The influence of microhydration on the ionization energy thresholds of uracil and thymine

In the present study the ionization energy thresholds (IET's) of uracil and thymine have been calculated (with the B3LYP, PMP2, and P3 levels of theory using the standard 6-31++G(d,p) basis set) with one to three water molecules placed in the first hydration shell. Then (B3LYP) polarizable continuum model (PCM) calculations were performed with one to three waters of the hydration shell included. Calculations show there is a distinct effect of microhydration on uracil and thymine. For uracil, one added water results in a decrease in the IET of about 0.15 eV. The second and third water molecules cause a further decrease by about 0.07 eV each. For thymine, the first water molecule is seen to decrease the IET by about 0.1 eV, while the second and third water molecules cause a further decrease of less than 0.1 eV each. The changes in IET calculated here for thymine with one to three waters of hydration are smaller than the experimental values determined by Kim et al. (Kim, S. K.; Lee, W.; Herschbach, D. R. J. Phys. Chem. 1996, 100, 7933). Preliminary results presented here indicate that the experimental results may involve keto-enol tautomers of thymine. The results of placing the microhydrated structures of uracil and thymine in a PCM cavity was seen to make very little difference in the IET when compared to the IET of ordinary uracil or thymine in a PCM cavity. The implications are that accurate calculations of the IET's of uracil and thymine can be obtained by simply considering long-range solvation effects.     

Influence of microhydration on the ionization energy thresholds of thymine: comparisons of theoretical calculations with experimental values

In the present study the ionization energy thresholds (IETs) of thymine, and thymine keto-enol tautomers, have been calculated (with the B3LYP, and P3 levels of theory using the standard 6-31++G(d,p) basis set) with 1-3 water molecules placed in the first hydration shell. Calculations show there is a distinct effect of microhydration on the IET of thymine. The first water molecule is seen to decrease the IET by about 0.1 eV, whereas the second and third water molecules cause a further decrease of less than 0.1 eV each. The changes in IET calculated here for thymine with 1-3 waters of hydration are smaller than the experimental values determined by Kim et al. (J. Phys. Chem. 1996, 100, 7933). Therefore calculations have been performed on the microhydrated keto-enol tautomers of thymine. The calculated results on the keto-enol tautomers are seen to be in better agreement with the experimental results. However, the keto-enol thymine tautomers are considerably higher in energy than the canonical form of thymine, and there is presently no good evidence that these thymine tautomers are actually present in a supersonic jet-cooled experiment.     

Flexible H2O2 in water: electronic structure from photoelectron spectroscopy and ab initio calculations

The effect of hydration on the electronic structure of H(2)O(2) is investigated by liquid-jet photoelectron spectroscopy measurements and ab initio calculations. Experimental valence electron binding energies of the H(2)O(2) orbitals in water are, on average, 1.9 eV red-shifted with respect to the gas-phase molecule. A smaller width of the first peak was observed in the photoelectron spectrum from the solution. Our experiment is complemented by simulated photoelectron spectra, calculated at the ab initio level of theory (with EOM-IP-CCSD and DFT methods), and using path-integral sampling of the ground-state density. The observed shift in ionization energy upon solvation is attributed to a combination of nonspecific electrostatic effects (long-range polarization) and of the specific interactions between H(2)O(2) and H(2)O molecules in the first solvation shell. Changes in peak widths are found to result from merging of the two lowest ionized states of H(2)O(2) in water due to conformational changes upon solvation. Hydration effects on H(2)O(2) are stronger than on the H(2)O molecule. In addition to valence spectra, we report oxygen 1s core-level photoelectron spectra from H(2)O(2)(aq), and observed energies and spectral intensities are discussed qualitatively.     

Theoretical elucidation of conflicting experimental data on vertical ionization potentials of microhydrated thymine

In a recent article we reported calculations of the ionization energy thresholds (IET) of microhydrated thymine (Close; et al. J. Phys. Chem. A, 2006, 110, 7485). Calculations showed a distinct effect of microhydration on the IET's of thymine. The first water molecule was seen to decrease the IET by about 0.1 eV, and the second and third water molecules caused a further decrease of less than 0.1 eV each. These changes in IET calculated for the canonical form of thymine with 1-3 waters of hydration are smaller than the experimental values determined by Kim et al. (J. Phys. Chem. C 1996, 100, 7933). In the present study it has been shown that there is considerable reorientation of the water molecules in microhydrated thymine upon ionization. This leads to the expectation that the experimental ionization energies may therefore represent an adiabatic process. The results presented here show that the changes in experimental ionization energies determined by Kim et al. for microhydrated thymine are in good agreement with the calculated adiabatic ionization energies.     

水环境对GC和AT碱基对质子转移的影响

采用B3LYP/DZP++的方法研究了第一水化层作用和连续化处理的水溶剂作用对鸟嘌呤-胞嘧啶(GC)碱基对和腺嘌呤-胸腺嘧啶(AT)碱基对质子转移反应的影响. GC和AT碱基对在连续化水溶剂作用下,均发生单质子转移(SPT1)和分步的双质子转移(DPT),而在第一水化层5 个水分子的作用下(GC·5H₂O,AT·5H₂O)或同时考虑第一水化层作用和连续化水溶剂作用(GC·5H₂O+PCM,AT·5H₂O+PCM)时,GC和AT碱基对的质子转移均只得到单质子转移反应(SPT1). 单质子转移过程中的活化能变化情况表明：第一水化层对GC和AT碱基对结构和质子转移影响较大,水环境对碱基对的作用主要发生在第一水化层.     

Two-dimensional hydration shells of alkali metal ions at a hydrophobic surface

We study the hydration shell formation of alkali metal ions at a graphite surface. Two-dimensional shell structures are found in the initial stage of hydration, in contrast to the three-dimensional structures in bulk water and clusters. Comparison of vibrational spectra with experiments identifies the shell structures and the thermally induced transition from the first to the second shell. We also found intriguing competition between hydration and ion-surface interaction, leading to different solvation dynamics between K and Na. Implications of these results in ionic processes at interfaces are elaborated.     

Speciation of the curium(III) ion in aqueous solution: a combined study by quantum chemistry and molecular dynamics simulation

The structures of aquo complexes of the curium(III) ion have been systematically studied using quantum chemical and molecular dynamics (MD) methods. The first hydration shell of the Cm3+ ion has been calculated using density functional theory (DFT), with and without inclusion of the conductor-like polarizable continuum medium (CPCM) model of solvation. The calculated results indicate that the primary hydration number of Cm3+ is nine, with a Cm-O bond distance of 2.47-2.48 A. The calculated bond distances and the hydration number are in excellent agreement with available experimental data. The inclusion of a complete second hydration shell of Cm3+ has been investigated using both DFT and MD methods. The presence of the second hydration shell has significant effects on the primary coordination sphere, suggesting that the explicit inclusion of second-shell effects is important for understanding the nature of the first shell. The calculated results indicate that 21 water molecules can be coordinated in the second hydration shell of the Cm3+ ion. MD simulations within the hydrated-ion model suggest that the second-shell water molecules exchange with the bulk solvent with a lifetime of 161 ps.     

Protons in non-ionic aqueous reverse micelles

Using molecular dynamics techniques, we investigate the solvation of an excess proton within an aqueous reverse micelle in vacuo, with the neutral surfactant diethylene glycol monodecyl ether [CH3(CH2)11(OC2H4)2OH]. The simulation experiments were performed using a multistate empirical valence bond Hamiltonian model. Our results show that the stable solvation environments for the excess proton are located in the water-surfactant interface and that its first solvation shell is composed exclusively by water molecules. The relative prevalence of Eigen- versus Zundel-like solvation structures is investigated; compared to bulk results, Zundel-like structures in micelles become somewhat more stable. Characteristic times for the proton translocation jumps have been computed using population relaxation time correlation functions. The micellar rate for proton transfer is approximately 40x smaller than that found in bulk water at ambient conditions. Differences in the computed rates are examined in terms of the hydrogen-bond connectivity involving the first solvation shell of the excess charge with the rest of the micellar environment. Simulation results would indicate that proton transfers are correlated with rare episodes during which the HB connectivity between the first and second solvation shells suffers profound modifications.     

Hybrid one-electron/many-electron methods for ionized states of molecular clusters

To describe singly-ionized states of molecular clusters we devised an effective Hamiltonian approach that combines (1) accurate monomer ionization potentials from many-electron wave functions with (2) polarization shifts and (3) effective monomer couplings obtained from a simple one-electron approach (the superposition-of-fragment-states (SFS) method [Valeev et al., J. Am. Chem. Soc., 2006, 128, 9882]). The accuracy of the intermolecular coupling parameters evaluated with SFS Hartree-Fock (HF) and Density-Functional-Theory (DFT) variants was evaluated for several weakly-bound dimers and compared against the state-of-the-art equation-of-motion ionization-potential coupled-cluster singles and doubles (EOM-IP-CCSD) data of Krylov and co-workers. The SFS-HF method produces coupling integrals accurate to a few percent, whereas SFS-DFT predictions are substantially worse. A hybrid approach combining SFS-HF couplings and shifts with EOM-IP-CCSD ionization potentials of monomers (denoted as SFS-EOM-IP-CCSD) was applied to ionized states of two conformers of a benzene dimer and ten representative DNA base pairs. The 16 considered SFS-EOM-IP-CCSD ionization potentials of the benzene dimer differed from the reference EOM-IP-CCSD IPs of Krylov and co-workers [Pieniazek et al., J. Chem. Phys. 2007, 127, 044317; Bravaya et al., Phys. Chem. Chem. Phys. 2010, 12, 2261] by less than 0.1 eV on average, and at most by 0.2 eV. For the DNA base pairs the mean absolute (median) deviation of the SFS-EOM-IP-CCSD IPs was 0.27 (0.23) eV; several deviations for non-Koopmans states were as large as 0.9 eV. The SFS-EOM-IP-CCSD method can be readily applied to large molecular clusters with computational effort scaling cubically with the size of the cluster.     

Structural and dynamic properties of water within the solvation layer around various conformations of the glycine-based polypeptide

Several conformations of the solvated glycine-based polypeptides were investigated using molecular dynamics simulations. Some properties of water in the neighboring space around these molecules were investigated. It was found that water forms a well-defined layer-the first solvation shell-around the peptide molecule, and thickness of this layer is independent of the peptide structure and is equal to approximately 0.28 nm. Within this layer, water molecules show marked orientations relative to a peptide surface. Using the two-particle contribution to entropy as a measure of structural ordering of water, we found that the first solvation shell contributes 95% or more to the total water ordering around the peptide molecule. In investigating the dynamic properties of water, diffusion coefficients and lifetime of the hydrogen bond, clear differences between solvation layer and the bulk water were observed. It was found that the translational diffusion coefficient, D(T), decreases by 30% or more compared to bulk water; also, the lifetime of the water-water hydrogen bond clearly increases. The rotational diffusion coefficient, however, decreases only slightly, no more than approximately 10%. These differences correspond to the slightly higher energy of the hydrogen bond, and to its slightly distorted geometry. Analyzing the translational dynamics of water in the vicinity of the peptide molecule, it was deduced that the structure of the first solvation shell becomes more rigid than the structure of the bulk water. Investigation of a "pure hydrophobic" form of the polypeptide shows that the structure and the properties of water within the solvation shell are predominantly determined by the hydrophobic effect. The specific interactions between water molecules and various charge groups of the peptide molecule modifies this effect only slightly.     

Hydration of alkali ions from first principles molecular dynamics revisited

Structural and dynamical properties of the hydration of Li(+), Na(+), and K(+) in liquid water at ambient conditions were studied by first principles molecular dynamics. Our simulations successfully captured the different hydration behavior shown by the three alkali ions as observed in experiments. The present analyses of the dependence of the self-diffusion coefficient and rotational correlation time of water on the ion concentration suggest that Li(+) (K(+)) is certainly categorized as a structure maker (breaker), whereas Na(+) acts as a weak structure breaker. An analysis of the relevant electronic structures, based on maximally localized Wannier functions, revealed that the dipole moment of H(2)O molecules in the first solvation shell of Na(+) and K(+) decreases by about 0.1 D compared to that in the bulk, due to a contraction of the oxygen lone pair orbital pointing toward the metal ion.     

Theoretical study of the solvation of fluorine and chlorine anions by water

The solvation of fluoride and chloride anions (F(-) and Cl(-), respectively) by water has been studied using effective fragment potentials (EFPs) for the water molecules and ab initio quantum mechanics for the anions. In particular, the number of water molecules required to fully surround each anion has been investigated. Monte Carlo calculations have been used in an attempt to find the solvated system X(-)(H(2)O)(n) (X = F, Cl) with the lowest energy for each value of n. It is predicted that 18 water molecules are required to form a complete solvation shell around a Cl(-) anion, where "complete solvation" is interpreted as an ion that is completely surrounded by solvent molecules. Although fewer water molecules may fully solvate the Cl(-) anion, such structures are higher in energy than partially solvated molecules, up to n > or = 18. Calculations on the F(-) anion suggest that 15 water molecules are required for a complete solvation shell. The EFP predictions are in good agreement with the relative energies predicted by ab initio energy calculations at the EFP geometries.     

Threshold-photoelectron spectroscopic study of methyl-substituted hydrazine compounds

The valence shell electronic structures of methylhydrazine (CH(3)NHNH(2)), 1,1-dimethylhydrazine ((CH(3))(2)NNH(2)) and tetramethylhydrazine ((CH(3))(4)N(2)) have been studied by recording threshold and conventional (kinetic energy resolved) photoelectron spectra. Ab initio calculations have been performed on ammonia and the three methyl substituted hydrazines, with the structures being optimized at the B3-LYP/6-31+G(d) level of theory. The ionization energies of the valence molecular orbitals were calculated using the Green's function method, allowing the photoelectron bands to be assigned to specific molecular orbitals. The ground-state adiabatic and vertical ionization energies, as determined from the threshold photoelectron spectra, were IE(a) = 8.02 +/- 0.16 eV and IE(v) = 9.36 +/- 0.02 eV for methylhydrazine, IE(a) = 7.78 +/- 0.16 eV and IE(v) = 8.86 +/- 0.01 eV for 1,1-dimethylhydrazine and IE(a) = 7.26 +/- 0.16 eV and IE(v) = 8.38 +/- 0.01 eV for tetramethylhydrazine. Due to the large geometry change that occurs upon ionization, these IE(a) values are all higher than the true thresholds. New features have been observed in the inner valence region and these have been compared with similar structure in the spectrum of hydrazine. The effect of resonant autoionization on the threshold photoelectron yield is discussed. New heats of formation (Delta(f)H) are proposed for the three hydrazines on the basis of G3 calculations: 107, 94, and 95 kJ/mol for methylhydrazine, 1,1-dimethyhydrazine and tetramethylhydrazine, respectively. The previously reported Delta(f)H for tetramethylhydrazine is shown to be erroneous.     

Hydration energies and structures of alkaline earth metal ions, M2+(H2O)n, n = 5-7, M = Mg, Ca, Sr, and Ba

The evaporation of water from hydrated alkaline earth metal ions, produced by electrospray ionization, was studied in a Fourier transform mass spectrometer. Zero-pressure-limit dissociation rate constants for loss of a single water molecule from the hydrated divalent metal ions, M(2+)(H(2)O)(n) (M = Mg, Ca, and Sr for n = 5-7, and M = Ba for n = 4-7), are measured as a function of temperature using blackbody infrared radiative dissociation. From these values, zero-pressure-limit Arrhenius parameters are obtained. By modeling the dissociation kinetics using a master equation formalism, threshold dissociation energies (E(o)) are determined. These reactions should have a negligible reverse activation barrier; therefore, E(o) values should be approximately equal to the binding energy or hydration enthalpy at 0 K. For the hepta- and hexahydrated ions at low temperature, binding energies follow the trend expected on the basis of ionic radii: Mg > Ca > Sr > Ba. For the hexahydrated ions at high temperature, binding energies follow the order Ca > Mg > Sr > Ba. The same order is observed for the pentahydrated ions. Collisional dissociation experiments on the tetrahydrated species result in relative dissociation rates that directly correlate with the size of the metals. These results indicate the presence of two isomers for hexahydrated magnesium ions: a low-temperature isomer in which the six water molecules are located in the first solvation shell, and a high-temperature isomer with the most likely structure corresponding to four water molecules in the inner shell and two water molecules in the second shell. These results also indicate that the pentahydrated magnesium ions have a structure with four water molecules in the first solvation shell and one in the outer shell. The dissociation kinetics for the hexa- and pentahydrated clusters of Ca(2+), Sr(2+), and Ba(2+) are consistent with structures in which all the water molecules are located in the first solvation shell.     

Asequential Monte Carlo quantum mechanics study of the hydrogen-bond interaction and the solvatochromic shift of the n-pi* transition of acrolein in water

The sequential Monte Carlo (MC) quantum mechanics (QM) methodology, using time-dependent density-functional theory (TD-DFT), is used to study the solvatochromic shift of the n-pi* transition of trans-acrolein in water. Using structures obtained from the isothermal-isobaric Metropolis MC simulation TD-DFT calculations, within the B3LYP functional, are performed for the absorption spectrum of acrolein in water. In the average acrolein makes one hydrogen bond with water and the hydrogen-bond shell is responsible for 30% of the total solvatochromic shift, considerably less than the shift obtained for the minimum-energy configurations. MC configurations are sampled after analysis of the statistical correlation and 100 configurations are extracted for subsequent QM calculations. All-electron TD-DFT B3LYP calculations of the absorption transition including acrolein and all explicit solvent molecules within the first hydration shell, 26 water molecules, give a solvatochromic shift of 0.18 +/- 0.11 eV. Using simple point charges to represent the solvent the shifts are calculated for the first, second, and third solvation shells. The results converge for the calculated shift of 0.20 +/- 0.10 eV in very good agreement with the experimentally inferred result of 0.20 +/- 0.05 eV. All average results presented are statistically converged.     

Structure and dynamics of the hydration shells of the Al3+ ion

First principles simulations of the hydration shells surrounding Al3+ ions are reported for temperatures near 300 degrees C. The predicted six water molecules in the octahedral first hydration shell were found to be trigonally coordinated via hydrogen bonds to 12 s shell water molecules in agreement with the putative structure used to analyze the x-ray data, but in disagreement with the results reported from conventional molecular dynamics using two-and three-body potentials. Bond lengths and angles of the water molecules in the first and second hydration shells and the average radii of these shells also agreed very well with the results of the x-ray analysis. Water transfers into and out of the second solvation shell were observed to occur on a picosecond time scale via a dissociative mechanism. Beyond the second shell the bonding pattern substantially returned to the tetrahedral structure of bulk water. Most of the simulations were done with 64 solvating water molecules (20 ps). Limited simulations with 128 water molecules (7 ps) were also carried out. Results agreed as to the general structure of the solvation region and were essentially the same for the first and second shell. However, there were differences in hydrogen bonding and Al-O radial distribution function in the region just beyond the second shell. At the end of the second shell a nearly zero minimum in the Al-O radial distribution was found for the 128 water system. This minimum is less pronounced minimum found for the 64 water system, which may indicate that sizes larger than 64 may be required to reliably predict behavior in this region.     

Accurate vertical ionization energy and work function determinations of liquid water and aqueous solutions

The absolute-scale electronic energetics of liquid water and aqueous solutions, both in the bulk and at associated interfaces, are the central determiners of water-based chemistry. However, such information is generally experimentally inaccessible. Here we demonstrate that a refined implementation of the liquid microjet photoelectron spectroscopy (PES) technique can be adopted to address this. Implementing concepts from condensed matter physics, we establish novel all-liquid-phase vacuum and equilibrated solution–metal-electrode Fermi level referencing procedures. This enables the precise and accurate determination of previously elusive water solvent and solute vertical ionization energies, VIEs. Notably, this includes quantification of solute-induced perturbations of water''s electronic energetics and VIE definition on an absolute and universal chemical potential scale. Defining and applying these procedures over a broad range of ionization energies, we accurately and respectively determine the VIE and oxidative stability of liquid water as 11.33 ± 0.03 eV and 6.60 ± 0.08 eV with respect to its liquid-vacuum-interface potential and Fermi level. Combining our referencing schemes, we accurately determine the work function of liquid water as 4.73 ± 0.09 eV. Further, applying our novel approach to a pair of exemplary aqueous solutions, we extract absolute VIEs of aqueous iodide anions, reaffirm the robustness of liquid water''s electronic structure to high bulk salt concentrations (2 M sodium iodide), and quantify reference-level dependent reductions of water''s VIE and a 0.48 ± 0.13 eV contraction of the solution''s work function upon partial hydration of a known surfactant (25 mM tetrabutylammonium iodide). Our combined experimental accomplishments mark a major advance in our ability to quantify electronic–structure interactions and chemical reactivity in liquid water, which now explicitly extends to the measurement of absolute-scale bulk and interfacial solution energetics, including those of relevance to aqueous electrochemical processes.

A generalised liquid-phase photoelectron spectroscopy approach is reported, allowing accurate, absolute energy scale ionisation energies of liquid water and aqueous solutions, as well as liquid water''s work function to be reported.     

Photoionization and ab initio study of Ba(H2O)n (n = 1-4) clusters

An experimental and theoretical study of the photoionization energies (IE's) of Ba(H(2)O)(n) clusters containing up to n = 4 water molecules has been performed. The clusters were generated by a pick-up source combining laser vaporization with pulsed supersonic expansion, and then photoionized by radiation of 272.5-340 nm. The experimentally determined IE(e)'s for n = 1 to 4 are 4.56 ± 0.05, 4.26 ± 0.05, 3.90 ± 0.05 and 3.71 ± 0.05 eV. This cluster size dependence of IE is reproduced within ±0.06 eV employing the mPW1PW91 density-functional and CCSD(T, Full) quantum-chemical methods combined with the 6-311++G(d,p) basis set for the H and O atoms and three different relativistic effective core potentials for Ba atoms. The calculations indicate that the lowest energy hydration structures represent the most relevant contributions to both the vertical and adiabatic ionization energies. Experimental and theoretical evidence correlates with the progressive surface-delocalization of the electron from the hydration cavity around the Ba atom and suggests that the intra-cluster electron transfer is possible even for small aggregates.     

Potential of mean force of hydrophobic association: dependence on solute size

The potentials of mean force (PMFs) were determined for systems involving formation of nonpolar dimers composed of methane, ethane, propane, isobutane, and neopentane, respectively, in water, using the TIP3P water model, and in vacuo. A series of umbrella-sampling molecular dynamics simulations with the AMBER force field was carried out for each pair in either water or in vacuo. The PMFs were calculated by using the weighted histogram analysis method (WHAM). The shape of the PMFs for dimers of all five nonpolar molecules is characteristic of hydrophobic interactions with contact and solvent-separated minima and desolvation maxima. The positions of all these minima and maxima change with the size of the nonpolar molecule, that is, for larger molecules they shift toward larger distances. The PMF of the neopentane dimer is similar to those of other small nonpolar molecules studied in this work, and hence the neopentane dimer is too small to be treated as a nanoscale hydrophobic object. The solvent contribution to the PMF was also computed by subtracting the PMF determined in vacuo from the PMF in explicit solvent. The molecular surface area model correctly describes the solvent contribution to the PMF together with the changes of the height and positions of the desolvation barrier for all dimers investigated. The water molecules in the first solvation sphere of the dimer are more ordered compared to bulk water, with their dipole moments pointing away from the surface of the dimer. The average number of hydrogen bonds per water molecule in this first hydration shell is smaller compared to that in bulk water, which can be explained by coordination of water molecules to the hydrocarbon surface. In the second hydration shell, the average number of hydrogen bonds is greater compared to bulk water, which can be explained by increased ordering of water from the first hydration shell; the net effect is more efficient hydrogen bonding between the water molecules in the first and second hydration shells.