Associate hydrations and energies of nucleotide bases as revealed by low-temperature field ionization mass-spectrometric data

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 Gln and m1.3(2)Thy Gln were determined from the temperature dependencies of the intensities of mass spectra peaks in the range 290-320 K.     

Hydration of complementary 9-methyladenine.1-methyluracil pairs at low temperatures according to data from field mass spectrometry

The hydration of nucleotide bases of m9Ade(A), m1Ura(U) and a complementary pair A.U was studied by field ionization mass-spectrometry at room and low (170 K) temperatures in vacuum. Enthalpies of A.U-pair formation and its monohydrate A.U(H2O) were measured using temperature dependences of association constants. From the analysis of intensities of mass-spectrum peaks, corresponding to monohydrates U(H2O), A(H2O), A.U(H2O), A.U-pair and initial components A, U, and also measured enthalpies it is supposed that monohydration of bases A and U essentially prevents the formation of the coplanar pair A.U. A qualitative information about the structure and energetics of hydrate clusters A(H2O)n, U(H2O)n and A.U(H2O)n for n = 1 divided by 7 was obtained from low temperature mass-spectra. The observed peculiarities in hydrate structures A(n = 5), U(n = 4), A.U(n = 4) are treated as a consequence of cyclization of water molecules around bases.     

Transition of stable isotope ratios of leaf water under simulated dew formation

Dew formation, a common meteorological phenomenon, is expected to intensify in the future. Dew can influence the H₂¹⁸O and HDO isotopic compositions of leaf water (δ_L), but the phenomenon has been neglected in many experimental and modelling studies. In this study, the dew effect on δ_L was investigated with a dark plant chamber in which dew formation was introduced. The H₂¹⁸O and HDO compositions of water vapour, dew water and leaf water of five species were measured for up to 48 h of dew exposure. Our results show that the exchanges of H₂¹⁸O and HDO in leaf water with the air continued in the darkness when the net H₂¹⁶O flux was zero. Our estimates of the leaf conductance using the isotopic mass balance method ranged from 0.035 to 0.087 mol m^?2 s^?1, in broad agreement of the night‐time stomatal conductance reported in the literature. In our experiments, the conductance of the C₄ species was 0.04 ± 0.01 mol m^?2 s^?1 and that of the C₃ plants was 0.10 ± 0.04 mol m^?2 s^?1. At the end of 16 h dew exposure, 72 (±17) and 94 (±11)% of the leaf water came from dew according to the ¹⁸O and D tracer, respectively.     

3D hydrogen bonded metal-organic frameworks constructed from [M(H2O)6][M′(dipicolinate)2] · mH2O (M/M′ = Zn/Ni or Ni/Ni). Identification of intercalated acyclic (H2O)6/(H2O)10 clusters

New heterodinuclear Zn^II/Ni^II (1) and homodinuclear Ni^II/Ni^II (2) water-soluble and air stable compounds of general formula [M(H₂O)₆][M′(dipic)₂] · mH₂O have been easily prepared by self-assembly of the corresponding metal(II) nitrates with dipicolinic acid (H₂dipic) in water solution at room temperature.  The compounds have been characterized by IR, UV/Vis and atomic absorption spectroscopies, elemental and X-ray single crystal diffraction (for 1 · 4H₂O and 2 · 5H₂O) analyses.  3D infinite polymeric networks are formed via extensive hydrogen bonding interactions involving all coordinated and crystallization water molecules, and all dipicolinate oxygens, thus contributing to additional stabilization of dimeric units, metal-organic chains and 2D layers.  In 1 · 4H₂O, the latter represent a rectangular-grid 2D framework with multiple channels if viewed along the c crystallographic axis, while in 2 · 5H₂O intercalated crystallization water molecules are associated to form acyclic nonplanar hexameric water clusters and water dimers which occupy voids in the host metal-organic matrix, with a structure stabilizing effect via host-guest interactions.  The hexameric cluster extends to the larger (H₂O)₁₀ one with an unusual geometry (acyclic helical octamer with two pendent water molecules) by taking into account the hydrogen bonds to water ligands in [Ni(H₂O)₆]²⁺.  The obtained Zn/Ni compound 1 relates to the recently reported family of heterodimetallic complexes [M(H₂O)₅M′(dipic)₂] · mH₂O (M/M′ = Cu/Co, Cu/Ni, Cu/Zn, Zn/Co, Ni/Co, m = 2, 3), what now allows to establish the orders of the metal affinity towards the formation of chelates with dipicolinic acid (Co^II > Ni^II > Zn^II > Cu^II) or aqua species (Co^II < Ni^II < Zn^II < Cu^II).     

Kinetics of Energetic O<Superscript>−</Superscript> Ions in the Discharge Plasmas of Water Vapor and H<Subscript>2</Subscript>O-Containing Mixtures

The process of relaxation of energetic O^– ions formed via dissociative attachment of electrons to molecules in the discharge plasmas of water vapor and H₂O: O₂ mixtures in a strong electric field is studied by the Monte Carlo method. The probability of energetic ions being involved in threshold ion–molecular processes is calculated. It is shown that several percent of energetic O^– ions formed via electron attachment to H₂O molecules in the course of plasma thermalization transform into OH^– ions via charge exchange or are destroyed with the formation of free electrons. The probabilities of charge exchange of O^– ions and electron detachment from them increase significantly (up to 90%) when O^– ions are formed via electron attachment to O₂ molecules in water vapor with an oxygen additive. This effect decreases with increasing oxygen fraction in the mixture but remains appreciable even when the fraction of H₂O molecules in the H₂O: O₂ mixture does not exceed several percent.     

Aromaticity of azines through dyotropic double hydrogen transfer reaction

The thermodynamic stabilities and IR spectra of the three water clusters (H₂O)_20, (H₂O)_54,, and (H₂O)₁₀₀ are studied by quantum-chemical computations. After full optimization of the (H₂O)_20,54,100 structures using the hybrid density functional B3LYP together with the 6-31+G(d,p) basis set, the electronic energies, zero-point energies, internal energies, enthalpies, entropies, and Gibbs free energies of the water clusters at 298 K are investigated. The OH stretching vibrational IR spectra of (H₂O)_20,54,100 are simulated and split into sub-spectra for different H-bond groups depending on the conformations of the hydrogen bonds. From the computed spectra the different spectroscopic fingerprint features of water molecules in different H-bond conformations in the water clusters are inferred.     

Ab initio and density functional theory (DFT) studies on triflic acid with water and protonated water clusters

The structure, stability and infrared spectral signatures of triflic acid (TA) with water clusters (W_n) and protonated water clusters (TAH⁺W_n, n?=?1???6) were computed using DFT and MP2 methods. Our calculations show that a minimum of three water molecules are necessary to stabilize the dissociated zwitterionic form of TA. It can be seen from the results that there is no significant movement of protons in smaller (n?=?1 and 2) and linear (n?=?1 – 6) types of water clusters. Further, the geometries of TAW_n clusters first form a neutral pair (NP) to contact ion pair (CIP), then form a solvent separated ion pair (SSIP) in a water hexamer. These findings reveal that proton transfer may take place through NP to CIP and then CIP to SSIP. The calculated binding energies (BEs) of ion pair clusters is always higher than that of NP clusters (i.e., more stable than the NP). Existing excess proton linear chain clusters transfer a proton to adjacent water molecules via a Grotthuss mechanism, whereas the same isomers in the branched motifs do not conduct protons. Examination of geometrical parameters and infrared frequencies reveals hydronium ion (H₃O⁺ also called Eigen cation) formation in both TAW_n and protonated TAW_n clusters. The stability of Eigen water clusters is three times higher than that of other non-Eigen water clusters. Our study shows clearly that formation of ion pairs in TAW_n and TAH⁺W_n clusters greatly favors proton transfer to neighboring water molecules and also enhances the stability of these complexes.     

Theoretical Study of the Water Exchange Reaction on Divalent Zinc Ion using Density Functional Theory

Recent ab initio studies reported in the literature have challenged the mechanistic assignments made on the basis of volume of activation data [1,2]. In addition to that ab initio molecular orbital calculations on hydrated zinc(II)-ions were used to elucidate the general role of this ion in metalloproteins [3]. Due to our interest in both inorganic reaction mechanisms and enzymatic catalysis we started a systematic investigation of solvent exchange processes on divalent zinc-ion using density functional calculations. Our investigations cover aqua complexes of the general form [Zn(H₂O)_n]²⁺·mH₂0 with n=3-6 and m=0-2, where n and m represent the number of water molecules in the coordination and solvation sphere, respectively.The complexes [Zn(H₂O)₅]²⁺·2H₂O and [Zn(H₂O)₄]²⁺·2H₂O turnend out to be the most stable zinc complexes with seven and six water molecules, respectively. This implies that a heptacoordinated zinc(II) complex, where all water molecules are located in the co-ordination sphere, should be energetically highly unfavorable and that [Zn(H₂O)₆]²⁺ can quite readily push two coordinated water molecules into the solvation sphere. For the pentaqua complex [Zn(H₂O)₅]²⁺ only one water molecule is easily lost to the solvation sphere, which makes the [Zn(H2O)₄]²⁺·H₂O complex the most favorable in order to consider the limiting dissociative and associative water exchange process of hexacoordinated zinc(II). The dehydration and hydration energies using the most stable zinc(II) complexes [Zn(H₂O)₄]²⁺·2H₂O, [Zn(H₂O)₅]²⁺·2H₂O and [Zn(H₂O)₄]²⁺·H₂O were calculated to be 24.1 and -21.0 kcal/mol, respectively.     

Water: Nanostructure and fluctuations

Recently a model of local organization of water was experimentally justified, in which tetrahedrally coordinated water clusters of 1–2 nanometers arise and disappear in liquid composed of H₂O molecules with partially broken hydrogen bonds [1, 2]. Here we show that the clusters can oscillate between two structural forms, of which one is common hexagonal ice I_h whereas another is formed of the modules participating in formation of hydration shells of biomolecules. It is suggested that such self-oscillations are responsible for observable fluctuations of various physical and chemical parameters of water.     

Effects of deuterium oxide on growth, proton extrusion, potassium influx, and in vitro plasma membrane activities in maize root segments

Elongation of subapical segments of maize (Zea mays) roots was greatly inhibited by ²H₂O in the incubation medium. Short-term exposure (30 min) to ²H₂O slightly reduced O₂ uptake and significantly increased ATP levels. ²H₂O inhibited H⁺ extrusion in the presence of both low (0.05 mm) and high (5 mm) external concentrations of K⁺ (about 30 and 53%, respectively at 50% [v/v] ²H₂O). Experiments on plasma membrane vesicles showed that H⁺-pumping and ATPase activities were greatly inhibited by ²H₂O (about 35% at 50% [v/v] ²H₂O); NADH-ferricyanide reductase and 1,3-β-glucan synthase activities were inhibited to a lesser extent (less than 15%). ATPase activities present in both the tonoplast-enriched and submitochondrial particle preparations were not affected by ²H₂O. Therefore, the effect of short incubation time and low concentration of ²H₂O is not due to a general action on overall cell metabolism but involves a specific inhibition of the plasma membrane H⁺ -ATPase. K⁺ uptake was inhibited by ²H₂O only when K⁺ was present at a low (0.05 mm) external concentration where absorption is against its electrochemical potential. The transmembrane electric potential difference (E_m) was slightly hyperpolarized by ²H₂O at low K⁺, but was not affected at the higher K⁺ concentrations. These results suggest a relationship between H⁺ extrusion and K⁺ uptake at low K⁺ external concentration.     

Components and fractions for differently bound water molecules of dipalmitoylphosphatidylcholine-water system as studied by DSC and H-NMR spectroscopy

Differently bound water molecules of dipalmitoylphosphatidylcholine (DPPC)-H₂O system were investigated with differential scanning calorimetry (DSC). According to a method previously reported by us, the ice-melting DSC curves of the DPPC-H₂O samples of varying water contents were deconvoluted into multiple components, and the ice-melting enthalpies for the individual deconvoluted components were used to estimate average molar ice-melting enthalpies for freezable interlamellar and bulk waters, respectively. With these average molar ice-melting enthalpies, the numbers of differently bound water molecules of the DPPC-H₂O system were calculated at varying water contents and were used to construct a water distribution diagram of this system. Furthermore, to evaluate the reliability of the present DSC deconvolution method, ²H-NMR T₁ measurements of DPPC-²H₂O system were carried out at 5 °C of the gel phase temperature, and components and fractions for differently bound water (²H₂O) molecules were estimated from the analysis of nonexponential magnetization recovery curves.     

X-ray crystal and molecular structures of the Ni(II) and Co(II) complexes of 2'-deoxyguanosine-5'-monophosphate.

The structures of [Ni(5′-dGMP)(H₂O)₅] and [Co(5′-dGMP)(H₂O)₅] have been solved by single-crystal x-ray diffraction techniques. Their common geometry consists of a metal ion octahedrally coordinated to the N₇ atom of guanine and five water ligands. The phosphate group of the nucleotide is hydrogenbonded to two of the coordinated water molecules.     

Effect of pH on H-2H exchange,H2 production and H2 uptake,catalysed by the membrane-bound hydrogenase of Paracoccus denitrificans

(1) The kinetics of isotope exchange catalysed by the membrane-bound hydrogenase of Paracoccus denitrificans have been studied by measuring H²H, H₂ or ²H₂ produced when the enzyme catalyses the exchange between ²H₂ and H₂O or H₂ and ²H₂O. (2) In the ²H₂-H₂O system the measured rate of H₂ production was always higher than that of H²H. The $\text{H}{}_2\text{H}{}^2\text{H}$ ratio remained constant (about 1.70) in the protein concentration range 0.08–1.32 mg. The very rapid formation of H₂ with respect to H²H is consistent with the hypothesis of a heterolytic cleavage of ²H₂ into a deuteron and an enzyme hydride that can exchange with the solvent. (3) In the H₂-²H₂O system, the exchange rate was much lower than in the ²H₂-H₂O system, indicating a marked isotopic effect of ²H₂O. (4) The H-²H exchange activity, determined from the initial velocity of H²H formation, is optimal at pH 4.5. A second maximum of activity is observed at pH 8.3. The pH value of 4.5 is also the pH optimum for H₂ production while at pH 8.3–8.5 there is a maximum of H₂ oxidation activity. (5) In ordinary H₂O the K_m for hydrogen uptake estimated either from H₂ consumption or from benzyl viologen reduction was 0.06–0.07 μM for both H₂ and ²H₂ indicating a strong affinity of the enzyme for hydrogen at pH 8.3–8.5. Shifting from H₂O to ²H₂O does not affect the K_m of the enzyme for H₂ but lowers the V_max value about 10-fold. The K_m for benzyl viologen and methyl viologen was 0.08 and 2 mM, respectively.     

Similarities and differences in interaction of K+ and Na+ with condensed ordered DNA. A molecular dynamics computer simulation study

Four 20 ns molecular dynamics simulations have been performed with two counterions, K⁺ or Na⁺, at two water contents, 15 or 20 H₂O per nucleotide. A hexagonal simulation cell comprised of three identical DNA decamers [d(5′-ATGCAGTCAG) × d(5′-TGACTGCATC)] with periodic boundary condition along the DNA helix was used. The simulation setup mimics the DNA state in oriented DNA fibers or in crystals of DNA oligomers. Variation of counterion nature and water content do not alter averaged DNA structure. K⁺ and Na⁺ binding to DNA are different. K⁺ binds to the electronegative sites of DNA bases in the major and the minor grooves, while Na⁺ interacts preferentially with the phosphate groups. Increase of water causes a shift of both K⁺ and Na⁺ from the first hydration shell of O1P/O2P and of the DNA bases in the minor groove with lesser influence for the cation binding to the bases in the major groove. Mobility of both water and cations in the K–DNA systems is faster than in the Na–DNA systems: Na⁺ organizes and immobilizes water structure around itself and near DNA while for K⁺ water is less organized and more dynamic.     

Quenching of electronically excited N2 molecules and Tb3+/Eu3+ ions by polyatomic sulfur‐containing gases upon triboluminescence of inorganic lanthanide salts

The triboluminescence of Eu₂(SO₄)₃·8H₂O and Tb₂(SO₄)₃·8H₂O crystals in an atmosphere of sulfur dioxide (SO₂) or sulfur hexafluoride (SF₆) was studied. Quenching of the gaseous (emitter N₂) and solid‐state (emitter Ln³⁺) components of the triboluminescence (TL) emission spectrum was seen when compared with the TL spectra of the crystals in air. One reason for the quenching is a reduction in the effective charge both on the crystal surface and in micro‐cracks under an SO₂ or SF₆ atmosphere, leading to a decrease in the probability of electrical breakdown and a reduction in electric field strength responsible for the electroluminescence excitation of lanthanide ions in TL. In an SO₂ atmosphere, there is an additional mode of quenching, as confirmed by quenching of the crystal photoluminescence (emitter Ln³⁺). It is supposed that this quenching is due to an exchange of energy on electronic excitation of the lanthanide ions to the vibrational sublevels of the SO₂ molecules adsorbed on the crystal surface. Another additional channel of TL quenching originates from non‐radiative transfer of excitation energy during collisions between the *N₂ and SO₂ molecules in the gaseous phase.     

Hydrolytic stability of SnCl4 and GaCl3 in the formation of [cis-SnCl4(H2O)2] · 18-crown-6 · 2H2O and [[2,2,2]cryptand + 2H][GaCl4]2

The combination of anhydrous SnCl₄ with 18-crown-6 in aqueous conditions results in formation of the non-hydrolysed product [cis-SnCl₄(H₂O)₂] · 18-crown-6 · 2H₂O. The X-ray crystal structure shows extensive intermolecular hydrogen bonding involving the cis-octahedral SnCl₄(H₂O)₂ units, the uncoordinated water molecules and the crown ether. Similarly, [2,2,2]cryptand reacts with an aqueous solution formed by adding anhydrous GaCl₃ to slightly acidic water, affording [[2,2,2]cryptand + 2H⁺][GaCl₄]₂.     

The effect of deuterium oxide on the stability of the collagen model peptides H‐(Pro‐Pro‐Gly)10‐OH,H‐(Gly‐Pro‐4(R)Hyp)9‐OH,and Type I collagen

The collagen triple helix has a larger accessible surface area per molecular mass than globular proteins, and therefore potentially more water interaction sites. The effect of deuterium oxide on the stability of collagen model peptides and Type I collagen molecules was analyzed by circular dichroism and differential scanning calorimetry. The transition temperatures (T_m) of the protonated peptide (Pro‐Pro‐Gly)₁₀ were 25.4 and 28.7°C in H₂O and D₂O, respectively. The increase of the T_m of (Pro‐Pro‐Gly)₁₀ measured calorimetrically at 1.0°C min^?1 in a low pH solution from the protonated to the deuterated solvent was 5.1°C. The increases of the T_m for (Gly‐Pro‐4(R)Hyp)₉ and pepsin‐extracted Type I collagen were measured as 4.2 and 2.2°C, respectively. These results indicated that the increase in the T_m in the presence of D₂O is comparable to that of globular proteins, and much less than reported previously for collagen model peptides [Gough and Bhatnagar, J Biomol Struct Dyn 1999, 17, 481–491]. These experimental results suggest that the interaction of water molecules with collagen is similar to the interaction of water with globular proteins, when the ratio of collagen to water is very small and collagen is monomerically dispersed in the solvent. © 2009 Wiley Periodicals, Inc. Biopolymers 93: 93–101, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

The quantum requirement for H2 production by anoxygenic phototrophic bacteria

Cultures from three groups of phototrophic bacteria (green sulphur bacteria, purple non-sulphur bacteria and purple sulphur bacteria) were investigated in respect of the quantum requirement for H₂ production (Q_H2). Rates of H₂ formation were determined by means of a Clark-type H₂ electrode with dense suspensions of whole cells and malate, acetate or sulphide as electron donor. At low light intensities (0–3 W·m^–2 of monochromatic light) the minimum quantum requirement was 8.6 quanta per H₂ with Chlorobium vibrioforme, 7.5 with Rhodospirillum rubrum, and 23.2 with Ectothiorhodospira shaposhnikovii. The physiological efficiency, defined as the measured Q_H2 compared to the theoretical value calculated from the energy requirement of the physiological processes involved, was 94%, 88%, or 28%, respectively. With increasing light intensities the quantum requirement also increased. Various hydrogenase inhibitors either inhibited both H₂ uptake and production (Cu²⁺, NO), or affected neither of these activities (CO, C₂H₂, N₂O, ethylenedinitrilotetraacetate). An uptake hydrogenase-deficient Hup^–-mutant of R. rubrum had higher rates of net H₂ production but a similar quantum requirement. The energetic efficiency of H₂ production by various biological and artificial systems is discussed.     

Experimental and theoretical study of energetics of complex formation between nucleic acid bases and the bases with amide group.

A number of nucleic acid base pairs and complexes between the bases and the amide group of acrylamide have been studied experimentally by using mass spectrometry and theoretically by the method of atom-atom potential function calculations. It has been found from temperature dependencies of peak intensities in mass spectra of m2.2.9(3) Gua.m1Ura, m9 Ade.m1Cyt, m2.2.9(3) Gua.m1Gua.m1Cyt pairs that enthalpy values, delta H, of the complex formation are equal to 14.2 +/- 1.1, 13.5 +/- 1.3 and 16.4 +/- 1.4 kcal/M, respectively, and those of acrylamide with m1.3(2) Ura and m1Thy corresponds to 9.7 +/- 1.0 and 6.8 +/- 0.6 kcal/M. There is a good agreement of the experimental data with calculations when taking into account both the amino-oxo and the amino-hydroxy tautomeric forms of guanine. A combined use of the data allows us to determine the energy, the modes of interaction and the structure of the complexes. The results are discussed in connection with the modelling of molecular structure of biopolymers by the method of classical potential functions, protein-nucleic acids recognition and fidelity of nucleic acids biosynthesis.     

Atomic Hydrogen Surrounded by Water Molecules,H(H2O)m,Modulates Basal and UV-Induced Gene Expressions in Human Skin In Vivo

Recently, there has been much effort to find effective ingredients which can prevent or retard cutaneous skin aging after topical or systemic use. Here, we investigated the effects of the atomic hydrogen surrounded by water molecules, H(H₂O)_m, on acute UV-induced responses and as well as skin aging. Interestingly, we observed that H(H₂O)_m application to human skin prevented UV-induced erythema and DNA damage. And H(H₂O)_m significantly prevented UV-induced MMP-1, COX-2, IL-6 and IL-1β mRNA expressions in human skin in vivo. We found that H(H₂O)_m prevented UV-induced ROS generation and inhibited UV-induced MMP-1, COX-2 and IL-6 expressions, and UV-induced JNK and c-Jun phosphorylation in HaCaT cells. Next, we investigated the effects of H(H₂O)_m on intrinsically aged or photoaged skin of elderly subjects. In intrinsically aged skin, H(H₂O)_m application significantly reduced constitutive expressions of MMP-1, IL-6, and IL-1β mRNA. Additionally, H(H₂O)_m significantly increased procollagen mRNA and also decreased MMP-1 and IL-6 mRNA expressions in photoaged facial skin. These results demonstrated that local application of H(H₂O)_m may prevent UV-induced skin inflammation and can modulate intrinsic skin aging and photoaging processes. Therefore, we suggest that modifying the atmospheric gas environment within a room may be a new way to regulate skin functions or skin aging.