Dynamic paths between neutral alanine–water and zwitterionic alanine–water clusters: single, double and triple proton transfer

Fluorescence Spectral Studies on the Interaction of Alanine and Valine with Resorcinol-Based Acridinedione Dyes in Aqueous Solution: A Comparative Study with Glycine

Photophysical studies were carried out for simple amino acids like alanine and valine with resorcinol-based aqueous acridinedione (ADDR) dyes. ADDR dyes exhibit interesting excited-state characteristics on altering the substituents at the 9th and 10th sites (Scheme 1). The longest-wavelength absorption maxima remain the same on adding the amino acids to the fluorophore, whereas the excited-state behavior varies significantly mostly based on the nature of the substituent at the 9th position. The absence of fluorescence enhancement was observed with addition of β-alanine, l-alanine, and l-valine to ADDR1 dye (photoinduced electron transfer, PET), whereas addition of glycine exhibits enhancement accompanied with a shift toward a longer-wavelength region. Interestingly, the addition of amino acids to non-PET dyes results in a fluorescence quenching accompanied with a larger shift toward the shorter-wavelength region. The properties of fluorophore and nonfluorophore dyes in the presence of alanine or valine are found to be entirely different from those of glycine. The interaction of alanine with ADDR dyes is predominantly through H-bonding, but the structural aspects of H-bonding interactions of alanine and water are completely different from those of glycine and water. The time-correlated single-photon counting method portrays the existence of fluorophore in two distinguishable microenvironments in the presence of amino acids. The fluorescence spectral technique used as a tool in elucidating the mode of interaction of dye with neutral amino acids in aqueous solution is illustrated in the present study.

Exploring the mechanism of isomerisation and water-migration in the water-complexes of amino-acid l-proline: electrostatic potential and vibrational analysis

This work reveals interesting pathways for water-migration and neutral ↔ zwitterionic isomerisation in the water complexes of l-proline.

Different proton transfer channels for the transformation of zwitterionic alanine-(H₂O)(n=2-4) to nonzwitterionic alanine-(H₂O)(n=2-4): a density functional theory study

We report here the various possibilities of proton transfer between the zwitterionic and the non-zwetterionic form of alanine (Ala) via (H₂O)(n=2-4) clusters by calculating the transition state structures of zwitterionic alanine (ZAla)-(H₂O)(n=2-4) and non-zwitterionic alanine (Ala)-(H₂O)(n=2-4) complexes at B3LYP/6-311++G(d,p) and CAM-B3LYP/6-311++G(d,p) level of theory. In order to determine the most feasible channel for proton transfer, the barrier energy corresponding to each channel was calculated. For the transformation of ZAla-(H₂O)(n=2) to Ala-(H₂O)(n=2), we identified eight channels for proton transfer. The lowest barrier energy (2.57 kcal mol⁻¹) channel, where ZAla-(H₂O)(n=2) transforms to Ala-(H₂O)(n=2) via triple proton transfer, is said to be the energetically most feasible channel. The values of barrier energy corresponding to the least energy pathway for proton transfer were calculated to be 1.14 and 9.82 kcal mol⁻¹ for n = 3 and n = 4 complexes, respectively, at B3LYP/6-311++G(d,p) level of theory. For complex n = 3, the structure where proton transfer takes place directly from -NH₃⁺ to -COO⁻ has the lowest energy pathway. However, the complexes for n = 2 and 3--the channels where proton transferred from -NH₃⁺ to -COO⁻ via two water molecules have the lowest barrier energy. For each n, the values of barrier energy calculated at CAM-B3LYP/6-311++G(d,p) level of theory were always less compared those calculated at B3LYP/6-311++G(d,p) level of theory. The value of rate constants corresponding to each proton transfer channel was also calculated.

Gas phase hydration of amino acids and dipeptides: effects on the relative stability of zwitterion vs. canonical conformers

This review highlights the effects of explicit water molecules on the structures of amino acids and dipeptides, focusing on the relative stability of canonical vs. zwitterionic conformers.

Efficiency of bulky protic solvent for SN2 reaction

We calculate and compare the effects of aprotic vs protic solvent on the rate of SN2 reaction [F- + C3H7OMs--> C3H7F + OMs-]. We find that aprotic solvent acetonitrile is more efficient than a small protic solvent such as methanol. Bulky protic solvent (tert-butyl alcohol) is predicted to be quite efficient, giving the rate constant that is similar to that in CH3CN. Our calculated relative activation barriers of the SN2 reaction in methanol, tert-butyl alcohol, and CH3CN are in good agreement with experimental observations.

Facile SN2 Reaction in Protic Solvent: Quantum Chemical Analysis

We study the effects of protic solvent (water, methanol, ethanol, and tert-butyl alcohol) and cation (Na+, K+, Cs+) on the unsymmetrical SN2 reaction X- + RY --> RX + Y- (X = F, Br; R = CH3,C3H7;Y = Cl, OMs). We describe a series of calculations for the S(N)2 reaction mechanism under the influence of cation and protic solvent, presenting the structures of pre- and postreaction complexes and transition states and the magnitude of the activation barrier. An interesting mechanism is proposed, in which the protic solvent molecules that are shielded from the nucleophile by the intervening cation act as a Lewis base to reduce the unfavorable Coulombic influence of the cation on the nucleophile. We predict that the reaction barrier for the S(N)2 reaction is significantly lowered by the cooperative effects of cation and protic solvent. We show that the cation and protic solvent, each of which has been considered to retard the SN2 reactivity of the nucleophile, can accelerate the reaction tremendously when they interact with the fluoride ion in an intricate, combined fashion. This alternative S(N)2 mechanism is discussed in relation to the recently observed phenomenal efficiency of fluorination in tert-alcohol media [Kim, D. W.; et al. J. Am. Chem. Soc. 2006, 128, 16394].

Ab Initio Molecular Dynamics Free-Energy Study of Microhydration Effects on the Neutral–Zwitterion Equilibrium of Phenylalanine

The structures and relative energies of the most stable conformers of both naked and microsolvated phenylalanine, Phe.(H(2)O)(n)(n=0-3), are calculated by density functional theory. For selected structures, coordination-constrained ab initio molecular dynamics simulations determine the proton-transfer mechanism connecting neutral and zwitterionic forms of Phe. The associated free-energy profiles are calculated by thermodynamic integration. While no zwitterionic free-energy minimum is found for naked Phe, microsolvation is found to stabilize the zwitterionic form. For cluster sizes n > or = 3, the proton-transfer equilibrium shifts towards the zwitterionic structure for specific proton-transfer pathways. The energetically most favourable interconversion path between the neutral and zwitterionic forms is through a H(2)O bridge with free-energy barriers as low as 14.4 kJ mol(-1) for Phe.(H(2)O)(3). The free energy required for breaking a carboxylic OH bond involved in intramolecular hydrogen bonding is typically lower than in the water-assisted case. However, the resulting zwitterion turns out to be unstable with respect to the backward proton-transfer reaction.

Conformational Flexibility of l-Alanine Zwitterion Determines Shapes of Raman and Raman Optical Activity Spectral Bands

Detailed analysis of Raman and Raman optical activity (ROA) of L-alanine zwitterion (ALAZW) revealed that shapes of the spectral bands are to a large extent determined by the rotation of the NH(3)(+), CO(2)(-), and CH(3) groups. Aqueous solution ALAZW spectra were measured down to 100 cm(-1) and compared to complex simulations based on ab initio (B3LYP/CPCM/6-31++G**) computations of molecular energies and spectral parameters. The bands exhibit different sensitivities to the motion of the rotating group; typically, for more susceptible bands the Raman signal becomes broader and the ROA intensity decreases. When these dynamical factors are taken into account in Boltzmann averaging of conformer contributions, simulated spectra not only better agree with the experiment, but shapes of the rotational potentials can be estimated. Effects of the molecular flexibility could be also demonstrated on differences in Raman spectra of the solution, crystalline, and glass (gellike) solid states of ALAZW. Experimental Raman and ROA spectra of four model dipeptides of different rigidities (Ala-Pro, Pro-Ala, Pro-Gly, and Gly-Pro) indicate that the broadening of spectral lines can be used as a general site-specific indicator of molecular rigidity or flexibility.

Double proton transfer and one-electron oxidation behavior in double H-bonded glycinamide-glycine complex in the gas phase

The behaviors of double proton transfer (DPT) occurring in a representative glycinamide-glycine complex have been investigated employing the B3LYP/6-311++G** level of theory. Thermodynamic and especially kinetic parameters, such as tautomerization energy, equilibrium constant, and barrier heights have been discussed, respectively. The relevant quantities involved in the DPT process including geometrical changes, interaction energies, and deformation energies have also been studied. Analogous to that of tautomeric process assisted with a formic acid molecule, the participation of a glycine molecule favors the proceeding of the proton transfer (PT) for glycinamide compared with that without mediator-assisted case. The DPT process proceeds with a concerted mechanism rather than a stepwise one because no zwitterionic complexes have been located during the DPT process. The barrier heights are 12.14 and 0.83 kcal/mol for the forward and reverse directions, respectively. However, both of them have been reduced by 3.10 and 2.66 kcal/mol to 9.04 and -1.83 kcal/mol with further inclusion of zero-point vibrational energy (ZPVE) corrections, where the disappearance of the reverse barrier height implies that the reverse reaction should proceed with barrierless spontaneously, analogous to those of DPTs occurring between glycinamide and formic acid (or formamide). Additionally, the oxidation process for the double H-bonded glycinamide-glycine complex has also been investigated. The oxidated product is characterized by a distonic radical cation due to the fact that one-electron oxidation takes place on glycine fragment and a proton has been transferred from glycine to glycinamide fragment spontaneously. As a result, the vertical and adiabatic ionization potentials for the neutral complex have been determined to be about 8.71 and 7.85 eV, respectively, where both of them have been reduced by about 0.54 (1.11) and 0.75 (1.13) eV relative to those of isolated glycinamide (glycine) due to the formation of the intermolecular H-bond.

On the stability of glycine-water clusters with excess electron: Implications for photoelectron spectroscopy

Calculations are presented for the glycine-(H(2)O)(n) (-) (n=0-2) anionic clusters with excess electron, with the glycine core in the canonical or zwitterion form. A variety of conformers are predicted, and their relative energy is examined to estimate thermodynamic stability. The dynamic (proton transfer) pathways between the anionic clusters with the canonical and the zwitterion glycine core are examined. Small barrier heights for isomerization from the zwitterion glycine-(H(2)O)(2) (-) anion to those with canonical glycine core suggest that the former conformers may be kinetically unstable and unfavorable for detection of neutral glycine zwitterion-(H(2)O)(n) (n=1,2) clusters by photodetachment, in accordance with the photoelectron spectroscopic experiments by Bowen and co-workers [Xu et al., J. Chem. Phys. 119, 10696 (2003)]. The calculated stability of the glycine-(H(2)O)(n) (-) anion clusters with canonical glycine core relative to those with zwitterion core indicates that the observation of the anionic conformers with the canonical glycine core would be much more feasible, as revealed by Johnson and co-workers [Diken et al. J. Chem. Phys. 120, 9902 (2004)].

Double proton transfer behavior and one-electron oxidation effect in double H-bonded glycinamide-formic acid complex

The behavior of double proton transfer occurring in a representative glycinamide-formic acid complex has been investigated at the B3LYP/6-311 + + G( * *) level of theory. Thermodynamic and, especially, kinetic parameters, such as tautomeric energy, equilibrium constant, and barrier heights have been discussed, respectively. The relevant quantities involved in the double proton transfer process, such as geometrical changes, interaction energies, and intrinsic reaction coordinate calculations have also been studied. Computational results show that the participation of a formic acid molecule favors the proceeding of the proton transfer for glycinamide compared with that without mediate-assisted case. The double proton transfer process proceeds with a concerted mechanism rather than a stepwise one since no ion-pair complexes have been located during the proton transfer process. The calculated barrier heights are 11.48 and 0.85 kcal/mol for the forward and reverse directions, respectively. However, both of them have been reduced by 2.95 and 2.61 kcal/mol to 8.53 and -1.76 kcal/mol if further inclusion of zero-point vibrational energy corrections, where the negative barrier height implies that the reverse reaction should proceed with barrierless spontaneously, analogous to that occurring between glycinamide and formamide. Furthermore, solvent effects on the thermodynamic and kinetic processes have also been predicted qualitatively employing the isodensity surface polarized continuum model within the framework of the self-consistent reaction field theory. Additionally, the oxidation process for the double H-bonded glycinamide-formic acid complex has also been investigated. Contrary to that neutral form possessing a pair of two parallel intermolecular H bonds, only a single H bond with a comparable strength has been found in its ionized form. The vertical and adiabatic ionization potentials for the neutral complex have been determined to be about 9.40 and 8.69 eV, respectively, where ionization is mainly localized on the glycinamide fragment. Like that ionized glycinamide-formamide complex, the proton transfer in the ionized complex is characterized by a single-well potential, implying that the proton initially attached to amide N4 in the glycinamide fragment cannot be transferred to carbonyl O13 in the formic acid fragment at the geometry of the optimized complex.

Solvent effects on glycine II. Water-assisted tautomerization

The water-assisted tautomerization of glycine has been investigated at the B3LYP/6-31+G** level using supermolecules containing up to six water molecules as well as considering a 1:1 glycine-water complex embedded in a continuum. The conformations of the tautomers in this mechanism do not display an intramolecular H bond, instead the functional groups are bridged by a water molecule. The replacement of the intramolecular H bond by the bridging water reduces the polarity of the N-H bond in the zwitterion and increases that of the O-H bond in the neutral, stabilizing the zwitterion. Both the charge transfer effects and electrostatic interactions stabilize the nonintramolecularly H-bonded zwitterion conformer over the intramolecularly hydrogen bonded one. The nonintramolecularly H-bonded neutral is favored only by charge transfer effects. Although there is no strong evidence whether the intramolecularly hydrogen bonded or non hydrogen bonded structures are favored in the bulk solution represented as a dielectric continuum, it is likely that the latter species are more stable. The free energy of activation of the water-assisted mechanism is higher than the intramolecular proton transfer channel. However, when the presumably higher conformational energy of the zwitterion reacting in the intramolecular mechanism is taken into account, both mechanisms are observed to compete. The various conformers of the neutral glycine may form via multiple proton transfer reactions through several water molecules instead of a conformational rearrangement.