Proton Transfer of Formamide + nH2O (n = 0−3): Protective and Assistant Effect of the Water Molecule

Mechanistic insight into the tautomerization of histidine initiated by water-catalyzed N-H and C-H cleavages

The N-H and C-H activation is of great significance in organic chemistry and chemical industry fields, especially, in the utilization of petroleum raw materials. High NδH (tautomer of natural histidine) content would increase Alzheimer's disease risk. To inhibit this and improve the activation of N-H and C-H bonds, the isomerization mechanism from NδH to NεH of histidine-containing dipeptide catalyzed by water cluster was explored. The results discovered that water cluster assists this reaction by reducing the activation energies from 68.20 to 9.60 kcal mol^-1, and its size not only affects the reaction rate but also determines the reaction pathway in a degree. Moreover, water cluster, taken as a potential green catalyst, is more effective on the reactions involving N-H and C-H bond cleavages than reported common toxic organometallic compounds and has different catalytic mechanisms. This work also provides some theoretical guidance for the modulation of Alzheimer's disease induced by histidine isomerization.

Infrared photodissociation spectroscopic studies of ScO(H2O)n=1–3Ar+ cluster cations: solvation induced reaction of ScO+ and water

We investigate the gaseous ScO(H₂O)_1–3Ar⁺ cations prepared by laser vaporization coupled with supersonic molecular beam using infrared photodissociation spectroscopy in the O–H stretching region.

Catalytic Effect of Aqueous Solution in Water-Assisted Proton-Transfer Mechanism of 8-Hydroxy Guanine Radical

Water-assisted proton-transfer process is a key step in guanine damage reaction by hydroxyl radical in aqueous solution. In this article, we quantitatively determine the solvent effect in water-assisted proton-transfer mechanism of 8-hydroxy guanine radical using combined quantum mechanics and molecular mechanism with an explicit solvation model. Atomic-level reaction pathway was mapped, which shows a synchronized two-proton-transfer mechanism between the assistant water molecule and 8-hydroxy guanine radical. The transition-state dipole moment is the largest along the reaction pathway, which electrostatically stabilizes the proton-transfer transition-state complex. The free-energy reaction barrier for this water-assisted proton-transfer reaction was calculated at 19.2 kcal/mol with the density functional theory/M08-SO/cc-pVTZ+/molecular mechanics level of theory. The solvent effect not only has a big impact on geometries, but also dramatically changes the energetics along the reaction pathway. Among the solvent effect contributions to the transition state, the solvent energy contribution is -28.5 kcal/mol and the polarization effect contribution is 19.9 kcal/mol. In total, the solvent effect contributes -8.6 kcal/mol to the free-energy barrier height, which means that the presence of aqueous solution has a catalytic effect on the reaction mechanism and enhances the proton-transfer reactivity in aqueous solution.

Chlorination of N-methylacetamide and amide-containing pharmaceuticals. Quantum-chemical study of the reaction mechanism

Chlorination of amides is of utmost importance in biochemistry and environmental chemistry. Despite the huge body of data, the mechanism of reaction between amides and hypochlorous acid in aqueous environment remains unclear. In this work, the three different reaction pathways for chlorination of N-methylacetamide by HOCl have been considered: the one-step N-chlorination of the amide, the chlorination via O-chlorinated intermediate, and the N-chlorination of the iminol intermediate. The high-level quantum chemical G3B3 composite procedure, double-hybrid B2-PLYPD, B2K-PLYP methods, and global hybrid M06-2X and BMK methods have been employed. The calculated energy barriers have been compared to the experimental value of ΔG(#)298 ≈ 87 kJ/mol, which corresponds to reaction rate constant k(r) ≈ 0.0036 M(-1) s(-1). Only the mechanism in which the iminol form of N-methylacetamide reacts with HOCl is consistent (ΔG(#)298 = 87.3 kJ/mol at G3B3 level) with experimental results. The analogous reaction mechanism has been calculated as the most favorable pathway in the chlorination of small-sized amides and amide-containing pharmaceuticals: carbamazepine, acetaminophen, and phenytoin. We conclude that the formation of the iminol intermediate followed by its reaction with HOCl is the general mechanism of N-chlorination for a vast array of amides.

Tautomerism of Uracil and 5-Bromouracil in a Microcosmic Environment with Water and Metal Ions. What Roles Do Metal Ions Play?

The base tautomerization processes of uracil/5-bromouracil were investigated in a microcosmic environment with both H2O and Na+ (W-M environment). It was found that uracil was more stable in the W-M environment than in the microcosmic environment with only water, which suggested that the metal ions and water work cooperated to maintain the classical nucleic acid bases. However, 5-bromouracil, a chemical mutagen, was found to be less stable than uracil in the W-M environment. Why the 5-bromouracil is easier to tautomerize and therefore induce gene mutation was explained to some extent. Further research revealed that the water molecule would assist the tautomerization in the W-M environment. However, the metal ions in different regions play absolutely opposite roles: in one region, the metal ions can prevent the base from tautomerizing, whereas in another region, the metal ion can assist the tautomerization process. Furthermore, from the viewpoint of ionization of the base, it seems BrU has a stronger tendency to lose the proton at N3, which is an intrinsic consequence of the bromine atom and is not affected by the metal cation.

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.

Reaction Mechanism of Uracil Bromination by HBrO: A New Way To Generate the Enol−Keto Form of 5-Bromouracil

Knowledge on the uracil bromination reaction is helpful for understanding the origin of the mutagenicity of 5-bromouracil (BrU). To get more details about this reaction, we explore the corresponding reaction mechanism by theoretical method. A total of seven pathways were studied for this purpose. The diketo form of BrU is observed as the main product in these pathways, which agrees well with experimental results. The most energy-favorable reaction pathway is found to be that Br and OH attacked the opposite sides of uracil. The reaction intermediate reported in the experiment is predicted to be reasonably stable. In the following step, a dehydration process occurs between H11 and O13-H14 when there are no explicit H(2)O taking part. However, when there are explicit water molecules in the environment, explicit H(2)O will lower the reaction barrier in the formation of reaction intermediates and the final product BrU. A proton-transfer process from C5 to O10 is facilitated by explicit H(2)O, which results in enol-keto form intermediate of this modified base (defined as BrU*). These results indicate a new way to generate the enol-keto form of BrU.

Microsolvation of Formamide: A Rotational Study

Microsolvated formamide clusters have been generated in a supersonic jet expansion and characterized using Fourier transform microwave spectroscopy. Three conformers of the monohydrated cluster and one of the dihydrated complex have been observed. Seven monosubstituted isotopic species have been measured for the most stable conformer of formamide...H(2)O, which adopts a closed planar ring structure stabilized by two intermolecular hydrogen bonds (N-H...O(H)-H...O=C). The two higher energy forms of formamide...H(2)O have been observed for the first time. The second most stable conformer is stabilized by a O-H...O=C and a weak C-H...O hydrogen bond, while, in the less stable form, water accepts a hydrogen bond from the anti hydrogen of the amino group. For formamide...(H(2)O)(2), the parent and nine monosubstituted isotopic species have been observed. In this cluster the two water molecules close a cycle with the amide group through three intermolecular hydrogen bonds (N-H...O(H)-H...O(H)-H...O=C), the nonbonded hydrogen atoms of water adopting an up-down configuration. Substitution (r(s)) and effective (r(0)) structures have been determined for formamide, the most stable form of formamide...H(2)O and formamide...(H(2)O)(2). The results on monohydrated formamide clusters can help to explain the observed preferences of bound water in proteins. Clear evidence of sigma-bond cooperativity effects emerges when comparing the structures of the mono- and dihydrated formamide clusters. No detectable structural changes due to pi-bond cooperativity are observed on formamide upon hydration.

Microenvironment Control of Methyl Rotation Induced by Proton Transfer

Methyl rotation induced by proton transfer was found for cis-N-methylacetamide (NMA). More interestingly, it was found that the microenvironment could control the methyl rotation. The atom-centered density matrix propagation (ADMP) method, a recently developed ab initio molecular dynamics, was further carried out to depict the trajectories for methyl rotation of NMA. Moreover, trajectories for methyl rotation of NMA complexed with water molecules were also calculated, and water molecules at the two different sites of NMA were found to reverse or cease the rotational direction of the methyl groups of NMA. This finding that microenvironment can not only control rotational direction of methyl groups but can also cease the rotation may be of significant importance for the control of molecular machines.

Influence of the number of water molecules on the mechanism of N-sulfinylaniline hydrolysis

The mechanism of the uncatalyzed hydrolysis of N-sulfinylaniline (Ph-N=S=O) has been studied with B3LYP/6-31+G(2d,2p) in the gas phase, with explicit treatment of water molecules. Hydrolysis involves water attack on sulfur, with a close to perpendicular alignment of a water molecule and the NSO plane in both prereaction complexes and transition states for the rate-determining step. Consequently, the distance of the weak S···O interaction, together with the efficiency of protonation of either nitrogen (attack across the N=S bond) or oxygen (attack across the S=O bond) atoms of the NSO group, determines the height of the activation barrier for hydrolysis. While the reaction with one water molecule is characterized by an unreasonably high enthalpy of activation, a cooperative effect from the weak interactions appears with the inclusion of a second water molecule, where both participate in the reaction, and the activation enthalpy drops significantly. The preference for attack across the S=O bond that is found in the reaction with one water molecule switches to a dominance of attack across the N=S bond in the reaction with three water molecules.Key words: N-sulfinylaniline, hydrolysis, mechanism, density functional theory (DFT).

Systematic Study of the Tautomerism of Uracil Induced by Proton Transfer. Exploration of Water Stabilization and Mutagenicity

To systematically investigate all the possible tautomerisms from uracil (U) and its enol form (U) induced by proton transfer, we describe a study of structural tautomer interconversion in the gas phase, in a continuum solvent, and in a microhydrated environment with 1 or 2 explicit water molecules, using density functional theory (DFT) calculations by means of the B3LYP exchange and correlation functions. A total of 62 geometries including 25 transition states were optimized, and the geometrical parameters have been discussed. Some rules of the configuration variation in tautomerization were summarized. The relative stabilities of all the tautomers were established. When a proton transfers from the di-keto form to the keto-enol form, water molecules in different regions show absolutely opposite effects: some assist, whereas others hinder the tautomerization. However, when a proton transfers from the keto-enol form to the di-enol form, water molecules in different regions show similar effects: the Gibbs free energy always increases and the activation energy always decreases. Additionally, some important factors that obviously affect the activation energy and Gibbs free energy were found and discussed in detail. The reasons that water molecules can assist or prevent the proton transfer were given. Furthermore, on the basis of our calculated results, we explain why it is hard to detect the di-enol form of uracil in general experiments.

Theoretical Study of the Effect of Water in the Process of Proton Transfer of Glycinamide

For the purpose of investigating the tautomerism from glycinamide (G) to glycinamidic acid (G*) induced by proton transfer, we carried out a study of structural interconversion of the two tautomers and the relative stabilizing influences of water during the tautomerization process. Throughout the study, we used density functional theory (DFT) calculations at the B3LYP/6-311++G** level of theory, also considering the correction functions, that is, the effect of basis set superposition error (BSSE). Totally, 42 geometries, including fourteen important transition states, were optimized, and their geometric parameters have also been discussed in detail. Water molecules were gradually put in three different regions in the vicinity of G and its tautomer G*. The calculation results indicate that water in two of these regions can protect G from tautomerizing to G*, while in another region, water can assist in the tautomerism; this reveals that water molecules have stabilization and mutagenicity effects for G simultaneously.