Structure and hydration of L-proline in aqueous solutions

The structure and hydration of L-proline in aqueous solution have been investigated using a combination of neutron diffraction with isotopic substitution, empirical potential structure refinement modeling, and small-angle neutron scattering at three concentrations, 1:10, 1:15, and 1:20 proline/water mole ratios. In each solution the carboxylate oxygen atoms from proline accept less than two hydrogen bonds from the surrounding water solvent and the amine hydrogen atoms donate less than one hydrogen bond to the surrounding water molecules. The solute-solute radial distribution functions indicate relatively weak interactions between proline molecules, and significant clustering or aggregation of proline is absent at all these concentrations. The spatial density distributions for the hydration of the COO- group in proline show a similar shape to that found previously in L-glutamic acid in aqueous solution but with a reduced coordination number.     

One water molecule stabilizes the cationized arginine zwitterion

Singly hydrated clusters of lithiated arginine, sodiated arginine, and lithiated arginine methyl ester are investigated using infrared action spectroscopy and computational chemistry. Whereas unsolvated lithiated arginine is nonzwitterionic, these results provide compelling evidence that attachment of a single water molecule to this ion makes the zwitterionic form of arginine, in which the side chain is protonated, more stable. The experimental spectra of lithiated and sodiated arginine with one water molecule are very similar and contain spectral signatures for protonated side chains, whereas those of lithiated arginine and singly hydrated lithiated arginine methyl ester are different and contain spectral signatures for neutral side chains. Calculations at the B3LYP/6-31++G** level of theory indicate that solvating lithiated arginine with a single water molecule preferentially stabilizes the zwitterionic forms of this ion by 25-32 kJ/mol and two essentially isoenergetic zwitterionic structure are most stable. In these structures, the metal ion either coordinates with the N-terminal amino group and an oxygen atom of the carboxylate group (NO coordinated) or with both oxygen atoms of the carboxylate group (OO coordinated). In contrast, the OO-coordinated zwitterionic structure of sodiated arginine, both with and without a water molecule, is clearly lowest in energy for both ions. Hydration of the metal ion in these clusters weakens the interactions between the metal ion and the amino acid, whereas hydrogen-bond strengths are largely unaffected. Thus, hydration preferentially stabilizes the zwitterionic structures, all of which contain strong hydrogen bonds. Metal ion size strongly affects the relative propensity for these ions to form NO or OO coordinated structures and results in different zwitterionic structures for lithiated and sodiated arginine clusters containing one water molecule.     

Dependence of the number of hydrogen bonds per water molecule on its distance to a hydrophobic surface and a thereupon-based model for hydrophobic attraction

A water molecule in the vicinity of a hydrophobic surface forms fewer hydrogen bonds than a bulk molecule because the surface restricts the space available for other water molecules necessary for its hydrogen-bonding. In this vicinity, the number of hydrogen bonds per water molecule depends on its distance to the surface. Considering the number of hydrogen bonds per bulk water molecule (available experimentally) as the only reference quantity, we propose an improved probabilistic approach to water hydrogen-bonding that allows one to obtain an analytic expression for this dependence. (The original version of this approach [Y. S. Djikaev and E. Ruckenstein, J. Chem. Phys. 130, 124713 (2009)] provides the number of hydrogen bonds per water molecule in the vicinity of a hydrophobic surface as an average over all possible locations and orientations of the molecule.) This function (the number of hydrogen bonds per water molecule versus its distance to a hydrophobic surface) can be used to develop analytic models for the effect of hydrogen-bonding on the hydration of hydrophobic particles and their solvent-mediated interaction. Presenting a model for the latter, we also examine the temperature effect on the solvent-mediated interaction of two parallel hydrophobic plates.     

Structure of bilirubin and its anion according to quantum chemical calculations and molecular dynamics simulation

Quantum chemical calculations of the structural characteristics of the bilirubin molecule and its anion are performed. Intramolecular hydrogen bonds are studied using NBO analysis. It is shown that hydrogen bonds in the bilirubin molecule are nonequivalent, and the bond formed by the keto oxygen of the pyrrole ring and the hydrogen of the carboxyl group belonging to the propionate residue is energetically more favorable. Structural characteristics of the molecular and ion forms of bilirubin in aqueous solution are studied by molecular dynamics simulation. It is found that intermolecular hydrogen bonds with water molecules are formed due to oxygen atoms of the carboxyl group and the keto group of bilirubin, and the probability of their formation by anions is much higher than that for molecules.     

Ions in water: the microscopic structure of concentrated NaOH solutions

A neutron diffraction experiment with isotopic H/D substitution on four concentrated NaOH/H(2)O solutions is presented. The full set of partial structure factors is extracted, by combining the diffraction data with a Monte Carlo simulation. These allow to investigate both the changes of the water structure in the presence of ions and their solvation shells. It is found that the interaction with the solute affects the tetrahedral network of hydrogen bonded water molecules in a manner similar to the application of high pressure to pure water. The solvation shell of the OH(-) ions has an almost concentration independent structure, although with concentration dependent coordination numbers. The hydrogen site coordinates a water molecule through a weak bond, while the oxygen site forms strong hydrogen bonds with a number of molecules that is on the average very close to four at the higher water concentrations and decreases to about three at the lowest one. The competition between hydrogen bond interaction and Coulomb forces in determining the orientation of water molecules within the cation solvation shell is visible in the behavior of the g(NaHw)(r) function     

The Crystal Structures of Two Polymorphic Forms of a Calcium(II) Complex with Pyridine-2,6-Dicarboxylate,Water and Nitrate Ligands

The calcium (II) complex: catena-mono(μ-pyridine-2,6-dicarboxylato-O:O:N;O') (diaqua-O)mono (nitrato-O:O)calcium(II) exists in two polymorphic forms. Each contains molecular ribbons in which adjacent Ca(II) ions are bridged by monodentate oxygen atoms donated by one carboxylate group of the pyridine-2,6-carboxylate ligand. Apart from this bridging oxygen atom, the Ca(II) ion is coordinated by two carboxylate oxygen atoms contributed by a different carboxylate group of the ligand molecule, the heteroring nitrogen atom, two water oxygen atoms and two oxygen atoms of a nitrate group giving rise to a distorted pentagonal bipyramid as a coordination polyhedron. The structures of the polymorphic modifications differ in the way in which the nitrate ligands are oriented with respect to the equatorial planes of the adjacent Ca(II) coordination polyhedra: the trans mode in the α-form; the cis mode in the β-form. In both forms, hydrogen bonds operate between the carboxylate oxygen atoms, water oxygen atoms and nitrate oxygen atoms.     

Intermolecular Hydrogen Bonds Formed Between Amino Acid Molecules in Aqueous Solution Investigated by Temperature-jump NanosecondTime-resolved Transient Mid-IR Spectroscopy

Carboxyl (COO?) vibrational modes of two amino acids histidine and glycine in D2O solution were investigated by temperature-dependent FTIR spectroscopy and temperature-jump nanosecond time-resolved IR di?erence absorbance spectroscopy. The results show that hydrogen bonds are formed between amino acid molecules as well as between the amino acid molecule and the solvent molecules. The asymmetric vibrational frequency of COO? around 1600-1610 cm?1 is blue shifted when raising temperature, indicating that the strength of the hydrogen bonds becomes weaker at higher temperature. Two bleaching peaks at 1604 and 1612 cm?1 were observed for histidine in response to a temperature jump from 10 ±C to 20 ±C. The lower vibrational frequency at 1604 cm?1 is assigned to the chain COO? group which forms the intermolecular hydrogen bond with NH3+ group, while the higher frequency at 1612 cm?1 is assigned to the end COO? group forming hydrogen bonds with the solvent molecules. This is because that the hydrogen bonds in the former are expected to be stronger than the latter. In addition the intensities of these two bleaching peaks are almost the same. In contrast, only the lower frequency at 1604 cm?1 bleaching peak has been observed for glycine. The fact indicates that histidine molecules form a dimer-like intermolecular chain while glycine forms a relatively longer chain in the solution. The rising phase of the IR absorption kinetics in response to the temperature-jump detected at 1604 cm?1 for histidine is about 30§10 ns, within the resolution limit ofour instrument, indicating that breaking or weakening the hydrogen bond is a very fast process.     

高岭石-水体系中水分子结构的分子动力学模拟

以Hendricks模型为初始结构, 利用CLAYFF力场对高岭石-水体系进行无晶体学限制的分子动力学模拟. 结果表明, 层间水有三种类型: I型类似于Costanzo提出的“洞水”分子, 其HH矢量(水分子中从一个氢原子位置指向另一个氢原子位置的方向矢量)平行于(001)平面, 而C2轴稍微倾斜于(001)面法线; II型类似于“连接水”, 一个氢氧键指向临近的层间四面体氧形成氢键, 另一个氢氧键与(001)面近似平行; III型水分子在层间近似保持为竖直状, 一个氢与层间四面体氧形成氢键, 而另一个氢与对面层的羟基氧形成氢键. 高岭石羟基氢沿(001)晶面法线的浓度曲线显示一部分羟基指向变为近似平行于(001)面, 羟基氧因此能够暴露出来与层间水分子氢形成氢键. 此外, 模拟中还观察到部分II型水分子氧偏离于层间的平均位置而更靠近四面体层, 这和Costanzo的实验结果一致, 可能是X射线谱图中(002)弱衍射峰出现的原因.     

聚N,N-二乙基丙烯酰胺低聚物水溶液的分子动力学研究

对50个单元构成的聚N,N-二乙基丙烯酰胺(PDEA)低聚物的水溶液体系进行了分子动力学的研究,分别模拟了300 K时的伸展链、310 K时的伸展链以及紧缩链与水构成的体系,对溶液中PDEA周围溶剂水分子的分布情况以及水分子形成氢键的情况进行了统计,结果表明在PDEA周围的水产生了比本体水更有序的结构,形成了更多的氢键,这种有序结构维持到第二水合层甚至更远.发生相分离后,PDEA与水分子形成的氢键大部分未被破坏,水合层中每个水分子形成的氢键数也没有明显变化,但水合层(形成有序结构的水分子)内水分子数目的减少使得总的氢键数目减少,从而造成体系能量增加及熵增加.同时还研究了聚合物及水分子的自扩散系数,表明PDEA影响周围水分子结构的同时,对水的动力学性质也产生了很大影响.     

Chiral NMR discrimination of secondary amines using (18-crown-6)-2,3,11,12-tetracarboxylic acid

[reaction: see text] Enantiomeric discrimination is observed in the (1)H NMR spectra of chiral secondary amines in the presence of (R)-(+)-(18-crown-6)-2,3,11,12-tetracarboxylic acid. Secondary amines are protonated by one of the carboxylic acid groups of the crown ether to produce the corresponding ammonium and carboxylate ions. The secondary ammonium ion likely forms two hydrogen bonds to crown ether oxygen atoms and an ion pair with the carboxylate anion.     

Structural and magnetic properties of vanadyl dichloride solvates: from molecular units to extended hydrogen-bonded solids

The preparation, structural characterization and magnetic properties of three solvent adducts of VOCl(2), trans-VOCl(2)(THF)(2)(H(2)O) (1), trans-VOCl(2)(H(2)O)(2).2Et(2)O (2) and cis-VOCl(2)(MeOH)(3) (3) are described. In these solids, hydrogen bonding among the inorganic complexes is the critical determinant of the formation of extended magnetic networks. Compound forms one-dimensional double chains where alternating monomers from the two branches of the chain are hydrogen bonded via the V-Cl ... H-O-V network (with an axial water molecule and equatorial chloride ions). Magnetic studies indicate no interaction among the vanadyl centers. The paramagnetism of 1 is consistent with the extension of the network from the hydrogen donor site of the axial water, which is orthogonal to the d(xy) magnetic orbital. Compound 2 forms one-dimensional chains with water molecules of adjacent monomers held together by hydrogen bonds to ether molecules (V-O-H ... O(ether) ... H -O-V). The chain network radiates only through the equatorial plane of the complex where the water molecules are located. The presence of the intervening solvent molecule between hydrogen bonds of the primary coordination sphere magnetically insulates metal centers and compound is also a simple paramagnet. Removal of the solvent turns on the magnetic interaction and neighboring spin centers couple antiferromagnetically. Compound 3 forms a layered structure via V-Cl ... H-O-V hydrogen bonding, where all the hydrogen donor sites participate in the formation of the network. The vanadyl spin centers, at distances of 5.5 and 6.5 A from each other, couple antiferromagnetically (J/k=-0.7 K). Thus, magnetic coupling among metal centers is achieved when the hydrogen bond network directly radiates from the coordination plane containing the magnetic orbital. These results further support the utility of hydrogen bond as a viable design element in the construction of low dimensional, magnetic solids.     

Molecular orbital theory of the hydrogen bond. 26. The hydration of uracil

Ab initio SCF calculations with the STO -3G basis set have been performed to determine the structure and stability of a 6:1 water:uracil heptamer in which water molecules are hydrogen bonded to uracil at each of the six hydrogen-bonding sites in the uracil molecular plane. The structure of the heptamer describes a stable arrangement of these six water molecules, which are the primary solvent molecules in the first solvation shell, and is suggestive of the arrangement of secondary solvent molecules in that shell in the nonpolar region of the uracil molecular plane. The stabilization energy of the heptamer is 49.6 kcal/mol, or 8.3 kcal/mol per water molecule. The hydrogen bonds between uracil and water are the primary factor in the stabilization of the complex, although water–water interactions and nonadditivity effects are also significant.     

Combined molecular mechanical and quantum mechanical potential study of a nucleophilic addition reaction in solution

The procedure of combined semiempirical quantum mechanical (AM1) and molecular mechanical potential⁷ was used to study the nucleophilic addition of hydroxide to formaldehyde in solution. The gas phase AM1 potential surface is approximately 26 kcal/mol more exothermic than the corresponding ab initio 6-31 + G* calculation results. The free energy profile for the reaction in solution was determined by means of molecular dynamic simulations. The resulting free energy of activation is approximately 5 kcal/mol. The difference of the free energy of solvation between the reactant and the product states is about 38 kcal/mol. As the reaction goes on, the number of hydrogen bonds formed by the hydroxide oxygen with the surrounding water molecules decreases, whereas the number of hydrogen bonds formed by the carbonyl oxygen increases. There is no significant change in the total number of hydrogen bonds between the solute and the solvent molecules, and the average number of these hydrogen bonds is between five and six during the entire reaction process. These results are consistent with previous studies using a model based on ad initio 6-31 + G* calculations in the gas phase. The reaction path in solution is different from the gas phase minimum energy reaction path. When the two reactants are at a large distance, the attack route of the hydroxide anion in solution is close to perpendicular to the formaldehyde plane, whereas in the gas phase the route is collinear with the carbonyl group. These results suggests that although AM1 does not yield accurate energies in the gas phase, valuable insights into the solvent effects can be obtained through computer simulations with this combined potential. This combined procedure could be applied to chemical reactions within macromolecules, in which a quantitative estimation of the effects of the environment would not be easily attainable by another technique. © 1994 by John Wiley & Sons, Inc.     

Poly[[aqua(μ7‐ethylenediaminetetraacetato)dicadmium(II)] monohydrate]

The title compound, {[Cd₂(C₁₀H₁₂N₂O₈)(H₂O)]·H₂O}_n, consists of two crystallographically independent Cd^II cations, one ethylenediaminetetraacetate (edta) tetraanion, one coordinated water molecule and one solvent water molecule. The coordination of one of the Cd atoms, Cd1, is composed of five O atoms and two N atoms from two tetraanionic edta ligands in a distorted pentagonal–bipyramidal coordination geometry. The other Cd atom, Cd2, is six‐coordinated by five carboxylate O atoms from five edta ligands and one water molecule in a distorted octahedral geometry. Two neighbouring Cd1 atoms are bridged by a pair of carboxylate O atoms to form a centrosymmetric [Cd₂(edta)₂]⁴⁻ unit located on the inversion centre, which is further extended into a two‐dimensional layered structure through Cd2—O bonds. There are hydrogen bonds between the coordinated water molecules and carboxylate O atoms within the layer. The solvent water molecules occupy the space between the layers and interact with the host layers through O—H...O and C—H...O interactions.     

Ionic hydrogen bonds controlling two-dimensional supramolecular systems at a metal surface

Hydrogen-bond formation between ionic adsorbates on an Ag(111) surface under ultrahigh vacuum was studied by scanning tunneling microscopy/spectroscopy (STM/STS), X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine structure (NEXAFS), and molecular dynamics calculations. The adsorbate, 1,3,5-benzenetricarboxylic acid (trimesic acid, TMA), self-assembles at low temperatures (250-300 K) into the known open honeycomb motif through neutral hydrogen bonds formed between carboxyl groups, whereas annealing at 420 K leads to a densely packed quartet structure consisting of flat-lying molecules with one deprotonated carboxyl group per molecule. The resulting charged carboxylate groups form intermolecular ionic hydrogen bonds with enhanced strength compared to the neutral hydrogen bonds; this represents an alternative supramolecular bonding motif in 2D supramolecular organization.     

Liquid structures of water, methanol, and hydrogen fluoride at ambient conditions from first principles molecular dynamics simulations with a dispersion corrected density functional

Using first principles molecular dynamics simulations in the isobaric-isothermal ensemble (T = 300 K, p = 1 atm) with the Becke-Lee-Yang-Parr exchange/correlation functional and a dispersion correction due to Grimme, the hydrogen bonding networks of pure liquid water, methanol, and hydrogen fluoride are probed. Although an accurate density is found for water with this level of electronic structure theory, the average liquid densities for both hydrogen fluoride and methanol are overpredicted by 50 and 25%, respectively. The radial distribution functions indicate somewhat overstructured liquid phases for all three compounds. The number of hydrogen bonds per molecule in water is about twice as high as for methanol and hydrogen fluoride, though the ratio of cohesive energy over number of hydrogen bonds is lower for water. An analysis of the hydrogen-bonded aggregates revealed the presence of mostly linear chains in both hydrogen fluoride and methanol, with a few stable rings and chains spanning the simulation box in the case of hydrogen fluoride. Only an extremely small fraction of smaller clusters was found for water, indicating that its hydrogen bond network is significantly more extensive. A special form of water with on average about two hydrogen bonds per molecule yields a hydrogen-bonding environment significantly different from the other two compounds.     

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

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

The Crystal and Molecular Structure of a New Calcium(II) Complex with Pyridine-2,6-DiCarboxylate,Water and Nitrate Ligands

Crystals of {catena-[μ-aqua-O]bis[μ-pyridine-2,6-dicarboxylato-O,N-O']} {[monoaqua-nitrato, O-calcium(II)] [diaqua-calcium(II)]} contain dimeric units composed of two calcium(II) ions and two ligand molecules, in which the calcium ions are bridged by two bidentate oxygen atoms, each donated by one carboxylic group of the ligand. The Ca(II) ion is also coordinated by one oxygen atom of the second carboxylate group and the hetero-ring nitrogen atom belonging to the same ligand molecule. The dimers form molecular chains through protons situated at the symmetry centers halfway between the non-bridging carboxylate oxygen atoms. In addition, both calcium ions in the dimer are bridged to calcium ions in adjacent dimers - each by a pair water oxygen molecules giving rise to two-dimensional molecular sheets. Coordination of the Ca ion in the dimer is completed either by two water oxygen atoms or by one water oxygen atom and an oxygen atom donated by a nitrate group. The molecular sheets are held together by an extended system of hydrogen bonds.     

2,3,5,6‐Tetrakis[3,5‐bis(trifluoromethyl)phenoxy]‐2,5‐bis(dimethylamino)2,3,5,6‐tetrabora‐1,4‐dioxane diethyl ether 0.667‐solvate

The title compound, C₃₆H₂₆B₄F₂₄N₂O₆·0.667C₄H₁₀O, has centrosymmetric tetraboradioxane molecules, half each of three of these comprising the asymmetric unit together with a molecule of diethyl ether. Disorder affects most of the CF₃ groups and one ethyl group of the solvent molecule. The B₄O₂ rings are approximately planar and contain two B atoms with trigonal geometry and two with distorted tetrahedral geometry, the B—O bonds for the four‐coordinate B atoms being longer than those for the three‐coordinate B atoms. N—H...O hydrogen bonds link two of the crystallographically independent molecules together in chains, while the third molecule forms discrete trimolecular clusters with two solvent molecules via N—H...O hydrogen bonds. This is the first crystallographically characterized example of a tetrabora‐dioxane molecule containing both four‐ and three‐coordinate B atoms.     

水与受质子溶剂氢键作用的IR研究

The interaction of water with solvents in H_2O-TBP-CCl_4 system and H_2O-p-dio-xan-CCl_4 system is studied with IR method. The absorbances of free water, 1:1 and 1:2 complex are observed and the absorbance frequencies of each species are assigned. In H_2O-TBP-CCl_4 system, there exists not only symmetric 1:2 complex but also unsymmetric one. The water molecule in unsymmetric 1:2 complex is considered to be hydrogen bonded with two kinds of oxygen atom in TBP. And the hydrogen bonds are different in strenghth. Because of diffeent spatial configurations of solvent molecules around water, more than one kind of 1:2 complex exist in H_2O-p-dioxan-CCl_4 system.