Substituent effect on the reaction mechanism of proton transfer in formamide

MP2 and B3LYP methods at 6‐311++G** basis set have been used to explore proton transfer in keto‐enol forms of formamide and to investigate the effect of substituent, i.e., H, F, Cl, OH, SH, and NH₂ on their transition states. Additionally, the vibrational frequencies of aforementioned compounds are calculated at the same levels of theory. It is proposed that the barrier heights values in kJ/mol for F, Cl, OH, and SH substituents are significantly greater than that of the bare tautomerization reaction, implying the importance of the substituents effect on the intramolecular proton transfer. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Targeted Car-Parrinello molecular dynamics: elucidating double proton transfer in formic acid dimer

The targeted molecular dynamics method, making possible the study of rare events, has been assessed in the framework of Car-Parrinello ab initio molecular dynamics. As a test case, we have studied the staggered-eclipsed rotation of ethane. The technique has subsequently been applied to investigate the nature of double proton transfer in formic acid dimer. The latter is found to follow a concerted transfer mechanism involving an essentially planar transition state. A "funnel-like region" of the potential energy surface is identified, where floppy intermolecular modes stiffen upon approaching the transition state.     

Effects of external electric fields on double proton transfer kinetics in the formic acid dimer

Molecules can be exposed to strong local electric fields of the order of 10(8)-10(10) V m(-1) in the biological milieu. The effects of such fields on the rate constant (k) of a model reaction, the double-proton transfer reaction in the formic acid dimer (FAD), are investigated. The barrier heights and shapes are calculated in the absence and presence of several static homogenous external fields ranging from 5.14 × 10(8) to 5.14 × 10(9) V m(-1) using density functional theory (DFT/B3LYP) and second order M?ller-Plesset perturbation theory (MP2) in conjunction with the 6-311++G(d,p) Pople basis set. Conventional transition state theory (CTST) followed by Wigner tunneling correction is then applied to estimate the rate constants at 25 °C. It is found that electric fields parallel to the long axis of the dimer (the line joining the two carbon atoms) lower the uncorrected barrier height, and hence increase the raw k. These fields also flatten the potential energy surface near the transition state region and, hence, decrease the multiplicative tunneling correction factor. The net result of these two opposing effects is that fields increase k(corrected) by a factor of ca. 3-4 (DFT-MP2, respectively) compared to the field-free k. Field strengths of ～3 × 10(9) V m(-1) are found to be sufficient to double the tunneling-corrected double proton transfer rate constant at 25 °C. Field strengths of similar orders of magnitudes are encountered in the scanning tunneling microscope (STM), in the microenvironment of a DNA base-pair, in an enzyme active site, and in intense laser radiation fields. It is shown that the net (tunneling corrected) effect of the field on k can be closely fitted to an exponential relationship of the form k = aexp(bE), where a and b are constants and E the electric field strength.     

Examination of formamide,formamidic acid,amidine dimers,and the double proton transfer transition states involving these dimers

Structures and relative energies were obtained for the hydrogen bonded dimers of formamide and formamidic acid using the 3-21G basis set. A double proton transfer transition state is claimed to link these two dimers. While the structure of the transition state was intermediate between those of the two dimers, the energy was only 7.6 kJ/mol greater than the less stable formamidic acid dimer. The activation energy from the formamide dimer side of the reaction was found to be 125 kJ/mol of dimer. A similar transition state was found for the amidine dimer system. The activation energy for this model reaction was found to be 66.9 kJ/mol of dimer.     

On the mechanism of proton transfer in imidazole

The force fields, in-plane vibrations, and relative intensities of Raman spectra have been calculated and analyzed for the N₁H and N₃H tautomers of imidazole, imidazolium cation, and their model structures. The results obtained for the isolated state of imidazole correspond to the intramolecular mechanism of proton transfer.     

An ab initio calculation on proton transfer in the benzoic acid dimer

We have made an ab initio calculation of the barriers for proton transfer in the hydrogen-bonded dimers of benzoic acid and acetic acid. Geometrical optimization values which are closer to the experiment one.     

The mechanism of double proton transfer in dimers of uracil and 2-thiouracil--the reaction force perspective

The intermolecular double proton transfer in dimers of uracil and 2-thiouracil is studied through density functional theory calculations. The reaction force framework provides the basis for characterizing the mechanism that in all cases has been associated to a dynamic balance between polarization and charge transfer effects. It has been found that the barriers for proton transfer depend upon the nature of the acceptor atoms and its position within the seminal monomer. Actually, the change in the nature of the hydrogen bonds connecting the two monomers along the reaction coordinate may favor or disfavor the double-proton transfer.     

Double proton transfer and charge transfer transitions in hydrogen-bonded systems: formic acid dimer

The barriers for double proton transfer in the ground and lowest Π-Π^* and Π-Π^* excited states of the formic acid dimer have been calculated within a modified INDO scheme. Analysis of the nature of the excited electronic states, with emphasis on charge-transfer transitions, has been performed. The results indicate a lower barrier in the excited Π-Π^* states than in the ground state.     

A non-empirical study of hydrogen bonding in the dimer of formamide

A non-empirical SCF calculation on the cyclic dimer of formamide in two different GTF basis sets has been performed and is compared to a similar calculation for the isolated monomer. The energy gain per H-bond is reasonable. Both the proton-donor and proton-acceptor show a global gain in electrons at the expense of the hydrogen of the bridge and of the C atoms. This gross changes in charge are reflected in the _1s values. They cover a gain for nitrogen and a loss for oxygen which are studied in detail on the difference density maps in the molecular plane. The covalent character of the H bond appears very small. Both basis sets yield similar conclusions.

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Zusammenfassung Eine SCF-Rechnung mit nicht empirischen Parametern wurde mit zwei verschiedenen aus Gauß aufgebauten Basissätzen für das zyklische Dimere und das Monomere des Formamid durchgeführt. Der Energiegewinn ist beträchtlich. Sowohl der Protonendonor als auch der -acceptor zeigen insgesamt einen Elektronengewinn auf Kosten des Brückenwasserstoffs und des Kohlenstoffatoms. Diese Änderung zeigt sich auch in den _1s -Werten. Der Gewinn und Verlust an -Elektronen für Stickstoff bzw. Sauerstoff wird an Hand von Elektronendichtekonturen untersucht. Der kovalente Charakter der Wasserstoffbrückenbindung ist sehr klein. Die beiden Basissätze führen zu ähnlichen Ergebnissen.

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Résumé Un calcul SCF non-empirique du dimère cyclique de la formamide a été fait dans deux bases de fonctions gaussiennes différentes et comparaison est faite avec le monomère isolé. Le gain d'énergie par liaison H est d'un ordre de grandeur raisonnable. Le donneur et l'accepteur de proton gagnent au total des électrons alors que l'hydrogène de la liaison H en perd ainsi que le carbone central; ces déplacements globaux se reflètent dans les valeurs des _1s correspondants. Ils couvrent un gain pour l'azote et une perte pour l'oxygène qui sont étudiés en détails sur les courbes d'isodensité différentielle dans le plan moléculaire. La liaison H apparait peu ou pas covalente. Les deux bases de gaussiennes choisies donnent les mêmes conclusions qualitatives.

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This work was supported by grant n CR 66-236 of the Institut National de la Santé et de la Recherche Médicale (Comité Cancer et Leucémie).     

Excited-state double proton transfer in 1-azacarbazole hydrogen-bonded dimers

1-azacarbazole hydrogen-bonded dimers undergo photoinduced double proton transfer reaction in their lowest excited singlet state. A second emission band with a maximum at 510 nm arises from a tautomer formed in the excited singlet state as a result of the double proton transfer process.     

Intramolecular single and double proton transfer in benzoxazole derivatives

The “double” derivatives of benzoxazole, bis-2,5-(2-benzoxazolyl)hydroquinone (II) and bis-3,6-(2-benzoxazolyl)-pyrocatochol (III), have been investigated. In (II), only one proton is transferred in the S₁ state. Primary and tautomeric forms exist in a rapidly established equilibrium. In (III), two tautomers were detected. One is generated in the S₁ state by a double proton transfer without a potential barrier, while the other, generated by a single proton transfer, is already present in trace amounts in the S₀ state.     

Symmetric double proton tunneling in formic acid dimer: a diabatic basis approach

A model of double proton tunneling in formic acid dimer is developed using a reaction surface Hamiltonian. The surface includes the symmetric OH stretch plus the in-plane stretch and bend interdimer vibrations. The surface Hamiltonian is coupled to a bath of five A1g and B3g normal modes obtained at the D2h transition state structure. Eigenstates are calculated using Davidson and block-Davidson iterative methods. Strong mode specific effects are found in the tunneling splittings for the reaction surface, where splittings are enhanced upon excitation of the interdimer bend motion. The results are interpreted within the framework of a diabatic representation of reaction surface modes. The splitting patterns observed for the reaction surface eigenstates are only slightly modified upon coupling to the bath states. Splitting patterns for the bath states are also determined. It is found that predicting these splittings is greatly complicated by subtle mixings with the inter-dimer bend states.     

The role of reaction force and chemical potential in characterizing the mechanism of double proton transfer in the adenine-uracil complex

A theoretical study of the intermolecular double proton transfer in the adenine-uracil base pair has been performed to model the double proton transfer in the adenine-thymine dimer. The mechanism is analyzed in terms of the reaction force profile, which indicates that the activation of the transfer occurs via structural rearrangements to bring the interacting molecules close to each other to let the donor and acceptor atoms in the right position to achieve the transfer. It is found that only when the first proton transfer is partially completed does the second proton get activated, thus illustrating the asynchronous nature of the double proton-transfer process in base pair systems.     

The inclusion of electron correlation in intermolecular potentials: applications to the formamide dimer and liquid formamide

A test of the quality of the electrostatic properties and polarizabilities used in the nonempirical molecular orbital (NEMO) potential is carried out for formamide by calculating the molecular dipole moment and polarizability at the second-order M?ller–Plesset (MP2) level of theory. The molecular dipole moment is 11% lower at the MP2 level than at the Hartree–Fock (HF) level, whereas the isotropic part of the polarizability is increased by 36% by adding electron correlation and using a considerably larger basis set. The atomic charges, dipole moments and polarizabilities obtained at the HF level are rescaled to get the correct molecular properties at the MP2 level. The potential minimum for the cyclic dimer of formamide is −17.50 kcal/mol with the MP2-scaled properties and is significantly lower than other potentials give. Two intermolecular potentials are constructed and used in subsequent molecular dynamics simulations: one with the regular NEMO potential and the other with the rescaled MP2 properties. A damping of the electrostatic field at short intermolecular distances is included in the present NEMO model. The average energies for liquid formamide are lower for the MP2-scaled model and are in good agreement with experimental results. The lowering of the simulation energy for the MP2-scaled potential indicates the strong dispersive interactions in liquid formamide. Received: 20 March 2000 / Accepted: 18 April 2000 / Published online: 18 August 2000     

Excited-state double proton transfer of 7-azaindole in water nanopools

The excited-state proton-transfer dynamics of 7-azaindole occurring in the water nanopools of reverse micelles has been investigated by measuring time-resolved fluorescence spectra and kinetics, as well as static absorption and emission spectra, with varying water content and isotope. 7-Azaindole molecules are found to exist in the bound-water regions of reverse micelles. The rate constant and the kinetic isotope effect of proton transfer are smaller than those in bulk water although both increase with the size of the water nanopool. The retardation of proton transfer in the bound regions is attributed to the increased free energy of prerequisite solvation to form a cyclically H-bonded 1:1 7-azaindole/water complex.     

A theoretical investigation on the excited state intramolecular single or double proton transfer mechanism of a salicyladazine system

Given the tremendous potential applications of excited state intramolecular proton transfer (ESIPT) systems, ESIPT molecules have received widespread attention. In this work, based on density functional theory (DFT) and time‐dependent DFT (TDDFT) methods, we theoretically study the excited state dynamical behaviors of salicyladazine (SA) molecules. Our simulated results show that the double intramolecular hydrogen bonds of SA are strengthened in the S₁ state via exploring bond distances, bond angles, and infrared (IR) vibrational spectra. Exploring the frontier molecular orbitals (MOs), we confirm that charge redistributions indeed have effects on excited state dynamical behaviors. The increased electronic densities on N atoms and the decreased electronic densities on O atoms imply that charge redistribution may trigger the ESPT process. Analyzing the constructed S₀‐state and S₁‐state potential energy surfaces (PESs), we confirm that only the excited state single proton transfer reaction can occur although SA possesses two intramolecular hydrogen bonds. In this work, we clarify the specific ESIPT mechanism, which may facilitate developing novel applications based on the SA system in future.     

A novel mechanism of proton transfer in protonated peptides

The study presents quantum-chemical calculations on proton transfer in protonated N-acetylglycyl-N1-methylglycinamide (AGA) as a short oligopeptide model. All calculations employ the B3LYP functional and the 6-31++G** basis set. Two different mechanisms of proton transfer are discussed. The rate-determining step of the first mechanism exhibits an energy barrier of about 17.7 kcal mol-1, and it is represented by an isomerization of the proton around the double bond of the carbonyl group. The second mechanism is based on the large conformational flexibility of AGA, where all carbonyl oxygens cooperate. The rate-determining step of this mechanism exhibits an energy barrier of only 8.3 kcal mol-1.     

Excited state proton transfer in 3-methyl-7-azaindole dimer. Symmetry control

The concerted double proton transfer undergone by the C(2)(h) dimer of 7-azaindole upon electronic excitation has also been reported to occur in 3-methyl-7-azaindole monocrystals and in dimers of this compound under free-jet conditions. However, the results obtained in this work for the 3-methyl-7-azaindole dimer formed in a 10(-4) M solution of the compound in 2-methylbutane suggest that the dimer produces no fluorescent signal consistent with a double proton transfer in the liquid phase or in a matrix. In this paper, the spectroscopic behavior of the doubly hydrogen bonded dimer of 3-methyl-7-azaindole is shown to provide a prominent example of molecular symmetry control over the spectroscopy of a substance. This interpretation opens up a new, interesting research avenue for exploring the ability of molecular symmetry to switch between proton-transfer mechanisms. It should be noted that symmetry changes in the 3-methyl-7-azaindole dimer are caused by an out-of-phase internal rotation of the two methyl groups.