Water dimer proton affinity from the kinetic method: dissociation energy of the water dimer

The proton affinity of water dimer was measured, using the kinetic method with nitrile reference bases, to be 808 +/- 6 kJ mol(-1). The difference between the measured value and the proton affinity of a single water molecule (690 +/- 4 kJ mol(-1)) reflects the difference in solvation energy for two neutral water molecules (the hydrogen bond energy of water dimer), and the energy for solvation of hydronium cation and water. Using the measured proton affinity of the dimer along with ancillary data yields an experimental value of the hydrogen bond energy of neutral water dimer, 18 +/- 9 kJ mol(-1), in good agreement with previous experimental and theoretical values. The proton affinity of the dimer measured by using alcohol references is ca 100 kJ mol(-1) too low, likely because the structure of the protonated cluster is not well-suited for kinetic method measurements. These results highlight the importance of choosing reference bases that form cluster ions consisting of a proton bound complex between the water dimer and the reference base.     

Quantitative information about the hydrogen bond strength in dilute aqueous solutions of methanol from the temperature dependence of the Raman spectra of the decoupled OD stretch

We have obtained quantitative information about the hydrogen bond strength in pure water and in dilute aqueous solutions of methanol by analyzing the temperature dependence of Raman spectra of the decoupled OD stretch from 21 to 160 degrees C with the hydrogen bond energy dispersion method. A minimum at 2440 cm(-1) assigned to strong icelike hydrogen bonds and a maximum at 2650 cm(-1) due to maximally (but not completely) broken hydrogen bonds result in all cases. The energy of the minimum decreases upon addition of methanol due to formation of stronger water-methanol hydrogen bonds, whereas the energy of the maximum increases because water hydrogen atoms in the vicinity of the methyl group might participate in "more broken" hydrogen bonds than in bulk water.     

Density functional calculations of ATP systems. 2. ATP hydrolysis at the active site of actin

The hydrolysis of adenosine 5'-triphosphate (ATP) at the active site of actin has been studied using density functional calculations. The active site is modeled by the triphosphate tail of ATP, an Mg cation, surrounding water molecules, and the nearby protein residues. Four reaction paths have been followed by constraining coordinates that allow phosphate stretching, nucleophilic attack of the catalytic water, and OH(-) formation via water deprotonation. The lowest-energy barrier (21.0 kcal/mol) is obtained for a dissociative reaction where the terminal phosphate breaks on approaching the catalytic water, followed by proton release via a proton wire mechanism. A higher barrier (39.6 kcal/mol) results for an associative reaction path where OH(-) is formed first, with a pentacoordinated phosphorus atom (P-O distances 2.1 A). Stretching the terminal bridging P-O bond results in bond rupture at 2.8 A with an energy barrier of 28.8 kcal/mol. The residues Gln137 and His161 are not important in the reactions, but insight into their roles in vivo has been obtained. The favored coordination of the end products H(2)PO(4)(-) and ADP(3-) includes a hydrogen bond and an O-Mg-O bridge between the phosphates as well as a hydrogen bond between H(2)PO(4)(-) and the Ser14 side chain. The total energy is 2.1 kcal/mol lower than in the initial reactants. Classical simulations of ATP- and ADP.P(i)-actin show few hydrolysis-induced differences in the protein structure, indicating that phosphate migration is necessary for a change in conformation.     

平面五元水分子簇的量子化学研究

选用Gaussian03的B3LYP/6-31G(d,p)、DMol3的BLYP/DNP和deMon的BLYP/TZVP等方法计算了甲烷水合物(结构-1)中平面五元水分子簇的结合能和氢键能,作了基组重叠误差(BSSE)和色散能(dispersion)的修正,估算了次级相互作用的贡献.在DMol3程序中使用了大型数值基组DNP,将基组重叠误差降至最低.在Gaussi-an03的B3LYP/6-31G(d,p)计算中,采用平衡法(Counterpoise)校正基组重叠误差.两种计算方法给出了一致的结果,证实了在使用6-31G(d,p)基组时,一对水分子在平衡距离的基组重叠误差高达8 kJ/mol.为估算色散能的贡献,使用了新近发展的包含色散能的密度泛函的DFT程序deMon计算了五元水分子簇.用多种方法计算出了经基组重叠误差和色散能修正的五元水分子簇的分子间结合能和氢键能的较为精确的势能超曲面,为甲烷和其他气体水合物的分子动力学模拟提供了依据.     

二水合甘氨酸两性离子复合体的结构和性能的理论研究

采用理论计算方法B3LYP, 在6-31++G**基组水平研究使甘氨酸质子化所需的最少水分子数目, 然后讨论水合两性离子复合体的结构和性能, 进而计算了二水合甘氨酸中性分子复合体(2W-GN)到二水合甘氨酸两性离子复合体(2W-GZ)的过渡态, 得到如下结论: (1)两个水分子可以使甘氨酸质子化, 能够形成稳定的二水合两性离子复合体. (2)甘氨酸与水分子之间通过氢键相互作用, 结合能较大, 复合体稳定; 在二水合甘氨酸复合体中, 水合甘氨酸中性分子比水合甘氨酸两性离子稳定. (3)由2W-GN到2W-GZ过程的反应活化能和氢键键能相近.     

N-甲替甲酰胺-水的氢键团簇的从头计算研究

The N-methylformamide（NMF）-water clusters were studied by ab inito calculations at MP2/6-31+G** and MP2 / 6-311 ++ G（d,p）levels. The equilibrium geometries and the dissociation channels and dissociation energies of both neutral and ionic NMF-H2O clusters are presented. For N-methylformamide,cis-form has lower energy than trans-form. In NMFH+,the proton prefers to link with the O atom of N-methylformamide. The results show that both cis- and trans- form of NMF can form a linear hydrogen bond with water. Although the energy of trans-NMF is higher than cis-NMF,trans-form exits more stably because it can form a double hydrogen bond with water. After the ionization of the NMF-H2O cluster,both the cis- and the trans-form will produce protonated products.     

Probing the acidity of p-substituted phenols in the excited state: electronic spectroscopy of the p-cyanophenol-water cluster.

The hydrogen bond structure of the p-cyanophenol-water cluster has been determined in the ground and first excited electronic state by rotationally resolved UV spectroscopy. The water molecule is trans-linearly bound to the hydroxy group of the p-cyanophenol moiety, with hydrogen bond distances considerably shorter in both electronic states than in the similar phenol-water cluster. The structure of the cluster has been elucidated by ab initio calculations at various levels of theory and compared to the experimental findings. The barriers to internal rotation of the water moiety were determined experimentally to be 275 and 183 cm(-1) for the ground and excited state, respectively. Hydrogen bond distances and the energy barrier to water torsion correlate with the pK(a) values of different substituted phenols for both electronic states.     

Vacuum ultraviolet (VUV) photoionization of small water clusters

Tunable vacuum ultraviolet (VUV) photoionization studies of water clusters are performed using 10-14 eV synchrotron radiation and analyzed by reflectron time-of-flight (TOF) mass spectrometry. Photoionization efficiency (PIE) curves for protonated water clusters (H2O)(n)H+ are measured with 50 meV energy resolution. The appearance energies of a series of protonated water clusters are determined from the photoionization threshold for clusters composed of up to 79 molecules. These appearance energies represent an upper limit of the adiabatic ionization energy of the corresponding parent neutral water cluster in the supersonic molecular beam. The experimental results show a sharp drop in the appearance energy for the small neutral water clusters (from 12.62 +/- 0.05 to 10.94 +/- 0.06 eV, for H2O and (H2O)4, respectively), followed by a gradual decrease for clusters up to (H2O)23 converging to a value of 10.6 eV (+/-0.2 eV). The dissociation energy to remove a water molecule from the corresponding neutral water cluster is derived through thermodynamic cycles utilizing the dissociation energies of protonated water clusters reported previously in the literature. The experimental results show a gradual decrease of the dissociation energy for removal of one water molecule for small neutral water clusters (3 相似文献   

Electrochemistry of a labile average-valence dicopper system

Electrochemical studies on an average-valent dicopper cryptate demonstrate the existence of a solvent-assisted disproportionation in acetonitrile, which is absent in water. The existence of this process was confirmed via absorption spectroscopy, which allowed the evaluation of thermodynamic parameters. The disproportionation equilibrium is enthalpically controlled, and the results suggest an upper limit for the bond energy of the one-electron Cu-Cu bond of 200 kJ mol(-1).     

DFT study on the mechanism of water-assisted dihydrogen elimination in group 6 octahedral metal hydride complexes

The reaction of water with octahedral bis-, tris- and tetrakis-(phosphine)tungsten, (phosphine)molybdenum and (phosphine)chromium complexes has been studied using B3LYP/def2-TZVPP level of DFT to elucidate dissociative, associative and hydride migratory insertion mechanisms for hydrogen elimination. In the dissociative mechanism, phosphine dissociation requires 19.3-28.5 kcal mol(-1) of energy. The phosphine-water ligand exchange is endergonic due to poor coordination ability of water to group 6 metals (binding energy 8.8-15.5 kcal mol(-1)). The ligand exchange leads to intermolecular M-HH(2)O dihydrogen interaction and facilitates dihydrogen elimination (G(act) = 6.8-15.5 kcal mol(-1)). In the associative mechanism, a water molecule in the first solvation shell interacts with the M-H bond through a dihydrogen bond (interaction energy 2.7-4.0 kcal mol(-1)) and leads to the elimination of H(2) by forming a hydroxide complex. Compared to the dissociative mechanism, G(act) of associative mechanisms are ～22 kcal mol(-1) higher. In the hydride migratory insertion mechanism, the hydride ligand shifts to the CO ligand (G(act) = 25.4-30.4 kcal mol(-1)) to afford a formyl complex and subsequently the H-H bond coupling occurs between formyl and water ligand (G(act) = 2.8-4.4 kcal mol(-1)). In many cases, the migratory insertion mechanism can simultaneously operate with the dissociative mechanism as a minor pathway, whereas owing to high G(act) value, the associative mechanism can be described as inactive in the reaction. The general argument that dihydrogen elimination is preceded by the formation of a dihydrogen intermediate is not applicable for the systems studied herein as the most favoured dissociative mechanism does not pass through such an intermediate. On the other hand, irrespective of the mechanisms, dihydrogen elimination invariably occurs with the formation of a dihydrogen bonded transition state. Our results also suggest that group 6 octahedral metal hydride complexes are attractive targets for the design of water splitting reactions.     

Quantum-mechanical simulation of the interaction of aluminum- and boron-containing zeolite clusters with molecules of water and ammonia

Quantum-mechanical computations of zeolite clusters with molecules of water and ammonia have been carried out. The clusters consisted of ten atoms of silicon and aluminum, where one atom of aluminum was also replaced with an atom of boron. Values of the bond length and bond angles have been obtained; the geometry of adsorption complexes and the bond energy for molecules of water and ammonia with atoms of aluminum and boron of a zeolite fragment have been determined. The computed values of bond energy for molecule probes yield the quantitative strength characteristic of zeolite aprotic acid centers.     

Bonding rearrangements of hydrogen-bonded complexes involving alkynes

Molecules containing a C-C triple bond, such as HC[triple bond]CH, FC[triple bond]CF, and the C[triple bond]CH radical, are allowed to interact with a partner molecule of H2O, NH3, or HF. Quantum chemical calculations show that these C[triple bond]CH...X H-bonded complexes are bound by up to 4 kcal x mol(-1). More importantly, they can rearrange in such a way that the partner molecule adds to the triple bond so as to form a double C=C bond. Whereas this process is strongly exoergic, there is a high-energy barrier to this rearrangement process. On the other hand, when a second water molecule is added to the complex, it can shuttle protons from the donor part of the complex to the acceptor, and thereby greatly reduce the rearrangement energy barrier. In the case of CCH + 2H2O, this barrier is computed to be less than 4 kcal x mol(-1).     

Accurate calculation of the binding energy of the water dimer

The binding energy of the water dimer is calculated at the MP2 level using efficient basis sets augmented with bond functions. The intermolecular energy is determined by the supermolecular approach and the basis set superposition error is corrected by the counterpoise method. Bond functions are found useful and very effective in recovering the dispersion energy, which is traditionally achieved by polarization functions. The calculated binding energy of the water dimer is systematically converged to a value of 4.75 kcal mol⁻ as bond functions are gradually added to nucleus-centered basis sets.     

Is the peptide bond formation activated by Cu(2+) interactions? Insights from density functional calculations

The catalytic role that Cu(2+) cations play in the peptide bond formation has been addressed by means of density functional calculations. First, the Cu(2+)-(glycine)2 --> Cu(2+)-(glycylglycine) + H2O reaction was investigated since mass spectrometry low collision activated dissociation (CAD) spectra of Cu(2+)-(glycine)2 led to the elimination of a water molecule, which suggested that an intracomplex peptide bond formation might have occurred. Results show that this intracomplex condensation is associated to a very high free energy barrier (97 kcal mol(-1)) and reaction free energy (66 kcal mol(-1)) because of the loss of metal coordination during the reaction. Second, on the basis of the salt-induced peptide formation theory, the condensation reaction between two glycines was studied in aqueous solution using discrete water molecules and the conductor polarized continuum model (CPCM) continuous method. It is found that the synergy between the interaction of glycines with Cu(2+) and the presence of water molecules acting as proton-transfer helpers significantly lower the activation barrier (from 55 kcal/mol for the uncatalyzed system to 20 kcal/mol for the Cu(2+) solvated system) which largely favors the formation of the peptide bond.     

Cooperative enhancement of water binding to crownophane by multiple hydrogen bonds: analysis by high level ab initio calculations.

The intermolecular interaction energy of the model system of the water-crownophane complex was analyzed. The water molecule has four hydrogen bonds, with the two hydrogen-donating phenolic hydroxy groups and two hydrogen-accepting oxygen atoms of the poly-oxyethylene chain of the crownophane in the complex. The MP2/6-311G(2d,2p) level calculations of the model system of the complex (hydrogen donating unit + hydrogen accepting unit + water) indicate that the binding energy of the water is 21.85 kcal/mol and that the hydrogen bond cooperativity increases the binding energy as much as 3.67 kcal/mol. The calculated interaction energies depend on the basis set, while the basis set dependence of the cooperative increment is negligible. Most of the cooperative increment is covered by the HF level calculation, which suggests that the major source of the hydrogen bond cooperativity in this system has its origin in induction. The BLYP/6-311G** and PW91/6-311G** level interaction energies of the model system are close to the MP2/6-311G** interaction energies, which suggests that the DFT calculations with these functionals are useful methods to evaluated the interactions of hydrogen bonded systems.     

N,N-二(对氟苄基)-N'-(2',3'-二脱氧-3'-硫代胞苷)甲脒水解反应的理论研究

采用密度泛函理论方法B3LYP/6-31++G(d,p)//B3LYP/6-31G(d,p)和导体极化连续模型B3LYP/CPCM/6-31++G(d,p)方法对苯环对位上有F取代的N,N-二(对氟苄基)-N′-(2′,3′-二脱氧-3′-硫代胞苷)甲脒(FBFA-3TC)水解反应机理和溶剂效应进行了研究. 考虑两条可能反应途径: 水分子首先进攻C=N双键的途径(Path A)和先进攻C-N单键的途径(Path B). 计算结果表明, 气相和水中两条途径的第一步都是速率控制步骤, Path A 比Path B 更有利. 对优势途径Path A的第二步反应的进一步研究发现, 中间体的羟基H原子转移到双键N比单键N更容易, 从而形成2′,3′-二脱氧-3′-硫代胞苷(3TC)的最终水解产物.     

Hydrogen‐Bond Free Energy of Local Biological Water

Here, we propose an experimental methodology based on femtosecond‐resolved fluorescence spectroscopy to measure the hydrogen (H)‐bond free energy of water at protein surfaces under isothermal conditions. A demonstration was conducted by installing a non‐canonical isostere of tryptophan (7‐azatryptophan) at the surface of a coiled‐coil protein to exploit the photoinduced proton transfer of its chromophoric moiety, 7‐azaindole. The H‐bond free energy of this biological water was evaluated by comparing the rates of proton transfer, sensitive to the hydration environment, at the protein surface and in bulk water, and it was found to be higher than that of bulk water by 0.4 kcal mol^?1. The free‐energy difference is dominated by the entropic cost in the H‐bond network among water molecules at the hydrophilic and charged protein surface. Our study opens a door to accessing the energetics and dynamics of local biological water to give insight into its roles in protein structure and function.     

Visualizing internal stabilization in weakly bound systems using atomic energies: hydrogen bonding in small water clusters

Atomic energies are used to visualize the local stabilizing and destabilizing energy changes in water clusters. Small clusters, (H(2)O)(n), from n = 2-5, at MP2/aug-cc-pVTZ geometries are evaluated using energies defined by the quantum theory of atoms in molecules (QTAIM). The atomic energies reproduce MP2 total energies to within 0.005 kcal mol(-1). Oxygen atoms are stabilized for all systems and hydrogen atoms are destabilized. The increased stability of the water clusters due to hydrogen bond cooperativity is demonstrated at an atomic level. Variations in atomic energies within the clusters are correlated to the geometry of the waters and reveal variations in the hydrogen bond strengths. The method of visualization of the energy changes applied here is especially suited for application to large biomolecules.     

Electron hydration dynamics in water clusters: A direct ab initio molecular dynamics approach

Electron attachment dynamics of excess electron in water cluster (H2O)n (n = 2 and 3) have been investigated by means of full-dimensional direct ab initio molecular dynamics (MD) method at the MP26-311++G(d,p) level. It was found that the hydrogen bond breaking due to the excess electron is an important process in the first stage of electron capture in water trimer. Time scale of electron localization and hydrogen bond breaking were determined by the direct ab initio MD simulation. The initial process of hydration in water cluster is clearly visualized in the present study. In n = 3, an excess electron is first trapped around the cyclic water trimer with a triangular form, where the excess electron is equivalently distributed on the three water molecules at time zero. After 50 fs, the excess electron is concentrated into two water molecules, while the potential energy of the system decreases by -1.5 kcal/mol from the vertical point. After 100 fs, the excess electron is localized in one of the water molecules and the potential energy decreases by -5.3 kcal/mol, but the triangular form still remained. After that, one of the hydrogen bonds in the triangular form is gradually broken by the excess electron, while the structure becomes linear at 100-300 fs after electron capture. The time scale of hydrogen bond breaking due to the excess electron is calculated to be about 300 fs. Finally, a dipole bound state is formed by the linear form of three water molecules. In the case of n = 2, the dipole bound anion is formed directly. The mechanism of electron hydration dynamics was discussed on the basis of theoretical results.     

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.