Microsolvation effect and hydrogen-bonding pattern of taurine-water TA-(H2O)n (n = 1-3) complexes

The microsolvation of taurine (TA) with one, two or three water molecules was investigated by a density functional theory (DFT) approach. Quantum theory of atoms in molecules (QTAIM) analyses were employed to elucidate the hydrogen bond (H-bond) interaction characteristics in TA-(H₂O)_n (n = 1–3) complexes. The results showed that the intramolecular H-bond formed between the hydroxyl and the N atom of TA are retained in most TA-(H₂O)_n (n = 1–3) complexes, and are strengthened via cooperative effects among multiple H-bonds from n = 1–3. A trend of proton transformation exists from the hydroxyl to the N atom, which finally results in the cleavage of the origin intramolecular H-bond and the formation of a new intramolecular H-bond between the amino and the O atom of TA. Therefore, the most stable TA-(H₂O)₃ complex becomes a zwitterionic complex rather than a neutral type. A many-body interaction analysis showed that the major contributors to the binding energies for complexes are the two-body energies, while three-body energies and relaxation energies make significant contributions to the binding energies for some complexes, whereas the four-body energies are too small to be significant.     

Microsolvation of aminoethanol: a study using DFT combined with QTAIM

The microsolvation of aminoethanol (AE) with one, two, three or four water molecules was investigated using a density functional theory (DFT) approach. Quantum theory of atoms in molecules (QTAIM) analyses were employed to elucidate the hydrogen-bonding characteristics of AE–(H₂O) _n (n = 1–4) complexes. The results showed that AE tends to break its intramolecular OH^AE···N^AE hydrogen bond (H-bond) upon microsolvation and form intermolecular H-bonds with water molecules, while complexes that retain the intramolecular OH^AE···N^AE H-bond show reduced stabilities. The intermolecular H-bond that forms between the nitrogen atom of AE and the hydroxyl of a water molecule is the strongest one for the most stable AE–(H₂O) _n (n = 1–4) complexes, and as n increases from 1 to 4 they grow stronger. The partial covalent character of this H-bond was confirmed by QTAIM analyses. Many-body interaction analysis showed that the relaxation energies and two- and three-body energies make significant contributions to the binding energies of the complexes.     

Associate Hydrations and Energies of Nucleotide Bases as Revealed by Low-Temperature Field Ionization Mass-Spectrometric Data

Abstract

The formation of water clusters, polyhydrates of nucleotide bases and their associates during simultaneous condensation of water and base molecules in vacuo onto a surface of a needle emitter cooled to 170 K was studied by field ionization mass spectrometry. It was found that different emitter temperatures are characterized by a specific distribution of intensities of cluster currents, depending on the number of water molecules in clusters. These distributions correlate with structural peculiarities and the relative energetics of formation of water clusters, polyhydrates of nucleotide bases and their associates at low temperature. The features observed in mass spectra for clusters m⁹Ade (H₂O)₅, m¹Ura (H₂O)₄ and m⁹Ade m¹Ura (H₂O)₂ are treated as a result of formation of energetically favorable structures stabilized by H-bonded bridges of water molecules.

The relative association constants and formation enthalpies of the noncomplementary pairs Ade Cyt, Gua Ura and the associates which model the aminoacid-base complexes m¹Ura Gin and m₂ ^1,3Thy Gin were determined from the temperature dependencies of the intensities of mass spectra peaks in the range 290–320 K.     

Theoretical studies on the structures,intra- and inter-molecular hydrogen bonding interactions in HNF and HNF–H2O clusters in the gaseous,aqueous and solid phases

Hydrazimium nitroformate ([N₂H₅]⁺[C(NO₂)₃]^? , HNF) is an ionic oxidiser used in solid propellants. Its properties are easily affected by H₂O because of its hygroscopicity. In this article, density functional theory (DFT) and molecular dynamics (MD) were employed to study the isolated HNF molecule and the HNF–H₂O cluster in gas phase and in the aqueous solution. Three stable conformations were obtained for HNF in the gas phase and in the aqueous solution, respectively, and each conformation can form several different HNF–H₂O clusters. Irrespective of whether it is in gas phase or in solution, intramolecular hydrogen bond interactions and other interactions (e.g. the binding energy, the dispersion energy, the second-order perturbation energy and the energy gap between frontier orbitals) of HNF are weaker in the clusters than in the isolated state. The initial decomposition energy of the cluster is lower than that of the isolated HNF molecule in both gaseous and aqueous phases, while the dissociation processes are the same. Molecular dynamic simulations showed that the clustered H₂O elongates and weakens the C–NO₂ bond in the solid HNF–H₂O cluster compared with that in the solid HNF. H₂O reduces and weakens intramolecular N–HΛO bonds too, and O–HΛN is the dominant intermolecular hydrogen bond between HNF and H₂O.     

1H NMR conformational study of sulfated and non-sulfated cholecystokinin fragment CCK27–33: Influence of the sulfate group on the peptide folding

¹H NMR study of cholecystokinin fragment (CCK_27–33) in (C²H₃)₂SO and in ²H₂O at different pH shows that sulfated (CCK₇) and non sulfated (NS-CCK₇) peptides are under preferentially folded conformations characterized by a β-turn including the sequence Gly-Trp-Met-Asp with a H-bond between the CO of Gly and the NH of Asp. This structure is probably stabilized by an ionic interaction between Tyr and Asp. Moreover, the N-terminal part of CCK₇ forms a C₇ structure with a weak H-bond between the CO of Gly and the NH of Trp. In this model all CCK₇ hydrophobic side chains are in close vicinity, far from the hydrophilic sulfate group. Full interaction with brain CCK₈ receptors could require both the sulfate group and the maintening of conformational constraints.     

Synthesis, X-ray crystal structures and spectroscopic properties of two Ni(II) complexes of pyridoxal Schiff’s bases with diamines: Importance of steric factor in stabilization of water helices in the lattices of metal complex

Two Ni(II) complexes of the ligands N,N′-dipyridoxylethylenediimine (L₁H₂) and N,N′-dipyridoxyl-1,3-propanediimine (L₂H₂) were synthesized and their structures were determined by X-ray crystallography. The complexes are of formula Ni(L₁). 3H₂O (1·3H₂O) and Ni(L₂) (2). Both the complexes were found to be luminescent, but the quantum yields are significantly low compared to those of free ligands or their Zn(II) complexes. In 1·3H₂O the metallo-organic fragment forms a staircase like network and three water molecules occupy the void space created by the staircase like network. The water molecules are strongly H-bonded between themselves forming a helical chain along ‘b’ axis. Complex 2, in spite of having same number of hydrogen bonding sites as that of 1, can not accommodate water clusters in their lattice. It is argued, that small steric factors, which may affect conformations of the hydrogen donor/acceptor sites, plays an important role in stabilization of water helices in lattices of metal complex.     

Molecular dynamics and quantum chemical studies of solvent effects on cyclo glycylglycine and glycylalanine dipeptides

Hydrogen bond (H-bond) interactions between the two cyclo dipeptides, cyclo(glycyl-glycine) (CGG) and cyclo(glycyl-alanine) (CGA), and water have been studied using molecular dynamics (MD) and quantum chemical methods. The MD studies have been carried out on CGG and CGA in water using fixed charge force field (AMBER ff03) for over 10 ns with a MD time step of 2 fs. The results of this study show that the solvation pattern influences the conformations of the cyclo dipeptides. Following molecular simulations, post Hartree–Fock and density functional theory methods have been used to explore the molecular properties of the cyclo dipeptides in gaseous and aqueous phase environments. The self-consistent reaction field theory has been used to optimise the cyclopeptides in diethyl ether (? = 4.3) and water (? = 78.5), and the solvent effects have been analysed. A cluster of eight water molecules leads to the formation of first solvation shell of CGG and CGA and the strong H-bonding mainly contributes to the interaction energies. The H-bond interactions have been analysed by the calculation of electron density ρ(r) and its Laplacian ▽²ρ(r) at bond critical points using atoms in molecules theory. The natural bond orbital analysis was carried out to reveal the nature of H-bond interactions. In the solvated complexes, the keto carbons registered the maximum NMR chemical shifts.     

Ab initio investigations on planar (MgO)n clusters (n = 1–5) and their hydrogen adsorption behaviour

Ab initio calculations (B3LYP and PBE-D3) of the structures, stabilities, vibrational, electronic and hydrogen adsorption behaviour of (MgO)_n clusters are performed using 6-311+ + G(d,p) basis set. The planar (MgO)_n clusters are found to be global minima for n ≤ 3 and local minima for n = 4 and 5. In addition, we have also analysed global minimum structures of (MgO)₄ and (MgO)₅. The binding energies suggest that their stabilities increase successively. Vibrational frequencies and IR intensities further support the enhanced stability with an increase in the size of (MgO)_n clusters. The highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) surfaces are used to explain and discuss the electronic properties. Finally, we have demonstrated hydrogen storage capacity of (MgO)_n clusters, considering hydrogen adsorption on planar as well as global minimum (MgO)₄ and (MgO)₅ clusters. We have noticed that four and five H₂ molecules can be easily adsorbed by (MgO)₄ and (MgO)₅ clusters having adsorption energy of 0.13–0.14 eV with mass ratio of 4.76%. Thus, the present study is expected to motivate further the applications of small clusters for efficient hydrogen energy storage.     

Synthesis, structure and thermal behaviour of two magnesium complexes containing the 1,4-bis(5-tetrazolyl)benzene ligand

The reaction between the 1,4-bis(5-tetrazolyl)benzene ligand (H₂btb) and different magnesium salts allowed the recovery of two different molecular salts, namely [Mg(H₂O)₆](btb) (1) and [Mg(H₂O)₆](Hbtb)₂·2H₂O (2). These crystalline materials were fully characterized by spectroscopic, thermal and diffraction methods. In both cases the octahedrally coordinated hexaaquo Mg(II) ions are linked through several strong H-bond interactions of the OH?N type to the btb anions, completely or partially deprotonated in 1 and 2, respectively. The thermal analysis has established that, in both cases, all water molecules are lost below 200 °C. Interestingly, the process is completely reversible upon exposure to water-saturated atmosphere. Unfortunately, the anhydrous phases are amorphous, and no structural information could be derived form our PD traces, even if a number of partially crystalline intermediates, formed during the dehydration processes, were observed by thermodiffractometric methods.     

Phospholipid hydration studied by deuteron magnetic resonace spectroscopy

Deuteron magnetic resonance spectra were obtained from ²H₂O in mixtures with egg lecithin, egg phosphatidylethanolamine, and ox brain sodium phosphatidylserine. The acid form of phosphatidylserine does not hydrate. Details of the different hydration “shells” were obtained by studying the spectral splittings as a function of ²H₂O concentration. Several different types of water are present, including bulk water (exchanging only slowly with water associated with the lipid), “trapped” water (not present with phosphatidylethanolamine), and up to three types of bound water. The spectral splittings characteristic of each water environment yielded information about the water binding energies and degrees of anisotropy of motion of the phospholipid polar groups; lecithin polar groups have least motional restriction and sodium phosphatidylserine most, while phosphatidylethanolamine binds water most tightly.Spectra of some lecithin and phosphatidylserine dispersions varied with time, due to a slow reorganization of randomly oriented multilamellar regions into longer, more ordered systems, with a length of about 1 μm. At ?20°C the timescales of the change were of the order of a week and a month for lecithin and phosphatidylserine respectively.Complex changes in the spectra were observed as the temperature was raised; these are interpreted in terms of changes in the motions of the phospholipid molecules.     

The polythiophene molecular segment as a sensor model for H<Subscript>2</Subscript>O,HCN, NH<Subscript>3</Subscript>, SO<Subscript>3</Subscript>, and H<Subscript>2</Subscript>S: a density functional theory study

Studying the interaction of some atmospheric gases (H₂O, HCN, NH₃, SO₃ and H₂S) with 3PT oligomers is important in the development of polymeric sensors for gas detection. In the present study, we studied the relaxed geometries, interaction energies, charge analysis, HOMO–LUMO orbital analysis, and UV–vis spectra of all interacted systems using first-principles density functional theory (DFT). All these analyses indicated the potential of polythiophene as an inexpensive polymeric sensor for the analytes mentioned. Interaction energy values of ?19.90, ?19.66, ?14.01, ?8.70, and ?4.76 kJ mol^?1 were achieved for adsorption of SO₃, H₂O, NH₃, HCN, and H₂S on 3PT, respectively. Consequently, clarification of their physical parameters became the major focus of this study.     

Studies of NAD(H) conformations in solution: A new method using the PMR spectra of cobalt ion—dinucleotide complexes

In aqueous solutions of NAD(H), there is an equilibrium between two different conformations : a “folded” conformation in which adenine and nicotinamide are staked together and an “unfolded” conformation in which the two rings are without interaction.The folded conformation is the more stable in aqueous solution whereas in organic solution it is the unfolded one.As we have previously shown, the PMR spectra of Co²⁺—NAD(H) complexes may be related with the coenzyme conformation giving suggest to a new method for NAD(H) conformational analysis.The results of this method applied to methanol ²H₂O and dioxane/²H₂O solutions are reported in this paper: they are in good accordance with those of spectrofluorimetric analysis.     

A theoretical investigation on the proton transfer tautomerization mechanisms of 2-thioxanthine within microsolvent and long range solvent

A relative complete study on the mechanisms of the proton transfer reactions of 2-thioxanthine was carried out with density functional theory. The models were designed with monohydrated and dihydrated microsolvent catalyses either with or without the presence of water solvent considered with the polarized continuum model (PCM). A total number of 114 complexes and 67 transition states were found with the B3LYP/6-311+G** calculations. The energies were refined with both B3LYP/aug-cc-pVTZ and PCM-B3LYP/aug-cc-pVTZ methods. The activation energies were reported with respect to the Gibbs free energies obtained in conjunction with the standard statistical thermodynamics. Possible reaction pathways were confirmed with the intrinsic reaction coordinates. Pathways via C8 atom on the imidazole ring, via the bridged C4 and C5 atoms between pyrimidine and imidazole rings and via N, O and S atom on the pyrimidine ring were examined. The results show that the most feasible pathway is the proton transfers within the long range solvent surrounding via the N, O and S atoms in the pyrimidine ring with di-hydrated catalysis: N(7)H?+?2H₂O?→?IM89?→?IM90?→?P13?+?2H₂O?→?IM91?→?IM92?→?P6?+?2H₂O?→?IM71?→?IM72?→?P7?+?2H₂O?→?IM107?→?IM108?→?P18?+?2H₂O?→?IM111?→?IM112?→?P19?+?2H₂O?→?IM113?→?IM114?→?P17?+?2H₂O?→?IM105?→?IM106?→?N(9)H?+?2H₂O that has the highest energy barrier of 44.0 kJ mol^?1 in the transition of IM89 to IM90 via TS54. The small energy barrier is in good agreement with the experimental observation that 2-TX tautomerizes at room temperature in water. In the aqueous phase, the most stable intermediate is found to be IM21 [N(7)H?+?2H₂O] and the possible co-existing species are the monohydrated IM1, IM9, IM39 and IM46, and the di-hydrated IM5, IM8, IM13, IM16, IM81, IM89, IM90, IM91 and IM106 complexes that have a relative concentration larger than 10^?6 (1 ppm) with respect to IM21.

Mechanism of protonation of the over-reduced Mn4CaO5 cluster in photosystem II

Based on characterization by X-ray absorption spectroscopy, it has been proposed that the Mn₄CaO₅ cluster in the crystal structure of the water-oxidizing enzyme, photosystem II (PSII), may represent an over-reduced form arising from reduction by the X-ray beam. Using a quantum mechanical/molecular mechanical approach, and assuming that all of the μ-oxo bridges are deprotonated in S₁, we analyzed the reduction process of the Mn₄CaO₅ cluster. In the crystal structure, the O atom (O5), which is linked with three Mn atoms and one Ca atom, has no H-bond. When reduced to S_–2, unexpectedly, a water molecule at Ca²⁺ (W3) reoriented itself, formed a H-bond with O5, and released a proton to O5, resulting in formation of OH⁻ at both W3 and O5. Once generated, the OH⁻ group at O5 was stable, because the W3…O5 H-bond had already disappeared. A weak binding of H₂O at Ca²⁺ led W3 to reorient and serve as a proton donor to O5 upon over-reduction.     

The influences of water solvent on the structures and stabilities of Na+–AD conformers

The influences of water solvent on the structures and stabilities of the complex ion conformers formed by the coordination of alanine dipeptide (AD) and Na⁺ have been investigated using supramolecular and polarizable continuum solvation models at the level of B3LYP/6-311++G**, respectively; 12 monohydrated and 12 dihydrated structures of Na⁺–AD complex ion were obtained after full geometrical optimization. The results showed that H₂O molecules easily bind with Na⁺ of Na⁺–AD complex ion, forming an ion-lone pair interaction with the Na–O bond length of 2.1–2.3 Å. Besides, H₂O molecules also can form hydrogen bonds O_W–H_W···O(1), O_W–H_W···O(2), N(1)–H(1)···O_W or N(2)–H(2)···O_W with O or N groups of the Na⁺–AD backbone. The most stable gaseous bidentate conformer C7AB of Na⁺–AD is still the most stable one in the solvent of water. However, the structure of the most unstable gaseous conformer α′B of Na⁺–AD collapses under the attack of H₂O molecules and changes into C7AB conformation. Computations with IEFPCM solvation model of self-consistent reaction field theory give that aqueous C5A is more stable than C7_eqB and that the stabilization energies of water solvent on monodentate conformers of Na⁺–AD complex ion (about 272–294 kJ/mol) are more than those on bidentate ones (about 243 kJ/mol).     

Thermal perturbation difference spectra and D2O vs H2O isothermal difference spectra of protein-model aromatic chromophores.

The thermal perturbation difference spectra of phenolic and indolic chromophores in water resemble the isothermal D₂O and H₂O spectra of these chromophores. For phenols approximately equal Δ? values are obtained in both types of spectra, but for their methyl ethers Δ? values of D₂O vs H₂O spectra are about half of those of the thermal perturbation spectra. Phenols and their methyl ethers were studied in deuterated ethylene glycol and glycerol vs the corresponding protiated solvent, and in nonprotic solvents containing 0.25–4% D₂O or H₂O. For phenols in D₂O vs H₂O, about one-third to one-half of the difference spectrum is attributed to solvent structure difference, and the remainder to the effects of replacing OH by OD and to differences in accepting hydrogen bonds from D₂O and H₂O. The refractive index difference between D₂O and H₂O was shown to be a minor contribution by means of experiments in which D₂O was at 5 dgC and H₂O at 47 dgC, conditions of equal refractive index (Na_D). D₂O vs H₂O and glycerol-d vs glycerol-h difference spectra of ribonuclease are about twice as large as expected from the known number of exposed tyrosyl side chains. Possible sources of error in D₂O vs H₂O spectra of proteins are discussed.     

Structures and excitation energies of ozone-water clusters O3(H2O)n (n = 1-4)

Hybrid density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations have been carried out for ozone-water clusters O₃(H₂O)_n (n = 1-4) in order to obtain hydration effects on the absorption spectrum of ozone. The first water molecule in n = 1 is bound to the ozone molecule by an oxygen orientation form in which the oxygen atom of H₂O orients the central oxygen atom of O₃. In n = 2, the water dimer is bound to O₃ and then the cyclic structure is formed as the most stable structure. For n = 3 (or n = 4), the cyclic water trimer (or tetramer) is bound by a hydrogen bond to the ozone molecule. The TD-DFT calculations of O₃(H₂O)_n (n = 0-4) show that the first and second excitation energies of O₃ are blue-shifted by the interaction with the water clusters. The magnitude of the spectral shift is largest in n = 2, and the shifts of the excitation energies are +0.07 eV for S₁ and +0.13 eV for S₂ states. In addition to the spectral shifts (S₁ and S₂ states), it is suggested that a charge-transfer band is appeared as a low-lying excited state above the S₁ and S₂ states. The origin of the spectrum shifts was discussed on the basis of theoretical results.     

A polyethylene-glycol-functionalized ring-like isopolymolybdate cluster

A new organic-inorganic hybrid compound, Na₆[HO(CH₂CH₂O)₄H]₃{Mo₃₆O₁₀₈(H₂O)₁₄(OH)₆[HO(CH₂CH₂O)₃H]₂} · ∼75H₂O (1) has been obtained in polyethylene glycol (PEG)/H₂O system with a good yield, and characterized by element analysis, IR, UV, TG, ¹³C NMR spectroscopy, electrochemistry and X-ray single crystal diffraction analysis. Compound 1 consists of the {Mo₃₆} clusters as the structural motif covalently decorated by PEG fragments. Such hybrid polyoxoanions are linked by Na⁺ counter-cations, leading to one-dimensional chains. The adjacent chains are closely packed together into a three-dimensional supramolecular framework via extensive H-bonding interactions among polyoxoanions and the isolated water molecules.     

All-electron scalar relativistic calculation of water molecule adsorption onto small gold clusters

An all-electron scalar relativistic calculation was performed on Au _n H₂O (n = 1–13) clusters using density functional theory (DFT) with the generalized gradient approximation at PW91 level. The calculation results reveal that, after adsorption, the small gold cluster would like to bond with oxygen and the H₂O molecule prefers to occupy the single fold coordination site. Reflecting the strong scalar relativistic effect, Au _n geometries are distorted slightly but still maintain a planar structure. The Au–Au bond is strengthened and the H–O bond is weakened, as manifested by the shortening of the Au–Au bond-length and the lengthening of the H–O bond-length. The H–O–H bond angle becomes slightly larger. The enhancement of reactivity of the H₂O molecule is obvious. The Au–O bond-lengths, adsorption energies, VIPs, HLGs, HOMO (LUMO) energy levels, charge transfers and the highest vibrational frequencies of the Au–O mode for Au _n H₂O clusters exhibit an obvious odd-even oscillation. The most favorable adsorption between small gold clusters and the H₂O molecule takes place when the H₂O molecule is adsorbed onto an even-numbered Au _n cluster and becomes an Au _n H₂O cluster with an even number of valence electrons. The odd–even alteration of magnetic moments is observed in Au _n H₂O clusters and may serve as material with a tunable code capacity of “0” and “1” by adsorbing a H₂O molecule onto an odd or even-numbered small gold cluster.     

Hydrothermal synthesis and crystal structure of a novel one-dimensional arsenic vanadate decorated with organonitrogen ligand: [H3V3O26(AsO4)4(phen)8(H2O)2] · 2H2O (phen=phenanthroline)

A novel organic-inorganic hybrid vanadium arsenate [H₃V₃O₂₆(AsO₄)₄(phen)₈(H₂O)₂] · 2H₂O 1 (phen=phenanthroline) was synthesized by the hydrothermal reaction of V₂O₅, VOSO₄, Na₂HAsO₄ · 7H₂O, phen and water. Its structure was determined by elemental analyses, XPS spectra, EPR spectrum, TG analysis, IR spectrum and single-crystal X-ray diffraction.