DFT study on the isomerization in vitamin B6

Isomerization and tautomerism reactions of the active form of vitamin B6, pyridoxal phosphate, are studied at B3LYP level of theory using 6-311++G(2df,p) basis set in gas and aqueous phases. Twenty-three transition state (TS) structures for vitamin B6 isomerization are optimized, including 13 TS structures for O–H and C–C rotations, 8 TS structures for imine–enamine tautomerism, and 2 TS structures for keto–enol tautomerism. Activation energy (E _a), imaginary frequency (υ), and Gibbs free energy of activation (ΔG ^#) for the isomerization reactions are calculated. The activation energies of the imine–enamine tautomerism are in the range of 190–280 kJ/mol and of O–H and C–C rotations are mainly less than 60 kJ/mol. Also, our calculation shows that the imine forms of B6 are mainly more stable than the enamine forms. Effect of microhydration on the TS structures and activation energies is also investigated. It is found that the presence of water molecules catalyzes only the imine–enamine tautomerism.     

Theoretical study on the isomerization and tautomerism in barbituric acid

Isomerization and tautomerism of 16 isomers of barbituric acid (BA) were studied at the MP2 and B3LYP levels of theory. Activation energies (E _a), imaginary frequencies (υ), and Gibbs free energies (ΔG ^#) of the amine-imine and keto-enol tautomerisms and O–H internal rotations were calculated. The activation energies of amine-imine tautomerisms were in the range of 110–200 kJ/mol and for keto-enol tautomerisms were larger than 200 kJ/mol. The calculated activation energies of internal O–H rotations were smaller than 60 kJ/mol. Effect of micro-hydration on the transition state structures and activation energies of the tautomerisms were also investigated. Water molecule catalyzed the tautomerisms and decreased the activation energies of both the amine-imine and keto-enol tautomerisms about 100–120 kJ/mol.     

Solvent-assisted catalysis mechanism on Keto–enol tautomerism of cyameluric acid

The keto–enol tautomerism of cyameluric acid, both in gas phase and in water and methanol solution, has been studied at the B3LYP/6-31++g(d,P) level of theory in this paper. The harmonic frequencies of all the structures are calculated. The results show that the transition states of the tautomerism are 4-membered ring conformations in gas phase, whereas 6-membered ring conformations in solution. In the first proton transfer, activation energy ΔE^# is 56.4 and 50.9 kJ/mol for water and methanol solution, respectively, which is much lower than that in gas phase (163.2 kJ/mol). Solvent molecules (water and methanol) produce an important catalytic effect in the tautomerism, especially for methanol-solvated system. NBO analysis shows that there is a strong interaction between cyameluric acid and solvent molecules in transition states. AIM charge analysis indicates that the keto–enol tautomerism shows a certain degree of proton transfer character. From the reaction enthalpy and reaction rate point of view, keto–enol tautomerism in water-solvated and methanol-solvated system is easier than that in gas phase. The keto–enol tautomerisms are endothermic both in gas phase and in solution, so the enol forms are less stable than the keto ones.     

The Keto–Enol Tautomerism of Biliverdin in Bacteriophytochrome: Could it Explain the Bathochromic Shift in the Pfr Form?†

Phytochromes are ubiquitous photoreceptors found in plants, eukaryotic algae, bacteria and fungi. Particularly, when bacteriophytochrome is irradiated with light, a Z‐to‐E (photo)isomerization takes place in the biliverdin chromophore as part of the Pr‐to‐Pfr conversion. This photoisomerization is concomitant with a bathochromic shift in the Q‐band. Based on experimental evidence, we studied a possible keto–enol tautomerization of BV, as an alternative reaction channel after its photoisomerization. In this contribution, the noncatalyzed and water‐assisted reaction pathways for the lactam–lactim interconversion through consecutive keto–enol tautomerization of a model BV species were studied deeply. It was found that in the absence of water molecules, the proton transfer reaction is unable to take place at normal conditions, due to large activation energies, and the endothermic formation of lactim derivatives prevents its occurrence. However, when a water molecule assists the process by catalyzing the proton transfer reaction, the activation free energy lowers considerably. The drastic lowering in the activation energy for the keto–enol tautomerism is due to the stabilization of the water moiety through hydrogen bonds along the reaction coordinate. The absorption spectra were computed for all tautomers. It was found that the UV–visible absorption bands are in reasonable agreement with the experimental data. Our results suggest that although the keto–enol equilibrium is likely favoring the lactam tautomer, the equilibrium could eventually be shifted in favor of the lactim, as it has been reported to occur in the dark reversion mechanism of bathy phytochromes.     

3,6-二羟基哒嗪质子转移过程的理论研究

为了探索3,6-二羟基哒嗪分子醇式和酮式结构互变异构化的反应机理,本研究组采用DFT B3LYP/6-311+G(d)方法对标题化合物异构化反应的势能面进行了研究,在探讨各种可能的反应途径中,发现至少有34种异构体和43种过渡态.结果表明,6-羟基-3(2H)-哒嗪酮不论是单体,与水形成配合物,还是二聚体,比其相对应的异构体能量低,表明在通常情况下是以6-羟基-3(2H)-哒嗪酮形式稳定存在的,这与前人通过实验数据对互变异构体的比率进行预测的结果是一致的;在考察的可能反应途径中,直接进行的分子内质子转移过程需要的活化能为142.2 kJ·mol^-1,水助催化时,反应活化能为41.3 kJ·mol^-1,考虑溶剂效应后,其活化能为59.2 kJ·mol^-1,二聚体双质子转移的活化能为16.8 kJ·mol^-1,二聚体双质子转移所需活化能最低,在室温下就可以进行.由此可见氢键在降低反应活化能方面起着重要的作用.     

组氨酸残基在芳基胺类N-乙酰基转移酶（NATs）乙酰化过程中有何作用？——量子化学研究

Arylamine N-acetyltransferases(NATs,EC 2.3.1.5)catalyze an acetyl group transfer from acetyl coenzyme A(AcCoA)to primary arylamines and play a very important role in the metabolism and bioactivation of drugs andcarcinogens.Experiments revealed that His-107 was likely the residues responsible for mediating acetyl transfer.The full catalytic mechanism of acetylation process has been examined by density functional theory.The results in-dicate that,if the acetyl group is directly transferred from the donor,p-nitrophenyl acetate,to the acceptor,cysteine,the high activation energy will be a great hindrance.These energies have dropped in a little range of 20—25 kJ/molwhen His-107 assisted the transfer process.However,when protonated His-107 mediated the reaction,the activa-tion energies have been dropped about 73—85 kJ/mol.Our calculations strongly supported an enzyme acetylationmechanism that experiences a thiolate-imidazolium pair,and verified the presumption from experiments.     

Mechanism of Gold(I)‐Catalyzed Conia‐ene Reaction of β‐Ketoesters with Alkynes: A DFT Study

Density functional calculations have been performed to comparatively investigate two possible pathways of Au(I)‐catalyzed Conia‐ene reaction of β‐ketoesters with alkynes. Our studies find that, under the assistance of trifluoromethanesulfonate (TfO), the β‐ketoester is the most likely to undergo Model II to isomerize into its enol form, in which TfO plays a proton transfer role through a 6‐membered ring transition state. The coordination of the Au(I) catalyst to the alkynes triple bond can enhance the eletrophilic capability and reaction activity of the alkynes moiety, which triggers the nucleophilic addition of the enol moiety on the alkynes moiety to give a vinyl‐Au intermediate. This cycloisomerizaion step is exothermal by 21.3 kJ/mol with an energy barrier of 56.0 kJ/mol. In the whole catalytic process, the protonation of vinyl‐Au is almost spontaneous, and the formation of enol is a rate‐limiting step. The generation of enol and the activation of Au(I) catalyst on the alkynes are the key reasons why the Conia‐ene reaction can occur in mild condition. These calculations support that Au(I)‐catalyzed Conia‐ene reactions of β‐ketoesters with alkynes go through the pathway 2 proposed by Toste.     

8-羟基喹啉单体及二聚体质子转移反应的理论研究

Density functional theory （DFT） of quantum chemistry method was employed to investigate proton transfer reactions of 8-hydroxyquinoline （8-HQ） monomers and dimers. By studying the potential energy curves of the isomerization, the most possible reaction pathway was found. The total energy of 8-hydroxyquinoline was lower than that of quinolin-8（1H）-one, whereas the order was reversed in dimers. The findings explained the contrary experimental phenomena. The minimum reaction barrier of intramolecular proton transfer was 47.3 kJ/mol while that in dimer was only 25.7 kJ/mol. Hence it is obvious that proton transfer reactions of 8-HQ monomer have a considerable rate but it is easier to proceed for 8-HQ dimer than monomers. It implied that the hydrogen bond played an important role in depressing the activation energy of reaction. The mechanism of the tautomerization was discussed on the basis of theoretical results.     

2-羟基咪唑在气相和水中的异构平衡和质子迁移的从头算计算和Monte Carlo模拟

采用从头算方法在MP2/6-31＋G^*水平上研究了2-羟基咪唑分子在孤立分子和一水合物的异构体的相对稳定性和可能的质子迁移反应, 分析了一个水分子的参与对2-羟基咪唑分子异构体的相对稳定性和质子迁移速率的影响, 采用Monte Carlo模拟方法研究了反应体系在水溶液中反应的溶剂化效应. 结果表明: 2-羟基咪唑分子的孤立分子和一水合物的最稳定异构体相同, 都为酮式. 直接质子迁移反应在水溶液中活化能垒有轻微增加, 但产物能量得到降低; 水助催化质子迁移反应在水溶液中的活化能垒和产物能量都得到明显降低. 综合气相和水相的计算结果, 2-羟基咪唑水助催化的质子迁移反应较易进行, 且在水溶液中进行容易, 可以很容易被实验观察到.     

Sodium chlorite–iodine–methyl acetoacetate oscillatory reaction investigated by UV–vis spectrophotometric method

A new sodium chlorite–iodine–methyl acetoacetate chemical oscillatory reaction was studied using UV–vis spectrophotometric method. The initial concentrations of methyl acetoacetate, sodium chlorite, iodine, sulfuric acid, and the pH value have great influence on the oscillation observed at wavelength of 585 nm. There is a pre-oscillatory or induction period; the amplitude and the number of oscillations are associated with the initial concentration of reactants. The equations for the I₃ ^?–starch complex reaction rate changing with reaction time and the initial concentrations in the oscillation stage were obtained. The time of induction period decreases with the initial concentration of methyl acetoacetate or sulfuric acid, and increases with the initial concentration of sodium chlorite. A good linear relationship exists. Oscillatory reaction can be accelerated by increasing temperature. The apparent activation energies in terms of the induction period and the oscillation period were 114.28 and 64.92 kJ/mol, respectively. It may indicate that the two stages have different reaction mechanisms. The reaction of producing enol isomer by keto-enol tautomerism is an important step to constrain the time of induction period.     

Proton magnetic resonance studies of tautomerism in substituted pyrimidines

Studies of line width and chemical shift vs. temperature for amide and hydroxyl proton magnetic resonance signals from: barbituric acid, dialuric acid, parabanic acid, alloxan and alloxan monohydrate dissolved in anhydrous dimethyl sulfoxide-d₆ are reported. The behavior of the amide signals shows that, between 20 and 65°C, none of the compounds listed exhibits lactim-lactam tautomerism. The amide proton resonance in uracil has also been investigated. The signal is a closely spaced, equal intensity, doublet due to the non-equivalence of H(1) and H(3). Again, no evidence of tautomerism is observed. Activation energies for the hydroxyl resonances in dialuric acid and alloxan monohydrate indicate hydrogen bonding between solute and solvent. The results of simple LCAO-MO calculations are in accord with the experimental conclusions concerning tautomeric equilibria.     

Modeling the Proton Transport in Orthoperiodic and Orthotelluric Acids and Their Salts

Orthoperiodic and orthotelluric acids, their salts MIO₆H₄ (M = Li, Rb, Cs) and CsH₅TeO₆, and dimers of the salt · acid type are calculated within density functional theory B3LYP and basis set LanL2DZ complemented by the polarizationd,p-functions. According to calculations, the salt · acid dimerization is energetically favorable for compounds MIO₆H₄ · H₅IO₆ (M = Rb, Cs) and CsIO₆H₄ · H₆TeO₆. The dimerization energy is equal to 138–146 kJ mol^–1. With relatively small activation energies equal to 4 kJ mol^–1 (M = Li) and 11 kJ mol^–1 (M = Rb, Cs), possible is rotation of octahedron IO₆ relative to the M atom in monomers of salt molecules. The proton transfer along an octahedron occurs with activation energies of 63–84 kJ mol^–1. The activation energy for the proton transfer between neighboring octahedrons of the type salt · acid acid · salt equals 8–17 kJ mol^–1. Quantum-chemical calculations nicely conform to x-ray diffraction and electrochemical data.     

Kinetics and mechanisms of transalkylation and disproportionation of meta‐diethylbenzene by triflic acid catalyst

The kinetics of transalkylation and isomerization of meta‐diethylbenzene in the presence of benzene using triflic acid as a catalyst has been investigated. High catalytic activity of the triflic acid catalyst was observed in homogeneous liquid‐phase reactions. On the basis of the product distribution obtained, transalkylation, disproportionation, and isomerization reactions have been considered and the main product of the reaction was ethylbenzene. These reactions are conducted in a closed liquid batch reactor with continuous stirring under dry nitrogen and atmospheric pressure over the temperature range of 288–308 K. The main transalkylation, disproportionation, and isomerization reactions occurred simultaneously and were considered as elementary reactions. The apparent activation energy of the transalkylation reaction was found to be 35.5 kJ/mol, while that of disproportionation reaction was 42.3 kJ/mol. The reproducibility of the experimental product distribution occurred with an average relative error of ±2%. © 2003 Wiley Periodicals, Inc. Int J Chem Kinet 35: 555–563, 2003     

2,6-二巯基嘌呤质子转移异构化的密度泛函理论研究

采用密度泛函B3LYP方法, 在6-311＋G(d,p)基组水平上对2,6-二巯基嘌呤质子转移引起的硫醇式与硫酮式互变异构反应进行了计算研究, 获得了互变异构过程的反应焓、活化能、活化吉布斯自由能和质子转移反应的速率常数等性质. 计算结果表明, 2,6-二巯基嘌呤无论是孤立分子还是一水合物, 其二硫酮式R是最稳定异构体. 由二硫酮式通过分子内质子转移向二硫醇式异构化共有6条反应通道, 其主通道(1)速控步骤的活化能为139.1 kJ•mol^－1, 速率常数为2.16×10^－12 s^－1; 当水分子参与反应以双质子转移机理异构化时, 活化能显著降低, 有利于硫酮式向硫醇式转变, 其主通道(7)速控步骤的活化能为61.3 kJ•mol^－1, 速率常数为1.33×10 s^－1. 计算结果还表明, 氢键作用在增大2,6-二巯基嘌呤氢键一水合物稳定性、降低质子转移异构化反应活化能等方面起着重要的作用.     

An Ab initio study of tautomerism between formhydroxamic acid and formhydroximic acid

Ab initio MO calculations including electron correlation with the 4-31G and 4-31G ** basis sets were performed in order to study the formhydroxamic acid-formhydroximic acid tautomerism. The geometries, relative energies, and activation energy of the tautomer and transition state were determined. Based on total-energy calculations at the MP 4/4-31G **//RHF /4-31G ** plus the scaled zero-point vibration energy level, the energy of formhydroxamic acid is determined to be lower than that of formhydroximic acid by 40.7 kJ/mol. The activation energy of the formhydroxamic acid-formhydroximic acid tautomerism via a 1,3-intramolecular hydrogen shift is 151.4 kJ/mol. © 1992 John Wiley & Sons, Inc.     

Electronic structure and the hydrogen-shift isomerization of hydrogen nitryl HNO2

Summary Electronic structure of hydrogen nitryl HNO₂, a yet not identified entity, and the path of its possible isomerization totrans-HONO have been investigated byab initio SCF and MRD-CI computations using the 6-31G** basis set. HNO₂ isC _2v -symmetric and its ground state (¹ A ₁) is less stable thantrans-HONO by 66 kJ/mol (with the SCF vibrational zero-point energy correction). The lowest two excited singlet states (¹ A ₂ and¹ B ₁) are nearly degenerate, their vertical excitation energies being predicted to be 4.8 eV. The isomerization path is traced by the CASSCF procedure and the activation barrier height is evaluated by the CI treatment. HNO₂ in its ground state isomerizes totrans-HONO by maintaining the planar (C _s-symmetric) structure. The activation energy is calculated to be 171 kJ/mol, which is clearly lower than the calculated H-N bond energy (253 kJ/mol). The transition state seems to be more adequately described as an interacting system of proton and the nitrite anion rather than as a pair of two fragment radicals.     

Hydration effect on the stability of the keto-enol tautomers of 5-hydroxy-6-methyluracil

The structure and energies of six tautomeric forms of 5-hydroxy-6-methyluracil (OMU) and their 1:n (n = 1−4) complexes with water were determined by the density functional theory (PBE/3z) method. The stability series of the tautomers and changes in it depending on the number of water molecules in the nearest environment of the tautomer were found. The effect of the water solvent was also included using the continuum (B3LYP/6-311+G(2d,p), COSMO) model. Both complex formation and medium effects significantly influenced the stability series of the tautomers. Although the decrease in the energy of the diketo form on hydration was smaller than for the enol states, diketo tautomer a remained the most stable form of OMU in solution. Inclusion of hydration in calculations suggests that the energies of three enol tautomers b–d were equalized (ΔH ≈ 5.5 kJ/mol). This should be taken into account for the conditions that facilitate the keto-enol tautomerism of OMU.     

Benzimidazole-based receptor for Zn2+ recognition in a biological system: a chemosensor operated by retarding the excited state proton transfer

A new benzimidazole-based receptor was developed with potential functional groups for excited state proton transfer (ESPT) through keto–enol tautomerism. The enol form of the receptor selectively recognizes Zn²⁺, allowing it to be used as a ratiometric fluorescence sensor in DMSO/CH₃CN (1:9, v/v). The binding event triggers a blue-shifted band through the modulation of charge transfer transitions. The sensor is applicable for recognizing Zn²⁺ in the cytoplasm of Saccharomyces cerevisiae.     

Hindered rotation about the amido N?C bond and the tautomeric equilibrium in N,N-dimethylacetoacetamide

The molecule N,N-dimethylacetoacetamide, which is subject to a keto–enol equilibrium process in solution, also exhibits hindered rotation about the amido N? C bond. The hindered rotation rates have been studied by lineshape fit methods of the nuclear magnetic resonance spectra. In spite of some overlap of the keto and enol N-methyl proton signals, the simultaneous measurement of the two distinct energy barriers in the two forms is possible as well as a determination of the keto–enol equilibrium. The differences in free energy of activation between keto and enol forms for the rotation barrier can be related to the conjugation energy of the N? C π system with the enolic hydrogen bonded ring. Appeal to the model compound acetylacetone reveals a consistent set of energies for the keto and enol forms in the ground and transition states for internal rotation. The opportunity has been taken to reexamine and compare the keto–enol system ethylacetoacetate. Long range, solvent, concentration and temperature sensitive scalar couplings ⁴J(HH) between the enolic –OH and the adjacent methyl group in acetoacetic ester have not hitherto been reported.     

Thermally induced polymerization of isobutylene in the presence of SnCl4: Kinetic study of the polymerization and NMR structural investigation of low molecular weight products

The polymerization reactivity of isobutylene/SnCl₄ mixtures in the absence of polar solvent, was investigated in a temperature interval from −78 to 60 °C. The mixture is nonreactive below −20 °C but slow polymerization proceeds from −20 to 20 °C with the initial rate r₀ of the order 10⁻⁵ mol · l⁻¹ · s⁻¹. The rate of the process increases with increasing temperature up to ∼10⁻² mol · l⁻¹ · s⁻¹ at 60 °C. Logarithmic plots of r₀ and M̄_n versus 1/T exhibit a break in the range from 20 to 35 °C. Activation energy is positive with values E = 21.7 ± 4.2 kJ/mol in the temperature interval from −20 to 35 °C and E = 159.5 ± 4.2 kJ/mol in the interval from 35 to 60 °C. The values of activation enthalpy difference of molecular weights in these temperature intervals are ΔH_Mn = −12.7 ± 4.2 kJ/mol and −38.3 ± 4.2 kJ/mol, respectively. The polymerization proceeds quantitatively, the molecular weights of products are relatively high, M̄_n = 1500–2500 at 35 °C and about 600 at 60 °C. It is assumed that initiation proceeds via [isobutylene · SnCl₄] charge transfer complex which is thermally excited and gives isobutylene radical‐cations. Oxygen inhibits the polymerization from −20 to 20 °C. Possible role of traces of water at temperatures above 20 °C is discussed. It was verified by NMR analysis that only low molecular weight polyisobutylenes are formed with high contents of exo‐ terminal unsaturated structures. In addition to standard unsaturated groups, new structures were detected in the products. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 1568–1579, 2000