Structures of Nickel(II) and Copper(II) Complexes of 14-Membered Macrocyclic Quadridentate Ligands

The structures of 41 Ni(II) and 17 Cu(II) complexes of macrocyclic quadridentate ligands have been analyzed, and are discussed about bond lengths, bond angles, conformations, and configurations, upon which many conclusions are formed. The inter- or intra-molecular hydrogen bonds exist among ligands and hydrates in many compounds and play an important role in the structures. There are exhibited two distinct peaks on the histogram of the average Ni-N distances, corresponding to four coordination and six coordination; these average Ni-N distances are 1.95(4) Å and 2.10(5) Å, respectively. The most probable structures of Ni(II) macrocyclic compounds have coordination number six for the metal ion, chair forms for six-membered rings, planar structure for the metal ion and the four donor atoms of the quadridentate ligand and an inversion center at the central metal ion.     

Spectroscopic characterization of microscopic hydrogen-bonding disparities in supercritical water

The local hydrogen-bonding environment in supercritical water (380 degrees C, 300 bars, density 0.54 gcm3) was studied by x-ray Raman scattering at the oxygen K edge. The spectra are compared to those of the gas phase, liquid surface, bulk liquid, and bulk ice, as well as to calculated spectra. The experimental model systems are used to assign spectral features and to quantify specific local hydrogen-bonding situations in supercritical water. The first coordination shell of the molecules is characterized in more detail with the aid of the calculations. Our analysis suggests that approximately 65% of the molecules in supercritical water are hydrogen bonded in configurations that are distinctly different from those in liquid water and ice. In contrast to liquid water the bonded molecules in supercritical water have four intact hydrogen bonds and in contrast to ice large variations of bond angles and distances are observed. The remaining approximately 35% of the molecules exhibit two free O-H bonds and are thus either not involved in hydrogen bonding at all or have one or two hydrogen bonds on the oxygen side. We determine an average O-O distance of 3.1+/-0.1 A in supercritical water for the H bonded molecules at the conditions studied here. This and the corresponding hydrogen bond lengths are shown to agree with neutron- and x-ray-diffraction data at similar conditions. Our results on the local hydrogen-bonding environment with mainly two disparate hydrogen-bonding configurations are consistent with an extended structural model of supercritical water as a heterogeneous system with small patches of bonded molecules in various tetrahedral configurations and surrounding nonbonded gas-phase-like molecules.     

A specific inhibitor design approach by means of molecular dynamics calculation for porcine pancreatic elastase

A 27-picosecond (ps) molecular dynamics calculation has been carried out for the 1:2 enzyme-ligand complex between porcine pancreatic elastase (PPE) and acetyl-alanine-proline-alanine (APA). A data analysis has been carried out using a total of 450 structures. During the simulation, the root-mean-square fluctuations (RMSF) increased compared with the x-ray data. Some differences of the hydrogen bond arrangement in the MD average structures are found especially for SER 195, suggesting the fluctuations of the ligand molecules. The radius of gyration decreased a little during the simulation. Although intermolecular hydrogen bonds between two substrates (APA1 and APA2) has not been found by a 1.65-Å high-resolution x-ray diffraction study, the MD calculation showed the intermolecular hydrogen bond between them to be 3.2 Å. The extended active site of PPE is so wide compared with the size of a tripeptide that such a hydrogen-bound hexapeptide can be more specific than tripeptides, which is consistent with the kinetic data previously reported.     

Dihydrogen bond cooperativity in (HCCBeH)n clusters

A theoretical study has been carried out on the clusters formed by the association of ethynylhydroberyllium (HC[triple bond]CBeH) monomers. The monomer presents a linear disposition with a dipole moment of 0.94 D. Clusters from two to six monomers have been calculated for three different configurations (linear, cyclic with dihydrogen bonds, and cyclic with hydrogen bonds to the pi-cloud), the third one being the most stable. The electronic properties of the clusters have been analyzed by means of the atoms in molecules and natural bond orbitals methodologies. Cooperative effects, similar to the ones described for standard hydrogen bonded clusters, are observed in those configurations where dihydrogen bonds are the main interacting force.     

Coherent molecular motion in aquatic environment. Extraction of correlation from noise

Molecular dynamics simulation of liquid water and system “argon-thin water film” has been performed. In was shown that time dependence of distances between oxygen atoms of water molecules, connected by hydrogen bonds, looks like random noise and these molecules are doomed to move concertedly. The average distance between the argon atoms dissolved in water is retained for some time, so the argon atoms included in the hydrogen bond networks, but not capable to participate in hydrogen bonds are involved in concerted motions. The problem of revealing the correlations in the motion of molecules and atoms is discussed.     

Investigating hydrogen bonds in liquid ethylene glycol structure by means of molecular dynamics

Models of liquid ethylene glycol are built by means of molecular dynamics at temperatures ranging between 268 and 443 K, with 1000 molecules in rectangular parallelepiped basic cells. The dependences of structures of O-H…O hydrogen bonds on modeling time and temperature are analyzed. It is found that the hydrogen bonds emerge at different sites of a model, thus forming a hydrogen bonds network that is continuously rebuilt under the action of thermal fluctuations. The number of hydrogen bonds in the models is observed to decrease when the temperature is raised. The energy of hydrogen bond formation is found to be ?20.0 ± 2.6 kJ mol^?1, the average bond lifetime is 370 ps at 268 K and 147 ps at 323 K, and the activation energy of hydrogen bond rupture at these temperatures is ～12.1 kJ mol^?1. It is concluded that the data on the breaking of H-bonds at temperatures of 323 to 443 K can be explained by the molecules moving away from each other as a result of diffusive motion, accompanied by rearrangement of the hydrogen bonds network. The concentration of dimers in the models is shown to be rather low, while the average energy of forming a dimer from two ethylene glycol molecules is ?35.4 kJ mol^?1.     

1,3‐Bis[2‐(2‐hydroxybenzylideneamino)phenoxy]propane

The title compound {systematic name: 2,2′‐[1,3‐propanediyldioxydi‐o‐phenylenebis(nitrilomethylidyne)]diphenol}, C₂₉H₂₆N₂O₄, exists as the phenol–imine form in the crystal, and there are strong intramolecular O—H⋯N hydrogen bonds, with O⋯N distances of 2.545 (2) and 2.579 (2) Å. The C=N imine bond distances are in the range 1.276 (2)–1.279 (2) Å and the C=N—C bond angles are in the range 123.05 (16)–124.64 (17)°. The configurations about the C=N bonds are anti (1E).     

Self‐Assembly of Iodine in Superfluid Helium Droplets: Halogen Bonds and Nanocrystals

We present evidence of halogen bond in iodine clusters formed in superfluid helium droplets based on results from electron diffraction. Iodine crystals are known to form layered structures with intralayer halogen bonds, with interatomic distances shorter than the sum of the van der Waals radii of the two neighboring atoms. The diffraction profile of dimer dominated clusters embedded in helium droplets reveals an interatomic distance of 3.65 Å, much closer to the value of 3.5 Å in iodine crystals than to the van der Waals distance of 4.3 Å. The profile from larger iodine clusters deviates from a single layer structure; instead, a bi‐layer structure qualitatively fits the experimental data. This work highlights the possibility of small halogen bonded iodine clusters, albeit in a perhaps limited environment of superfluid helium droplets. The role of superfluid helium in guiding the trapped molecules into local potential minima awaits further investigation.     

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

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

Monte Carlo Simulation of the Local Ordering of Water Molecules. II. Spatial Correlations and Hydrogen Bonds

The Monte Carlo method is used to calculate spatial distribution functions of oxygen and hydrogen atoms within a large-size water model (33666 SPC/E water molecules) under atmospheric pressure at room temperature. The work focuses on structural interpretation of local densities of water at the distances of about 3–5 Å from its molecules. The distribution of the distances between water molecules connected by chains of two or more hydrogen bonds indicates that the molecules between the first and second peaks of the radial distribution function (RDF) are mainly second and, to a lesser extent, third neighbors along the chain of bonds.     

Hydrogen bond and residence dynamics of ion-water and water-water pairs in supercritical aqueous ionic solutions: dependence on ion size and density

We have carried out a series of molecular dynamics simulations to investigate the hydrogen bond and residence dynamics of X(-)-water (X=F, Cl, and I) and pairs in aqueous solutions at a temperature of 673 K. The calculations are done at six different water densities ranging from 1.0 to 0.15 g cm(-3). The hydrogen bonds are defined by using a set of configurational criteria with respect to the anion(oxygen)-oxygen and anion(oxygen)-hydrogen distances and the anion(oxygen)-oxygen-hydrogen angle for an anion(water)-water pair. The F(-)-water hydrogen bonds are found to have a longer lifetime than all other hydrogen bonds considered in the present study. The lifetime of Cl(-)-water hydrogen bonds is shorter than that of F(-)-water hydrogen bonds but longer than the lifetime of water-water hydrogen bonds. The lifetimes of I(-)-water and water-water hydrogen bonds are found to be very similar. Generally, the lifetimes of both anion-water and water-water hydrogen bonds are found to be significantly shorter than those found under ambient conditions. In addition to hydrogen bond lifetimes, we have also calculated the residence times and the orientational relaxation times of water molecules in ion(water) hydration shells and have discussed the correlations of these dynamical quantities with the observed dynamics of anion(water)-water hydrogen bonds as functions of the ion size and density of the supercritical solutions.     

Hydrogen bonding in selected vanadates: a Raman and infrared spectroscopy study

Water plays an important role in the stability of minerals containing the deca and hexavanadates ions. A selection of minerals including pascoite, huemulite, barnesite, hewettite, metahewettite, hummerite has been analysed. Infrared spectroscopy combined with Raman spectroscopy has enabled the spectra of the water HOH stretching bands to be determined. The use of the Libowitsky type function allows for the estimation of hydrogen bond distances to be determined. The strength of the hydrogen bonds can be assessed by these hydrogen bond distances. An arbitrary value of 2.74A was used to separate the hydrogen bonds into two categories such that bond distances less than this value are considered as strong hydrogen bonds whereas hydrogen bond distances greater than this value are considered relatively weaker. Importantly infrared spectroscopy enables the estimation of hydrogen bond distances using an empirical function.     

Charge‐transfer‐to‐solvent absorption spectra of I−(H2O)3–5 at a finite temperature via simulation

Ground‐state equilibrium Born–Oppenheimer molecular dynamics on I^?(H₂O)_3–5 clusters at ～200 K are performed to sample configurations for calculating the charge‐transfer‐to‐solvent (CTTS) absorption spectra for these clusters. When there are more water molecules in clusters, the calculated CTTS spectra are found to become more intense with the absorption maxima shifting to higher energies, which is in agreement with experimental results. In addition, compared with the findings for optimized structures, the absorption energies of the iodide 5p orbitals are red‐shifted at ～200 K because, on average, the distances between the iodide and the dangling hydrogen atoms are increased at finite temperatures which weakens the interactions between the iodide and water molecules in the clusters. Moreover, the number of ionic hydrogen bonds in the clusters are also reduced. However, it is found that all dangling hydrogen atoms must be considered to obtain a good correlation between the CTTS excitation energy and the average distance between the iodide and the dangling hydrogen atoms, which indicates the existence of the strong interactions of the CTTS electron with all of the dangling hydrogen atoms.     

Crystal structure of 1:1 Complexes between urea and two crown ether derivatives of phthalic acid, 2,3,5,6,8,9,11,12,14,15-decahydrobenzo[1,4,7,10,13,16]hexaoxacyclo-octadecin-18,19-dicarboxylic acid (i) and 2,3,5,6,8,9,11,12-octahydro-benzo[1,4,7,10,13]pentaoxacyclopentadecin-15,16-dicarboxylic acid (II)

The crystal structures of the titlke compounds have been determined by X-ray diffraction. Urea, I crystallizes in the triclinic PI space group with cell dimensions a = 8.336(2), b = 11.009(2), c = 13.313(2) Å, α = 105.55(3), β = 103.62(3), γ = 104.63(3)° and Z = 2 final R value 0.072 for 2105 observations. Urea, II crystallizes in the orthorhombic P2₁2₁2₁ space group with cell dimensions a = 8.750(2), b = 10.844(3) and c = 21.215(3) Å and Z = 4, final R value 0.083 for 599 observations. All the hydrogen atoms were located in the complex urea, I ; urea molecules form hydrogen bonded dimers about centers of symmetry, these dimers are sandwiched between macrocyclic rings forming one simple and one bifurcated hydrogen bond from the “endo” hydrogen atoms to the ether oxygen atoms. These units are held by hydrogen bonding between the urea molecules and carboxylic acids in two other units; these hydrogen bonds are cyclic involving eight atoms -(N-H(exo)…O(keto)-C-O-H…O(urea)-C)-. Only one carboxylic acid group per molecule takes part in these hydrogen bonds, the other forms a short, 2.490(7) Å, internal bond to the acceptor keto oxygen atom. N(H)…O bonds range from 2.930(7) to 3.206(7) Å, O(H)…O is 2.475(6) Å. In the complex urea, II each urea is hydrogen bonded to three different host molecules and vice versa; the urea “endo” hydrogen atoms bond to the ether oxygen atoms, while both “exo” hydrogen atoms take part in cyclic hydrogen bonds to carboxylic acids. There is not internal hydrogen bond. N(H)…O bonds range from 2.83 to 3.26(2) A and the O-…O bonds are 2.55 and 2.56(2) Å.     

4‐Amino‐3‐methyl‐6‐phenyl‐1,2,4‐triazin‐5(4H)‐one (metamitron) and 4‐amino‐6‐methyl‐3‐phenyl‐1,2,4‐triazin‐5(4H)‐one (isometamitron)

The title structures, both C₁₀H₁₀N₄O, are substitutional isomers. The N—N bond lengths are longer and the C=N bond lengths are shorter by ca 0.025 Å than the respective average values in the C=N—N=C group of asymmetric triazines; the assessed respective bond orders are 1.3 and 1.7. There are N—H⋯O and N—H⋯N hydrogen bonds in both structures, with 4‐­amino‐3‐methyl‐6‐phenyl‐1,2,4‐triazin‐5(4H)‐one containing a rare bifurcated N—H⋯N,N hydrogen bond. The structures differ in their mol­ecular stacking and the hydrogen‐bonding patterns.     

Structures and energetics of hydrated oxygen anion clusters

Hydration of the atomic oxygen radical anion is studied with computational electronic structure methods, considering (O(-))(H(2)O)(n) clusters and related proton-transferred (OH(-))(OH)(H(2)O)(n)(-)(1) clusters having n = 1-5. A total of 67 distinct local-minimum structures having various interesting hydrogen bonding motifs are obtained and analyzed. On the basis of the most stable form of each type, (O(-))(H(2)O)(n)) clusters are energetically favored, although for n > or = 3, there is considerable overlap in energy between other members of the (O(-))(H(2)O)(n) family and various members of the (OH(-))(OH)(H(2)O)(n)(-)(1) family. In the lower-energy (O(-))(H(2)O)(n) clusters, the hydrogen bonding arrangement about the oxygen anion center tends to be planar, leaving the oxygen anion p-like orbital containing the unpaired electron uninvolved in hydrogen bonding with any water molecule. In (OH(-))(OH)(H(2)O)(n)(-)(1) clusters, on the other hand, nonplanar arrangements are the rule about the anionic oxygen center that accepts hydrogen bonds. No instances are found of OH(-) acting as a hydrogen bond donor. Those OH bonds that form hydrogen bonds to an anionic O(-) or OH(-) center are significantly stretched from their equilibrium value in isolated water or hydroxyl. A quantitative inverse correlation is established for all hydrogen bonds between the amount of the OH bond stretch and the distance to the other oxygen involved in the hydrogen bond.     

An empirical potential for the O-H ⋯ O hydrogen bond: Part 2. Comparison with observed hydrogen bond geometries

The room temperature distribution of O-H ? O hydrogen bond geometries has been predicted by a Monte Carlo calculation, with an empirical potential energy function for the hydrogen bond. The results are compared with a recent survey of hydrogen bonds in carbohydrate crystal structures. The calculated and observed distributions of the O-H ? O angle have mean values of 165.5° and 167.1° respectively. Both the theoretical and experimental results suggest that short O ? H hydrogen bonds tend to be more linear than long O ? H bonds. The distribution of hydrogen bonding within the lone pair plane of the acceptor oxygen atom is predicted to be broader than the distribution perpendicular to this plane, in agreement with the experimental data. The empirical hydrogen bond function, in conjunction with the molecular mechanics program MMI, has also been used to predict the geometries of inter-residue hydrogen bonds in five disaccharides. The O ? H distances and O-H ? O angles are reproduced with r.m.s. deviations of 0.06 Å and 9° respectively.     

Synthesis,Crystal and Molecular Structure of Mono- and Diaquadi(acetato-O)-Bis(2,4′-Bipyridyl) Copper(II)

The title compound has been synthesized and characterized by elemental analysis and conductivity studies. The crystal and molecular structure has been determined. There are two different types of molecules in the crystal: mono- and diaquadi(acetato-O)-bis(2,4'-bipyridyl) copper (II). Both copper atoms occupy special positions. The copper atoms show almost ideal square pyramidal (4 + 1) and square bipyramidal (4 + 2) coordination. Due to the Jahn-Teller effect, the axial Cu-O(water) bond distances are longer than respective equatorial Cu-O(acetate) bond distances. The bond valences of the copper were computed. An intramolecular strong hydrogen bond linking O(water) and O(acetate) atoms exists in the molecule. The differences of geometrical environment for copper in mono- and diaquadi(acetato-O)-bis(2,4'-bipyridyl) copper(II) are imposed by strong intermolecular hydrogen bonds creating a linear infinite chain structure along crystallographic x axis. Also weak intramolecular hydrogen bonds are present in the molecule.     

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

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

A 1:1 cocrystal of 4‐(dimethylamino)benzaldehyde and 6‐phenyl‐1,3,5‐triazine‐2,4‐diamine

The crystal structure of the title compound, C₉H₁₁NO·C₉H₉N₅, contains one molecule of each component in the asymmetric unit. Approximately planar clusters of four molecules are formed by N—H...N and N—H...O hydrogen bonds, and further N—H...N hydrogen bonds link adjacent clusters to form pleated ribbons. π–π interactions are found between triazine and aldehyde benzene rings in different clusters, generating stacks along the monoclinic b axis. The intramolecular geometry of the two components is similar to that found in other crystal structures containing these molecules. Both molecules are approximately planar, except for methyl H atoms, with a small twist about the C—C bond linking the phenyl and triazine rings.