Theoretical investigation of the intermolecular H-bonding and proton transfer in cytosine assisted by water and methanol

Abstract  

This investigation is devoted to study of the electronic structure of several H-bonded complexes of cytosine tautomers with water and methanol. The stability of these “supersystems” (aggregates) was estimated by calculating the bonding energies ΔE and ΔE _b. The energy barriers of water/methanol-assisted tautomeric conversions were calculated (intermolecular proton transfer), and the electronic structures of the transition states were studied. Each transition state of the proton-transfer reaction was determined as a first-order saddle point on the potential energy surface (full coordinate hyperspace). The crystal structure of the tetramer of cytosine monohydrate was also investigated. It was found that this structure is close to a conical intersection.     

Theoretical study of intermolecular proton transfer reaction in isolated 5-hydroxyisoxazole–water complexes

A systematic investigation in isolated 5-hydroxyisoxazole–water complexes (5-HIO · (H₂O)_nn = 1–3) is performed at the DFT level, employing B3LYP/6-31G(d, p) basis set. Single-point energy calculations are also performed at the MP2 level using B3LYP/6-31G(d, p) optimized geometries and the 6-311++G(d, p) basis set. The computational results show that the keto tautomer K₂ is the most stable isomer in the gas phase, and the tautomer K₁ to be the next most stable tautomer. Hydrogen bonding between HIO and the water molecule(s) will dramatically lower the barrier by a concerted multiple proton transfer mechanism. The proton transfer process of 3WE_cis ↔ 3WK₁ and 2WE_trans ↔ 2WK₂ is found to be more efficient in two tautomerization, and the barrier heights are 7.03 and 14.15 kcal/mol at B3LYP/6-31G(d, p) level, respectively. However, the proton transfer reaction between E_cis and K₁ cannot happen without solvent-assisted.     

黄嘌呤异构体质子转移异构化反应机理的理论研究

采用量子化学密度泛函B3LYP/6-31G(d,p)和M06-2X/6-311++G(d,p)方法对黄嘌呤两种酮式异构体X(1,3,7)与X(1,3,9)间质子转移引起的互变异构反应机理进行了计算研究,获得了异构化反应过程的反应焓﹑活化吉布斯自由能和质子转移反应的速率常数等参数。水相计算采用极化连续(PCM)模型。结果表明,由于可能的氢迁移顺序差异,分子内由X(1,3,7)向X(1,3,9)异构化可能共有16条反应通道,涉及11个中间体和20个过渡态,其主反应通道速控步骤的活化吉布斯自由能为183.10k J/mol,速率常数为5.17×10-20s-1,其余各通道速控步骤活化吉布斯自由能均较高,而且整体水溶剂效应不利于质子转移的发生。     

Role of base assisted proton transfer in N-heterocyclic carbene-catalyzed intermolecular Stetter reaction

The mechanism of the NHC-catalyzed intermolecular Stetter reaction between benzaldehyde and cyclopropene has been investigated using the PCM-M062X/6-311++G(3df,2p)//M062X/6-31+G(d,p) level of DFT. Compared to the direct reaction, a substantial reduction in the activation free energy by 10.6–14.4 kcal/mol is observed when the reaction is performed in the presence of water, 1,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD), and 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU). The bases promote the proton transfer step of the reaction to yield the Breslow intermediate. An early concerted transition state has been located for the stereocontrolling C–C bond formation step (ΔG^# = 26.6 kcal/mol) which is used to explain the diastereomeric ratio observed in the experiment.     

Spectroscopic studies of intermolecular hydrogen bonding and proton transfer complexes of chromotropic acid with some amines in methanol

The proton transfer reactions between chromotropic acid (CTA) and some amines including benzylamine (BA), triethylamine (TEA), pyrrolidine (PY) and 1,8-bis(dimethylamino) naphthalene (DMAN) have been investigated spectrophotometrically in methanol. A long wavelength band at 365 nm has been recorded due to the proton transfer (PT) complex formation. The proton transfer equilibrium constants K_PT were estimated utilizing the minimum–maximum absorbances method. It has been found that K_PT were not depend on the amine pKa values, but strongly depend on the formed structures of the PT complexes. Job^’s method of continuous variations and photometric titrations were applied to identify the compositions of the formed PT complexes where 1:1 complexes (proton donor: proton acceptor) were produced. Due to the rapidity and simplicity of the proton transfer reactions and the stability of the formed complexes, a rapid and accurate spectrophotometric method for the determination of CTA was proposed for the first time.     

Control of proton transfer: intramolecular vs intermolecular

[reaction: see text] Proton transfer in ketonization of enolates is a critical step in a myriad of organic reactions. Its stereochemistry has been the object of our studies since we reported kinetic protonation from the less hindered face of the molecule under kinetic control some decades ago. Very recently, we have succeeded in reversing the stereochemistry using 2-pyridyl groups to deliver the proton. We now report intramolecular delivery by other moieties and control of intramolecular versus intermolecular proton delivery.     

5-氟胞嘧啶气相及水助质子转移异构化的理论研究

采用密度泛函B3LYP/6-311G**方法,对6种5-氟胞嘧啶异构体孤立分子的稳定性及质子转移引起的酮式-烯醇式、氨基式-亚胺式互变异构反应机理进行了计算研究,获得了零点能、吉布斯自由能及质子转移过程的反应焓、活化能、活化吉布斯自由能和速率常数等参数.计算结果表明,气相中烯醇-氨基式FC4是最稳定的异构体.分子内质子转移设计了FC1→FC2和FC1→FC6两条通道,分别标记为P(1)和P(2),各通道速控步骤的活化能和速率常数分别为155.9 kJ·mol-1,4.70×10-15 s-1和173.1 kJ·mol-1,1.41×10-18 s-1.水助催化时,相应通道P(3) 和P(4) 速控步骤的活化能和速率常数分别为51.0 kJ·mol-1,1.41×103 s-1和88.2 kJ·mol-1,4.53×10-3 s-1.可见,水分子的加入极大地降低了质子转移的活化能垒.另外发现,水分子参与形成协同的双质子转移机理比水助单质子转移机理更利于降低活化能垒.     

Thermodynamics and kinetics of intramolecular water assisted proton transfer in Na+ -1-methylcytosine water complexes

High-level ab initio predictions of the tautomerization equilibrium and rate constants of water-assisted proton transfer of 1-methyl-cytosine (MeC) to its MeC* imino tautomeric form in the presence of up to two water molecules (W) and the Na(+) cation were carried out. The calculated energy values were used to obtain the thermodynamic parameters and equilibrium concentration of MeC, its rare tautomer, and their complexes with up to two water molecules and the Na (+) cation. The rate constants for the tautomerization were obtained by using the instanton approach (a quasiclassical method based on the least-action principle). Hydration of MeC by one water molecule leads to an increase of the concentration of the MeC* tautomer in the equilibrium mixture and a decrease of the barrier of the MeC* formation (to 15.6 kcal/mol). If the Na(+) cation is present, the tautomeric form is much less favored, and the tautomerization barrier increases to 25.2 kcal/mol. It was found that MeC monohydrate has both the highest equilibrium (2.9 x 10(-2)) and rate (7.9 x 10(5) s(-1)) constants of tautomerization in comparison to the MeC*NaW and MeC*Na2W complexes containing the Na(+) cation. Moreover, this study also allows one to estimate the concentration of MeC present in the cell during DNA synthesis as the unwanted tautomer, which in forming a mismatched base pair can cause spontaneous point mutations. Kinetic simulations have demonstrated that the low values of equilibrium (10(-14)-10(-13)) and rate constants (10(-17)-10(-16) s(-1)) of tautomerization make contribution of the MeC*Na(+)W and MeC*Na(+)2W complexes to the point mutations in DNA unlikely. In contrast to these Na(+) complexes, MeC*W can reach an equilibrium concentration of 2.9 x 10(-2) within 10(-7) s; thus, it can increase the probability of the point mutations.     

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.     

Ultrafast excited-state intermolecular proton transfer of cyanine fluorochrome dyes

Steady-state and time-resolved emission spectroscopy techniques were employed to study the excited-state proton transfer (ESPT) to water and D(2)O from QCy7, a recently synthesized near-infrared (NIR)-emissive dye with a fluorescence band maximum at 700 nm. We found that the ESPT rate constant, k(PT), of QCy7 excited from its protonated form, ROH, is ~1.5 × 10(12) s(-1). This is the highest ever reported value in the literature thus far, and it is comparable to the reciprocal of the longest solvation dynamics time component in water, τ(S) = 0.8 ps. We found a kinetic isotope effect (KIE) on the ESPT rate of ~1.7. This value is lower than that of weaker photoacids, which usually have KIE value of ~3, but comparable to the KIE on proton diffusion in water of ~1.45, for which the average time of proton transfer between adjacent water molecules is similar to that of QCy7.     

Intra- and intermolecular proton transfer reactions in 2-phenyl substituted benzazoles

The present review describes the salient features of inter- and intramolecular proton transfer reactions of 2-(2′-aminophenyl)-, 2-(3′-aminophenyl)-, 2-(4′-aminophenyl)-, 2-(2′-hydroxyphenyl)-, 2-(3′-hydroxyphenyl)- and 2-(4′-hydroxyphenyl)-benzimidazoles, benzoxazoles and benzothiazoles. Fluorescence quantum yield of the phototautomer produced by the intramolecular hydrogen bonding decreases on going from benzimidazole to benzoxazole to benzothiazole. This indicates that the rate of internal conversion increases in the order of compounds as mentioned above. The biprotonic phototautomerism or the presence of intermolecular proton transfer has led to the formation of (i) nonfluorescent zwitterions in case of hydroxyphenyl derivatives and the ground state precursor of this species in neutral molecules, (ii) nonfluorescent monoanions from fluorescent monoanions and (iii) nonfluorescent monocations from monocations in case of aminophenyl derivatives. In the case of 2-(4′-aminophenyl)-substituted compounds, the first protonation has always led to the formation of two types of monocations; one by protonating the amino group and the other by protonating the tertiary nitrogen atom. The former is more stable in aqueous media and the latter in non-polar media.     

别嘌醇质子迁移过程的理论研究

别嘌醇(Allopurinol)是次黄嘌呤的位置异构体,是唯一在临床上应用的黄嘌呤氧化酶抑制剂.     

Mechanochromism of piroxicam accompanied by intermolecular proton transfer probed by spectroscopic methods and solid-phase changes

Structural and solid-state changes of piroxicam in its crystalline form under mechanical stress were investigated using cryogenic grinding, powder X-ray diffractometry, diffuse-reflectance solid-state ultraviolet-visible spectroscopy, variable-temperature solid-state (13)C nuclear magnetic resonance spectroscopy, and solid-state diffuse-reflectance infrared Fourier transform spectroscopy. Crystalline piroxicam anhydrate exists as colorless single crystals irrespective of the polymorphic form and contains neutral piroxicam molecules. Under mechanical stress, these crystals become yellow amorphous piroxicam, which has a strong propensity to recrystallize to a colorless crystalline phase. The yellow color of amorphous piroxicam is attributed to charged piroxicam molecules. Variable-temperature solid-state (13)C NMR spectroscopy indicates that most of the amorphous piroxicam consists of neutral piroxicam molecules; the charged species comprise only about 8% of the amorphous phase. This ability to quantify the fractions of charged and neutral molecules of piroxicam in the amorphous phase highlights the unique capability of solid-state NMR to quantify mixtures in the absence of standards. Other compounds of piroxicam, which are yellow, are known to contain zwitterionic piroxicam molecules. The present work describes a system in which proton transfer accompanies both solid-state disorder and a change in color induced by mechanical stress, a phenomenon which may be termed mechanochromism of piroxicam.     

Excited-state intermolecular proton transfer of firefly luciferin V. Direct proton transfer to fluoride and other mild bases

We studied the direct proton transfer (PT) from electronically excited D-luciferin to several mild bases. The fluorescence up-conversion technique is used to measure the rise and decay of the fluorescence signals of the protonated and deprotonated species of D-luciferin. From a base concentration of 0.25 M or higher the proton transfer rates to the fluoride, dihdyrogen phosphate or acetate bases are fast and comparable. The fluorescence signals are nonexponential and complex. We suggest that the fastest decay component arises from a direct proton transfer process from the hydroxyl group of D-luciferin to the mild base. The proton donor and acceptor molecules form an ion pair prior to photoexcitation. Upon photoexcitation solvent rearrangement occurs on a 1 ps time-scale. The PT reaction time constant is ～2 ps for all three bases. A second decay component of about 10 ps is attributed to the proton transfer in a contact pair bridged by one water molecule. The longest decay component is due to both the excited-state proton transfer (ESPT) to the solvent and the diffusion-assisted PT process between a photoacid and a base pair positioned remotely from each other prior to photoexcitation.     

Excited-state proton transfer from pyranine to acetate in methanol

Excited-state proton transfer (ESPT) of pyranine (8-hydroxypyrene-1,3,6-trisulphonate, HPTS) to acetate in methanol has been studied by steady-state and time-resolved fluorescence spectroscopy. The rate constant of direct proton transfer from pyranine to acetate (k ₁) is calculated to be ∼1 × 10⁹ M⁻¹ s⁻¹. This is slower by about two orders of magnitude than that in bulk water (8 × 10¹⁰ M⁻¹ s⁻¹) at 4 M acetate.     

DFT investigation on the intramolecular and intermolecular proton transfer processes in 2-aminobenzothiazole (ABT) in the gas phase and in different solvents

DFT at the B3LYP/6-311++G(d,p) level of theory was performed to geometrically, thermodynamically, and kinetically investigate the tautomerism process of 2-aminobenzothiazole (ABT) with n water molecules (n = 1–3) and without water in the gas phase and in different solvents with a gradual increase in their dielectric constants. The geometries of the envisaged tautomers were optimized in the gas phase and in solution with the polarized continuum model (PCM). Equilibrium and rate constants for the forward and reverse intra-/intermolecular isolated and water-assisted tautomerism reactions were also calculated. The results suggest that the activation energy of the transition state of direct proton transfer in the isolated reaction is very high and that the rate constant is very slow (~ 10^?24 s), reflecting that the reaction is thermodynamically unfavored, whereas the barrier differences between the transition states of the tautomers decrease gradually as the number of water molecules increases from one to three. Moreover, the rate constants of the proposed reactions are ~ 10²³–10²⁵ faster than those of the isolated reaction, and the water-assisted tautomerism paths can be performed quickly, especially with the assistance of two molecules of water.

     

Control of emission by intermolecular fluorescence resonance energy transfer and intermolecular charge transfer

Control of emission by intermolecular fluorescence resonant energy transfer (IFRET) and intermolecular charge transfer (ICT) is investigated with the quantum-chemistry method using two-dimensional (2D) and three-dimensional (3D) real space analysis methods. The work is based on the experiment of tunable emission from doped 1,3,5-triphenyl-2-pyrazoline (TPP) organic nanoparticles (Peng, A. D.; et al. Adv. Mater. 2005, 17, 2070). First, the excited-state properties of the molecules, which are studied (TPP and DCM) in that experiment, are investigated theoretically. The results of the 2D site representation reveal the electron-hole coherence and delocalization size on the excitation. The results of 3D cube representation analysis reveal the orientation and strength of the transition dipole moments and intramolecular or intermolecular charge transfer. Second, the photochemical quenching mechanism via IFRET is studied (here "resonance" means that the absorption spectrum of TPP overlaps with the fluorescence emission spectrum of DCM in the doping system) by comparing the orbital energies of the HOMO (highest occupied molecular orbital) and the LUMO (lowest unoccupied molecular orbital) of DCM and TPP in absorption and fluorescence. Third, for the DCM-TPP complex, the nonphotochemical quenching mechanism via ICT is investigated. The theoretical results show that the energetically lowest ICT state corresponds to a pure HOMO-LUMO transition, where the densities of the HOMO and LUMO are strictly located on the DCM and TPP moieties, respectively. Thus, the lowest ICT state corresponds to an excitation of an electron from the HOMO of DCM to the LUMO of TPP.     

Barrier-free intermolecular proton transfer induced by excess electron attachment to the complex of alanine with uracil

The photoelectron spectrum of the uracil-alanine anionic complex (UA)(-) has been recorded with 2.540 eV photons. This spectrum reveals a broad feature with a maximum between 1.6 and 2.1 eV. The vertical electron detachment energy is too large to be attributed to an (UA)(-) anionic complex in which an intact uracil anion is solvated by alanine, or vice versa. The neutral and anionic complexes of uracil and alanine were studied at the B3LYP and second-order M?ller-Plesset level of theory with 6-31++G(*) (*) basis sets. The neutral complexes form cyclic hydrogen bonds and the three most stable neutral complexes are bound by 0.72, 0.61, and 0.57 eV. The electron hole in complexes of uracil with alanine is localized on uracil, but the formation of a complex with alanine strongly modulates the vertical ionization energy of uracil. The theoretical results indicate that the excess electron in (UA)(-) occupies a pi(*) orbital localized on uracil. The excess electron attachment to the complex can induce a barrier-free proton transfer (BFPT) from the carboxylic group of alanine to the O8 atom of uracil. As a result, the four most stable structures of the uracil-alanine anionic complex can be characterized as a neutral radical of hydrogenated uracil solvated by a deprotonated alanine. Our current results for the anionic complex of uracil with alanine are similar to our previous results for the anion of uracil with glycine, and together they indicate that the BFPT process is not very sensitive to the nature of the amino acid's hydrophobic residual group. The BFPT to the O8 atom of uracil may be relevant to the damage suffered by nucleic acid bases due to exposure to low energy electrons.     

Facile Ru-H2 heterolytic activation and intramolecular proton transfer assisted by basic N-centers in the ligands

The use of the phosphine PPh2py instead of PPh3 in complexes of the type [Cp*RuH(P)2] enormously alters the kinetic control of the proton-transfer reactions over this compound and its chemical behavior. The reaction at low temperature of [Cp*RuH(PPh2py)2], 2, with HBF4 gives as products the classical dihydride trans-[Cp*RuH2(PPh2py)2](BF4), 3 (1 equiv of HBF4) or the dihydrogen-bonded complex [Cp*RuHH(PPh2pyH)(PPh2py)](BF4)2, 4 (2 equiv of HBF4). These complexes exhibit very accessible intramolecular processes of proton transfer, and finally, a slow release of H2 takes place at room temperature. Derivatives 2 and 3 are active catalysts for the deuterium labeling of H2 using methanol-d4 as an isotopic source. This demonstrates that the release of hydrogen is reversible, that the heterolytic activation of H2 is an easy process, and that acid species participate in the intramolecular proton-transfer processes. These observations are supported by reaction-coordinate calculations at the DFT/B3LYP level that show the existence of a low-energy reaction path that easily transforms the classical trans dihydride complex into the nonclassical cis dihydrogen compound in a reversible way, through the involvement of hydrogen- and dihydrogen-bonded intermediates and the essential participation of the pyridine centers. The different energy minima of this reaction profile are very accessible through low-energy transition states, all of which have been located.