Theoretical study of one‐carbon unit transfer between methyl‐AICA and N1‐methyl‐N1‐acryloyl‐formamide

The mechanism of one‐carbon unit transfer between 1‐methyl‐5‐amino‐4‐carboxamide imidazole (M‐AICA) and N¹‐methyl‐N¹‐acryloyl‐formamide (the model molecule of 10‐f‐H4F) is investigated by the Hartree–Fock and DFT methods, respectively, at the 6‐31G* basis level. There are two different channels for the proton transfer, resulting in two reaction pathways with different properties. The results indicate that both channels can complete the reaction, but path a is slightly favored due to its lower active energy barrier. Furthermore, the influence of 4‐carboxamindde in M‐AICA is also discussed. This group can stabilize the reactant and intermediates, and reduce the active energy barrier through the intermolecular hydrogen bond. The intermolecular hydrogen bond results in an enlarged conjugation system and makes the transition states more stable. Our results are in agreement with experiments. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

ONIOM study of one‐carbon unit transfer from imidazolidine to dUMP analogue

The ONIOM quantum mechanics method is used in this article to study one‐carbon unit transfer from an imidazolidine to 6‐aminouracil derivates. The computation results show that this reaction can be completed via three paths, owing to the three different proton transfer modes. Each path experiences three processes of nucleophile attacking, proton transferring, and bond rupturing. The focus of discussion falls on the proton transfer process. By analyzing the calculation results, we find that the direct proton transfer is the preferable pathway. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

细胞内第二信使3',5'-环核苷酸酯质子迁移机理的理论研究

应用密度泛函理论B3LYP/6-31G**计算方法对气相中细胞内第二信使3¢,5¢-环核苷酸酯(cAMPm)质子迁移机理进行了理论研究,此外,在相同水平上模拟了水分子作催化剂的反应机理。计算结果表明cAMPm两种构象Bm 和Dm之间的转化经过一个环状过渡态,其中,两分子水参与的H 迁移反应的势能面最低,反应更容易进行。我们的计算结果为研究相关的磷酸二酯的H质子迁移反应提供了理论依据。     

Theoretical insights into the excited‐state process of 4‐tert‐butyl‐2‐(5‐(5‐tert‐butyl‐2‐methoxyphenyl)thiazolo[5,4‐d]thiazol‐2‐yl)‐phenol

In this paper, we theoretically explore the motivation and behaviors of the excited‐state intramolecular proton transfer (ESIPT) reaction for a novel white organic light‐emitting diode (WOLED) material 4‐tert‐butyl‐2‐(5‐(5‐tert‐butyl‐2‐methoxyphenyl)thiazolo[5,4‐d]thiazol‐2‐yl)‐phenol (t‐MTTH). The “atoms in molecules” (AIM) method is adopted to verify the formation and existence of the hydrogen bond O? H···N. By analyzing the excited‐state hydrogen bonding behaviors via changes in the chemical bonding and infrared (IR) vibrational spectra, we confirm that the intramolecular hydrogen bond O? H···N should be getting strengthened in the first excited state in four kinds of solvents, thus revealing the tendency of ESIPT reaction. Further, the role of charge‐transfer interaction is addressed under the frontier molecular orbitals (MOs), which depicts the nature of the electronic excited state and supports the ESIPT reaction. Also, the electron distribution confirms the ESIPT tendency once again. The scanned and optimized potential energy curves according to variational O? H coordinate in the solvents demonstrate that the proton transfer reaction should occur in the S₁ state, and the potential energy barriers along with ESIPT direction support this reaction. Based on the excited‐state behaviors reported in this work, the experimental spectral phenomenon has been reasonably explained.     

Quantum chemical modeling of 1,1‐proton transfer reaction catalyzed by a cofactor‐independent α‐methylacyl‐CoA racemase

α‐Methylacyl‐CoA racemases (AMACR) are essential enzymes for branched‐chain lipids and drugs metabolism. AMACR catalyzes the chiral inversion of (2R) and (2S)‐methylacyl‐CoA esters in both directions. In this study, we investigated the catalytic mechanism of Mycobacterium tuberculosis (MCR) α‐methylacyl‐CoA racemase by using the density functional theory with the hybrid functional B3LYP. Our calculations elucidate and support the mechanism proposed by Prasenjit Bhaumik. His126 and Asp156 serve as the acid/base‐pair residues in the 1,1‐proton transfer catalytic reaction. From the optimized structures, it can be seen that an enolate intermediate is formed and the possibility of forming a ketene or a carbanion intermediate is excluded. By comparing the energy barriers, we could consider that the deprotonation step is the rate‐determined step in the invert direction from (S)‐ to (R)‐enantiomer. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Electrochemical Oxidation of 8‐Oxo‐2′‐Deoxyguanosine on Glassy Carbon,Gold, Platinum and Tin(IV) Oxide Electrodes

Cyclic voltammetry was used to investigate the oxidation of 8‐oxo‐2′‐deoxyguanosine (8‐oxo‐dG) on the glassy carbon (GC), platinum, gold and SnO₂ electrodes over a range of the sweep rate, 8‐oxo‐dG concentration and the solution pH. Reaction mechanism that is common to all these electrodes involves the two‐electron two‐proton charge transfer step followed by the irreversible chemical reaction(s). Rate of the charge transfer reaction decreases with the increasing solution pH (GC, Pt, Au), and depends on the nature of the electrode material following the sequence GC>Pt, Au>>SnO₂. These effects can be related to the degree of oxidation of the electrode surface (Pt, Au, SnO₂), or to the density of the active surface sites (GC). Any of these electrodes can be used for the fabrication of an amperometric detector for 8‐oxo‐dG .     

Study of the Photochemical Properties and Conical Intersections of [2,2′‐Bipyridyl]‐3‐amine‐3′‐ol

The two isoelectronic bipyridyl derivatives [2,2′‐bipyridyl]‐3,3′‐diamine and [2,2′‐bipyridyl]‐3,3′‐diol are experimentally known to undergo very different excited‐state double‐proton‐transfer processes, which result in fluorescence quantum yields that differ by four orders of magnitude. In a previous study, these differences were explained from a theoretical point of view, because of topographical features in the potential energy surface and the presence of conical intersections (CIs). Here, we analyze the photochemical properties of a new molecule, [2,2′‐bipyridyl]‐3‐amine‐3′‐ol [BP(OH)(NH₂)], which is, in fact, a hybrid of the former two. Our density functional theory (DFT), time‐dependent DFT (TDDFT), and complete active space self‐consistent field (CASSCF) calculations indicate that the double‐proton‐transfer process in the ground and first singlet π→π* excited state in BP(OH)(NH₂) presents features that are between those of their “parents”. The presence of two CIs and the role they may play in the actual photochemistry of BP(OH)(NH₂) and other bipyridyl derivatives are also discussed.     

9,10‐Diphenylanthracene as a matrix for MALDI‐MS electron transfer secondary reactions

The most common secondary‐ionization mechanism in positive ion matrix‐assisted laser desorption/ionization (MALDI) involves a proton transfer reaction to ionize the analyte. Peptides and proteins are molecules that have basic (and acidic) sites that make them susceptible to proton transfer. However, non‐polar, aprotic compounds that lack basic sites are more difficult to protonate, and creating charged forms of this type of analyte can pose a problem when conventional MALDI matrices are employed. In this case, forming a radical molecular ion through electron transfer is a viable alternative, and certain matrices may facilitate the process. In this work, we investigate the performance of a newly developed electron‐transfer secondary reaction matrix: 9,10‐diphenylanthracene (9,10‐DPA). The use of 9,10‐DPA as matrix for MALDI analysis has been tested using several model compounds. It appears to promote ionization through electron transfer in a highly efficient manner as compared to other potential matrices. Thermodynamic aspects of the observed electron transfers in secondary‐ionization reactions were also considered, as was the possibility for kinetically controlled/endothermic, electron‐transfer reactions in the MALDI plume. Copyright © 2012 John Wiley & Sons, Ltd.     

A comparative study of open‐close and related rotamers methods to evaluate the intramolecular hydrogen bond energies in 3‐imino‐propen‐1‐ol and its derivatives

MP2 study of O? H…N intramolecular hydrogen bond (IMHB) in 3‐imino‐propen‐1‐ol and its derivatives were performed and their IMHB energies were obtained using the related rotamers and open‐close methods. Also the topological properties of electron density distribution and charge transfer energy associated with IMHB were gained by quantum theory of atoms in molecules and natural bond orbital theory, respectively. The computational results reveal that the related rotamers method energies are well correlates with geometrical parameters, topological parameters at hydrogen bond and ring critical points, integrated properties, proton transfer barrier and charge transfer energy of O? H…N unit. Surprisingly, it was found that the open‐close hydrogen bond energies cannot represent good linear correlations with these parameters. Consequently, we extrapolate a number of equations that can be used in estimation of O? H…N IMHB energy in complex biological systems. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Calculated geometries of dications of bis odd‐membered π‐ring systems containing a NCN fragment and related π‐systems. An opposite out‐of‐plane rotation of the 4n π‐ring subsystems

Quantum chemical calculations have been carried out on dications of bis odd‐membered π‐ring systems containing a NCN fragment and related π‐systems. An opposite out‐of‐plane rotation of both subsystems was found if these systems contain 4n π‐electrons (antiaromatic). A planar situation was found for 4n+2 π‐electrons (aromatic). The geometric representations could be compared with X‐ray crystallographic three‐dimensional structures of related compounds. Calculations at different levels clearly show that separation of the σ‐ and π‐electron contribution is an effective way to elucidate the origin of the geometrical changes. We also give attention to some fundamental aspects of the subsystems related to the 1,3‐azolium cations because of their biochemical relevance such as fast C₂? H proton exchange. We postulate that at least two molecules of water are involved in this process. The significance of a trigonal pyramidal (TP) geometry has been emphasized. © 2001 Wiley Periodicals, Inc. Int J Quantum Chem, 2001     

Theoretical studies of the hydrolysis reaction of 5′‐AMP

The hydrolysis reaction mechanisms of the phosphate group, with and without an adenosine connected to it, have been theoretically investigated at the B3LYP/6‐31G** level. It is found that each reaction is single‐channel with a two‐step process. When H₂O approaches the phosphate group, a penta‐coordinated intermediate (IM1‐a) is formed first, followed by the H transfer reaction with P? O broken at the same time. This process belongs to the addition‐elimination process, similar to the carboxylate. In addition, the solvent effect has been studied by the polarizable continuum model (PCM). Our present calculations have rationalized and verified all the possible reaction channels. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Electrochemical Initiated C‐N Coupling of 3‐Methylcatechol and n‐Hexylamine in a Flow Cell Monitored with ESI‐MS

The electrochemical initiated heterocoupling of 3‐methylcatechol and n‐hexylamine was investigated. The oxidation of 3‐methylcatechol was performed in an electrochemical flow cell with glassy carbon as the working electrode. As a result, the two‐electron, two‐proton oxidised chinone intermediate undergoes a C‐N coupling reaction in the presence of an amine (Michael addition). This mono coupling product can undergo a second two‐electron, two‐proton oxidation depending on acidic or basic conditions and substrate ratios. This flow cell was coupled on‐line with electrospray ionisation mass spectrometry to identify the possible coupling products. Higher substrate concentrations were performed off‐line as first scale‐up experiments in a two‐step procedure.     

Absorption and Emission Sensitivity of 2‐(2′‐Hydroxyphenyl)benzoxazole to Solvents and Impurities

2‐(2′‐Hydroxyphenyl)benzoxazole (HBO) is known for undergoing intramolecular proton transfer in the excited state to result in the emission of its tautomer. A minor long‐wavelength absorption band in the range 370–420 nm has been reported in highly polar solvents such as dimethylsulfoxide (DMSO). However, the nature of this species has not been entirely clarified. In this work, we provide evidence that this long‐wavelength absorption band might have been caused by base or metal salt impurities that are introduced into the spectral sample during solvent transport using glass Pasteur pipettes. The contamination by base or metal salt could be avoided by using borosilicate glass syringes or nonglass pipettes in sample handling. Quantum chemical calculations conclude that solvent‐mediated deprotonation is too energetically costly to occur without the aid of a base of an adequate strength. In the presence of such a base, the deprotonation of HBO and its effect on emission are investigated in dichloromethane and DMSO, the latter of which facilitates deprotonation much more readily than the former. Finally, the absorption and emission spectra of HBO in 13 solvents are reported, from which it is concluded that ESIPT is hindered in polar solvents that are also strong hydrogen bond acceptors.     

The Cyclic Hydrogen‐Bonded 6‐Azaindole Trimer and its Prominent Excited‐State Triple‐Proton‐Transfer Reaction

The compound 6‐azaindole undergoes self‐assembly by formation of N(1)?H???N(6) hydrogen bonds (H bonds), forming a cyclic, triply H‐bonded trimer. The formation phenomenon is visualized by scanning tunneling microscopy. Remarkably, the H‐bonded trimer undergoes excited‐state triple proton transfer (ESTPT), resulting in a proton‐transfer tautomer emission maximized at 435 nm (325 nm of the normal emission) in cyclohexane. Computational approaches affirm the thermodynamically favorable H‐bonded trimer formation and the associated ESTPT reaction. Thus, nearly half a century after Michael Kasha discovered the double H‐bonded dimer of 7‐azaindole and its associated excited‐state double‐proton‐transfer reaction, the triply H‐bonded trimer formation of 6‐azaindole and its ESTPT reaction are demonstrated.     

Theoretical Study on the Substituent Effect on the Excited‐State Proton Transfer in the 7‐Azaindole‐Water Derivatives

The first excited‐state proton transfer (ESPT ) in 7AI ‐H₂O complex and its derivatives, in which the hydrogen atom at the C₂ position in pyrrole ring was replaced by halogen atom X (X = F, Cl, Br), were studied at the TD ‐M06‐2X/6‐31 + G(d, p) level. The double proton transfer took place in a concerted but asynchronous protolysis pathway. The vibrational‐mode selectivity of excited‐state double proton transfer in the model system was confirmed. The specific vibrational‐mode could shorten the reaction path and accelerate the reaction rate. The substituent effects on the excited‐state proton transfer process were discussed. When the H atom at C₂ position in 7AI ‐H₂O complex was replaced by halogen atom, some geometrical parameters changed obviously, the barrier height of ESDPT reduced, and the asynchronicity of proton transfer enlarged. The above changes correlated with the Pauling electronegativity of halogen atom.     

Different catalysis role of in‐loop and out‐of‐loop waters in assisting HNS/HSN proton transfer isomerizations: Bridging vs. surrounding effect

In this work, a density function theory (DFT) study is presented for the HNS/HSN isomerization assisted by 1–4 water molecules on the singlet state potential energy surface (PES). Two modes are considered to model the catalytic effect of these water molecules: (i) water molecule(s) participate directly in forming a proton transfer loop with HNS/HSN species, and (ii) water molecules are out of loop (referred to as out‐of‐loop waters) to assist the proton transfer. In the first mode, for the monohydration mechanism, the heat of reaction is 21.55 kcal · mol^?1 at the B3LYP/6‐311++G** level. The corresponding forward/backward barrier lowerings are obtained as 24.41/24.32 kcal · mol^?1 compared with the no‐water‐assisting isomerization barrier T (65.52/43.87 kcal · mol^?1). But when adding one water molecule on the HNS, there is another special proton‐transfer isomerization pathway with a transition state 10T′ in which the water is out of the proton transfer loop. The corresponding forward/backward barriers are 65.89/65.89 kcal · mol^?1. Clearly, this process is more difficult to follow than the R–T–P process. For the two‐water‐assisting mechanism, the heat of reaction is 19.61 kcal · mol^?1, and the forward/backward barriers are 32.27/12.66 kcal · mol^?1, decreased by 33.25/31.21 kcal · mol^?1 compared with T. For trihydration and tetrahydration, the forward/backward barriers decrease as 32.00/12.60 (30T) and 37.38/17.26 (40T) kcal · mol^?1, and the heat of reaction decreases by 19.39 and 19.23 kcal · mol^?1, compared with T, respectively. But, when four water molecules are involved in the reactant loop, the corresponding energy aspects increase compared with those of the trihydration. The forward/backward barriers are increased by 5.38 and 4.66 kcal · mol^?1 than the trihydration situation. In the second mode, the outer‐sphere water effect from the other water molecules directly H‐bonded to the loop is considered. When one to three water molecules attach to the looped water in one‐water in‐loop‐assisting proton transfer isomerization, their effects on the three energies are small, and the deviations are not more than 3 kcal · mol^?1 compared with the original monohydration‐assisting case. When adding one or two water molecules on the dihydration‐assisting mechanism, and increasing one water molecule on the trihydration, the corresponding energies also are not obviously changed. The results indicate that the forward/backward barriers for the three in‐loop water‐assisting case are the lowest, and the surrounding water molecules (out‐of‐loop) yield only a small effect. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

A combined experimental,theoretical, and Van't Hoff model study for identity methyl,proton, hydrogen atom,and hydride exchange reactions. Correlation with three‐center four‐, three‐, and two‐electron systems

We have studied carbon transfer reactions following an S_N2 reaction profile. With ab initio calculations and experimental geometries concerning the nature of the various complexes indicated as stable, intermediate, and transition state we were able to show the additional value of van't Hoff's tetrahedral configuration by changing its geometry via a trigonal pyramid into a trigonal bipyramid. The ratio of the apical bond and corresponding tetrahedral bond distances is then nearly 1.333. The relevance of this approach has also been shown for identity proton‐(hydrogen atom‐, and hydride‐) in‐line reactions. The use of this geometrical transmission will be demonstrated for the hydrogen bonding distances in e.g., DNA duplexes and other biological (supra) molecular systems. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Steady‐State Spectroscopy of the 2‐(N‐methylacetimidoyl)‐1‐naphthol Molecule

The steady‐state spectroscopy of 2‐(N‐methylacetimidoyl)‐1‐naphthol (MAN) reveals composite absorption and emission spectra from 298 to 193 K in hexane. The ground electronic state (So) absorption can be assigned to the sum of three molecular structures: the OH normal tautomer, and two NH proton transfer tautomers. The NH‐structures are the most stable ones in equilibrium with the OH tautomer for the S₀ state. On photoexcitation of the OH tautomer the excited state intramolecular proton transfer is undergone, and the corresponding NH emission is monitored at 470 nm. On photoexcitation of the NH tautomers the previous emission is monitored in addition to another emission at 600 nm, which is ascribed to intramolecular hydrogen‐bonded (IHB) nonplanar NH structures generated from the IHB planar NH tautomers. A Jab?oński diagram is introduced which gathers all the experimental evidence as well as the theoretical calculations executed at the DFT‐B3LYP and TD‐DFT levels. The MAN molecule is compared with other analogs such as 1‐hydroxy‐2‐acetonaphthone (HAN), 2‐(1?‐hydroxy‐2?‐naphthyl)benzimidazole and methyl 1‐hydroxy‐2‐naphthoate to validate the theoretical calculations. Photoexcitation of MAN generates two emission bands at longer wavelengths than that of the emission band of HAN. The MAN molecule exhibits a great photostability in hydrocarbon solution which depends on the photophysics of the NH tautomers (keto forms).     

Efficient measurement of the sign and the magnitude of long‐range proton‐carbon coupling constants from a spin‐state‐selective HSQMBC‐COSY experiment

A spin state‐selective Heteronuclear Single‐Quantum Multiple‐Bond Connectivities (HSQMBC‐COSY) experiment is proposed to measure the sign and the magnitude of long‐range proton‐carbon coupling constants (ⁿJ(CH); n > 1) either for protonated or for non‐protonated carbons in small molecules. The simple substitution of the selective 180° ¹H pulse in the original selHSQMBC pulse scheme by a hard one allows the simultaneous evolution of both proton‐proton and proton‐carbon coupling constants during the refocusing period and enables a final COSY transfer between coupled protons. The successful implementation of the IPAP principle leads to separate mixed‐phase α/β cross‐peaks from which ⁿJ(CH) values can be easily measured by analyzing their relative frequency displacements in the detected dimension. Copyright © 2012 John Wiley & Sons, Ltd.     

Theoretical study of the ring‐closing reaction of 5′‐AMP to cAMP and H2O in the gas phase

The ring‐closing reaction of 5′‐adenosine monophosphate (5′‐AMP) to generate cyclic 3′, 5′‐adenosine monophosphate (cAMP) and H₂O was theoretically investigated at the B3LYP/6‐31G**level. It was found that the ring‐closing reaction of 5′‐AMP may proceed in a synchronous way or in a stepwise way. For the latter, the reaction is a multichannel elimination reaction including inner H transfer. The potential energy surface of Path 3 is lowest in all the ring‐closing reaction paths. In addition, H shuttling reaction with the participation of a water molecule to act as a shuttle were also studied at the same level. The calculations indicate that the participation of a water molecule facilitates hydrogen transfer reaction. Our present calculations rationalized all the possible reaction channels. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005