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.     

Complex dynamics of proton and deuteron transfer in double hydrogen bond of benzoic acid isotopes

This paper deals with spin-lattice relaxation due to classical jumps and incoherent tunnelling of protons and deuterons in hydrogen bonds in solids. An analysis of experimental spin-lattice relaxation data for carboxylic acids suggests that tunnelling does not contribute to spin-lattice relaxation above the temperature at which the thermal energy of molecules and the potential barrier height are equal. It is also shown that contributions to the spin-lattice relaxation rate due to classical motion and incoherent tunnelling in excited vibrational states are negligible for fast proton transfer. However, for deuterons this contribution to spin-lattice relaxation is significant.     

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.     

Excited-state double proton transfer dynamics of model DNA base pairs: 7-hydroxyquinoline dimers

The excited-state double proton transfer of model DNA base pairs, 7-hydroxyquinoline dimers, in benzene has been investigated using picosecond time-resolved fluorescence spectroscopy. Upon excitation, whereas singly hydrogen-bonded noncyclic dimers do not go through tautomerization within the relaxation time of 1400 ps, doubly hydrogen-bonded cyclic dimers undergo excited-state double proton transfer on the time scale of 25 ps to form tautomeric dimers, which subsequently undergo a conformational change in 180 ps to produce singly hydrogen-bonded tautomers. The rate constant of the double proton transfer reaction is temperature-independent, showing a large kinetic isotope effect of 5.2, suggesting that the rate is governed mostly by tunneling.     

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.     

Isotope effects associated with tunneling and double proton transfer in the hydrogen bonds of benzoic acid

The isotope effects associated with double proton transfer in the hydrogen bonds of benzoic acid (BA) dimers have been measured using field-cycling (1)H NMR relaxometry and quasielastic neutron scattering. By studying mixed isotope (hydrogen and deuterium) samples, the dynamics of three isotopologues, BA-HH, BA-HD, and BA-DD, have been investigated. Low temperature measurements provide accurate measurements of the incoherent tunneling rate, k(0). This parameter scales accurately with the mass number, m, according to the formula k(0)=(E/m)e(-Fm) providing conclusive evidence that the proton transfer process is a strongly correlated motion of two hydrons. Furthermore, we conclude that the tunneling pathway is the same for the three isotopologue species. Measurements at higher temperatures illuminate the through barrier processes that are mediated via intermediate or excited vibrational states. In parallel with the investigation of proton transfer dynamics, the theoretical and experimental aspects of studying spin-lattice relaxation in single crystals of mixed isotope samples are investigated in depth. Heteronuclear dipolar interactions between (1)H and (2)H isotopes contribute significantly to the overall proton spin-lattice relaxation and it is shown that these must be modeled correctly to obtain accurate values for the proton transfer rates. Since the sample used in the NMR measurements was a single crystal, full account of the orientation dependence of the spin-lattice relaxation with respect to the applied B field was incorporated into the data analysis.     

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.     

Compression effect on structure and proton transfer in crystalline benzoic acid

Geometry optimizations for an isolated dimer and a crystal of benzoic acid were performed in order to evaluate the equilibrium geometries and the energy difference between the dimers in isolated and crystalline states using model potentials. The optimization in the crystal field results in a shortening of the O⋯O distance in comparison with that in an isolated dimer. The magnitude of the shortening agrees well with the difference between the observed values of the O⋯O distance in the gaseous (2.703 Å) and crystalline (2.64 Å) states. The energy increase due to this shortening is estimated to be about 0.24–0.40 kcal mol⁻¹ and is found to be one of the causes of the discrepancy between the barrier height of 1–2 kcal mol⁻¹ measured by NMR for crystalline carboxylic acids and that of 7.1–9.1 kcal mol⁻¹ calculated by the ab initio method for the isolated dimer.     

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.     

Hydrogen bonding in substituted formic acid dimers

The hydrogen-bonded dimers of formic acid derivatives XCOOH (X = H, F, Cl, and CH3) have been investigated using density functional theory (B3LYP) and second-order M?ller-Plesset perturbation (MP2) methods, with the geometry optimization carried out using 6-311++G(2d,2p) basis set. The dimerization energies calculated using aug-cc-pVXZ (with X = D and T) basis have been extrapolated to infinite basis set limit using the standard methodology. The results indicate that the fluorine-substituted formic acid dimer is the most stable one in comparison to the others. Topological analysis carried out using Bader's atoms in molecules (AIM) theory shows good correlation of the values of electron density and its Laplacian at the bond critical points (BCP) with the hydrogen bond length in the dimers. Natural bond orbital (NBO) analysis carried out to study the charge transfer from the proton acceptor to the antibonding orbital of the X-H bond in the complexes reveals that most of the dimers are associated with conventional H-bonding except a few, where improper blue-shifting hydrogen bonds are found to be present.     

Excited-state double proton transfer of 7-azaindole dimers in a low-temperature organic glass

The excited-state double proton transfer of model DNA base pairs, 7-azaindole (7AI) dimers, is explored in a low-temperature organic glass of n-dodecane using picosecond time-resolved fluorescence spectroscopy. Reaction mechanisms are found to depend on the conformations of 7AI dimers at the moment of excitation; whereas planar conformers tautomerize rapidly (<10 ps), twisted conformers undergo double proton transfer to form tautomeric dimers on the time scale of 250 ps at 8 K. The proton transfer is found to consist of two orthogonal steps: precursor-configurational optimization and intrinsic proton transfer via tunneling. The rate is almost isotope independent at cryogenic temperatures because configurational optimization is the rate-determining step of the overall proton transfer. This optimization is assisted by lattice vibrations below 150 K or by librational motions above 150 K.     

Raman jet spectroscopy of formic acid dimers: low frequency vibrational dynamics and beyond

The vibrational dynamics of formic acid dimer is quite regular at low fundamental excitation frequencies, whereas it evolves into a complex and irregular vibrational signature in the OH stretching region. This is evidenced by the first Raman investigation of the jet-cooled formic acid dimer and its three deuterated isotopomers. Subtle isotope effects in the inter-monomer stretching mode, which is directly observed for the first time at 194 cm(-1), find an interpretation based on hydrogen bond weakening due to quantum delocalization of the protons. The reported high-frequency jet spectra should provide essential experimental stepping stones towards a more complete understanding of this planar prototype for strong double hydrogen bonding.     

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.     

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.     

Partition potential for hydrogen bonding in formic acid dimers

The ground-state energy and density of 4 low-energy conformations of the formic acid dimer were calculated via partition density functional theory (PDFT). The differences between isolated and PDFT monomer densities display similar deformation patterns for primary and secondary hydrogen bonds (HBs) among all 4 dimers. In contrast, the partition potential shows no transferable features in the bonding regions. These observations highlight the global character of the partition potential and the cooperative effect that occurs when a dimer is bound via more than 1 HB. We also provide numerical confirmation of the intuitive (but unproven) observation that fragment deformation energies are larger for systems with larger binding energies.     

Negative influence of pKa on activation energy barrier: A case study for double proton transfer reaction in inorganic acid dimers

Strength of acid can be determined by means of pK_a value. Attempts have been made to find a relationship between pK_a and activation energy barrier for a double proton transfer (DPT) reaction in inorganic acid dimers. Negative influence of pK_a is observed on activation energy (E_a) which is contrary to the general convention of pK_a. Four different levels of theories with two different basis sets have been used to calculate the activation energy barrier of the DPT reaction in inorganic acid dimers. A model based on first and second order polynomial has been created to find the relationship between activation energy for DPT reaction. © 2018 Wiley Periodicals, Inc.     

Polar isomer of formic acid dimers formed in helium nanodroplets

The infrared spectrum of formic acid dimers in helium nanodroplets has been observed corresponding to excitation of the "free" OH and CH stretches. The experimental results are consistent with a polar acyclic structure for the dimer. The formation of this structure in helium, as opposed to the much more stable cyclic isomer with two O-H...O hydrogen bonds, is attributed to the unique growth conditions that exist in helium droplets, at a temperature of 0.37 K. Theoretical calculations are also reported to aid in the interpretation of the experimental results. At long range the intermolecular interaction between the two monomers is dominated by the dipole-dipole interaction, which favors the formation of a polar dimer. By following the minimum-energy path, the calculations predict the formation of an acyclic dimer having one O-H...O and one C-H...O contact. This structure corresponds to a local minimum on the potential energy surface and differs significantly from the structure observed in the gas phase.     

Tunneling in the proton transfer between two water molecules

SCF CNDO calculations were performed for the species H₅O⁺₂ at several positions of the intervening proton and at interoxygen distances of 2.65, 2.70 and 2.75 Å. The energy profile was fitted to a potential energy function containing a quadratic term plus a gaussian. The eigenvalues and eigenvectors were obtained by using the variational method with the eigenfunctions of the parabolic potential as basis set. The results indicate that at 2.65 Å the top of the barrier is below the first energy level and that at 2.75 Å the first two energy levels are below the top of the barrier with the splitting of the symmetric-antisymmetric pair of 0.00132 au indicating that tunneling occurs at a frequency of 10¹⁴ reciprocal seconds.     

High pressure effects on benzoic acid dimers: Vibrational spectroscopy

To understand pressure effects on dimer structure stability, Raman and FTIR spectroscopies were used to examine changes in H-bonded dimers of benzoic acid (BA). Experiments were performed on single crystals compressed to 33 GPa in a diamond anvil cell (DAC). Several changes in Raman spectra were observed in the range 6–8 GPa indicating modification in the dimer structure suggesting the lowering of molecular symmetry. Pressure increase above 15 GPa induced strong luminescence and a gradual change of the crystal color from white to yellow/brownish. FTIR measurements on the sample released from 33 GPa indicated formation of a new compound. It is proposed that molecules of this compound are composed of the hydroxyl group associated with alcohol, carbonyl group associated with ketone, and the sp³ hydrocarbon groups. This study demonstrates that sufficient high pressure compression and subsequent decompression can lead to significant changes in the H-bonded dimer structure, including the breaking of bonds and formation of new chemical compound.