Global Minimum‐Energy Structure and Spectroscopic Properties of I2.−⋅n H2O Clusters: A Monte Carlo Simulated Annealing Study

The vibrational (IR and Raman) and photoelectron spectral properties of hydrated iodine‐dimer radical‐anion clusters, I₂^.? ? n H₂O (n=1–10), are presented. Several initial guess structures are considered for each size of cluster to locate the global minimum‐energy structure by applying a Monte Carlo simulated annealing procedure including spin–orbit interaction. In the Raman spectrum, hydration reduces the intensity of the I? I stretching band but enhances the intensity of the O? H stretching band of water. Raman spectra of more highly hydrated clusters appear to be simpler than the corresponding IR spectra. Vibrational bands due to simultaneous stretching vibrations of O? H bonds in a cyclic water network are observed for I₂^.? ? n H₂O clusters with n≥3. The vertical detachment energy (VDE) profile shows stepwise saturation that indicates closing of the geometrical shell in the hydrated clusters on addition of every four water molecules. The calculated VDE of finite‐size small hydrated clusters is extrapolated to evaluate the bulk VDE value of I₂^.? in aqueous solution as 7.6 eV at the CCSD(T) level of theory. Structure and spectroscopic properties of these hydrated clusters are compared with those of hydrated clusters of Cl₂^.? and Br₂^.?.     

Effects of microsolvation and aqueous solvation on the tautomers of histidine: a computational study on energy, structure and IR spectrum

Microsolvation and combined microsolvation-continuum approaches are employed to investigate the structures and energies of canonical and zwitterionic histidine conformers. The effect of hydration on the relative conformational stability is examined. The strategy of exploring singly and doubly hydrated structures and the possible microsolvation patterns are described. We find that bonding water molecule may significantly change the relative conformational stabilities. In gas phase, the singly and doubly hydrated canonical forms are more stable than their zwitterionic counterparts. In solution, the continuum solvent model shows that bare zwitterionic form is more stable than bare canonical form by 1.1 kcal/mol. This energy separation is increased to 2.2 and 3.4 kcal/mol with inclusion of one and two explicit water molecules, respectively. We have also observed that the doubly hydrated structures obtained by combining two water molecules simultaneously to the solute molecule are preferred over the stepwise hydration. Hydrogen bond energies for the most stable hydrated histidine tautomers are determined by the atoms in molecules theory. The infrared (IR) spectra for the most stable singly and doubly hydrated structures of both histidine tautomers in gas phase are characterized. The stretching frequencies for NH of imidazole ring and OH of COOH are red shifted due to the hydrations. The IR spectra for the most stable zwitterionic tautomers in solution are also presented and discussed in connection with the comparison to the experiments. The pKa values obtained for the ring protonated zwitterions with two explicit water molecules appear to be in good agreement with the experiments.     

The Structural Features of the Hydrated Ferrous Ion Clusters: [Fe(H2O) n ]2+ (n?=?1–19)

The low-lying structures of the hydrated ferrous ion clusters [Fe(H₂O) _n ]²⁺ (n?=?1?C19) were extensively searched at the level of the density functional theory. The results show that the first hydration shell consists of six water molecules, and the second hydration shell contains seven water molecules. Furthermore, it is found that all the lowest-energy states of [Fe(H₂O) _n ]²⁺ (n?=?1?C19) clusters are spin quintet states. These lowest-energy states keep well even at finite temperatures. The analyses of the successive water binding energy and natural charges population on ferrous ion clearly show that the influence of ferrous ion on the surrounding water molecules goes beyond the second hydration shell.     

Computational Exploration of Conformations of Glycine-Arginine and a Deduced Model on Global Minimum Configurations of Dipeptides in Gas Phase

An extensive computational study on the conformations of gaseous dipeptide glycinearginine, GlyArg, has been performed. A large number of trail structures were generated by systematically sampling the potential energy surface (PES) of GlyArg. The trial structures were successively optimized with the methods of PM3, HF/3-21G^*, BHandHLYP/6-31G^*, and BHandHLYP/6-311++G^** in order to reliably find the low energy conformations. The conformational energies were finally determined with the methods of BHandHLYP, camB3LYP, B97D, and MP2 using the basis set of 6-311++G(3df,3pd). The results establish firmly that gaseous GlyArg exists primarily in its canonical form, in sharp contrast with ArgGly that adopts the zwitterionic form. Important data such as the rotational constants, dipole moments, vertical ionization energies, temperature distributions and IR spectra of the low energy conformers are represented for the understanding of the future experiments. Moreover, considering the global minima of all amino acids and many dipeptides, combined with the hydrophobicities of amino acids, a model predicting whether the global minimum configuration of a dipeptide is canonical or zwitterionic is developed.     

Comparative studies between hydrated hydrogen bonded and stacked DNA base pair

Influence of hydration on the Watson–Crick guanine–cytosine hydrogen bonded (h-bonded) base pair (GC) and stacked pair (G/C) was investigated in their first hydration shell. An electrostatic based approach has been used to identify the potential binding sites for water molecules around GC and G/C pairs. Several geometries of the complexes, GC…(H₂O)_n and G/C…(H₂O)_n (n=1–6) were investigated using HF/6-31G** and HF/6-31G++** methods. Further minimization calculations were performed at both B3P86/6-31G** and MP2/6-31G** levels to assess the role of electron correlation contribution in the hydration process. It can be concluded from the present findings that the stacked base-pair hydrate better than the corresponding h-bonded base pair, and DNA base pairs can accommodate up to 4–5 water molecules whereas stacked pair do accommodate 5–6 water molecules.     

Theoretical studies on photoelectron and IR spectral properties of Br2.-(H2O)n clusters

We report vertical detachment energy (VDE) and IR spectra of Br2.-.(H2O)n clusters (n=1-8) based on first principles electronic structure calculations. Cluster structures and IR spectra are calculated at Becke's half-and-half hybrid exchange-correlation functional (BHHLYP) with a triple split valence basis function, 6-311++G(d,p). VDE for the hydrated clusters is calculated based on second order Moller-Plesset perturbation (MP2) theory with the same set of basis function. On full geometry optimization, it is observed that conformers having interwater hydrogen bonding among solvent water molecules are more stable than the structures having double or single hydrogen bonded structures between the anionic solute, Br2.-, and solvent water molecules. Moreover, a conformer having cyclic interwater hydrogen bonded network is predicted to be more stable for each size hydrated cluster. It is also noticed that up to four solvent H2O units can reside around the solute in a cyclic interwater hydrogen bonded network. The excess electron in these hydrated clusters is localized over the solute atoms. Weighted average VDE is calculated for each size (n) cluster based on statistical population of the conformers at 150 K. A linear relationship is obtained for VDE versus (n+3)(-1/3) and bulk VDE of Br2.- aqueous solution is calculated as 10.01 eV at MP2 level of theory. BHHLYP density functional is seen to make a systematic overestimation in VDE values by approximately 0.5 eV compared to MP2 data in all the hydrated clusters. It is observed that hydration increases VDE of bromine dimer anion system by approximately 6.4 eV. Calculated IR spectra show that the formation of Br2.--water clusters induces large shifts from the normal O-H stretching bands of isolated water keeping bending modes rather insensitive. Hydrated clusters, Br2.-.(H2O)n, show characteristic sharp features of O-H stretching bands of water in the small size clusters.     

Extensive computational study on coordination of transition metal cations and water molecules to glutamic acid

On the basis of the conformations of glutamic acid (Glu) and analysis of possible metal cation coordination and hydration modes, conformations of Glu metalated with transition metal cations (TMCs), Cu(+/2+), Zn(+/2+), and Fe(+/2+/3+) and hydrations of Glu-Cu(+/2+) and Glu-Zn(+/2+) complexes by up to three water molecules are determined by extensive computational searches. The BHandHLYP functional is chosen as the main computational method as its overall performance for treating the spin multiplicity of TMCs is similar to that of CCSD(T) and better than that of MP2 and B3LYP. All mono- and divalent TMCs prefer tridentate coordination to canonical Glu, while Fe(3+) favors a bidentate coordination to zwitterionic Glu. The ground state of Glu-Fe(+) is found to be a spin sextet. Metal ion affinities of Glu for the TMCs are determined, and an excellent agreement with the experiment for Cu(+) may be obtained if the entropic effect is properly accounted for. Effects of hydration on the stabilities of different Glu-Cu(+/2+)/Zn(+/2+) structures are discussed, and the hydration energies for up to three water molecules are obtained. For the global minimum to take the zwitterionic form, Glu-Zn(+) requires only monohydration, Glu-Zn(2+) needs to be trihydrated, while Glu-Cu(+/2) should be hydrated with four or more water molecules.     

Structures and isomerization of neutral and zwitterion serine–water clusters: Computational study

Calculations are presented for the structure and the isomerization reaction of various conformers of the bare serine, neutral serine–(H₂O)_n and serine zwitterion–(H₂O)_n (n = 1, 2) clusters. The effects of binding water molecules on the relative stability and the isomerization processes are examined. Hydrogen bonding between serine and the water molecule(s) may significantly affect the relative stability of conformers of the neutral serine–(H₂O)_n (n = 1, 2) clusters. The sidechain (OH group) in serine is found to have a profound effect on the structure and isomerization of serine–(H₂O)_n (n = 1, 2) clusters. Conformers with the hydrogen bonding between water and the hydroxyl group of serine are predicted. A detailed analysis is presented of the isomerization (proton transfer) pathways between the neutral serine–(H₂O)₂ and serine zwitterion–(H₂O)₂ clusters by carrying out the intrinsic reaction coordinate analysis. At least two water molecules need to bind to produce the stable serine zwitterion–water cluster in the gas phase. The isomerization for the serine–(H₂O)₂ cluster proceeds by the concerted double and triple proton transfer mechanism occurring via the binding water molecules, or via the hydroxyl group. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Computer-assisted study of characteristics of water clusters in the presence of nitrogen dioxide

The interaction of IR radiation with water clusters that have absorbed NO₂ molecules is studied by the molecular dynamics method in terms of the polarizable model. Induced dipole moments of H₂O and NO₂ molecules diminish during the addition of one to six NO₂ molecules to (H₂O)₅₀ cluster. The integral intensity of IR absorption by a system consisting of (NO₂) _i (H₂O)₅₀ heteroclusters with 1 ≤ i ≤ 6 decreases, whereas the power of heat emission rises as compared with an (H₂O) _n system. The decrease in the IR absorption and the increase in the IR emission by water clusters with the capture of NO₂ molecules are nonmonotonic. The absorption of NO₂ molecules by water clusters causes a noticeable reduction in the intensity of the first peak and the confluence of the fourth and fifth peaks in the Raman spectrum.     

Thermal decomposition of HfCl4 as a function of its hydration state

The thermogravimetric behavior of HfCl₄ powders with different hydration states has been compared. Strongly hydrated powders consist of HfOCl₂·nH₂O with n>4. Partially hydrated powders consist of particles with a HfCl₄ core and a hydrated outerlayer of HfOCl₂·nH₂O with n in the range of 0-8. Hydrated powders decomposed at temperature lower than 200 °C whereas the decomposition of partially hydrated powders was completed at a temperature of around 450 °C. The observed differences in decomposition temperature is related to the structure of HfOCl₂·nH₂O, which is different if n is higher or smaller than 4 and leads to intermediate compounds, which decompose at different temperatures.     

The investigation on the relative stability of different clusters of thiourea dioxide in water using gas phase quantum chemical calculations

The relative stability of different clusters of thiourea dioxide (TDO) in water is examined using gas phase quantum chemical calculations at the MP2 and B3LYP level with 6‐311++G(d,p) basis set. The possible equilibrium structures and other energetic and geometrical data of the thiourea dioxide clusters, TDO‐(H₂O)_n (n is the number of water molecules), are obtained. The calculation results show that a strong interaction exists between thiourea dioxide and water molecules, as indicated by the binding energies of the TDO clusters progressively increased by adding water molecules. PCM model is used to investigate solvent effect of TDO. We obtained a negative hydration energy of ?20.6 kcal mol^?1 and free‐energy change of ?21.0 kcal mol^?1 in hydration process. On the basis of increasing binding energies with adding water molecules and a negative hydration energy by PCM calculation, we conclude thiourea dioxide can dissolve in water molecules. Furthermore, the increases of the C? S bond distance by the addition of water molecules show that the strength of the C? S bonds is attenuated. We find that when the number of water molecules was up to 5, the C? S bonds of the clusters, TDO‐(H₂O)₅ and TDO‐(H₂O)₆ were ruptured. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Effect of microhydration on the atmospherically important metastable carbonyl sulfide anion: Structure,energetic, and infrared study

Structure, energetics, and vibrational frequency of the microhydrated carbonyl sulfide anion [OCS^?? (H₂O)_n (n = 1–6)] have been explored by the systematic ab initio study to have a comprehensive understanding about the hydration‐induced stabilization phenomenon of OCS^?. Water binds with the OCS^? in single hydrogen‐bonded (SHB) or double hydrogen‐bonded (DHB) fashion with O? H S and O? H O contacts. Maximum five water molecules can stay in a cyclic water network of these hydrated clusters forming interwater hydrogen bonding (IHB) with each other and out of this, maximum of two water molecules can bind directly to the OCS^? in (DHB) arrangement. The stabilization energy values of OCS^?? (H₂O)_n depict that ion–water interaction is significant up to four water molecules and beyond that OCS^? is stabilized by IHB between the water molecules. The CO stretching frequency of OCS^? gets red shifted, whereas CS stretching frequency gets blue shifted on hydration. Charge analysis of hydrated clusters of OCS^? indicates that negative charge moves toward oxygen from sulfur on hydration. © 2015 Wiley Periodicals, Inc.     

Application of FTIR spectroscopy in the study of lattice vibration for mixed crystals

FT-IR spectroscopy was utilized to characterize the structure hydration and dehydration of mucin in vitro. The results indicated that both the protein chain and carbohydrate moiety are hydrated with the water molecules. In addition, the hydration and dehydration mechanism of mucin are quite different in H₂O and D₂O media.     

A molecular dynamics study on Rh3+ hydration: development and application of a first principles hydrated ion–water interaction potential

The Rh³⁺ aquaion exhibits one of the largest residence times of water molecules in the first hydration shell. The extreme stability of this hexahydrated ion in water solutions makes Rh³⁺ an extremely suitable candidate to be studied using the hydrated ion model. According to this approach, the representative cationic entity in aqueous solution is the ion plus its first hydration shell (i.e. the hydrated ion) and not the bare ion. Our group has successfully applied that concept in the framework of classical statistical simulations based on first principles ion–water interaction potentials. The methodology is now applied to the [Rh(H₂O)₆]³⁺ case based on a previous generalization in which some of the contributions were found to be transferable among the cases already studied (Cr³⁺, Al³⁺, Mg²⁺, Be²⁺). In this contribution a flexible hydrate model is presented, in which rigid first-shell water molecules have rotational and translational degrees of freedom, allowing for internal dynamics of the hydrated ion entity. The potential presented is thoroughly tested by means of a set of molecular dynamics simulations. Structural, dynamical, energetic and spectroscopic information is retrieved from the simulations, allowing the estimation of properties such as ion hydration energy, vibrational spectra of the intermolecular modes, cation mobility, rotational dynamics of the hydrated ion and first-shell water molecules and residence times of the second-shell water molecules. Extension of the Ewald sum to terms r^–4, r^–6 and r^–7 is presented and applied to systems of different size ([Rh(H₂O)₆]³⁺+(n–6)H₂O, n=50, 100, 200, 500, 1000 and 2500) and cutoff radii.Contribution to the Jacopo Tomasi Honorary Issue     

Neutral 4‐phenyl‐1‐[phenyl(pyridin‐2‐yl)methylidene]semicarbazide and its salt forms with inorganic anions

Semicarbazones can exist in two tautomeric forms. In the solid state, they are found in the keto form. This work presents the synthesis, structures and spectroscopic characterization (IR and NMR spectroscopy) of four such compounds, namely the neutral molecule 4‐phenyl‐1‐[phenyl(pyridin‐2‐yl)methylidene]semicarbazide, C₁₉H₁₆N₄O, (I), abbreviated as HBzPyS, and three different hydrated salts, namely the chloride dihydrate, C₁₉H₁₇N₄O⁺·Cl^?·2H₂O, (II), the nitrate dihydrate, C₁₉H₁₇N₄O⁺·NO₃^?·2H₂O, (III), and the thiocyanate 2.5‐hydrate, C₁₉H₁₇N₄O⁺·SCN^?·2.5H₂O, (IV), of 2‐[phenyl({[(phenylcarbamoyl)amino]imino})methyl]pyridinium, abbreviated as [H₂BzPyS]⁺·X^?·nH₂O, with X = Cl^? and n = 2 for (II), X = NO₃^? and n = 2 for (III), and X = SCN^? and n = 2.5 for (IV), showing the influence of the anionic form in the intermolecular interactions. Water molecules and counter‐ions (chloride or nitrate) are involved in the formation of a two‐dimensional arrangement by the establishment of hydrogen bonds with the N—H groups of the cation, stabilizing the E isomers in the solid state. The neutral HBzPyS molecule crystallized as the E isomer due to the existence of weak π–π interactions between pairs of molecules. The calculated IR spectrum of the hydrated [H₂BzPyS]⁺ cation is in good agreement with the experimental results.     

Sequential bond energies of water to sodium glycine cation

Absolute bond dissociation energies of water to sodium glycine cations and glycine to hydrated sodium cations are determined experimentally by competitive collision-induced dissociation (CID) of Na⁺Gly(H₂O)_x, x = 1–4, with xenon in a guided ion beam tandem mass spectrometer. The cross sections for CID are analyzed to account for unimolecular decay rates, internal energy of reactant ions, multiple ion–molecule collisions, and competition between reaction channels. Experimental results show that the binding energies of water and glycine to the complexes decrease monotonically with increasing number of water molecules. Ab initio calculations at four different levels show good agreement with the experimental bond energies of water to Na⁺Gly(H₂O)_x, x = 0–3, and glycine to Na⁺(H₂O), whereas the bond energies of glycine to Na⁺(H₂O)_x, x = 2–4, are systematically higher than the experimental values. These discrepancies may provide some evidence that these Na⁺Gly(H₂O)_x complexes are trapped in excited state conformers. Both experimental and theoretical results indicate that the sodiated glycine complexes are in their nonzwitterionic forms when solvated by up to four water molecules. The primary binding site for Na⁺ changes from chelation at the amino nitrogen and carbonyl oxygen of glycine for x = 0 and 1 to binding at the C terminus of glycine for x = 2–4. The present characterization of the structures upon sequential hydration indicates that the stability of the zwitterionic form of amino acids in solution is a consequence of being able to solvate all charge centers.     

Hydration of gas-phase gramicidin S (M + 2H)2+ ions formed by electrospray: The transition from solution to gas-phase structure

The hydration of doubly protonated gas-phase ions of gramicidin S formed by electrospray ionization was investigated. Under “gentle” electrospray conditions, a near Gaussian distribution of (M + 2H + nH₂O)²⁺ ions with n up to 50 can be readily formed. These extensively hydrated gas-phase ions should have structures similar to those in solution. For intermediate extents of hydration, the “naked” or unsolvated ion is present in unusually high abundance. This is attributed to a competition between solvation of the charges by water vs intramolecular self-solvation via hydrogen bonding. In addition, “magic” numbers of attached water molecules are observed for n = 8, 11, and 14. These magic numbers are attributed to favorable arrangements of water molecules surrounding the charge and surface of the peptide in the gas phase. These results are indicative of a gentle stepwise transformation from the solution-phase structure of the ion to the preferred gas-phase structure as solvent evaporates from the hydrated ions.     

Supramolecular Open‐Framework of a Bipyridinium‐Carboxylate Based Copper Complex with High and Reversible Water Uptake

The rigid zwitterionic ligand 1,1′‐bis(4‐carboxylatphenyl)‐(4,4′‐bipyridinium) (pc1) and copper(II) ions give rise to a linear complex [Cu(pc1)₂(H₂O)₄]²⁺, which self assembles in a pseudo tetragonal supramolecular arrangement leading to the supramolecular open‐framework [Cu(pc1)₂(H₂O)₄](Cl)₂ · 8H₂O exhibiting an open structure including water molecules and chlorides in pores. The dehydration of this material occurs at relatively low temperature (70 °C) and results in structure modification accompanied by shrinking of the crystals. Characterization of the obtained material by FT‐IR spectroscopy reveals appearance of coordinated carboxylates groups, which may indicate the formation of coordination polymer after dehydration. Water adsorption (maximum uptake 0.23 g H₂O per g) on dehydrated material allows to restore the initial structure. A large hysteresis in water adsorption‐desorption isotherm is characteristic of a significant modification of the structure during the hydration‐dehydration cycle which is in line with the structural transition determined from thermodiffractometry and FT‐IR spectroscopy.     

Double resonance spectroscopy of different conformers of the neurotransmitter amphetamine and its clusters with water

In this paper the conformational landscape of amphetamine in the neutral ground state is examined by both spectroscopy and theory. Several spectroscopic methods are used: laser-induced fluorescence (LIF), resonance-enhanced two-photon ionization (R2PI), dispersed fluorescence and IR/R2PI hole burning spectroscopy. The latter two methods provide for the first time vibrationally resolved spectra of the neutral ground state of dl-amphetamine and the amphetamine–(H₂O)_1,2 complexes. Nine stable conformers of the monomer were found by DFT (B3LYP/6-311++G(d,p)) and ab initio (MP2/6-311++G(d,p)) calculations. For conformer analysis the vibrations observed in the IR/R2PI hole burning and dispersed fluorescence spectra obtained from single vibronic levels (SVLF) of a selected conformer were compared with the results of an ab initio normal mode analysis. By this procedure three S₀ → S₁ transitions in the R2PI spectrum were assigned to three different conformer structures. Another weak transition earlier attributed to another conformer could be assigned to a vibronic band of one of the three conformers. Furthermore spectra of amphetamine–(H₂O)_1,2 are tentatively assigned.     

Theoretical Study of the Dimerization of Chlorophyll (a) and Its Hydrates: Implication for Chlorophyll (a) Aggregation

Dimeric structures chlorophyll (a) (Chla) and their mono‐ and dihydrated have been suggested to play an important role in the mechanism of photoreaction center chlorophyll special pairs PSI and PSII. Despite their functional importance, the molecular basis structures for interacting two Chla molecules and the structural stabilization role of H₂O in the formation of hydrated Chla dimer complexes is poorly understood. In this article, the different coordination modes between two interacting Chla molecules and the configurational (orientation and distance) features between the dimer and bound H₂O molecules are characterized by means of super molecule approach the density functional theory DFT. An estimation of the thermodynamic quantities is made for Chla dimerization and hydration processes. The results indicate that structure including ester linkages via H₂O hydrogen bonding is the most favorable conformation for the dihydrated chlorophyll (a) dimer at B3LYP/6‐31G*‐DCP level of calculation. The dispersion interaction is shown to be of great significance for the Chla dimer stabilization. In aqueous nonpolar solvent, the thermodynamics show that Chla has a slightly stronger driving force for full hydration than for dimerization and that hydration of the dimers is rather weakly exergonic. The tetrahydrated dimers having a similar arrangement to that in crystals of ethyl chlorophyllide (a) dihydrate are found to be more stable than the Chla dihydrated dimer. The data underscore the key role of H‐bonding in the stability of Chla‐H₂O adducts and, in particular, the great importance of the Chla monomeric dihydrated species in the hydration and dimerization of Chla in aqueous media. Clearly, the Chla dihydrates (Chla‐2 H₂O) are found more stable than the monohydrates (Chla‐H₂O) and the Chla dimers (Chla₂), owing to a particular structure in which cooperative interactions occur between the H₂O molecules and Chla. Calculations also indicate that the most thermodynamically preferred pathway for the formation of Chla dimer hydrates can be represented by two steps: the first corresponds to the formation of Chla monomeric dihydrates and the second is the dimerization of the dihydrates on to tetrahydrated Chla dimers. These results allow to obtain a new possible pathway for Chla dimer formation processes and could provide new insights to the aggregation of chlorophyll (a) in solution.