Picosecond proton transfer studies in water-alcohols solutions

Picosecond proton ejection rates from 8-hydroxy-1,3,6-pyrene trisulfonate and 2-naphthol-6-sulfonate in water-alcohol solutions have been found to decrease rapidly with increasing alcohol concentrations. It was found that the rate of proton transfer decreases more rapidly in water propanol solutions than in water ethanol solutions. This phenomenon can be interpreted in terms of water breaking structure by the organic solvent.     

A three-dimensional He-NaH potential energy surface for rovibrational energy transfer studies

A three-dimensional potential energy surface for the He-NaH van der Waals complex is calculated at the coupled cluster singles-and-doubles with noniterative inclusion of connected triples [CCSD(T)] level of theory. Estimates of CCSD(T) interaction energies for an infinitely large basis set is obtained using a basis set extrapolation scheme. The He-NaH potential energy surface is much different than the He-LiH surface. In particular, the He-NaH system has a binding energy of De=19.73 cm(-1) in comparison to De=176.7 cm(-1) for He-LiH. These minima are at the theta=180 degrees linear geometry where the helium is located at the metal end of the metal hydride. The He-NaH and He-LiH potentials are very similar for the theta=0 degrees linear geometry. The He-NaH potential energy surface supports one vibrational bound state with E=-1.48 cm(-1). Since this energy is smaller than the accuracy of the potential energy surface, the existence of a bound He-NaH complex is questionable.     

Neutron diffraction and computer simulation studies of D-xylose

Neutron diffraction with isotopic substitution (NDIS) experiments and molecular dynamics (MD) simulations have been used to examine the pentose D-xylose in aqueous solution. By specifically labeling D-xylose molecules with a deuterium atom at the nonexchangeable hydrogen position on C4, it was possible to extract information about the atomic structuring around just that specific position. The MD simulations were found to give satisfactory agreement with the experimental NDIS results and could be used to help interpret the scattering data in terms of the solvent structuring as well as the intramolecular hydroxyl conformations. Although the experiment is challenging and on the limit of modern instrumentation, it is possible by careful analysis, in conjunction with MD studies, to show that the conformation trans to H4 at 180 degrees is strongly disfavored, in excellent agreement with the MD results. This is the first attempt to use NDIS experiments to determine the rotameric conformation of a hydroxyl group.     

细菌紫红质中氢键相互作用和质子转移机理的分子模拟

用CHARMM程序以细菌紫红质1R84晶体为模型, 模拟了在等温定容条件下细菌紫红质在1 ps过程中的变化, 分析了与质子传递相关的ASP85, ASP212和水分子与视黄醛间氢键的结构变化情况. 考虑到氨基酸残基和席夫碱质子的不同距离, 考察了EC和PC两种结构的变化情况, 探讨了紫红质中质子传递的可能途径. 模拟结果表明1R84中可能的质子连续传递的机理是质子由席夫碱向水传递, 再由水向ASP85传递. 发现Asp212在模拟过程中保持EC结构, 这样可能更有利于顺序质子传递.     

Semiempirical mo studies on the proton transfer equilibria of amides

Intramolecular proton transfer equilibria of acetamide and methyl carbamate have been studied by AMI MO calculations, and the results are compared with those of the MNDO method. It was found that the two semi- empirical methods predict essentially the same proton transfer mechanism, but MNDO tends to overestimate the activation barriers. Participation of one solvate vater in the proton transfer led to a considerable lovering of the activation barrier, by nearly the same amount, in both methods. One notable conflict between the two methods was that the methoxy-O-protonated form of methyl carbamate, in the gas phase, can be a local energy minimum with MNDO, whereas it leads to dissociation into two species Instead of an optimized structure with AM1. It was concluded that the MNDO method can be useful for this type of process, especially when one is interested in the relative activation barriers only.     

Spectroscopic studies on proton transfer and hydrogen bonding in p-nitrophenol-donor systems

The interaction of p-nitrophenol with several electron-donors has been studied in aprotic and protic solvents by electronic absorption spectroscopy. The equilibrium data for different kinds of equilibria in 1,2-dichloroethane, n-butanol and acetonitrile have been obtained and discussed. The strong hydrogen bonding interaction between p-nitrophenol and a variety of electron donors has been investigated in heptane by electronic absorption spectroscopy. The interesting correlations obtained in terms of Mulliken's charge transfer model have been examined and extended in many cases.     

A computer simulation of trapping electrophoresis

The gel electrophoretic migration of streptavidin-DNA complexes is severely altered by the phenomenon known as “trapping electrophoresis.” We present a first computer simulation study of this process. Our simulations use the very efficient biased reptation algorithm. The steady state is characterized by a large increase in band broadening and interband separation. However, we also find that for a narrow range of molecular sizes, the separation power of gel electrophoresis is greatly increased. We discuss the implications of our findings for the possible improvement of DNA sequencing technologies. © 1992 John Wiley & Sons, Inc.     

Fluorescent probe based on intramolecular proton transfer for fast ratiometric measurement of cellular transmembrane potential

Development of fast-response potentiometric probes for measuring the transmembrane potential Vm in cell plasma membranes remains a challenge. To overcome the limitations of the classical charge-shift potentiometric probes, we selected a 3-hydroxychromone fluorophore undergoing an excited-state intramolecular proton transfer (ESIPT) reaction that generates a dual emission highly sensitive to electric fields. To achieve the highest sensitivity to the electric field associated to Vm, we modified the fluorophore by adding two rigid legs containing terminal polar sulfonate groups to allow a deep vertical insertion of the fluorophore into the membrane. Fluorescence spectra of the new dye in lipid vesicles and cell membranes confirm the fluorophore location in the hydrophobic region of the membranes. Variation of Vm in lipid vesicles and cell plasma membranes results in a change of the intensity ratio of the two emission bands of the probe. The ratiometric response of the dye in cells is approximately 15% per 100 mV, and is thus quite large in comparison with most single-fluorophore, fast-response probes reported to date. Combined patch-clamp/fluorescence data further show that the ratiometric response of the dye in cells is faster than 1 ms. Analysis of the excitation and emission shifts further suggests that the probe responds to changes in Vm by a mechanism based on electrochromic modulation of its ESIPT reaction. Thus, for the first time, the ESIPT reaction has been successfully applied as a sensing principle for detection of transmembrane potential, allowing to couple classical electrochromic band shifts with changes in the relative intensities of the two well-separated emission bands. The fast two-band ratiometric response as well as the relatively high sensitivity of the new probe are the key features that make it useful for rapid detection of Vm changes in cell suspensions and single cells. Moreover, the new design principles proposed in the present work should allow further improvement of the probe sensitivity.     

Transmission coefficient calculation for proton transfer in triosephosphate isomerase based on the reaction path potential method

A global potential energy surface has been constructed through interpolation of our recently developed reaction path potential for chemical reactions in enzymes which is derived from combined ab initio quantum mechanical and molecular mechanical calculations. It has been implemented for the activated molecular dynamics simulations of the initial proton transfer reaction catalyzed by triosephosphate isomerase. To examine the dynamical effects on the rate constants of the enzymatic reaction, the classical transmission coefficient kappa(t) is evaluated to be 0.47 with the reactive flux approach, demonstrating considerable deviations from transition state theory. In addition, the fluctuations of protein environments have small effects on the barrier recrossing, and the transmission coefficient kappa(t) strongly depends on the fluctuations of atoms near the active site of the enzyme.     

Chemical potential of triatomic polar liquids; a computer simulation study

The chemical potential of liquid sulphur dioxide and liquid water is investigated by molecular dynamics simulation. The calculation is based upon the Widom test-particle method. An empirical procedure is applied in order to reduce drastically the computing time needed to sample the computer-generated configurations. The influence of the choice of the effective pair potential is discussed.     

AM1 studies on the potential energy surface for the proton transfer in protonated water clusters,H+(H2O)n

The potential energy surfaces for the proton transfer processes in H⁺(H₂O)_n with n=2 ～ 11 have been studied using the semiempirical AM1 method. Two model systems were adopted: branched and linear systems. The branched system showed a tendency to form a bulk cluster, while the linear system showed a tendency toward a constant barrier height with increasing number of water molecules in the model system. The potential energy surfaces were discussed using Marcus theory. In the case of H⁺ (H₂O)_n with n=10 and 11, the intrinsic barrier to the proton transfer was found to be around 1.0 kcal/mol.     

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.     

Time-resolved studies of water dynamics and proton transfer at the alumina-air interface

The present study aims to understand the dynamical properties of water and OH groups layered on an alumina surface mainly by means of femtosecond IR-pump IR-probe transient absorption spectroscopy. The experimental results obtained demonstrate the existence of several kinds of O-H vibrators on the surface of alumina membranes, distinguishing them by their behavior on the femtosecond time scale and by the anisotropy of their spectral response. In the high-frequency region (>3400 cm-1), the absorption is due to well-packed aluminol groups and to physisorbed water patches on the surface. When pumping at 3200 cm-1, physisorbed water hydrogen-bonded to AlOH2+ groups is observed. The anisotropy measurements demonstrate the existence of an efficient energy-transfer mechanism among the water molecules characterized by a time constant of 400 +/- 100 fs. The persisting anisotropy at long times, especially in the case of AlOH groups and of the structured physisorbed water layer on top of them, proves the anisotropic structuring induced by the surface. The excitation at 3000 cm-1 enables the detection of a photon-induced proton-transfer reaction. The proton back-transfer reaction time constant is 350 +/- 50 fs. From anisotropy measurements, we estimate the proton hopping time to be 900 +/- 100 fs in a locally extended water network lying on the surface.     

Activation free energy for proton transfer in solution

Path integral molecular dynamics methods are employed to compute the free energy for proton transfer reactions for strongly hydrogen bonded systems in a polar solvent. The free energy profile is calculated using several different techniques, including: integration of the mean force acting on the proton path with its centroid constrained at different values, the integral form of the free energy calculation in the constrained-reaction-coordinate-dynamics ensemble and direct simulation of the unconstrained dynamics. The results show that estimates of the free energy barrier obtained by harmonic extrapolation are likely to be in error. Both quantum and classical results for the free energy are obtained and compared with simulations using adiabatic quantum dynamics. Comparison of the quantum and classical results show that there are quantum corrections to the solvent contributions to the free energy.     

Computational models for proton transfer in biological systems

A computational scheme based on a “mixed basis set” approach is applied to the study of the structure and the energetics in proton transfer systems. Five hydrogen-bonded systems of the type (CH₃H_nA ‥ H ‥ BH_mCH₃)⁺, where A and B can be N, O, or S, have been investigated with various minimal and extended basis sets. Calculations with the extended basis set yield double-well potential energy curves, which the minimal basis set is unable to reproduce. Calculations with the mixed basis set, constructed from an extended basis set on the atoms engaged in the hydrogen transfer part and a minimal basis set on the rest of the molecule, give predictions of geometries, potential energy curves, and relative energies similar to the results from the extended basis set. Inclusion of polarization functions in the mixed basis set becomes essential in systems that contain third row atoms. This scheme should become useful in studies of large molecules in which different parts can be represented at different levels of computational complexity.     

A computer simulation of model discotic dimers

We set up a model for discotic liquid crystal dimers and study, by means of Monte Carlo simulations, their phase behaviour and self–assembling properties, in comparison with the simpler monomeric case. Each discotic dimer is described by two oblate Gay–Berne ellipsoids connected by a flexible spacer, modelled by a harmonic “spring” of three different lengths. We find that dimerization in general yields produces a significant change on the phase behaviour, with an increase of the columnar–nematic transition temperature, a widening of the nematic region and the apparent suppression of the crystalline phase in favour of the columnar phase up to very low temperatures. Longer spacers prove to ease the formation of columns and to increase the orientational order. Contribution to the Fernando Bernardi memorial issue.