radical

The singlet and triplet potential energy surfaces (PESs) for the gas-phase bimolecular self-reaction of HOO*, a key reaction in atmospheric environments, have been investigated by means of quantum-mechanical electronic structure methods (CASSCF and CASPT2). All the reaction pathways on both PESs consist of a first step involving the barrierless formation of a prereactive doubly hydrogen-bonded complex, which is a diradical species lying about 8 kcal/mol below the energy of the reactants at 0 K. The lowest energy reaction pathway on both PESs is the degenerate double hydrogen exchange between the HOO* moieties of the prereactive complex via a double proton transfer mechanism involving an energy barrier of only 1.1 kcal/mol for the singlet and 3.3 kcal/mol for the triplet at 0 K. The single H-atom transfer between the two HOO* moieties of the prereactive complex (yielding HOOH + O2) through a pathway keeping a planar arrangement of the six atoms involves a conical intersection between either two singlet or two triplet states of A' and A" symmetries. Thus, the lowest energy reaction pathway occurs via a nonplanar cisoid transition structure with an energy barrier of 5.8 kcal/mol for the triplet and 17.5 kcal/mol for the singlet at 0 K. The simple addition between the terminal oxygen atoms of the two HOO* moieties of the prereactive complex, leading to the straight chain H2O4 intermediate on the singlet PES, involves an energy barrier of 7.3 kcal/mol at 0 K. Because the decomposition of such an intermediate into HOOH + O2 entails an energy barrier of 45.2 kcal/mol at 0 K, it is concluded that the single H-atom transfer on the triplet PES is the dominant pathway leading to HOOH + O2. Finally, the strong negative temperature dependence of the rate constant observed for this reaction is attributed to the reversible formation of the prereactive complex in the entrance channel rather than to a short-lived tetraoxide intermediate.     

Gas-phase proton-transfer pathways in protonated histidylglycine

Pathways for proton transfer in the histidylglycine cation are examined in the gas-phase environment with the goal of understanding the mechanism by which protons may become mobile in proteins with basic amino acid residues. An extensive search of the potential energy surface is performed using density functional theory (DFT) methods. After corrections for zero-point energy are included, it is found that all the lowest energy barriers for proton transfer between the N-terminus and the imidazole ring have heights of only a few kcal/mol, while those between the imidazole ring and the backbone amide oxygen have heights of approximately 15 kcal/mol when the proton is moving from the ring to the backbone and only a few kcal/mol when moving from the backbone to the imidazole ring. In mass spectrometric techniques employing collision-induced dissociation to dissociate protein complex ions or to fragment peptides, these barriers can be overcome, and the protons mobilized. Copyright (c) 2008 John Wiley & Sons, Ltd.     

Formamide tautomerization: catalytic role of formic acid

Formic acid catalyzed tautomeric conversion of formamide to formamidic acid has been investigated by use of ab initio and density functional theoretical calculations. In a 1:1 dimeric complex between formamide and formic acid, the tautomeric conversion occurs via double-hydrogen transfer within an eight-member hydrogen-bonded cyclic network. The results predict that the energy barrier of the catalytic process is reduced by more than a factor of 4 compared to that in the isolated formamide molecule in the gas phase, and the tautomerization in the 1:1 complex is several kcal/mol less endothermic than that of the isolated molecule. The potential energy surface corresponding to this double hydrogen transfer process indicates that a concerted transfer of both the hydrogen atoms along the hydrogen bond directions is energetically favorable, and no minimum for an ionic intermediate, which may arise for stepwise transfer, was predicted. The unique configuration of the transition state has been identified by starting the reaction from both the tautomeric forms, and the transition state was subjected to IRC calculation.     

The ground-state tunneling splitting of various carboxylic acid dimers

Carboxylic acid dimers in gas phase reveal ground-state tunneling splittings due to a double proton transfer between the two subunits. In this study we apply a recently developed accurate semiclassical method to determine the ground-state tunneling splittings of eight different carboxylic acid derivative dimers (formic acid, benzoic acid, carbamic acid, fluoro formic acid, carbonic acid, glyoxylic acid, acrylic acid, and N,N-dimethyl carbamic acid) and their fully deuterated analogs. The calculated splittings range from 5.3e-4 to 0.13 cm(-1) (for the deuterated species from 2.8e-7 to 3.3e-4 cm(-1)), thus indicating a strong substituent dependence of the splitting, which varies by more than two orders of magnitude. One reason for differences in the splittings could be addressed to different barriers heights, which vary from 6.3 to 8.8 kcal/mol, due to different mesomeric stabilization of the various transition states. The calculated splittings were compared to available experimental data and good agreement was found. A correlation could be found between the tunneling splitting and the energy barrier of the double proton transfer, as the splitting increases with increased strength of the hydrogen bonds. From this correlation an empirical formula was derived, which allows the prediction of the ground-state tunneling splitting of carboxylic acid dimers at a very low cost and the tunneling splittings for parahalogen substituted benzoic acid dimers is predicted.     

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.     

Proton exchanges between phenols and ammonia or amines: a computational study

Density functional theory calculations at the B3LYP/6-31+G(d,p) level of theory have been performed to explore proton exchanges between phenols and ammonia or amines, which can be used to account for previous NMR experiments. For the parent phenol-NH(3) system, a transition state with a symmetric phenolate-NH(4)(+)-like structure, which lies about 35 kcal mol(-1) in energy above the hydrogen-bonded complex, has been successfully located. An intrinsic reaction coordinate (IRC) analysis indicates that the proton exchange is a concerted process, which can be roughly divided into four continuous subprocesses. A series of para-substituted phenol-NH(3) systems have been considered to investigate the substituent effect. Whereas introduction of an electron-withdrawing group on the phenol appreciably reduces the barrier, an opposite effect is observed for an electron-donating group. Moreover, it has been disclosed that there exists a good linear correlation between the activation barriers and the interaction energies between the phenols and NH(3), indicating the important role of proton transfer (or hydrogen bonding) in determining the proton exchange. Also considered are the proton exchanges between phenol and amines and those for some sterically hindered systems. The results show that the phenol tends to exchange hydrogen with the amines, preferably the secondary amines, and that the steric effect is favorable for the proton exchange, which imply that, as the IRC analysis suggested, besides the proton transfer, the flip of the ammonium-like moiety may play a significant role in the course of proton exchange. For all of these systems, we investigated the solvent effects and found that the barrier heights of proton exchange decrease remarkably as compared to those in a vacuum due to the ion pair feature of the transition state. Finally, we explored the phenol radical cation-NH(3) system; the barrierless proton transfer and remarkably low barrier (5.2 kcal mol(-1)) of proton exchange provide further evidence for the importance of proton transfer in the proton exchange.     

锰配合物催化CO2加氢生成甲酸的理论研究

采用密度泛函理论(DFT)对锰配合物催化二氧化碳加氢生成甲酸的反应进行了理论研究. 整个催化循环主要包括氢气活化和二氧化碳氢化2个阶段. 计算结果表明, 甲酸的参与明显降低了氢气活化的反应能垒; 二氧化碳的氢化过程遵循外层机理并且氢转移是分步进行的, 决速步骤为氢负离子的转移过程, 自由能垒为21.0 kJ/mol. 对配合物中硫原子上的取代基R进行了调变, 研究结果表明, 当R为吸电子基团时能降低氢气裂解和二氧化碳氢化过程中质子转移的能垒, 而当R为推电子基团时有利于氢负离子的转移,当R=CF₃时整个反应的能量跨度(80.4 kJ/mol)最小.     

A Marcus treatment of rate constants for protonation of ring-substituted alpha-methoxystyrenes: intrinsic reaction barriers and the shape of the reaction coordinate

Rate and equilibrium constants were determined for protonation of ring-substituted -methoxystyrenes by hydronium ion and by carboxylic acids to form the corresponding ring-substituted alpha-methyl alpha-methoxybenzyl carbocations at 25 degrees C and I = 1.0 (KCl). The thermodynamic barrier to carbocation formation increases by 14.5 kcal/mol as the phenyl ring substituent(s) is changed from 4-MeO- to 3,5-di-NO2-, and as the carboxylic acid is changed from dichloroacetic to acetic acid. The Br?nsted coefficient alpha for protonation by carboxylic acids increases from 0.67 to 0.77 over this range of phenyl ring substituents, and the Br?nsted coefficient beta for proton transfer increases from 0.63 to 0.69 as the carboxylic acid is changed from dichloroacetic to acetic acid. The change in these Br?nsted coefficients with changing reaction driving force, (inverted theta)alpha/ (inverted theta) deltaG(av) degrees=(inverted theta)beta/(inverted theta)delta G(av) degrees= 1/8lambda = 0.011, is used to calculate a Marcus intrinsic reaction barrier of lambda= 11 kcal/mol which is close to the barrier of 13 kcal/mol for thermoneutral proton transfer between this series of acids and bases. The value of alpha= 0.66 for thermoneutral proton transfer is greater than alpha= 0.50 required by a reaction that follows the Marcus equation. This elevated value of beta may be due to an asymmetry in the reaction coordinate that arises from the difference in the intrinsic barriers for proton transfer at the oxygen acid reactant and resonance-stabilized carbon acid product.     

Ab initio model study on acetylcholinesterase catalysis: potential energy surfaces of the proton transfer reactions

Ab initio molecular orbital (MO) and hybrid density functional theory (DFT) calculations have been applied to the initial step of the acylation reaction catalyzed by acetylcholinesterase (AChE), which is the nucleophiric addition of Ser200 in catalytic triads to a neurotransmitter acetylcholine (ACh). We focus our attention mainly on the effects of oxyanion hole and Glu327 on the potential energy surfaces (PESs) for the proton transfer reactions in the catalytic triad Ser200-His440-Glu327. The activation barrier for the addition reaction of Ser200 to ACh was calculated to be 23.4 kcal/mol at the B3LYP/6-31G(d)//HF/3-21G(d) level of theory. The barrier height under the existence of oxyanion hole, namely, Ser200-His440-Glu327-ACh-(oxyanion hole) system, decreased significantly to 14.2 kcal/mol, which is in reasonable agreement with recent experimental value (12.0 kcal/mol). Removal of Glu327 from the catalytic triad caused destabilization of both energy of transition state for the reaction and tetrahedral intermediate (product). PESs calculated for the proton transfer reactions showed that the first proton transfer process is the most important in the stabilization of tetrahedral intermediate complex. The mechanism of addition reaction of ACh was discussed on the basis of theoretical results.     

Mechanisms of acid decomposition of dithiocarbamates. 4. Theoretical calculations on the water-catalyzed reaction

A theoretical study of the water-catalyzed dithiocarbamic acid cleavage has been performed using N-methyl- (MeDTC) and N-phenyldithiocarbamic acid (PhDTC) as model molecules. Calculations have been carried out within the Density Functional Theory (DFT) formalism, using the B3LYP hybrid functional together with medium-sized basis sets, both in gas phase and by considering solvent effects through dielectric continuum methods. According to the results obtained, both in gas phase and in solution, MeDTC decomposes through a proton-transfer step assisted by a water molecule (this being the rate-determining step), leading to a zwitterionic intermediate, followed by a fast N-C bond-breaking process. In the case of PhDTC, the theoretical results point to a one-step mechanism in which the N-C bond breaking takes place in a concerted manner with the proton transfer. The calculated Delta Delta G(++) of the proton-transfer step for MeDTC and PhDTC is 4.0 kcal mol(-1), which is similar to the experimental values. For both compounds the water-assisted intramolecular proton transfer occurs with a twisting of the CS(2) group that inhibits the resonance of the thiocarbamic group, making the nitrogen more basic and therefore favoring the proton transfer. The difference in the torsional barrier has been calculated to be ca. 5 kcal mol(-1), and it is therefore concluded that most of the activation barrier of the reaction is due to the torsional barrier of the CS(2) group.     

Formic acid catalyzed hydrolysis of SO3 in the gas phase: a barrierless mechanism for sulfuric acid production of potential atmospheric importance

Computational studies at the B3LYP/6-311++G(3df,3pd) and MP2/6-311++G(3df,3pd) levels are performed to explore the changes in reaction barrier height for the gas phase hydrolysis of SO(3) to form H(2)SO(4) in the presence of a single formic acid (FA) molecule. For comparison, we have also performed calculations for the reference reaction involving water assisted hydrolysis of SO(3) at the same level. Our results show that the FA assisted hydrolysis of SO(3) to form H(2)SO(4) is effectively a barrierless process. The barrier heights for the isomerization of the SO(3)···H(2)O···FA prereactive collision complex, which is the rate limiting step in the FA assisted hydrolysis, are found to be respectively 0.59 and 0.08 kcal/mol at the B3LYP/6-311++G(3df,3pd) and MP2/6-311++G(3df,3pd) levels. This is substantially lower than the ~7 kcal/mol barrier for the corresponding step in the hydrolysis of SO(3) by two water molecules--which is currently the accepted mechanism for atmospheric sulfuric acid production. Simple kinetic analysis of the relative rates suggests that the reduction in barrier height facilitated by FA, combined with the greater stability of the prereactive SO(3)···H(2)O···FA collision complex compared to SO(3)···H(2)O···H(2)O and the rather plentiful atmospheric abundance of FA, makes the formic acid mediated hydrolysis reaction a potentially important pathway for atmospheric sulfuric acid production.     

Different Catalytic Effects of a Single Water Molecule: The Gas‐Phase Reaction of Formic Acid with Hydroxyl Radical in Water Vapor

The effect of a single water molecule on the reaction mechanism of the gas‐phase reaction between formic acid and the hydroxyl radical was investigated with high‐level quantum mechanical calculations using DFT–B3LYP, MP2 and CCSD(T) theoretical approaches in concert with the 6‐311+G(2df,2p) and aug‐cc‐pVTZ basis sets. The reaction between HCOOH and HO has a very complex mechanism involving a proton‐coupled electron transfer process (pcet), two hydrogen‐atom transfer reactions (hat) and a double proton transfer process (dpt). The hydroxyl radical predominantly abstracts the acidic hydrogen of formic acid through a pcet mechanism. A single water molecule affects each one of these reaction mechanisms in different ways, depending on the way the water interacts. Very interesting is also the fact that our calculations predict that the participation of a single water molecule results in the abstraction of the formyl hydrogen of formic acid through a hydrogen atom transfer process (hat).     

Overtone-induced decarboxylation: a potential sink for atmospheric diacids

Atmospheric photochemistry induced by solar excitation of vibrational overtone transitions has recently been demonstrated to be of importance in cleaving weak bonds (in HO(2)NO(2)) and inducing intramolecular rearrangement followed by reaction (in H(2)SO(4)). Here, we propose another potentially important process: the decarboxylation of organic acids. To demonstrate this possibility, we have calculated the decarboxylation pathways for malonic acid and its monohydrate. The barrier to the gas-phase decarboxylation was calculated to be in the range 26-28 kcal/mol at the B3LYP/6-311++G(3df,3pd) level of theory, in good agreement with previous results. The transition state is a six-membered ring structure which is accessed via concerted O-H and C-C stretches; excitation of v(OH) > or = 3 of either one of the OH stretching modes is sufficient to supply the energy needed for the decarboxylation. A low-energy isomer of the malonic acid-water complex forms an eight-membered, multiply hydrogen bonded structure, bound by 3-6 kcal/mol, somewhat less stable than the lowest energy, six-membered ring isomer. Decarboxylation of such complexes uses water as a catalyst; the water accepts an acidic proton from one malonic acid group and transfers a proton to the carbonyl of the other acid group. The barrier for this process is 20-22 kcal/mol, suggesting that complexes excited to v(OH) > or = 2 possess sufficient energy to react. Using estimated absorption cross sections for the OH overtone transitions, we suggest that the overtone-induced decarboxylation of malonic acid and its water complex is competitive with wet deposition of the acid and with gas-phase reaction with OH for removal of the acid.     

Fundamental reaction pathway and free energy profile for inhibition of proteasome by Epoxomicin

First-principles quantum mechanical/molecular mechanical free energy calculations have been performed to provide the first detailed computational study on the possible mechanisms for reaction of proteasome with a representative peptide inhibitor, Epoxomicin (EPX). The calculated results reveal that the most favorable reaction pathway consists of five steps. The first is a proton transfer process, activating Thr1-O(γ) directly by Thr1-N(z) to form a zwitterionic intermediate. The next step is nucleophilic attack on the carbonyl carbon of EPX by the negatively charged Thr1-O(γ) atom, followed by a proton transfer from Thr1-N(z) to the carbonyl oxygen of EPX (third step). Then, Thr1-N(z) attacks on the carbon of the epoxide group of EPX, accompanied by the epoxide ring-opening (S(N)2 nucleophilic substitution) such that a zwitterionic morpholino ring is formed between residue Thr1 and EPX. Finally, the product of morpholino ring is generated via another proton transfer. Noteworthy, Thr1-O(γ) can be activated directly by Thr1-N(z) to form the zwitterionic intermediate (with a free energy barrier of only 9.9 kcal/mol), and water cannot assist the rate-determining step, which is remarkably different from the previous perception that a water molecule should mediate the activation process. The fourth reaction step has the highest free energy barrier (23.6 kcal/mol) which is reasonably close to the activation free energy (～21-22 kcal/mol) derived from experimental kinetic data. The obtained novel mechanistic insights should be valuable for not only future rational design of more efficient proteasome inhibitors but also understanding the general reaction mechanism of proteasome with a peptide or protein.     

Electronic Factors Influencing the Decarboxylation of beta-Keto Acids. A Model Enzyme Study

A theoretical study of the mechanism of decarboxylation of beta-keto acids is described. A cyclic transition structure was found with essentially complete proton transfer from the carboxylic acid to the beta-carbonyl group. The activation barrier for decarboxylation of formylacetic acid is predicted to be 28.6 kcal/mol (MP4SDTQ/6-31G//MP2/6-31G) while loss of CO(2) from its anion exhibits a barrier of only 20.6 kcal/mol (MP4SDTQ/6-31+G//MP2/6-31+G). Barrier heights of decarboxylation of malonic acid and alpha,alpha-dimethylacetoacetic acid are predicted to be 33.2 and 26.7 kcal/mol, respectively. Model enzyme studies using a thio methyl ester of malonate anion suggests that the role of malonyl-CoA is to afford a polarizable sulfur atom to stabilize the developing enolate anion in the transition structure for decarboxylation. Adjacent positively charged ammonium ions are also observed to stabilize the loss of CO(2) from a carboxylate anion by through-bond Coulombic stabilization of the transition structure.     

The 6-31B(d) basis set and the BMC-QCISD and BMC-CCSD multicoefficient correlation methods

Three new multicoefficient correlation methods (MCCMs) called BMC-QCISD, BMC-CCSD, and BMC-CCSD-C are optimized against 274 data that include atomization energies, electron affinities, ionization potentials, and reaction barrier heights. A new basis set called 6-31B(d) is developed and used as part of the new methods. BMC-QCISD has mean unsigned errors in calculating atomization energies per bond and barrier heights of 0.49 and 0.80 kcal/mol, respectively. BMC-CCSD has mean unsigned errors of 0.42 and 0.71 kcal/mol for the same two quantities. BMC-CCSD-C is an equally effective variant of BMC-CCSD that employs Cartesian rather than spherical harmonic basis sets. The mean unsigned error of BMC-CCSD or BMC-CCSD-C for atomization energies, barrier heights, ionization potentials, and electron affinities is 22% lower than G3SX(MP2) at an order of magnitude less cost for gradients for molecules with 9-13 atoms, and it scales better (N6 vs N,7 where N is the number of atoms) when the size of the molecule is increased.     

Computational study of phosphatase activity in soluble epoxide hydrolase: high efficiency through a water bridge mediated proton shuttle

Recently, a new branch of fatty acid metabolism has been opened by the novel phosphatase activity found in the N-terminal domain of the, hence bifunctional, soluble epoxide hydrolase (sEH). Importantly, this finding has also provided a new site for drug targeting in sEH's activity regulation. Classical MD and hybrid Car-Parrinello QM/MM calculations have been performed to investigate the reaction mechanism of the phosphoenzyme intermediate formation in the first step of the catalysis. The results support a concerted multi-event reaction mechanism: (1) a dissociative in-line nucleophilic substitution for the phosphoryl transfer reaction; (2) a double proton transfer involved in the formation of a good leaving group in the transition state. The presence of a water bridge in the substrate/enzyme complex allowed an efficient proton shuttle, showing its key role in speeding up the catalysis. The calculated free energy of the favored catalytic pathway is approximately 19 kcal/mol, in excellent agreement with experimental data.