Investigation of the intermolecular proton transfer in the supersystems adenine-methanol/ethanol/i-propanol: MP2 and DFT levels study

Twelve H-bonded supersystems constructed between the adenine tautomers and methanol, ethanol, and i-propanol were studied at the B3LYP and MP2 levels of theory using 6-311G(d,p) and 6-311++G(d,p) basis functions. The thermodynamic parameters of the complex formations were calculated in order to estimate the exact stability of the supersystems. It was proven that the calculated energy barriers of the alcohol-assisted proton transfers are about 60% lower than those of the intramolecular proton transfers in adenine found earlier (Gu and Leszczynski in J Phys Chem A 103:2744–2750, 1999). Figure H-bonded complex between i-propanol and adenine     

DFT study of the gas phase proton transfer in guanine assisted by water, methanol, and hydrogen peroxide

A computational study of hydrogen-bonded complexes between the oxo-/hydroxo-amino N7/9H tautomers of guanine and water, methanol, and hydrogen peroxide has been performed at the B3LYP/6-31+G(d) level of theory. The mechanisms of the water-, methanol-, and hydrogen peroxide-assisted proton transfers in guanine were studied and compared with the intramolecular proton transfer in guanine in the gas phase. It was found that the assisted proton transfers pass through about three times lower energy barriers than those found for isolated guanine tautomers. Figure DFT study of the gas phase proton transfer in guanine assisted by water, methanol and hydrogen peroxide     

DFT and MP2 study of the interaction between corannulene and alkali cations

Corannulene is an unsaturated hydrocarbon composed of fused rings, with one central five-membered ring and five peripheral six-membered rings. Its structure can be considered as a portion of C₆₀. Corannulene is a curved π surface, but unlike C₆₀, it has two accessible different faces: one concave (inside) and one convex (outside). In this work, computational modeling of the binding between alkali metal cations (Li⁺, Na⁺, and K⁺) and corannulene has been performed at the DFT and MP2 levels. Different corannulene···M⁺ complexes have been studied and the transition states interconnecting local minima were located. The alkali cations can be bound to a five or six membered ring in both faces. At the DFT level, binding to the convex face (outside) is favored relative to the concave face for the three alkali cations studied, as it was previously published. This out preference was found to decrease as cation size increases. At the MP2 level, although a similar trend is found, some different conclusions related to the in/out preference were obtained. According to our results, migration of cations can take place on the convex or on the concave face. Also, there are two ways to transform a concave complex in a convex complex: migration across the edge of corannulene and bowl-to-bowl inversion.     

Computational (DFT and TD DFT) study of the electron structure of the tautomers/conformers of uridine and deoxyuridine and the processes of intramolecular proton transfers

Six uridine and six deoxyuridine isomers were studied at the B3LYP and TD B3LYP theoretical level and 6–31+G(d) basis function. The stability and the excited states of the isomers were studied in order to clarify some known experimental data. It was established that the rotation of the oxo uracil ring in uridine is energetically more likely to occur in the excited state than in the ground state, driven by the bright ¹ ππ* state and the dark charge transfer ¹nπ* state. Very high energy barriers (on the S_o) were found for thermal intramolecular proton transfer processes.     

Aspartate-histidine interaction in the retinal schiff base counterion of the light-driven proton pump of Exiguobacterium sibiricum

One of the distinctive features of eubacterial retinal-based proton pumps, proteorhodopsins, xanthorhodopsin, and others, is hydrogen bonding of the key aspartate residue, the counterion to the retinal Schiff base, to a histidine. We describe properties of the recently found eubacterium proton pump from Exiguobacterium sibiricum (named ESR) expressed in Escherichia coli, especially features that depend on Asp-His interaction, the protonation state of the key aspartate, Asp85, and its ability to accept a proton from the Schiff base during the photocycle. Proton pumping by liposomes and E. coli cells containing ESR occurs in a broad pH range above pH 4.5. Large light-induced pH changes indicate that ESR is a potent proton pump. Replacement of His57 with methionine or asparagine strongly affects the pH-dependent properties of ESR. In the H57M mutant, a dramatic decrease in the quantum yield of chromophore fluorescence emission and a 45 nm blue shift of the absorption maximum with an increase in the pH from 5 to 8 indicate deprotonation of the counterion with a pK(a) of 6.3, which is also the pK(a) at which the M intermediate is observed in the photocycle of the protein solubilized in detergent [dodecyl maltoside (DDM)]. This is in contrast with the case for the wild-type protein, for which the same experiments show that the major fraction of Asp85 is deprotonated at pH >3 and that it protonates only at low pH, with a pK(a) of 2.3. The M intermediate in the wild-type photocycle accumulates only at high pH, with an apparent pK(a) of 9, via deprotonation of a residue interacting with Asp85, presumably His57. In liposomes reconstituted with ESR, the pK(a) values for M formation and spectral shifts are 2-3 pH units lower than in DDM. The distinctively different pH dependencies of the protonation of Asp85 and the accumulation of the M intermediate in the wild-type protein versus the H57M mutant indicate that there is strong Asp-His interaction, which substantially lowers the pK(a) of Asp85 by stabilizing its deprotonated state.     

A MP2 and DFT study of the influence of complexation on the aromatic character of phosphole

This work is focused in three topical subjects: intermolecular interactions, metal ions, and aromaticity. A comprehensive MP2/6-31 + G* and B3LYP/6-31 + G* study of the influence of cation-π interactions on the aromatic character of phosphole was conducted. For this purpose, the structures of complexes were optimized at both theoretical level and different magnetic properties were evaluated. The main conclusion is the increase of the aromatic character of the phosphole when complexes with Li⁺, Be²⁺, and Al³⁺ are formed.     

Short-strong hydrogen bonds and a low barrier transition state for the proton transfer reaction in RNase A catalysis: a quantum chemical study

There is growing evidence that some enzymes catalyze reactions through the formation of short-strong hydrogen bonds as first suggested by Gerlt and Gassman. Support comes from several experimental and quantum chemical studies that include correlation energies on model systems. In the present study, the process of proton transfer between hydroxyl and imidazole groups, a model of the crucial step in the hydrolysis of RNA by the enzymes of the RNase A family, is investigated at the quantum mechanical level of density functional theory and perturbation theory at the MP2 level. The model focuses on the nature of the formation of a complex between the important residues of the protein and the hydroxyl group of the substrate. We have also investigated different configurations of the ground state that are important in the proton transfer reaction. The nature of bonding between the catalytic unit of the enzyme and the substrate in the model is investigated by Bader's atoms in molecule theory. The contributions of solvation and vibrational energies corresponding to the reactant, the transition state and the product configurations are also evaluated. Furthermore, the effect of protein environment is investigated by considering the catalytic unit surrounded by complete proteins--RNase A and Angiogenin. The results, in general, indicate the formation of a short-strong hydrogen bond and the formation of a low barrier transition state for the proton transfer model of the enzyme.     

Relationship of proton release at the extracellular surface to deprotonation of the schiff base in the bacteriorhodopsin photocycle.

The surface potential of purple membranes and the release of protons during the bacteriorhodopsin photocycle have been studied with the covalently linked pH indicator dye, fluorescein. The titration of acidic lipids appears to cause the surface potential to be pH-dependent and causes other deviations from ideal behavior. If these anomalies are neglected, the appearance of protons can be followed by measuring the absorption change of fluorescein bound to various residues at the extracellular surface. Contrary to widely held assumption, the activation enthalpies of kinetic components, deuterium isotope effects in the time constants, and the consequences of the D85E, F208R, and D212N mutations demonstrate a lack of direct correlation between proton transfer from the buried retinal Schiff base to D85 and proton release at the surface. Depending on conditions and residue replacements, the proton release can occur at any time between the protonation of D85 and the recovery of the initial state. We conclude that once D85 is protonated the proton release at the extracellular protein surface is essentially independent of the chromophore reactions that follow. This finding is consistent with the recently suggested version of the alternating access mechanism of bacteriorhodopsin, in which the change of the accessibility of the Schiff base is to and away from D85 rather than to and away from the extracellular membrane surface.     

Coupling of electron and proton transfer in the photosynthetic water oxidase

According to current estimates, the photosynthetic water oxidase functions with a quite restricted driving force. This emphasizes the importance of the catalytic mechanisms in this enzyme. The general problem of coupling electron and proton transfer is discussed from this viewpoint and it is argued that 'weak coupling' is preferable to 'strong coupling'. Weak coupling can be achieved by facilitating deprotonation either before (proton-first path) or after (electron-first path) the oxidation step. The proton-first path is probably relevant to the oxidation of tyrosine Y(Z) by P-680. Histidine D1-190 is believed to play a key role as a proton acceptor facilitating Y(Z) deprotonation. The pK(a) of an efficient proton acceptor is submitted to conflicting requirements, since a high pK(a) favors proton transfer from the donor, but also from the medium. H-bonding between Y(Z) and His, together with the Coulombic interaction between negative tyrosinate and positive imidazolium, are suggested to play a decisive role in alleviating these constraints. Current data and concepts on the coupling of electron and proton transfer in the water oxidase are discussed.     

Interaction of internal water molecules with the schiff base in the L intermediate of the bacteriorhodopsin photocycle

In the photocycle of bacteriorhodopsin (BR), the first proton movement, from the Schiff base to Asp85, occurs after the formation of the L intermediate. In L, the C [double bond] N bond of the Schiff base is strained, and the nitrogen interacts strongly with its counterion. The present study seeks to detect the interaction of internal water molecules with the Schiff base in L using difference FTIR spectroscopy at 170 K. The coupled modes of the hydrogen-out-of plane bending vibrations (HOOPs) of the N-H and C(15)-H of the protonated Schiff base are detected as a broad band centered at 911 cm(-1) for BR. A set of bands at 1073, 1064, and 1056 cm(-1) for L is shown to arise from the coupling of the HOOP with the overtones of interacting water O-H vibrations. Interaction with water was shown by the decreased intensity of the HOOPs of L in H(2)(18)O and by the influence of mutants that have been shown to perturb specific internal water molecules in BR. In contrast, the HOOP band of initial BR was not affected by these mutations. In D85N, the coupled HOOP of BR is depleted, while the coupled HOOPs of L are shifted. The results indicate that the Schiff base interacts with water in the L state but in a different manner than in the BR state. Moreover, the effects of mutations suggest that cytoplasmic water close to Thr46 (Wat46) either interacts stronger with the Schiff base in L or that it is important in stabilizing another water that does.     

Assignment of the low field proton nuclear magnetic resonance spectrum of yeast phenylalanine transfer RNA to specific base pairs

High-resolution proton nuclear magnetic resonance spectra at 220 and 300 MHz have been used to investigate the base-pairing structure of fragments of yeast tRNA^Phe, of chemically modified tRNA^Phe and of intact tRNA^Phe. To a very good approximation the positions of the fragment spectra are additive within 0·2 part per million, indicating that factors responsible for certain structural features in the intact molecule are already present in the smaller fragments (half molecules, hairpins and $\text{3}\text{4}$ molecules). A simple first-order ring-current shift theory taken in conjunction with the cloverleaf model for tRNA^Phe (RajBhandary et al., 1967) has been used to predict the low-field (? 15 to ?11 part per million) nuclear magnetic resonance spectra and make assignments of the resolved resonances to ring NH protons of specific base pairs. The general agreement between the predicted and observed spectra to within 0·2 part per million confirms in detail the cloverleaf model for the secondary structure of tRNA^Phe in solution. It is also established that ring-current shifts are the principal factor responsible for the wide range of shifts observed in the low-field spectra. As a result it is evident that the resonances are very sensitive to small changes in the secondary structure and in some cases changes in the interbase distance as small as 0·2 Å could easily be detected. It is also clear from the analysis that certain of the resonances are sensitive to the tertiary structure of the molecule and specific examples are discussed. As with our previous study, we find no evidence for any strong Watson-Crick type base pairs beyond those predicted by the cloverleaf structure.     

Excited state intramolecular proton transfer in 3-hydroxy flavone and 5-hydroxy flavone: A DFT based comparative study

Potential energy (PE) curves for the intramolecular proton transfer in the ground (GSIPT) and excited (ESIPT) states of 3-hydroxy-flavone (3HF) and 5-hydroxy-flavone (5HF) were studied using DFT/B3LYP (6-31G (d,p)) and TD-DFT/B3LYP (6-31G (d,p)) level of theory respectively. Our calculations suggest the non-viability of ground state intramolecular proton transfer for both the compounds. Calculated PE curves of 3HF for the ground and excited singlet states proton transfer process explain its four state laser diagram. Excited states PE calculations support the ESIPT process to both 5HF and 3HF. The difference in ESIPT emission process of 3HF and 5HF have been explained in terms of HOMO and LUMO electron distribution of the enol and keto tautomer of these two compounds.     

Location of the low temperature water flow barrier in stems

Experiments are described indicating the magnitude and location of the low temperature barrier to lateral water flow in stems of cotton (Gossypium hirsutum L. `Auburn 7-683'). Rehydration of wilted stem tissues was performed at 6 C and 32 C. Compared with the 32 C control, a 13-fold increase in the rehydration halftime was recorded at 6 C when water entered the secondary phloem tissues across the vascular cambium from the secondary xylem. However, only a 3-fold increase in the rehydration halftime occurred when water entered phloem tissues through the cortex, and most of this increase was due to the higher viscosity of water at the lower temperature. These results show that the cambial region of an intact cotton stem markedly resists the radial flow of water at lower temperatures. This resistance was not demonstated by other stem tissues.     

Linear free energy relationship for the anomeric effect: MP2, DFT and ab initio study of 2-substituted-1,4-dioxanes

The anomeric effect of 2-substituted 1,4-dioxane derivatives was calculated and compared with the values for substituted cyclohexane. The bond lengths, bond angles, torsion angles, and relative energies of axial and equatorial conformers of 2-substituted 1,4-dioxanes were calculated by the second-order Møller–Plesset (MP2), density functional theory (DFT/B3LYP), and Hartree–Fock (HF) methods using 6-31G^∗ basis set. The energy differences between the axial and equatorial conformers, endo and exo-anomeric effects, repulsive non-bond and H-bonding interactions were investigated. A linear free energy relationship (LFER) between calculated (MP2/6-31G^∗) anomeric effect and inductive substituent constants (σ_I) was obtained for 2-substituted-1,4-dioxanes (slope = 6.19 and r² = 0.967). The calculated energy differences indicate lower equatorial orientation for 2-substituted-1,4-dioxanes compared to the 2-substituted-tetrahydropyrans. The contribution of resonance, hyperconjugation, inductive, steric, hydrogen bonding, electrostatic interaction, and level of theory influences the anomeric effect.     

Hydration switch model for the proton transfer in the Schiff base region of bacteriorhodopsin

In a light-driven proton-pump protein, bacteriorhodopsin (BR), protonated Schiff base of the retinal chromophore and Asp85 form ion-pair state, which is stabilized by a bridged water molecule. After light absorption, all-trans to 13-cis photoisomerization takes place, followed by the primary proton transfer from the Schiff base to Asp85 that triggers sequential proton transfer reactions for the pump. Fourier transform infrared (FTIR) spectroscopy first observed O-H stretching vibrations of water during the photocycle of BR, and accurate spectral acquisition has extended the water stretching frequencies into the entire stretching frequency region in D(2)O. This enabled to capture the water molecules hydrating with negative charges, and we have identified the water O-D stretch at 2171 cm(-1) as the bridged water interacting with Asp85. We found that retinal isomerization weakens the hydrogen bond in the K intermediate, but not in the later intermediates such as L, M, and N. On the basis of the observation particularly on the M intermediate, we proposed a model for the mechanism of proton transfer from the Schiff base to Asp85. In the "hydration switch model", hydration of a water molecule is switched in the M intermediate from Asp85 to Asp212. This will have raised the pK(a) of the proton acceptor, and the proton transfer is from the Schiff base to Asp85.     

DFT and MP2 study on the electrophilic addition reaction of bromine to exo-tricyclo[3.2.1.02.4]oct-6-ene

The geometry and electronic structure of exo-tricyclo[3.2.1.0^2,4]oct-6-ene (exo-TCO) was investigated using DFT methods. The two faces of the endo-pyramidalised double bond of the molecule are not equivalent. The exo face of the double bond has regions with high electron density (q _i,HOMO) and greater negative potential. Molecular complexes of exo-TCO with bromine were investigated using the B3LYP/6-311++G(d,p) method; the exo-TCO . . . Br₂(exo) molecular complex was found to be relatively more stable than the exo-TCO . . . Br₂(endo) complex. The cationic intermediates of the reaction were studied by DFT and MP2 methods. The solvent effect was evaluated using the self-consistent isodensity polarised continuum model (SCI-PCM). The exo-bromonium cation was found to be more stable than the endo-bromonium cation. Exo-facial selectivity due to electronic and steric factors was observed upon addition of bromine to exo-TCO. The multicentre nonclassical delocalised bromocarbonium cation IV and the exo-bridged-bromonium cation I are more stable than the rearrangement cation V. The reaction products are formed via exo-bridged-bromonium I and nonclassical IV cations, which are the most stable intermediates and whose stabilities barely differ. The mechanism of the addition reaction is also discussed.     

Combined DFT and electrostatics study of the proton pumping mechanism in cytochrome c oxidase

Cytochrome c oxidase is a redox-driven proton pump which converts atmospheric oxygen to water and couples the oxygen reduction reaction to the creation of a membrane proton gradient. The structure of the enzyme has been solved; however, the mechanism of proton pumping is still poorly understood. Recent calculations from this group indicate that one of the histidine ligands of enzyme's CuB center, His291, may play the role of the pumping element. In this paper, we report on the results of calculations that combined first principles DFT and continuum electrostatics to evaluate the energetics of the key energy generating step of the model-the transfer of the chemical proton to the binuclear center of the enzyme, where the hydroxyl group is converted to water, and the concerted expulsion of the proton from delta-nitrogen of His291 ligand of CuB center. We show that the energy generated in this step is sufficient to push a proton against an electrochemical membrane gradient of about 200 mV. We have also re-calculated the pKa of His291 for an extended model in which the whole Fe(a3)-CuB center with their ligands is treated by DFT. Two different DFT functionals (B3LYP and PBE0), and various dielectric models of the protein have been used in an attempt to estimate potential errors of the calculations. Although current methods of calculations do not allow unambiguous predictions of energetics in proteins within few pKa units, as required in this case, the present calculation provides further support for the proposed His291 model of CcO pump and makes a specific prediction that could be targeted in the experimental test.     

MP2, DFT and DFT-D study of the dimers of diazanaphthalenes: a comparative study of their structures,stabilisation and binding energies

Diazanaphthalenes (DAPs) are a broad class of N-heteroaromatic compounds with several technological and biological applications. Some of these applications are attributed to the ability of DAP molecules to form associated dimers through non-covalent interactions. A study of the types and strength of the interactions involved is crucial for understanding the preferred geometries and energetics of the dimers. In this study, the dimers of five DAPs are investigated by means of Møller–Plesset second order perturbation theory, hybrid meta-GGA [density functional theory methods (DFT): DFT/MPWB1K, DFT/M05-2X and DFT/M06-2X] and DFT dispersion-corrected (DFT-D/ωB97XD) methods to elucidate their dimers' preferred geometries, relative energies and nature of the interactions between monomer units. The results indicate that the monomer units of the dimers are held by either intermolecular hydrogen bonds or π…π stacking interactions, and that the preferred dimers are those in which the monomer units interact through π…π stacking interactions. A comparison across structures suggests that the position of the N atom in the ring has significant role in determining the relative energy and binding strength of the dimers. A comparison among the different methods utilised for the study indicates that DFT/M06-2X method provides binding energies that are close to those of DFT-CCSD(T) correction scheme and could therefore be considered as the best method for describing the binding properties of DAP dimers.