Uncatalyzed peptide bond formation between two double amino acid molecules in the gas phase

The gas phase mechanism for peptide bond formation between two double amino acid (DAA) molecules ((NH₂)₂C(COOH)₂) is investigated in the absence of any catalysts. Two different paths, concerted and stepwise, each leading to both cis and trans DAA‐DAA dipeptide products (four mechanisms total) are examined on the basis of theoretical calculations carried out at the CCSD(T)/aug‐cc‐pVDZ//MP2/aug‐cc‐pVDZ level. The investigation indicates that the concerted mechanism leading to the trans configuration of the peptide bond in the DAA‐DAA dipeptide product is thermodynamically favored by about 5 kcal mol^?1 and requires slightly less energy than the remaining pathways considered. Moreover, the peptide bond formation process between two DAA molecules in the gas phase resembles the analogous reactions between two natural amino acids.     

Reaction HFCO + 2H2O — Calculated Mechanisms

Three possible reaction mechanisms of methanoyl fluoride with 2H₂O include a concerted and a stepwise hydrolysis of HFCO into HCOOH + HF, and a pure catalytic decomposition of HFCO into HF + CO. Among these, the two H₂O molecules acting as catalyst to decompose HFCO has the lowest calculated barrier, 25.1 kcal/mol with respect to the reactant‐adduct complex, whereas the barriers for the concerted and stepwise hydrolytic reactions in which one H₂O acts as a reactant and the other H₂O as catalyst are similar, 30.8 kcal/mol for concerted and 29.9 kcal/mol for stepwise. The formation of transoid HCOOH in the hydrolysis of HFCO is more favorable than cisoid HCOOH.     

Insights into the mechanism of methionine oxidation catalyzed by metal (Cu2+, Zn2+, and Fe3+)—Amyloid beta (Aβ) peptide complexes: A computational study

In this DFT study, a mechanism of the oxidation of methionine (Met) amino acid residue catalyzed by the metal (Cu²⁺, Zn²⁺, and Fe³⁺) bound amyloid beta (Aβ) peptide has been proposed. Based on experimental information, two different mechanisms: (1) stepwise and (2) concerted mechanisms for this important process have been investigated. The B3LYP calculations suggest that in the stepwise mechanism, the two separate pathways leading to the same sulfoxide product [Met(O)] go through prohibitively high barriers of 27.3 and 35.1 kcal/mol, therefore it is ruled out. In the concerted mechanism, the Cu²⁺‐Aβ complex has been found to be the most efficient catalyst with the computed barrier of 14.3 kcal/mol. The substitutions of Cu²⁺ by Zn²⁺ and Fe³⁺ increase barriers to 19.6 and 16.9 kcal/mol, respectively and make the reaction thermodynamically less favorable. It was also found that, in comparison with the cysteine (Cys) residue, Met is more susceptible toward oxidation. Its substitution with Cys slightly increased the barrier to 15.8 kcal/mol for the Cu²⁺‐Aβ complex. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009     

An ab initio study on the allene-isocyanic acid and ketene-vinylimine [2 + 2] cycloaddition reaction paths

The reaction paths of [2 + 2] cycloadditions of allene (H2C=C=CH2) to isocyanic acid (HN=C=O) and ketene (H2C=C=O) to vinylimine (H2C=C=NH), leading to all the possible 14 four-membered ring molecules, were investigated by the MP2/aug-cc-pVDZ method. In the two considered reactions, the 2-azetidinone (beta-lactam) ring compounds were predicted to be the most stable thermodynamically in the absence of an environment. Although 4-methylene-2-azetidinone is the most stable product of the ketene-vinylimine cycloaddition, its activation barrier is higher than that for 4-methylene-2-iminooxetane by ca. 6 kcal/mol. Therefore, the latter product can be obtained owing to kinetic control. The activation barriers in the allene-isocyanic acid reactions are quite high, 50-70 kcal/mol, whereas in the course of the ketene-vinylimine cycloaddition they are equal to ca. 30-55 kcal/mol. All the reactions studied were found to be concerted and mostly asynchronous. Simulation of the solvent environment (toluene, tetrahydrofuran, acetonitrile, and water) by using Tomasi's polarized continuum model with the integral equation formalism (IEF-PCM) method showed the allene-isocyanic reactions remained concerted, yet the activation barriers were somewhat higher than those in the gas phase, whereas the ketene-vinylimine reactions became stepwise. The larger the solvent dielectric constant, the lower the activation barriers found. The lowest-energy pathways in the gas phase and in solvent were confirmed by intrinsic reaction coordinate (IRC) calculations. The atoms in molecules (AIM) analysis of the electron density distribution in the transition-state (TS) structures allowed us to distinguish pericyclic from pseudopericyclic from nonplanar-pseudopericyclic types of reactions.     

Transition states for the dimerization of 1,3-cyclohexadiene: a DFT, CASPT2, and CBS-QB3 quantum mechanical investigation

Quantum mechanical calculations using restricted and unrestricted B3LYP density functional theory, CASPT2, and CBS-QB3 methods for the dimerization of 1,3-cyclohexadiene (1) reveal several highly competitive concerted and stepwise reaction pathways leading to [4 + 2] and [2 + 2] cycloadducts, as well as a novel [6 + 4] ene product. The transition state for endo-[4 + 2] cycloaddition (endo-2TS, DeltaH(double dagger)(B3LYP(0K)) = 28.7 kcal/mol and DeltaH(double dagger)(CBS-QB3(0K)) = 19.0 kcal/mol) is not bis-pericyclic, leading to nondegenerate primary and secondary orbital interactions. However, the C(s) symmetric second-order saddle point on the B3LYP energy surface is only 0.3 kcal/mol above endo-2TS. The activation enthalpy for the concerted exo-[4 + 2] cycloaddition (exo-2TS, DeltaH(double dagger)(B3LYP(0K)) = 30.1 kcal/mol and DeltaH(double dagger)(CBS-QB3(0K)) = 21.1 kcal/mol) is 1.4 kcal/mol higher than that of the endo transition state. Stepwise pathways involving diallyl radicals are formed via two different C-C forming transition states (rac-5TS and meso-5TS) and are predicted to be competitive with the concerted cycloaddition. Transition states were located for cyclization from intermediate rac-5 leading to the endo-[4 + 2] (endo-2) and exo-[2 + 2] (anti-3) cycloadducts. Only the endo-[2 + 2] (syn-3) transition state was located for cyclization of intermediate meso-5. The novel [6 + 4] "concerted" ene transition state (threo-4TS, DeltaH(double dagger)(UB3LYP(0K)) = 28.3 kcal/mol) is found to be unstable with respect to an unrestricted calculation. This diradicaloid transition state closely resembles the cyclohexadiallyl radical rather than the linked cyclohexadienyl radical. Several [3,3] sigmatropic rearrangement transition states were also located and have activation enthalpies between 27 and 31 kcal/mol.     

Computational study on the reaction mechanism of atmospheric oxidation of ethanol with ozone

The reaction of C₂H₅OH and O₃ on the singlet potential energy surface is carried out using the MP2 and CCSD(T)//MP2 theoretical approaches in connection with the 6-311++G(d,p) basis set. Three pre-reactive complexes C1, C2, and C3 are formed between ethanol and ozone at atmospheric pressure and 298.15 K temperature. With variety of the complexes, seven types of product are obtained which four types of them have enough thermodynamic stability. In thermodynamic approach, the most favor product begins with the formation of pre-reactive C2 complex and produces the CH₃CH(OH)₂ + O₂ as final adduct in a process that is computed to be exothermic by ?53.759 kcal/mol and spontaneous reaction by ?51.833 kcal/mol in Gibbs free energy. In kinetic viewpoint, the formation of CH₃COH + cis-H₂O₃ as a final adducts is the most favor path.     

Theoretical study on the reaction pathways of HFCO + H2O

For the reaction of methanoyl fluoride with water, both optimized structures and vibrational wavenumbers of reaction intermediates, transition structures and product complexes were calculated and characterized with theory at the MP2/6-311++G(d,p) level. Including a catalytic path and concerted and stepwise hydrolysis paths, possible reaction mechanisms were also investigated. The catalytic reaction of HFCO yielding HF and CO has the smallest activation barrier, 29.6 kcal/mol, whereas for the concerted hydrolysis 33.0 kcal/mol is required to overcome the barrier to form transoid HCOOH + HF, which is less than for the stepwise counterpart, 42.0 kcal/mol.     

Ab initio studies of isomerization and dissociation reactions of methyl peroxynitrate

Using the CCSD(T)/cc-pVDZ//B3LYP/6-311G(2d,2p) method, we calculated the detailed potential energy surfaces (PESs) for the unimolecular isomerization and decomposition of methyl peroxynitrate (CH₃O₂NO₂). The results show that there are the two most stable isomers, IS1a and IS1b, which are a pair of mirror image isomers. From IS1a and IS1b, different isomerization and unimolecular decomposition reaction channels have been studied and discussed. Among them, the predominant thermal decomposition pathways are those leading to CH₃O₂ + NO₂ and cis-CH₃ONO + O₂. The former is the lowest-energy path through the direct O–N bond rupture in IS1a or IS1b. The PES along the O–N bond in IS1a has been scanned, where the energy of IS1a reaches maximum value of 23.5 kcal/mol when the O–N bond is stretched to about 2.8 Å. This energy is 2.7 kcal/mol larger than the O–N bond dissociation energy (BDE) and 2.8 kcal/mol larger than the experimental active energy. In addition, because the energy barriers of IS1a isomerization to IS2a are 23.8 kcal/mol, close to the 20.8 kcal/mol O–N BDE in IS1a or IS1b, the isomerization reaction may compete with the direct bond rupture dissociation reaction.     

Geometries and stabilities of various configurations of benzene dimer: details of novel V-shaped structure revealed

Benzene dimer configurations namely T-shaped, parallel-displaced, sandwich, and V-shaped that were proposed by experimental studies are investigated using second- and fourth-order Møller–Plesset perturbation theory. The MP2 method with aug-cc-pVDZ and aug-cc-pVTZ basis sets unequivocally shows that the parallel-displaced configuration is considerably more stable than T-shaped structure. On the other hand, the MP4(SDTQ)/aug-cc-pVDZ level predicts that the T-shaped and parallel-displaced configurations are nearly isoenergetic, which is parallel to the previous results of estimated CCSD(T)/CBS level reported recently. The lowest energy T-shaped configuration is stabilized by 0.17 kcal/mol over the parallel-displaced configuration at the MP4(SDTQ)/aug-cc-pVDZ level. Although the structures of all the four different types of configurations are found to be stable at both MP2 and full MP4 methods, the V-shaped configuration is the least stable among them. The calculated interaction energy of ?2.3 kcal/mol for the lowest energy T-shaped structure at the MP4(SDTQ)/aug-cc-pVDZ level is in good agreement with the experimental value of ?2.4 ± 0.4 kcal/mol. We conclude that the MP4(SDTQ) with a reasonably good basis set can be used for systems involving π–π interactions to obtain qualitative and quantitative results.     

Thermochemical kinetics of bromine nitrate,bromine nitrite,halogen hydroperoxides,dichlorine pentoxide,peroxycarboxylic acids,and diacyl peroxides

Heats of formation of BrONO₂, BrONO, BrOOH, FOOH, FOOCl, CF₃C(O)OOH, HC(O)OOH, CH₃C(O)OOH, and [CH₃C(O)O]₂ are estimated from bond contributions taken from J. Phys. Chem., 100, 10150 (1996). They agree within ±2 kcal/mol with recent experimental or ab initio data. The resulting BDE(O(SINGLEBOND)O)=36 kcal/mol value in diacetyl peroxide requires the concerted assistance of exothermic C(SINGLEBOND)C(O) weakening in the transition state of its decomposition into free radicals. It also implies the existence of a previously unrecognized 12 kcal/mol nonbonded repulsion in acyl anhydrides. The formation of chloryl chlorate with ΔH_f(O₂ClOClO₂)=50 kcal/mol, a marginally stable species toward dissociation into (ClO₃+OClO), may account for observations made in the [O(³P+OClO] system at low temperatures. © 1998 John Wiley & Sons, Inc. Int J Chem Kinet: 30: 41–45, 1998.     

Binding of anticancer drug Ru(η 6 -C6H5(CH2)2OH)Cl2(DAPTA) to DNA purine bases and amino acid residues: a theoretical study

The hydrolyzed Ru(η ⁶ -C₆H₅(CH₂)₂OH)Cl₂(DAPTA) (DAPTA = 3,7-diacetyl-1,3,7-triaza-5-phosphabicyclo[3.3.1]nonane) binding to guanine(G), adenine (A), cytosine(C), cysteine (Cys), and histidine (His) residues were explored using the B3LYP hybrid functional and IEF-PCM solvation models. The computed activation barriers for the reactions of diaqua complex were lower than those of chloroaqua complex except for binding to cytosine. For the chloroaqua complex, the activation free energy was lowest when binding to cytosine (10.5 kcal/mol). Whereas, the substitution reaction of diaqua complex binding to cysteine showed the lowest activation free energy with 10.1 kcal/mol, closely followed by histidine (15.8 kcal/mol), adenine (20.1 kcal/mol), cytosine (20.7 kcal/mol), and guanine (24.4 kcal/mol) by turns. It could be deduced that the completely hydrolyzed Ru(η ⁶ -C₆H₅(CH₂)₂OH)Cl₂(DAPTA) compounds might preferentially bind to amino acids residues in vivo. In addition, to simulate the protein and DNA environment in vivo, a detailed investigation of the activation free energies for the substitution reactions in dependence of the dielectric constant ε (4, 24, and 78.39) was systematically performed as well. The calculated results demonstrated that the environmental effect had a little impact on these substitution reactions.     

Quantum mechanical and molecular mechanics approach with a multilayered-quantum representation study of solvent effects and potentials of mean force for the CH<Subscript>3</Subscript>CH<Subscript>2</Subscript>Cl + ClO<Superscript>−</Superscript> S<Subscript>N</Subscript>2 reaction in aqueous solution

The bimolecular nucleophilic substitution reaction of CH₃CH₂Cl + ClO^? in aqueous solution was investigated using a multilayered-quantum representation, quantum mechanical and molecular mechanics approach with an explicit water model. Ten configurations along the reaction pathway including reactant complex, transition state and product complex were analyzed in the presence of the aqueous solution. The obtained free energy activation barrier under the CCSD(T)/MM representation is 13.2 kcal/mol, while it is 11.7 kcal/mol under the DFT/MM representation which agrees very well with the DFT calculation, at 11.0 kcal/mol, with a polarizable continuum solvent model. The solvent effects including the solvation free energy contribution and the polarization effect raise the free activation barrier by 9.8 kcal/mol. The rate constant, at 298 K, is 5.27 × 10^?17 cm³/molecule/s which is about seven orders of magnitude smaller than that in the gas phase (1.10 × 10^?10 cm³/molecule/s). All in all, the aqueous solution plays an essential role in shaping the reaction pathway for this reaction in water.     

Theoretical study of the neutral hydrolysis of methyl formate via a concerted and stepwise water-assisted mechanism using free-energy curves and molecular dynamics simulation

A procedure previously described by us is used for the theoretical study of chemical reactions in solution by means of molecular dynamics simulation, with solute–solvent interaction potentials LJ (12-6-1) derived from ab initio quantum calculations. We apply the procedure to the case of the neutral hydrolysis of methyl formate, HCOOCH₃ + 3H₂O → HCOOH + CH₃OH + 2H₂O in aqueous solution, via concerted and stepwise water-assisted mechanisms. We use the solvent as reaction coordinate, and the free-energy curves for the calculation of the activation energies. The theoretical calculation for the thermodynamics of this hydrolysis reaction in aqueous solution, assisted by three water molecules, is in agreement with the available experimental information. In particular our study gives values of ΔG ^≠ = 28.88 and 28.17 kcal/mol for the concerted and stepwise mechanisms, close to the experimental activation barrier of 28.8 kcal/mol, and a significant improvement over the values of 48.05 and 45.66 kcal/mol found in another similar study using the PCM model.     

Investigation of ethylene dimerization over faujasite zeolite by the ONIOM method.

Ethylene dimerization was investigated by using an 84T cluster of faujasite zeolite modeled by the ONIOM3(MP2/6-311++G(d,p):HF/6-31G(d):UFF) method. Concerted and stepwise mechanisms were evaluated. In the stepwise mechanism, the reaction proceeds by protonation of ethylene to form the surface ethoxide and then C--C bond formation between the ethoxide and the second ethylene molecule to give the butoxide product. The first step is rate-determining and has an activation barrier of 30.06 kcal mol(-1). The ethoxide intermediate is rather reactive and readily reacts with another ethylene molecule with a smaller activation energy of 28.87 kcal mol(-1). In the concerted mechanism, the reaction occurs in one step of simultaneous protonation and C--C bond formation. The activation barrier is calculated to be 38.08 kcal mol(-1). Therefore, the stepwise mechanism should dominate in ethylene dimerization.     

Theoretical analysis of concerted and stepwise mechanisms of the hetero-Diels–Alder reaction of butadiene with formaldehyde and thioformaldehyde

The concerted and stepwise mechanisms of the hetero-Diels–Alder reaction of butadiene with formaldehyde and thioformaldehyde were studied by a CASSCF molecular orbital method. The energy barrier of the concerted reaction of butadiene with formaldehyde is about 21 kcal/mol higher than that of butadiene with thioformaldehyde at the CAS-MP2 calculation level. For the stepwise reaction paths, the energy barrier for the first step process of the reaction of butadiene with formaldehyde is about 17 kcal/mol above that of butadiene with thioformaldehyde. The concerted pathways for both systems are more favorable by 9–12 kcal/mol than the stepwise pathways. The electronic mechanisms for the concerted reactions of both reaction systems are also discussed by a CiLC analysis.     

DFT study on the mechanism of Pd(OAc)<Subscript>2</Subscript>-catalyzed hydrothiolation of alkenes bearing heteroatoms with benzenethiol

The work reports the theoretical investigation of the mechanism and regioselectivity of the Pd(OAc)₂-catalyzed hydrothiolation of heteroatom-substituted alkenes with benzenethiol leading to Markovnikov-type product. The reaction process includes: (1) activation of the S–H bond for benzenethiol by the catalyst Pd(OAc)₂; (2) migratory insertion of the alkenes bearing heteroatoms into the Pd–S bond; (3) AcOH molecule attacks Pd–C bonds to give the product and release the catalyst. In addition, the computed results shown that Pd(OAc)₂-catalyzed hydrothiolation take place by two possible channels and get anti-Markovnikov-type or Markovnikov-type species. The Markovnikov-type reaction channel is more favored with the energy barriers of 21.9–25.6 versus 28.5–31.2 kcal/mol for the anti-Markovnikov-type pathway. The theoretical results and the experimental observations of Tamai and co-workers are consistent. This reaction would proceed in mild conditions and afford the Markovnikov-type products in high yields and regioselectivity.     

Theoretical analysis of concerted and stepwise mechanisms of Diels-Alder reactions of butadiene with silaethylene and disilene

The concerted and the stepwise mechanisms of the Diels-Alder reactions of butadiene with silaethylene and disilene were studied by ab initio MO methods. For the reaction of butadiene and silaethylene, an asymmetric concerted process that is almost stepwise and two stepwise processes were located. For the first step of the stepwise process, the C-Si bond formation is more favorable than the C-C bond formation. The activation energy barrier of the concerted transition state is only 0.89 kcal/mol lower than that of the first-step transition state of the C-Si bond formation for the stepwise process by the CASPT2 calculation level. For the reaction of butadiene and disilene, the activation energy barrier of the concerted-type transition state constrained with Cs symmetry is about 9 kcal/mol higher than that of the stepwise transition state by the CASSCF method. The energy barrier of the first step of the stepwise reaction disappears at the CASPT2/6-311++G(d,p) calculation level including the nondynamical correlation energy, although the reaction of the butadiene with disilene occurs through the stepwise-like process.     

Can methylene amidogene and its isomers be formed by a concerted reaction?

We have explored the possibility of occurrence of the concerted formation of the methylene amidogene radical and its cis isomer from H₂ and CN at energy regimes of over 60 kcal/mol relative to the ground state of the radical. We have concluded that for the cases of parallel and perpendicular orientations of H₂ and CN, a concerted reaction is possible in principle provided that H₂ is vibrationally excited. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

The Low Energy of Concert in Many Symmetry‐Allowed Cycloadditions Supports a Stepwise‐Diradical Mechanism

The thesis of this paper is that orbital symmetry allowedness does not guarantee concert. The activation energy (E_a) for concerted Diels–Alder and 1,3‐dipolar cycloadditions must be substantially lower than that for a stepwise‐diradical pathway because the diradical has two fewer bonding electrons than anything on the concerted reaction coordinate, including the transition state. Two bonding electrons provide tens of kcal/mol of stabilization. The difference between the experimental E_a and that for diradicals is called the energy of concert (E_con). If experiment represents concert, E_con must be large, and if it represents diradicals E_con will be very small. In this paper, 42 examples are adduced in which firm experimental data show that E_con = 0. These cycloadditions cannot be concerted. While concert remains possible for all cycioadditions not proven stepwise, there is none with compelling evidence for concert.     

Quantum Monte Carlo investigation of the H-shift and O2-loss channels of cis-2-butene-1-peroxy radical

Owing to importance in combustion processes, O₂-loss and 1, 6-H-shift in cis-2-butene-1-peroxy radical have been investigated. Energies for these processes and the barrier height of the latter are computed using the diffusion Monte Carlo (DMC) method. The DMC energy for the 1, 6-H-shift was determined to be 4.56 ± 0.19 kcal/mol with barrier height of 26.79 ± 0.20 kcal/mol. The energy for O₂-loss was found to be 14.93 ± 0.24 kcal/mol. Quantitative differences between the findings of the present study and previous CBS-QB3 results indicate a discrepancy between high-level methods for the resonance-stabilized radicals. Further study is needed to identify the origin of these differences.