Energetics and dynamics of proton transfer reactions along short water wires

Proton transfer (pT) reactions in biochemical processes are often mediated by chains of hydrogen-bonded water molecules. We use hybrid density functional calculations to study pT along quasi one-dimensional water arrays that connect an imidazolium-imidazole proton donor-acceptor pair. We characterize the structures of intermediates and transition states, the energetics, and the dynamics of the pT reactions, including vibrational contributions to kinetic isotope effects. In molecular dynamics simulations of pT transition paths, we find that for short water chains with four water molecules, the pT reactions are semi-concerted. The formation of a high-energy hydronium intermediate next to the proton-donating group is avoided by a simultaneous transfer of a proton from the donor to the first water molecule, and from the first water molecule into the water chain. Lowering the dielectric constant of the environment and increasing the water chain length both reduce the barrier for pT. We study the effect of the driving force on the energetics of the pT reaction by changing the proton affinity of the donor and acceptor groups through halogen and methyl substitutions. We find that the barrier of the pT reaction depends linearly on the proton affinity of the donor but is nearly independent of the proton affinity of the acceptor, corresponding to Br?nsted slopes of one and zero, respectively.     

Molecular Ionization from Carbon Nanotube Paper

Ambient ionization is achieved by spraying from a carbon nanotube (CNT)‐impregnated paper surface under the influence of small voltages (≥3 V). Organic molecules give simple high‐quality mass spectra without fragmentation in the positive or negative ion modes. Conventional field ionization is ruled out, and it appears that field emission of microdroplets occurs. Microscopic examination of the CNT paper confirms that the nanoscale features at the paper surface are responsible for the high electric fields. Raman spectra imply substantial current flows in the nanotubes. The performance of this analytical method was demonstrated for a range of volatile and nonvolatile compounds and a variety of matrices.     

Excited-state intermolecular proton transfer of firefly luciferin V. Direct proton transfer to fluoride and other mild bases

We studied the direct proton transfer (PT) from electronically excited D-luciferin to several mild bases. The fluorescence up-conversion technique is used to measure the rise and decay of the fluorescence signals of the protonated and deprotonated species of D-luciferin. From a base concentration of 0.25 M or higher the proton transfer rates to the fluoride, dihdyrogen phosphate or acetate bases are fast and comparable. The fluorescence signals are nonexponential and complex. We suggest that the fastest decay component arises from a direct proton transfer process from the hydroxyl group of D-luciferin to the mild base. The proton donor and acceptor molecules form an ion pair prior to photoexcitation. Upon photoexcitation solvent rearrangement occurs on a 1 ps time-scale. The PT reaction time constant is ～2 ps for all three bases. A second decay component of about 10 ps is attributed to the proton transfer in a contact pair bridged by one water molecule. The longest decay component is due to both the excited-state proton transfer (ESPT) to the solvent and the diffusion-assisted PT process between a photoacid and a base pair positioned remotely from each other prior to photoexcitation.     

Effects of size constraint on water filling process in nanotube

Molecular dynamics (MD) simulation and the potential of mean force (PMF) analysis are used to investigate the structural properties of water molecules near the end of nanotube for the whole process from the initial water filling up to the configuration stabilization inside the carbon nanotubes (CNTs). Numerical simulations showed that when a small-sized nanotube is immersed into the water bath, the size constraint will induce a prevailing orientation for the water molecule to diffuse into the tube and this effect can persist approximately 3.3 angstroms from the end of CNT. As the structure within the CNTs stabilizes, the ambient structural properties can indirectly reflect their corresponding properties inside the nanotube. Our results also showed that there exists a close correlation between the PMF analysis and the results of MD simulations, and the properties at nanometer scale are closely related to the size-constraint effect.     

聚苯乙烯修饰碳纳米管表面的研究

利用原子转移自由基聚合方法合成了端基具有一个卤素的聚苯乙烯, 并通过叠氮化反应得到端基为叠氮基团的聚苯乙烯. 利用叠氮基与单壁或复壁碳纳米管的反应， 将聚苯乙烯接到碳纳米管的表面上, 实现了碳纳米管的化学修饰. 通过FTIR, XPS, TEM, UV和Raman光谱等技术证明了聚苯乙烯以共价键形式结合到碳纳米管表面上. 利用TGA估算出连接在碳纳米管上的聚苯乙烯的含量, 并推测出复壁碳纳米管中较多的结构缺陷更有利于聚合物的接枝.     

Nonequilibrium molecular dynamics simulation of water transport through carbon nanotube membranes at low pressure

Nonequilibrium molecular dynamics (NEMD) simulations are used to investigate pressure-driven water flow passing through carbon nanotube (CNT) membranes at low pressures (5.0 MPa) typical of real nanofiltration (NF) systems. The CNT membrane is modeled as a simplified NF membrane with smooth surfaces, and uniform straight pores of typical NF pore sizes. A NEMD simulation system is constructed to study the effects of the membrane structure (pores size and membrane thickness) on the pure water transport properties. All simulations are run under operating conditions (temperature and pressure difference) similar to a real NF processes. Simulation results are analyzed to obtain water flux, density, and velocity distributions along both the flow and radial directions. Results show that water flow through a CNT membrane under a pressure difference has the unique transport properties of very fast flow and a non-parabolic radial distribution of velocities which cannot be represented by the Hagen-Poiseuille or Navier-Stokes equations. Density distributions along radial and flow directions show that water molecules in the CNT form layers with an oscillatory density profile, and have a lower average density than in the bulk flow. The NEMD simulations provide direct access to dynamic aspects of water flow through a CNT membrane and give a view of the pressure-driven transport phenomena on a molecular scale.     

径向电场对纳米管中水分子通量的影响

水分子在纳米通道中的运动对于生命活动、纳米器件的设计等都有着重要的意义. 现在已经证实, 在(6,6)的碳纳米管中, 水分子会以单分子水链的形式协同通过碳纳米管. 但是如何控制水分子的流量仍然是一个困难的课题. 本文研究了在径向电场作用下, 碳纳米管中水分子通量的变化趋势和碳纳米管的开关行为.发现在碳纳米管两端存在200 MPa的压力差时, 电场强度从1 V·nm^-1增加到3 V·nm^-1, 水分子通量线性减小. 当径向电场强度增加到3 V·nm^-1时, 碳纳米管处于关闭状态, 水分子无法通过碳纳米管. 进一步, 我们发现水偶极与碳纳米管管轴夹角的平均值的概率分布和翻转频率都与水分子在纳米管中的个数有很大关系.     

质子水合结构的振动态密度分析

使用基于多态经验价键模型的分子动力学模拟, 对水溶液中质子的水合结构及其在质子传递过程中的动力学过程进行了研究. 在价键模型的方法下, 质子的水合结构主要以H₉O₄⁺(Eigen)以及过渡态的H₅O₂⁺(Zundel)结构形态存在, 且在这两种结构中以Eigen的形态表现明显. 通过对质子传递过程中不同水合结构的态密度频谱分析, 发现一个在2000~3000 cm^-1范围内的明显连续的宽吸收谱带, 主要归因于Eigen结构的贡献, 这些特征峰的出现与水合氢离子第一溶剂化层内的强氢键作用密切相关. 对于Zundel的结构, 在1760 cm^-1处出现一个较为明显的肩峰, 归属为质子传递模式的特征振动. 通过对质子水合结构态密度频谱的分析, 可望增强对于稀酸溶液红外光谱中的连续宽吸收带以及质子传递的微观动力学过程的理解.     

"Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis

Proton transfers are fundamental to chemical processes in solution and biological systems. Often, the well-known Grotthuss mechanism is assumed where a series of sequential "proton hops" initiates from the donor and combines to produce the net transfer of a positive charge over a long distance. Although direct experimental evidence for the sequential proton hopping has been obtained recently, alternative mechanisms may be possible in complex molecular systems. To understand these events, all accessible protonation states of the mediating groups should be considered. This is exemplified by transfers through water where the individual water molecules can exist in three protonation states (water, hydronium, and hydroxide); as a result, an alternative to the Grotthuss mechanism for a proton transfer through water is to generate a hydroxide by first protonating the acceptor and then transfer the hydroxide toward the donor through water. The latter mechanism can be most generally described as the transfer of a "proton hole" from the acceptor to the donor where the "hole" characterizes the deprotonated state of any mediating molecule. This pathway is distinct and is rarely considered in the discussion of proton-transfer processes. Using a calibrated quantum mechanical/molecular mechanical (QM/MM) model and an effective sampling technique, we study proton transfers in two solution systems and in Carbonic Anhydrase II. Although the relative weight of the "proton hole" and Grotthuss mechanisms in a specific system is difficult to determine precisely using any computational approach, the current study establishes an energetics motivated framework that hinges on the donor/acceptor pKa values and electrostatics due to the environment to argue that the "proton hole" transfer is likely as important as the classical Grotthuss mechanism for proton transport in many complex molecular systems.     

Molecular modeling of proton transport in the short-side-chain perfluorosulfonic acid ionomer

An explanation for the superior proton conductivity of low equivalent weight (EW) short-side-chain (SSC) perfluorosulfonic acid membranes is pursued through the determination of hydrated morphology and hydronium ion diffusion coefficients using classical molecular dynamics (MD) simulations. A unique force field set for the SSC ionomer was derived from torsion profiles determined from ab initio electronic structure calculations of an oligomeric fragment consisting of two side chains. MD simulations were performed on a system consisting of a single macromolecule of the polymer (EW of 580) with the general formula F3C-[CF(OCF2CF2SO3H)-(CF2)7]40-CF3 at hydration levels corresponding to 3, 6, and 13 water molecules per sulfonic acid group. Examination of the hydrated morphology indicates the formation of hydrogen bond "bridges" between distant sulfonate groups without significant bending of the polytetrafluoroethylene backbone. Pair correlation functions of the system identify the presence of ion cages consisting of hydronium ions hydrogen-bonded to three sulfonate groups at the lowest water content. Such structures exhibit very low S-OH3+ separations, well below 4 A and severely inhibit vehicular diffusion of the protons. The number of sulfonate groups in the first solvation shell of a given hydronium ion correlates well with the differences between Nafion and the SSC polymer (Hyflon). The calculated hydronium ion diffusion coefficients of 2.84 x 10-7, 1.36 x 10-6, and 3.47 x 10-6 cm2/s for water contents of 3, 6, and 13, respectively, show only good agreement to experimentally measured values at the lowest water content, underscoring the increasing contribution of proton shuttling or hopping at the higher hydration levels. At the highest water content, the vehicular diffusion accounts for only about 1/5 of the total proton transport similar to that observed in Nafion.     

Minimum energy pathways for proton transfer between adjacent sites exposed to water

The capacity to transfer protons between surface groups is an innate property of many proteins. The transfer of a proton between donor and acceptor, located as far as 6-7 A apart, necessitates the participation of water molecules in the process. In a previous study we investigated the mechanism of proton transfer (PT) between bulk exposed sites, a few ?ngstr?ms apart, using as a model the proton exchange between the proton-binding sites of the fluorescein molecule in dilute aqueous solution.1 The present study expands the understanding of PT reactions between adjacent sites exposed to water through the calculation the minimum energy pathways (MEPs) by the conjugate peak refinement algorithm2 and a quantum-mechanical potential. The PT reaction trajectories were calculated for the fluorescein system with an increasing number of water molecules. The MEP calculations reveal that the transition state is highly strained and involves a supramolecular structure in which fluorescein and the interconnecting water molecules are covalently bonded together and the protons are shared between neighboring oxygens. These findings are in accord with the high activation energy, as measured for the reaction, and indicate that PT reactions on the surface proceed by a semi- or fully concerted rather than stepwise mechanism. A similar mechanism is assumed to be operative on the surface of proteins and renders water-mediated PT reactions as highly efficient as they are.     

Periodicity in proton conduction along a H‐bonded chain. Application to biomolecules

Molecular complexes are constructed to simulate proton transfer channels of the influenza A virus and of the active site of carbonic anhydrase. These complexes consist of proton donor and acceptor groups connected by a chain of water molecules. Quantum chemical calculations on the methylimidazole(H⁺)? H₂O? CH₃COO^? model of the M2 virus channel indicate free translational motion of the water molecule between donor and acceptor, as well as concerted transfer of both H‐bond protons. The proton transfer barrier does not depend on the position of the bridged water molecule and varies linearly with the difference of electrostatic potentials between the donor and acceptor. When the water chain is elongated, and with various donor and acceptor models, periodicity appears in the H‐bond lengths and the progression of proton transfer in each link. This “wave” is shown to propagate along the chain, as it is driven by the displacement of a single proton. One can thereby estimate the velocity of the proton wave and proton conduction time. Computations are performed to examine the influence of immersing the system within a polarizable medium. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Unusual "amphiphilic" association of hydrated protons in strong acid solution

The solvation structure of the hydrated excess proton in concentrated aqueous HCl solution is studied using the self-consistent iterative multi-state empirical valence bond method. At 0.43-0.85 M concentrations, hydronium cations are found to form unusual cation pairs. This behavior is consistent with our earlier finding that hydronium cations can have an "amphiphilic" character due in part to the asymmetric nature of their hydrogen bonding to nearby water molecules. The existence of these hydronium amphiphilic pairs is further supported by a Car-Parrinello ab initio molecular dynamics simulation at 1.0 M HCl concentration. It is also found that the hydronium cation pairs are stabilized by a delocalization of the hydrated excess proton charge defects involving additional water molecules. At the higher concentrations of 1.68 and 3.26 M, the abundance of such hydronium pairs decreases, and the analysis of the radial distribution functions indicates the possible formation of an aggregate structure with longer-ranged order.     

Factors governing the protonation state of Zn-bound histidine in proteins: a DFT/CDM study

We have performed systematic theoretical studies to elucidate the factors governing the His protonation/deprotonation state in Zn-binding sites, especially those containing the ubiquitous Zn-His-Asp/Glu triad. Specifically, we have addressed the following three questions: (1) How does the transfer of the Zn-bound His imidazole proton to the second-shell Asp/Glu carboxylate oxygen depend on the composition of the other first-shell ligands and the solvent accessibility of the metal-binding site? (2) Can any second-shell ligand with a proton acceptor group such as the backbone carbonyl oxygen also act as a proton acceptor? (3) What is the effect of the Asp/Glu in the Zn-His-Asp/Glu triad on the Zn-bound water protonation state? To address these questions, we used a combination of quantum mechanical and continuum dielectric methods to compute the free energies for deprotonating a Zn-bound imidazole/water in various Zn complexes. The calculations show that whether the Zn-bound His is protonated or deprotonated depends on (1) the solvent accessibility of the metal-binding site, and (2) the Lewis acid ability of Zn, which is indirectly determined by both the first- and the second-shell Zn ligands. The calculations also show that the effect of the Zn-His-Asp/Glu interaction on the nucleophilicity of the Zn-bound water depends on the solvent accessibility of the catalytic Zn site. Furthermore, they show that the Asp/Glu side chain in the Zn-His-Asp/Glu triad can increase the negative charge of its partner, His, and create an anionic hole that may stabilize a cation in buried cavities, provided that the Zn complex is cationic/neutral. The findings of this work are in accord with available experimental data.     

Proton transport in a binary biomimetic solution revealed by molecular dynamics simulation

We report the simulation results of the proton transport in a binary mixture of amphiphilic tetramethylurea (TMU) molecules and water. We identify different mechanisms that either facilitate or retard the proton transport. The efficiency of these mechanisms depends on the TMU concentration. The overall picture is more complicated than a recent suggestion that the presence of amphiphilic molecules suppresses the proton mobility by slowing down the reorientation of the surrounding water molecules. It has also been suggested that the hydronium ion induces local water orientational order, which results in an ordered region that has to move along with the proton potentially slowing down the proton transport as suggested by experiment. We find that water-wire like structures formed at low amphiphile concentrations facilitate proton transfer, and reduction of the hydrogen bond connectivity induced at high concentrations retards it.     

Hydroxide and hydronium ion adsorption — A survey

The propensity of hydroxide and hydronium ions to accumulate at interfaces is the subject of ongoing scientific debate. Electrokinetic and surface force measurements suggest elevated interfacial concentrations of hydroxide ions across a wide range of pHs. Contrary to this, however, surface-sensitive spectroscopic techniques and molecular dynamic (MD) simulations indicate that hydronium ions have strong surface affinity under similar conditions. Here we review results obtained for gas/water, oil/water and solid/water interfaces. Emphasis is placed on ion adsorption phenomena occurring on polymer films of different hydrophobicity and structure. The results clearly show that asymmetric water ion adsorption is independent of the hydrophobicity of the solid surface. Recently obtained data reveal significant effects of the hydroxide and hydronium ions even on the charging of hydrophobic polymers in the presence of multivalent electrolytes and on the charging of zwitterionic lipid membranes.     

Proton mobility in thin ice films: a revisit

We have examined proton transport through an ice film in the temperature range 73-140 K by initially adding hydronium ions into the interior of the film and then monitoring the build-up of hydronium ion population at the film surface. The result confirms that the proton exhibits limited mobility in the ice film at low temperature, but it becomes highly mobile at temperature above 130 K. Based on this result we suggest an explanation of the anomalous experimental observations in the literature for the proton mobility in ice films.     

正渗透过程中纳米碳管膜的盐水通道行为

以纳米碳管(CNT)仿生构筑正渗透(FO)膜, 采用分子动力学模拟的方法考察水和盐在由CNT(6,6)、CNT(7,7)、CNT(8,8)、CNT(9,9)、CNT(10,10)、CNT(11,11)等不同尺寸纳米碳管构筑膜中, 于2.5、3.75、5.0mol·L^-1等不同汲取液浓度下的传递行为. 纳秒级的模拟得到水分子在不同尺寸纳米碳管膜内的分布, 水通量的变化以及盐截留等情况. 模拟结果表明, 由CNT(8,8)构筑的正渗透膜表现出优异的通水阻盐性能.     

Imidazole facilitates electron transfer from organic reductants

In cyclic voltammetry studies at pH 8, imidazole facilitates oxidation of organic compounds that normally lose hydrogen atoms. High concentrations of imidazole shift the oxidizing wave of ascorbic acid, 2,3-dimethoxy-5-methyl-1,4-hydroquinone, and the vitamin E analogue Trolox toward lower potentials. By contrast, imidazole has no effect on the cyclic voltammogram of methyl viologen, which undergoes electron rather than hydrogen-atom transfer. The effect of imidazole is observed at pH 8.0 but only to a lesser extent at pH 5.5 indicating that imidazole must be unprotonated to facilitate oxidation. Digital simulation shows that these results are consistent with a mechanism in which imidazole acts as a proton acceptor permitting concerted proton/electron transfer by the organic reductant.