How Many Methanol Molecules Can Solvate a Glycine: a PBE1PBE Approach

Microsolvation of glycine in methanol clusters is explored by the use of DFT calculation method. The lowest energy conformations within 16.72 kJ·mol-1 of the glycine clustering with one to six methanol molecules, which are obtained at the B3LYP/6-31+G(d) level of theory, are reoptimized at PBE1PBE/6-311+G(d,p). The calculated results agree with our previous results with B3LYP (Chin. J. Chem. Phys. 22 (2009) 577) that the clusters of two forms (Z-and N-form) tend to be isoenergetic when the number of the solvate molecules reaches six. Furthermore, this result is in good agreement with the experiment of the tryptophan-methanol clusters, implying that the present treatments are reasonable and reliable. The results also indicate that nine methanol molecules are not enough to fully solvate a glycine molecule, and a tentative estimation is obtained that ten methanol molecules may fully solvate a glycine molecule, which consists with the experiment results.     

Incremental solvation of nonionized and zwitterionic glycine

Microsolvation and combined microsolvation-continuum approaches are employed in order to examine the structures and relative energies of nonionized (N) and zwitterionic (Z) glycine clusters. Bridging structures are predicted to be the global minima after 3-5 discrete water molecules are included in the calculations. Calculations incorporating electron correlation stabilize the zwitterionic structures by about 7-9 kcal/mol relative to the N structures regardless of the number of discrete water molecules considered. Continuum calculations stabilize the Z structures relative to N structures; this effect decreases as the number of discrete water molecules is increased. Eight water molecules do not appear to fully solvate glycine.     

A theoretical investigation of the relative stability of hydrated glycine and methylcarbamic acid--from water clusters to interstellar ices

We have theoretically investigated how the low-energy conformers of the neutral and the zwitterionic forms of glycine as well as methylcarbamic acid are stabilized by the presence water. The MP2/6-311++G(d,p) method was utilized to conduct calculations on glycine and methylcarbamic acid in both isolated clusters and in clusters embedded in the conductor-like polarizable continuum model (C-PCM), where the clusters explicitly contain between one and ten water molecules. The neutral forms of glycine and methylcarbamic acid were found to have similar hydration energies, whereas the neutral methylcarbamic acid was determined to be approximately 32 kJ mol(-1) more stable than the neutral glycine in the isolated clusters and 30 kJ mol(-1) more stable in the C-PCM embedded clusters. Both the number and strength of the hydrogen bonding interactions between water and the zwitterions drive the stability. This lowers the relative energy of the glycine zwitterion from 50 kJ mol(-1) above neutral glycine, when there are two water molecules in the clusters to 11 kJ mol(-1) below for the clusters containing ten water molecules. For the methylcarbamic acid clusters with two water molecules, the zwitterion is 51 kJ mol(-1) higher in energy than the neutral form, but it remains 13 kJ mol(-1) above the neutral methylcarbamic acid in the clusters containing ten water molecules. When the bulk water environment is simulated by the C-PCM calculations, we find both the methylcarbamic acid and glycine zwitterionic forms have similar energies at 20 kJ mol(-1) above the neutral methylcarbamic acid energy and 10 kJ mol(-1) lower than the neutral glycine energy. Although neither methylcarbamic acid nor glycine have been detected in the interstellar medium yet, our findings indicate that methylcarbamic acid is the more stable product from methylamine and carbon dioxide reactions in a water ice. This suggests that methylcarbamic acid likely plays a role in the intermediate steps if glycine is formed in the interstellar medium.     

Microsolvation of uracil and its conjugate bases: a DFT study of the role of solvation on acidity

The effect of microsolvation on the deprotonation energies of uracil was examined using DFT. The structures of uracil and its N(1) and N(3) conjugate bases were optimized with zero to six associated water molecules. Multiple configurations (upward of 93) of these hydrated clusters were located at PBE1PBE/6-311+G(d,p). Trends in these geometries are discussed, with the waters generally forming chains with small numbers of waters (one-three), rings (three-five waters), or cages (five-six waters). The difference in energy between the N1 and N3 conjugate bases is 13 kcal mol(-1) in the gas phase, and it decreases with each added water up to four. At this point the energy difference has been halved, but addition of a fifth or sixth water has little effect on the energy difference. This is understood in terms of the water structures and their ability to stabilize the negatively charged atoms in the conjugate bases.     

Gas-Phase Reactions of hydrated alkaline earth metal ions, M2+(H2O) n (M = Mg, Ca, Sr, Ba and n = 4–7), with benzene

Gas-phase reactions of hydrated divalent alkaline earth metal ions and benzene were investigated by electrospray ionization Fourier-transform mass spectrometry. Rate constants for solvent-exchange reactions were determined as a function of hydration extent for Mg2+, Ca2+, Sr2+, and Ba2+ clusters containing four to seven water molecules each. All of the strontium and barium clusters react quickly with benzene. Barium reacts slightly faster than the corresponding strontium cluster with the same number of water molecules attached. For calcium, clusters with four and five water molecules react quickly, whereas those with six and seven water molecules do not. Magnesium with four water molecules reacts quickly, but not when five through seven water molecules are attached. The slow reactivity observed for some of these clusters indicates that the cation-pi interaction between the metal ion and benzene is partially screened by the surrounding water molecules. The reactivity of magnesium with seven water molecules is intermediate that of the hexa- and pentahydrate and the tetrahydrate. This result is consistent with the seventh water molecule being in the outer shell and much more weakly bound. The unusual trend in reactivity observed for magnesium may be due to the presence of mixed shell structures observed previously. These results are the first to provide information about the relative importance of cation-pi interactions in divalent metal ions as a function of metal hydration extent. Such studies should also provide a model and some insight into the relative binding affinities of divalent metal ions to aromatic residues on peptides and proteins.     

Clustering of glycine molecules in aqueous solution studied by molecular dynamics simulation

The nature of glycine--glycine interactions in aqueous solution has been studied using molecular dynamics simulations at four different concentrations and, in each case, four different temperatures. Although evidence is found for formation of small, transient hydrogen-bonded clusters of glycine molecules, the main type of interaction between glycine molecules is found to be single NH...OC hydrogen bonds. Double-hydrogen-bonded "dimers", which have often been cited as a significant species present in aqueous solutions of glycine, are only observed infrequently. When double-hydrogen-bonded dimers are formed, they dissociate quickly (typically within less than ca. 4 ps), although the broken hydrogen bonds have a higher than average probability of reforming. Several aspects of the clustering of glycine molecules are investigated as a function of both temperature and concentration, including the size distribution of glycine clusters, the radii of gyration of the clusters, and aspects of the lifetimes of glycine-glycine hydrogen bonding by means of hydrogen-bond correlation functions. Diffusion coefficients for the glycine clusters and water molecules are also investigated and provide results in realistic agreement with experimental results.     

Vibrational spectra of alpha-amino acids in the zwitterionic state in aqueous solution and the solid state: DFT calculations and the influence of hydrogen bonding

The zwitterionic forms of the two simplest alpha-amino acids, glycine and l-alanine, in aqueous solution and the solid state have been modeled by DFT calculations. Calculations of the structures in the solid state, using PW91 or PBE functionals, are in good agreement with the reported crystal structures, and the vibrational spectra computed at the optimized geometries provide a good fit to the observed IR and Raman spectra in the solid state. DFT calculations of the structures and vibrational spectra of the zwitterions in aqueous solution at the B3-LYP/cc-pVDZ level were found to require both explicit and implicit solvation models. Explicit solvation was modeled by inclusion of five hydrogen-bonded water molecules attached to each of the five possible hydrogen-bonding sites in the zwitterion and the integration equation formalism polarizable continuum model (IEF-PCM) was employed, providing a satisfactory fit to observed IR and Raman spectra. Band assignments are reported in terms of potential-energy distributions, which differ in some respects to those previously reported for glycine and l-alanine.     

Density functional theory study of 1:1 glycine-water complexes in the gas phase and in solution

We present a systematic study of 1:1 glycine-water complexes involving all possible glycine conformers. The complex geometries are fully optimized for the first time both in the gas phase and in solution using three DFT methods (B3LYP, PBE1PBE, X3LYP) and the MP2 method. We calculate the G3 energies and use them as the reference data to gauge hydrogen bond strength in the gas phase. The solvent effects are treated via the integral equation formalism-polarizable continuum model (IEF-PCM). Altogether, we locate fifty-two unique nonionized (N) structures and six zwitterionic (Z) structures in the gas phase, and fifty-five N structures and thirteen Z structures in solution. Both correlation and solvation are shown to be important in geometry determination. We found that in the gas phase, a water molecule binds more strongly to the carboxylic acid group of glycine than to its amine group, whereas in solution phase the reverse is true. The most stable Z structure is isoenergetic with the most stable N structure.     

Investigations on mixed water-clusters: Gas phase titration with cyclopentanone and identification of some isomers by time-of-flight mass spectrometry

Mixed-clusters of water with cyclopentanone have been investigated using high resolution time-of-flight mass spectrometry. These clusters are synthesized in a gas-aggregation source at comparatively higher temperature. They contain water-cluster at the core and cyclopentanone molecules hydrogen bonded through ketone oxygen with the dangling OH available at the core. Thus these mixed-clusters may also be considered as the products of a titration in gas phase. The growth reaction reveals that all clusters are protonated. From the configuration of dimer and tetramer, it is suggested that the proton resides as an Eigen ion in the core. The protonated mixed-clusters containing six, seven and eight water molecules substantiate the hydronium contained hexa, hepta and octamer water-cluster structures predicted by [KJ(H₃O)⁺] model calculations. For clusters with 9–19 water molecules, the core appears to have configurations that give less than the predicted number of dangling bonds. In large size clusters having more than 20 water molecules, the water-core appears to have open configuration like the melted structures obtained as a result of increase in temperature.     

Dissociation of hydrogen fluoride in HF(H(2)O)(7)

We have previously demonstrated that H-bond arrangement has a significant influence on the energetics, structure and chemistry of water clusters. In this work, the effect of H-bond orientation on the dissociation of hydrogen fluoride with seven water molecules is studied by means of graph theory and high level ab initio methods. It is found that cubic structures of HF(H(2)O)(7) are more stable than structures of other topologies reported in the literature. Electronic calculations on all possible H-bond orientations of cubie-HF(H(2)O)(7) show that ionized structures are energetically more favorable than nonionized ones. This is an indication that seven water molecules might be capable of ionizing hydrogen fluoride.     

Comparison of model chemistry and density functional theory thermochemical predictions with experiment for formation of ionic clusters of the ammonium cation complexed with water and ammonia; atmospheric implications

The G2, G3, CBS-QB3, and CBS-APNO model chemistry methods and the B3LYP, B3P86, mPW1PW, and PBE1PBE density functional theory (DFT) methods have been used to calculate deltaH(o) and deltaG(o) values for ionic clusters of the ammonium ion complexed with water and ammonia. Results for the clusters NH4(+) (NH3)n and NH4(+) (H2O)n, where n = 1-4, are reported in this paper and compared against experimental values. Agreement with the experimental values for deltaH(o) and deltaG(o) for formation of NH4(+) (NH3)n clusters is excellent. Comparison between experiment and theory for formation of the NH4(+) (H2O)n clusters is quite good considering the uncertainty in the experimental values. The four DFT methods yield excellent agreement with experiment and the model chemistry methods when the aug-cc-pVTZ basis set is used for energetic calculations and the 6-31G* basis set is used for geometries and frequencies. On the basis of these results, we predict that all ions in the lower troposphere will be saturated with at least one complete first hydration shell of water molecules.     

Clusters of hydrated methane sulfonic acid CH3SO3H.(H2O)n (n = 1-5): a theoretical study

Ab initio and density functional methods have been used to examine the structures and energetics of the hydrated clusters of methane sulfonic acid (MSA), CH3SO3H.(H2O)n (n = 1-5). For small clusters with one or two water molecules, the most stable clusters have strong cyclic hydrogen bonds between the proton of OH group in MSA and the water molecules. With three or more water molecules, the proton transfer from MSA to water becomes possible, forming ion-pair structures between CH3SO3- and H3O+ moieties. For MSA.(H2O)3, the energy difference between the most stable ion pair and neutral structures are less than 1 kJ/mol, thus coexistence of neutral and ion-pair isomers are expected. For larger clusters with four and five water molecules, the ion-pair isomers are more stable (>10 kJ/mol) than the neutral ones; thus, proton transfer takes place. The ion-pair clusters can have direct hydrogen bond between CH3SO3- and H3O+ or indirect one through water molecule. For MSA.(H2O)5, the energy difference between ion pairs with direct and indirect hydrogen bonds are less than 1 kJ/mol; namely, the charge separation and acid ionization is energetically possible. The calculated IR spectra of stable isomers of MSA.(H2O)n clusters clearly demonstrate the significant red shift of OH stretching of MSA and hydrogen-bonded OH stretching of water molecules as the size of cluster increases.     

Solvent effects on glycine. I. A supermolecule modeling of tautomerization via intramolecular proton transfer

The relative stabilities of glycine tautomers involved in the intramolecular proton transfer are investigated computationally by considering glycine-water complexes containing up to five water molecules. The supermolecule results are compared with continuum calculations. Specific solute-solvent interactions and solvent induced changes in the solute wave function are considered using the natural bond orbitals (NBO) method. The stabilization of the zwitterion upon solvation is explained by the changes in the wave functions localized on the forming and breaking bonds as well as by the different interaction energies in the zwitterionic and neutral clusters. Only the neutral species exist in mono- and dihydrated clusters and in the gas phase. In the smaller clusters, zwitterions are mainly stabilized by conformational effects, whereas in larger clusters, in particular when glycine is solvated on both sides of its heavy atom backbone, polarization effects dominate the stability of a given tautomer. Generally, the strength of the solute-solvent interactions is governed by the intermolecular charge transfer interactions. As the solvation progresses, the hypothetical gaseous zwitterion is better solvated than the gaseous neutral, making zwitterion to neutral tautomerization progressively less exothermic for clusters containing up to three water molecules, and endothermic for larger clusters. The neutral isomer does not exist for some solvent arrangements with five water molecules. Only solvent arrangements in which water molecules do not interact with the reactive proton are considered. Hence, the experimentally observed double well potential energy surface may be due to such an interaction or to a different reaction mechanism.     

Quantum-chemical study of structurization of water in the cavity of cucurbit[6]uryl

Structurization of water in the cavity of cucurbit[6]uryl was studied using the highly effective PRIRODA quantum-chemical program package, the PBE functional, and the TZ atomic basis. The structural and energy characteristics of the formation of small water clusters in the cavitand void were calculated. The maximum possible number of molecules in the void was found to be six.     

Microhydration of protonated glycine: an ab initio family tree

The incremental hydration of the glycine cation is investigated using an ab initio approach fully correcting for basis set superposition errors and explicitly incorporating electron-correlation effects. Structures with zero to four surrounding water molecules have been determined. It is demonstrated that the successive aggregates follow a Darwinian family tree, the most stable complexes systematically belonging to the same branch of the tree. In strong contrast with neutral glycine, the direct hydrogen bonding to the glycine cation is favored over bridging water structures. The agreement between experimental and theoretical hydration enthalpies and Gibbs free energies is impressive, as ab initio estimates almost systematically fit the experimental error bars. For GlyH(+)-(H2O) and GlyH(+)-(H2O)3, we show that two structures are generated by the experimental setup. The present approach also resolves most of the previous theory/experiment discrepancies and provides patterns for the evolution of the vibrational spectra: a decrease of the hydrogen-bond stretching frequency indicating second-shell water molecules. Additionally, the impact of bulk solvent solvation is investigated, as four discrete water molecules still do not fully hydrate the protonated glycine.     

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.     

DFT Calculation of Glycine with Methanols Clusters

Density functional theory （DFT） calculations are reported for the structures of neutral and zwitterionic glycine-（CHaOH）n where n=1-6. Initial geometries of the clusters of neutral and zwitterionic glycine with 1-6 methanol molecules are fully optimized at B3LYP/6-31＋G^＊ level of theory. The lowest energy configurations are located and their hydrogen bond structures are analyzed. Theoretical prediction reveals that the methanols prefer to locate near the carboxylic acid group for the small clusters （n_〈3） with the neutral form while the configurations with the methanols bridging the acid and the amino group are favorite in the zwitterionic form clusters. When the number of the methanol molecules in the clusters reaches five and six, the two forms tend to be isoenergetic.     

Polarization effects and charge separation in AgCl-water clusters

Structural, energetic, vibrational, and electronic properties of salt ion pairs (AgCl and NaCl) in water (W) clusters were investigated by density functional theory. In agreement with recent theoretical studies of NaCl-water clusters, structures where the salt ion pair is separated by solvent molecules or solvent separated ion pair (SSIP) were found in AgCl-W(6) and AgCl-W(8) aggregates. Our results indicate that for small AgCl-water clusters, contact ion pair (CIP) structures are energetically more stable than SSIP, whereas an opposite tendency was observed for NaCl-water clusters. In comparison with CIP, SSIP are characterized by extensive electronic density reorganization, reflecting enhanced polarization effects. A major difference between AgCl-water and NaCl-water CIP aggregates concerns charge transfer. In AgCl-water CIP clusters, charge is transferred from the solvent (water) to the ion pair. However, in NaCl-water CIP clusters charge is transferred from the ion pair to the water molecules. The electronic density reorganization in the aggregates was also discussed through the analysis of electronic density difference isosurfaces. Time dependent density functional theory calculations show that upon complexation of AgCl and NaCl with water molecules, excitation energies are significantly blueshifted relative to the isolated ion pairs ( approximately 2 eV for AgCl-W(8) SSIP). In keeping with results for NaI-water clusters [Peslherbe et al., J. Phys. Chem. A 104, 4533 (2000)], electronic oscillator strengths of transitions to excited states are weaker for SSIP than for CIP structures. However, our results also suggest that the difference between excitation energies and oscillator strengths of CIP and SSIP structures may decrease with increasing cluster size.     

Computer Simulation of the Stability of Water Clusters Containing Nitrogen Oxide Molecules

The stability of water clusters containing nitrogen oxide molecules is studied by the molecular dynamics method. The composition and size of thermodynamically stable heteroclusters are determined. The inclusion of two molecules of nitrogen oxide into aggregates containing seven or more water molecule increases the cluster stability. The correlation between the stability of heteroclusters and the ratio of self-diffusion coefficients of molecules of different kinds is observed. The real part of the cluster permittivity is maximal in the vicinity of the frequency of 200 cm^–1. The inclusion of nitrogen oxide molecules into water clusters increases the characteristic frequency of dielectric relaxation. In general, heteroclusters are more stable with respect to perturbations caused by an external electric field than pure clusters with the same number of water molecules. The clusterization of water vapors accompanied by absorption of polar molecules of impurity favors a decrease in the greenhouse effect.