Toward theoretical analysis of long-range proton transfer kinetics in biomolecular pumps

Motivated by the long-term goal of theoretically analyzing long-range proton transfer (PT) kinetics in biomolecular pumps, researchers made a number of technical developments in the framework of quantum mechanics-molecular mechanics (QM/MM) simulations. A set of collective reaction coordinates is proposed for characterizing the progress of long-range proton transfers; unlike previous suggestions, the new coordinates can describe PT along highly nonlinear three-dimensional pathways. Calculations using a realistic model of carbonic anhydrase demonstrated that adiabatic mapping using these collective coordinates gives reliable energetics and critical geometrical parameters as compared to minimum energy path calculations, which suggests that the new coordinates can be effectively used as reaction coordinate in potential of mean force calculations for long-range PT in complex systems. In addition, the generalized solvent boundary potential was implemented in the QM/MM framework for rectangular geometries, which is useful for studying reactions in membrane systems. The resulting protocol was found to produce water structure in the interior of aquaporin consistent with previous studies including a much larger number of explicit solvent and lipid molecules. The effect of electrostatics for PT through a membrane protein was also illustrated with a simple model channel embedded in different dielectric continuum environments. The encouraging results observed so far suggest that robust theoretical analysis of long-range PT kinetics in biomolecular pumps can soon be realized in a QM/MM framework.     

Proton transfer reactions in aqueous solution of 2-vinylquinoline copolymers

Fluorescence spectra of atactic and isolaclic poly-2-vinylquinoline and copolymers of 2-vinylquinoline and four non fluorescent comonomers have been measured as a function of pH. The homopolymers and the copolymers with pyrrolidone show two band fluorescence spectra; their intensity ratio changes with pH, polymer concentration and excitation wavelength. For the other copolymers the emission of the protonated heterocycle is only a shoulder of the emission of the neutral form. A kinetic scheme has been proposed to explain these results.     

Excited state proton transfer in guanine in the gas phase and in water solution: a theoretical study

Theoretical investigations were performed to study the phenomena of ground and electronic excited state proton transfer in the isolated and monohydrated forms of guanine. Ground and transition state geometries were optimized at both the B3LYP/6-311++G(d,p) and HF/6-311G(d,p) levels. The geometries of tautomers including those of transition states corresponding to the proton transfer from the keto to the enol form of guanine were also optimized in the lowest singlet pipi* excited state using the configuration interaction singles (CIS) method and the 6-311G(d,p) basis set. The time-dependent density function theory method augmented with the B3LYP functional (TD-B3LYP) and the 6-311++G(d,p) basis set was used to compute vertical transition energies using the B3LYP/6-311++G(d,p) geometries. The TD-B3LYP/6-311++G(d,p) calculations were also performed using the CIS/6-311G(d,p) geometries to predict the adiabatic transition energies of different tautomers and the excited state proton transfer barrier heights of guanine tautomerization. The effect of the bulk aqueous environment was considered using the polarizable continuum model (PCM). The harmonic vibrational frequency calculations were performed to ascertain the nature of potential energy surfaces. The excited state geometries including that of transition states were found to be largely nonplanar. The nonplanar fragment was mostly localized in the six-membered ring. Geometries of the hydrated transition states in the ground and lowest singlet pipi* excited states were found to be zwitterionic in which the water molecule is in the form of hydronium cation (H3O(+)) and guanine is in the anionic form, except for the N9H form in the excited state where water molecule is in the hydroxyl anionic form (OH(-)) and the guanine is in the cationic form. It was found that proton transfer is characterized by a high barrier height both in the gas phase and in the bulk water solution. The explicit inclusion of a water molecule in the proton transfer reaction path reduces the barrier height drastically. The excited state barrier height was generally found to be increased as compared to that in the ground state. On the basis of the current theoretical calculation it appears that the singlet electronic excitation of guanine may not facilitate the excited state proton transfer corresponding to the tautomerization of the keto to the enol form.     

A theoretical method of researching ion-molecule reactions in solution

A method has been devised for researching the mechanisms of ion-molecule reactions in aqueous solutions, which involves deriving an approximate reaction path by means of a model Hamiltonian, in which the medium is described by a set of point Langevin dipoles. At the stationary points on the PES derived in that way, the solvation may be simulated by means of a more accurate scheme for the medium, namely by direct optimization of the potential energy for the solvate shell. The method has been tested on the reaction CO₂+OH^–HCO₃ ^–. The model Hamiltonian has been constructed by MINDO/3. Good agreement with experiment is obtained.Translated from Teoreticheskaya i Éxperimental'naya Khimiya, Vol. 23, No. 3, pp. 281–288, May–June, 1987.     

3-卤代吡唑质子转移过程的理论研究

采用密度泛函B3LYP/6-311G**方法,对3-卤(-F、-Cl、-Br)代吡唑几何构型进行了全自由度优化,获得了它们的几何结构和电子结构。计算结果显示,N1-H型的稳定性大于N2-H型。计算并考察了3-卤代吡唑进行结构互变的质子转移过程的四种可能途径:(a)分子内质子转移;(b)水助质子转移;(c)同种二聚体双质子转移;(d)异种二聚体双质子转移。计算结果表明(以3-氟代吡唑为例),途径d所需要的活化能最小(54.89 kJ/mol),而途径a所需要的活化能最大(198.83kJ/mol),途径b和c的活化能居中间分别为(104.05 kJ/mol和69.05 kJ/mol)。研究还表明氢键在降低活化能方面起着重要的作用,卤素(-F、-Cl、-Br)对活化能的影响不大。     

Temperature dependence of the rate of rapid reactions of proton transfer in aqueous solution

Conclusions The kinetics of the reactions of proton transfer from aqua-complexes of transition metals to the dianion of dibromocresolsulfophthalein in aqueous solution at temperatures from 8 to 50° was studied by the temperature jump method.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 2, pp. 299–305, February, 1974.Deceased.     

Long-range proton transfer in aqueous Acid-base reactions

We study the mechanism of proton transfer (PT) in the aqueous acid-base reaction between the photoacid 8-hydroxy-1,3,6-pyrenetrisulfonic acid (HPTS) and acetate by probing the vibrational resonances of HPTS, acetate, and the hydrated proton with femtosecond mid-infrared laser pulses. We find that PT takes place in a distribution of hydrogen-bound reaction complexes that differ in the number of water molecules separating the acid and the base. The number of intervening water molecules ranges from 0 to 5, which, together with a strongly distance-dependent PT rate, explains the observed highly nonexponential reaction kinetics. The kinetic isotope effect for the reaction is determined to be 1.5, indicating that tunneling does not play a significant role in the transfer of the proton. Rather, the transfer mechanism is best described in terms of the adiabatic PT picture as it has been formulated by Hynes and co-workers [Staib, A.; Borgis, D.; Hynes, J. T. J. Chem. Phys. 1995, 102, 2487. Ando, K.; Hynes, J. T. J. Phys. Chem. B 1997, 101, 10464.], where solvent fluctuations play an essential role in forming the correct hydrogen-bond configuration and solvent polarization to facilitate PT.     

Proton transfer to photoexcited aromatic compounds in solution

This review paper will summarize work carried out during the last thirty years in the area of proton transfer to the aromatic ring of photoexcited aromatic compounds. The aromatic ring has been predicted to be much more basic in the singlet excited state than in the ground state. However, only recently has there been systematic and quantitative studies in this area. This review will highlight the significant new insights now available and demonstrate that there is much more to be learned in the excited state acid-base chemistry of aromatic rings.     

A scaling theoretical analysis of vibrational relaxation experiments: rotational effects and long-range collisions

Expressions for the quantum number scaling of vibration—translation (VT) and vibration—vibration (VV) rates are derived. The derivation uses the recently developed scaling theory of non-reactive processes and invokes the assumption of rotational equilibrium. However, the VV and VT scaling relationships include rotational effects through the rotational energy gaps and the rotational distributions. The variables in this theory are a fundamental set of rates and the average collision range, l_c, for the particular inelastic process. The physically transparent meaning of these variables, combined with the a priori nature of the scaling coefficients, allows one to investigate actual dynamical effects and not just merely fit data. A detailed analysis of VV energy transfer in the COCO system is presented. Three conclusions are drawn: (1) rotational effects are crucially important in the scaling of the rates; (2) the process is predominantly long-range with l_c = 5.5 ± 0.5 au; and, (3) the available experimental data is consistent with single quanta vibrational changes in the VV rates.     

Bimodal proton transfer in acid-base reactions in water

We investigate one of the fundamental reactions in solutions, the neutralization of an acid by a base. We use a photoacid, 8-hydroxy-1,3,6-trisulfonate-pyrene (HPTS; pyranine), which upon photoexcitation reacts with acetate under transfer of a deuteron (solvent: deuterated water). We analyze in detail the resulting bimodal reaction dynamics between the photoacid and the base, the first report on which was recently published. We have ascribed the bimodal proton-transfer dynamics to contributions from preformed hydrogen bonding complexes and from initially uncomplexed acid and base. We report on the observation of an additional (6 ps)(-1) contribution to the reaction rate constant. As before, we analyze the slower part of the reaction within the framework of the diffusion model and the fastest part by a static, sub-150 fs reaction rate. Adding the second static term considerably improves the overall modeling of the experimental results. It also allows to connect experimentally the diffusion controlled bimolecular reaction models as defined by Eigen-Weller and by Collins-Kimball. Our findings are in agreement with a three-stage mechanism for liquid phase intermolecular proton transfer: mutual diffusion of acid and base to form a "loose" encounter complex, followed by reorganization of the solvent shells and by "tightening" of the acid-base encounter complex. These rearrangements last a few picoseconds and enable a prompt proton transfer along the reaction coordinate, which occurs faster than our time resolution of 150 fs. Alternative models for the explanation of the slower "on-contact" reaction time of the loose encounter complex in terms of proton transmission through a von Grotthuss mechanism are also discussed.     

Proton transfer in nanoconfined polar solvents. II. Adiabatic proton transfer dynamics

The reaction dynamics for a model phenol-amine proton transfer system in a confined methyl chloride solvent have been simulated by mixed quantum-classical molecular dynamics. In this approach, the proton vibration is treated quantum mechanically (and adiabatically), while the rest of the system is described classically. Nonequilibrium trajectories are used to determine the proton transfer reaction rate constant. The reaction complex and methyl chloride solvent are confined in a smooth, hydrophobic spherical cavity, and radii of 10, 12, and 15 A have been considered. The effects of the cavity radius and the heavy atom (hydrogen bond) distance on the reaction dynamics are considered, and the mechanism of the proton transfer is examined in detail by analysis of the trajectories.     

Photo-excited intramolecular charge transfer and excited state intramolecular proton transfer behaviors for HPIBT system: A theoretical investigation

Given facile synthetic route and excellent photo stability, excited state intramolecular proton transfer (ESIPT)-active luminous materials have gained more and more attention. Here, we focus on photo-induced excitation process and the ESIPT reaction process for the novel 5-benzothiazol-2-yl-6-hydroxy-2-methyl-isoindole-1,3-dione (HPIBT) molecule. On the level of chemical geometries and infrared spectra, we verify that O─H⋯N of HPIBT should be enhanced. We find that a proton is likely to be attracted by enhanced electronic densities around N, that is, charge transfer impetus ESIPT trend. Combing potential energy curves and searching for transition state, we clarify the ultrafast ESIPT mechanism of HPIBT due to a low barrier, which legitimately explains previous experimental characteristics.     

Evidence for long-range glycosyl transfer reactions in the gas phase

A long-range glycosyl transfer reaction was observed in the collision-induced dissociation Fourier transform (CID FT) mass spectra of benzylamine-labeled and 9-aminofluorene-labeled lacto-N-fucopentaose I (LNFP I) and lacto-N-difucohexaose I (LNDFH I). The transfer reaction was observed for the protonated molecules but not for the sodiated molecules. The long-range glycosyl transfer reaction involved preferentially one of the two L-fucose units in labeled LNDFH I. CID experiments with labeled LNFP I and labeled LNFP II determined the fucose with the greatest propensity for migration. Further experiments were performed to determine the final destination of the migrating fucose. Molecular modeling supported the experiments and reaction mechanisms are proposed.     

A general theoretical model for electron transfer reactions in complex systems

In this paper we present a general theoretical-computational model for treating electron transfer reactions in complex atomic-molecular systems. The underlying idea of the approach, based on unbiased first-principles calculations at the atomistic level, utilizes the definition and the construction of the Diabatic Perturbed states of the involved reactive partners (i.e. the quantum centres in our perturbation approach) as provided by the interaction with their environment, including their mutual interaction. In this way we reconstruct the true Adiabatic states of the reactive partners characterizing the electron transfer process as the fluctuation of the electronic density due to the fluctuating perturbation. Results obtained by using a combination of Molecular Dynamics simulation and the Perturbed Matrix Method on a prototypical intramolecular electron transfer (from 2-(9,9'-dimethyl)fluorene to the 2-naphthalene group separated by a steroidal 5-α-androstane skeleton) well illustrate the accuracy of the method in reproducing both the thermodynamics and the kinetics of the process.     

Parallel proton transfer pathways in aqueous acid-base reactions

We study the mechanism of proton transfer (PT) between the photoacid 8-hydroxy-1,3, 6-pyrenetrisulfonic acid (HPTS) and the base chloroacetate in aqueous solution. We investigate both proton and deuteron transfer reactions in solutions with base concentrations ranging from 0.25 M to 4 M. Using femtosecond midinfrared spectroscopy, we probe the vibrational responses of HPTS, its conjugate photobase, the hydrated proton/deuteron, and chloroacetate. The measurement of these four resonances allows us to follow the sequence of proton departure from the acid, its uptake by the water solvent, and its arrival at the base. In recent studies it was shown that proton transfer to carboxylate bases proceeds via Grotthuss conduction through a water wire connecting the acid and the base [Mohammed et al., Science 310, 83 (2005);Agnew. Chem. Int. Ed. 46, 1458 (2007);Siwick and Bakker, J. Am. Chem. Soc. 129, 13412 (2007); J. Phys. Chem. B 112, 378 (2008)]. Here we show that, for the weaker base chloroacetate, an alternative channel for proton transfer arises. In this channel the proton is first transferred to the water solvent and only later taken up from the water by the base. We study the base concentration dependence of the two competing channels.     

Dynamics of competitive reactions: endothermic proton transfer and exothermic substitution

Dynamics of an endothermic proton-transfer reaction, F(-) with dimethyl sulfoxide, and an endothermic proton-transfer reaction with a competing exothermic substitution (S(N)2) channel, F(-) with borane-methyl sulfide complex, were investigated using a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR) and kinetic modeling. The two proton-transfer reactions have slightly positive and a small negative overall free energy changes, respectively. Energy-dependent rate constants were measured as a function of F(-) ion translational energy, and the resulting kinetics were modeled with the RRKM (Rice-Ramsperger-Kassel-Marcus) theory. The observed rate constants for the proton-transfer reactions of F(-) with dimethyl sulfoxide and with borane-methyl sulfide complex are identical, with a value of 0.17 x 10(-9) cm(3) molecule(-1) s(-1); for the S(N)2 reaction, k = 0.90 x 10(-9) cm(3) molecule(-1) s(-1) at 350 K. Both proton-transfer reactions have positive entropy changes in the forward direction and show positive energy dependences. The competing S(N)2 reaction exhibits negative energy dependence and becomes less important at higher energies. The changes of the observed rate constants agree with RRKM theory predictions for a few kcal/mol of additional kinetic energy. The dynamic change of the branching ratio for the competing proton transfer and the substitution reactions results from the competition between the microscopic rate constants associated with each channel.