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.     

价键结构函数与键函数 2.水分子的计算和分析

应用键表酉群方法对水分子进行了计算分析, 并用键函数定量讨论了成键电子对之间.成键电子对与孤电子对之间及孤电子对间的相互作用,计算表明H~2O中氧原子与两个HIs成键的两个杂化轨道密度重心偏离O-H联线,氧原子实际上以两个P轨道与HIs成键.     

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.     

A survey of O-H⋯O hydrogen bond geometries determined by neutron diffraction

An analysis of the geometries of one hundred O-H?O hydrogen bonds observed by neutron diffraction in 24 crystal structures shows the following results. Twenty-Five of the hydrogen bonds can be described as bifurcated, indicating that this form of association is more common than previously supposed. Of the linear hydrogen bonds, those engaged in cooperative, or self associated, arrangements have a mean bond length of 1.805(9) Å, compared with 1.869(23) Å for the non-cooperative hydrogen bonds. This difference is significant at the 99.5 percent level. The mean O-H?O valence angle is 167.1(8)°, and there is evidence at the 92.5 percent significance level that the shorter O?H bonds are more linear. There is a preferred direction of hydrogen bonding with respect to the acceptor oxygen atom, which is in, or close to, the plane containing the oxygen lone pair orbitals, but there is no evidence of a preferred direction within that plane.     

Neutron crystallographic and molecular dynamics studies of the structure of ammonia-cellulose I: rearrangement of hydrogen bonding during the treatment of cellulose with ammonia

The hydrogen bond arrangement in a complex of cellulose with ammonia has been studied using neutron crystallography in combination with molecular dynamics simulations. The O6 atom of the hydroxymethyl group is donor in a highly occupied hydrogen bond to an ammonia molecule. This rotating ammonia molecule is donor in partially occupied and transient hydrogen bonds to the O2, O3 and O6 atoms of the hydroxyl groups of other chains. The hydrogen atom bound to the O3 atom is disordered but it is almost always involved in some type of hydrogen bonding. It is donated in a hydrogen bond most of the time to the O5 atom on the same chain. However, it also rotates away from this O5 atom to be donated to an ammonia molecule part of the time. On the other hand the hydrogen atom bound to the O2 atom is free from hydrogen bonding most of the time. It is donated in a hydrogen bond to the O6 atom on a neighboring chain only with a relatively small probability. These results provide new insights into how hydrogen bonds are rearranged during the conversion of cellulose I to cellulose III_I by ammonia treatment.     

Density functional theory and topological analysis on the hydrogen bonding interactions in cysteine‐thymine complexes

Hydrogen bonding interactions between amino acids and nucleic acid bases constitute the most important interactions responsible for the specificity of protein binding. In this study, complexes formed by hydrogen bonding interactions between cysteine and thymine have been studied by density functional theory. The relevant geometries, energies, and IR characteristics of hydrogen bonds (H‐bonds) have been systematically investigated. The quantum theory of atoms in molecule and natural bond orbital analysis have also been applied to understand the nature of the hydrogen bonding interactions in complexes. More than 10 kinds of H‐bonds including intra‐ and intermolecular H‐bonds have been found in complexes. Most of intermolecular H‐bonds involve O (or N) atom as H‐acceptor, whereas the H‐bonds involving C or S atom usually are weaker than other ones. Both the strength of H‐bonds and the structural deformation are responsible for the stability of complexes. Because of the serious deformation, the complex involving the strongest H‐bond is not the most stable structures. Relationships between H‐bond length (ΔR_X‐H), frequency shifts (Δv), and the electron density (ρ_b) and its Laplace (?²ρ_b) at bond critical points have also been investigated. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Molecular orbital studies of gas-phase interactions between complex molecules

Describing interactions among large molecules theoretically is a challenging task. As an example, we investigated gas-phase interactions between a linear nonionic oligomer and various model compounds (cofactors), which have been reported to associate experimentally, using PM3 semiempirical molecular orbital theory. As oligomer, we studied the hexamer of poly(ethylene oxide) (PEO), and as cofactors, we studied corilagin and related compounds containing phenolic groups (R-OH). These systems are of interest because they are models for PEO/cofactor flocculation systems, used in industrial applications. The PM3 delocalized molecular orbitals (DLMO) describe the bonding between (PEO)6 and cofactors, and some of them cover the complete complex. The DLMOs which cover the traditionally considered hydrogen bonds R-OH...O or R-CH...O show a distinct "pinch", a decrease of the electron density, between the H...O atoms. Calculations of Gibbs free energy, entropy, and enthalpy show that the PEO/cofactor complexes do not form at room temperature, because the loss of entropy exceeds the increase in enthalpy. The change in enthalpy is linearly related to the change in entropy for the different complexes. Even though bond lengths, bond angles, DLMOs, and electron densities for the PEO/cofactor complexes are consistent with the definition of hydrogen bonds, the number of intermolecular R-OH...O and R-CH...O bonds does not correlate with the enthalpy of association, indicating that the bonding mechanism for these systems is the sum of many small contributions of many delocalized orbitals.     

Relation between intramolecular NH...S hydrogen bonds and coordination number in mercury(II) complexes with carbamoylbenzenethiol derivatives

A novel series of bis(carbamoylthiophenolato)mercury(II) complexes, [Hg(S-RNHCOC6H4)2] (1, R = 2-t-Bu; 2, R = 2-CH3; 3, R = 2-C6H5CH2; 4, R = 4-t-Bu), and a tetrakis(carbamoylthiophenolato)mercury(II) complex, (NEt4)2[Hg-(S-2-CH3NHCOC6H4)4] (5), were synthesized and characterized by 1H NMR, IR, 199Hg NMR, and crystallographic analyses. The bis(carbamoylthiophenolato)mercury complexes 1-3 do not have intramolecular NH...S hydrogen bonds between the amide NH group and the sulfur atom coordinated to mercury, whereas the tetrakis(thiophenolato)mercury complex 5 does have an intramolecular NH...S hydrogen bond. A relatively weak NH...S hydrogen bond in 5 can be seen in the 1H NMR spectra and the IR spectra in chloroform and in the solid state. The 199Hg NMR spectra in bis(carbamoylthiophenolato)mercury complexes 1-4 show a downfield shift, with an increase in the flow of electrons to mercury(II) from the oxygen atom due to the intramolecular Hg...O bonding interaction. Conversely, the 199Hg NMR spectra in 5 show a high-field shift with a decrease in the flow of electrons to mercury(II) from the sulfur atom due to the intramolecular NH...S hydrogen bond.     

The charge density distribution in a model compound of the catalytic triad in serine proteases

Combined low temperature (28(1) K) X-ray and neutron diffraction measurements were carried out on the co-crystallised complex of betaine, imidazole, and picric acid (1). The experimental charge density was determined and compared with ab initio theoretical calculations at the B3LYP/6-311G(d,p) level of theory. The complex serves as a model for the active site in, for example, the serine protease class of enzymes, the so-called catalytic triad. The crystal contains three short strong N-H...O hydrogen bonds (HBs) with dN...O < 2.7 A. The three HBs have energies above 13 kcalmol(-1), although the hydrogen atoms are firmly localized in the "nitrogen wells". This suggests that low-barrier hydrogen bonding in catalytic enzyme reactions may be a sufficient, but not a necessary, condition for obtaining transition-state stabilization. Structural analysis (e.g., covalent N-H bond lengthening) indicates that the hydrogen bond between H3A and 08 of imidazole and betaine respectively (HB2) is slightly stronger than the bond between H1A and O1A of imidazole and picric acid (HB1), although HB1 is shorter than HB2: (dN...O(HB1)= 2.614(1) A, dN...O(HB2) = 2.684(1) A, dH...O(HB1) = 1.630(1) A, dH...O(HB2)= 1.635(1) A, dN-H(HB1) = 1.046(1) A, dN-H(HB2) = 1.057(1) A). Furthermore, the charge density analysis reveals that HB2 has a larger covalent character than HB1, with considerable polarization of the density towards the acceptor atom. The Gatti and Bader source function (S) is introduced to the analysis of strong HBs. The source function is found to be a sensitive measure for the nature of a hydrogen bond, and comparison with low-barrier and single-well hydrogen bonding systems (e.g., benzoylacetone and nitromalonamide) shows that the low-barrier hydrogen bond (LBHB) state is characterized by an enormously increased hydrogen atom source contribution to the bond critical point in the HB. In this context, HB2 can be characterized as intermediate between localized HBs and delocalized LBHBs.     

Two polymorphs of bis(2‐carbamoylguanidinium) fluorophosphonate dihydrate

Two polymorphs of bis(2‐carbamoylguanidinium) fluorophosphonate dihydrate, 2C₂H₇N₄O⁺·FO₃P²⁻·2H₂O, are presented. Polymorph (I), crystallizing in the space group Pnma, is slightly less densely packed than polymorph (II), which crystallizes in Pbca. In (I), the fluorophosphonate anion is situated on a crystallographic mirror plane and the O atom of the water molecule is disordered over two positions, in contrast with its H atoms. The hydrogen‐bond patterns in both polymorphs share similar features. There are O—H...O and N—H...O hydrogen bonds in both structures. The water molecules donate their H atoms to the O atoms of the fluorophosphonates exclusively. The water molecules and the fluorophosphonates participate in the formation of R⁴₄(10) graph‐set motifs. These motifs extend along the a axis in each structure. The water molecules are also acceptors of either one [in (I) and (II)] or two [in (II)] N—H...O hydrogen bonds. The water molecules are significant building elements in the formation of a three‐dimensional hydrogen‐bond network in both structures. Despite these similarities, there are substantial differences between the hydrogen‐bond networks of (I) and (II). The N—H...O and O—H...O hydrogen bonds in (I) are stronger and weaker, respectively, than those in (II). Moreover, in (I), the shortest N—H...O hydrogen bonds are shorter than the shortest O—H...O hydrogen bonds, which is an unusual feature. The properties of the hydrogen‐bond network in (II) can be related to an unusually long P—O bond length for an unhydrogenated fluorophosphonate anion that is present in this structure. In both structures, the N—H...F interactions are far weaker than the N—H...O hydrogen bonds. It follows from the structure analysis that (II) seems to be thermodynamically more stable than (I).     

N‐tert‐Butyl‐N′‐[5‐cyano‐2‐(4‐methylphenoxy)phenylsulfonyl]urea,a new TXA2 receptor antagonist

The title compound, C₁₉H₂₁N₃O₄S, crystallizes in the space group P2/c with two molecules in the asymmetric unit. The conformation of both molecules is very similar and is mainly determined by an intramolecular N—H...O hydrogen bond between a urea N atom and a sulfonyl O atom. The O and second N atom of the urea groups are involved in dimer formation via N—H...O hydrogen bonds. The intramolecular hydrogen‐bonding motif and conformation of the C—SO₂—NH(C=O)—NH—C fragment are explored and compared using the Cambridge Structural Database and theoretical calculations. The crystal packing is characterized by π–π stacking between the 5‐cyanobenzene rings.     

2‐(Benzoylsulfanyl)acetic acid and 2,5‐dioxopyrrolidin‐1‐yl 2‐(benzoylsulfanyl)acetate by powder X‐ray diffraction studies

The structures of the title compounds, C₉H₈O₃S, (I), and C₁₃H₁₁NO₅S, (II), were determined by X‐ray powder diffraction. Both were solved using the direct‐space parallel tempering algorithm and refined using the Rietveld method. In (I), the C—S—C bond angle is slightly smaller than normal, indicating more p character in the bonding orbitals of the S atom. The carboxylic acid group joins across an inversion centre to form a dimer. The crystal packing includes a weak C—H...O hydrogen bond between an aromatic C—H group and a carboxylic acid O atom to form a two‐dimensional network parallel to (10). The C—S—C bond angle in (II) is larger than its counterpart in (I), indicating that the S atom of (II) has less p character in its bonding orbitals than that of (I), according to Bent's rule. The crystal structure of (II) includes weak C—H...O hydrogen bonds between the H atoms of the methylene groups and carbonyl O atoms, forming a three‐dimensional network.     

Structures,vibrational frequencies,topologies, and energies of hydrogen bonds in cysteine‐formaldehyde complexes

The hydrogen bonding interactions between cysteine (Cys) and formaldehyde (FA) were studied with density functional theory regarding their geometries, energies, vibrational frequencies, and topological features of the electron density. The quantum theory of atoms in molecules and natural bond orbital analyses were employed to elucidate the interaction characteristics in the Cys‐FA complexes. The intramolecular hydrogen bonds (H‐bonds) formed between the hydroxyl and the N atom of cysteine moiety in some Cys‐FA complexes were strengthened because of the cooperativity. Most of intermolecular H‐bonds involve the O atom of cysteine/FA moiety as proton acceptors, while the strongest H‐bond involves the O atom of FA moiety as proton acceptor, which indicates that FA would rather accept proton than providing one. The H‐bonds formed between the CH group of FA and the S atom of cysteine in some complexes are so weak that no hydrogen bonding interactions exist among them. In most of complexes, the orbital interaction of H‐bond is predominant during the formation of complex. The electron density (ρ_b) and its Laplace (?²ρ_b) at the bond critical point significantly correlate with the H‐bond parameter δR, while a linearly relationship between the second‐perturbation energy E(2) and ρ_b has been found as well. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

The orientation of N-H...O=C and N-H...N hydrogen bonds in biological systems: How good is a point charge as a model for a hydrogen bonding atom?

In order to design new ligands for protein-binding sites of unknownstructure, it would be useful to predict the likely sites of hydrogenbonding of an unknown protein fragment to a known molecule. The positions ofmaxima and minima in the electrostatic potential at appropriate distancesfrom the van der Waals surface were calculated for various small molecules,nucleic acid bases, peptide units and amino acid side chains containinggroups which can form the biologically important N-H...O=C andN-H...N hydrogen bonds. Their ability to predict the positions of H andO/N in hydrogen bonded complexes, as predicted by optimising theelectrostatic interactions of pairs of such molecules constrained by themolecular shapes, was assessed. It is shown that extrema in theelectrostatic potential around the isolated molecules give worthwhilepredictions for the locations of hydrogen bonding partners. For moleculesbound by a single N-H...O=C hydrogen bond, the electrostatic maximumassociated with the H is usually less than 1 Å from an acceptor atom,while a C=O electrostatic minimum is generally less than 1.5 Å fromthe hydrogen bond proton. However, a significant number of hydrogen bondsform to the opposite lone pair from the electrostatic minimum, in which casethe separation is up to 3.3 Å. This reflects the broad electrostaticpotential well around a carbonyl oxygen between the lone pair directions.The model predicts when neighbouring atoms drastically change the hydrogenbonding characteristics of an N-H or C=O group. Although the geometries ofhydrogen bonded complexes are influenced by the other van der Waals contactsbetween the molecules, particularly multiple hydrogen bonds, theseinfluences are constant when considering hydrogen bonding to a specificuncharacterised binding site. Hence, the consideration of stericallyaccessible electrostatic extrema will be useful in the design of newligands.     

Evaluation of the individual hydrogen bonding energies in N-methylacetamide chains

The individual hydrogen bonding energies in N-methylacetamide chains were evaluated at the MP2/6-31+G** level including BSSE correction and at the B3LYP/6-311++G(3df,2pd) level including BSSE and van der Waals correction. The calculation results indicate that compared with MP2 results, B3LYP calculations without van der Waals correction underestimate the individual hydrogen bonding energies about 5.4 kJ mol^?1 for both the terminal and central hydrogen bonds, whereas B3LYP calculations with van der Waals correction produce almost the same individual hydrogen bonding energies as MP2 does for those terminal hydrogen bonds, but still underestimate the individual hydrogen bonding energies about 2.5 kJ mol^?1 for the hydrogen bonds near the center. Our calculation results show that the individual hydrogen bonding energy becomes more negative (more attractive) as the chain becomes longer and that the hydrogen bonds close to the interior of the chain are stronger than those near the ends. The weakest individual hydrogen bonding energy is about ?29.0 kJ mol^?1 found in the dimer, whereas with the growth of the N-methylacetamide chain the individual hydrogen bonding energy was estimated to be as large as ?62.5 kJ mol^?1 found in the N-methylacetamide decamer, showing that there is a significant hydrogen bond cooperative effect in N-methylacetamide chains. The natural bond orbital analysis indicates that a stronger hydrogen bond corresponds to a larger positive charge for the H atom and a larger negative charge for the O atom in the N-H?O=C bond, corresponds to a stronger second-order stabilization energy between the oxygen lone pair and the N-H antibonding orbital, and corresponds to more charge transfer between the hydrogen bonded donor and acceptor molecules.     

Mechanism of glucose oxidation by quinoprotein soluble glucose dehydrogenase: insights from molecular dynamics studies

We have generated 3 ns molecular dynamic (MD) simulations, in aqueous solution, of the bacterial soluble glucose dehydrogenase enzyme.PQQ.glucose complex and intermediates formed in PQQ reduction. In the MD structure of enzyme.PQQ.glucose complex the imidazole of His144 is hydrogen bonded to the hydroxyl hydrogen of H[bond]OC1(H) of glucose. The tightly hydrogen-bonded triad Asp163-His144-glucose (2.70 and 2.91 A) is involved in proton abstraction from glucose concerted with the hydride transfer from the C1[bond]H of glucose to the >C5[double bond]O quinone carbon of PQQ. The reaction is assisted by Arg228 hydrogen bonding to the carbonyl oxygen of >C5[double bond]O. The rearrangement of [bond](H)C5(O-)[bond]C4([double bond]O)[bond] of II to [bond]C5(OH)[double bond]C4(OH)[bond] of PQQH(2) hydroquinone is assisted by general acid protonatation of the >C4[double bond]O oxygen by protonated His144 and hydrogen bonds of Arg228 to the oxyanion O5. The continuous hydrogen bonding of the amide side chain of Asn229 to >C4[double bond]O4 oxygen and that of the O5 oxygen of the cofactor to Wat89 is observed throughout the entire reaction.     

Theoretical study of hydrogen bonding interaction in nitroxyl (HNO) dimer: interrelationship of the two N-H...O blue-shifting hydrogen bonds

The hydrogen bonding interactions of the HNO dimer have been investigated using ab initio molecular orbital and density functional theory (DFT) with the 6-311++G(2d,2p) basis set. The natural bond orbital (NBO) analysis and atom in molecules (AIM) theory were applied to understand the nature of the interactions. The interrelationship between one N-H...O hydrogen bond and the other N-H...O hydrogen bond has been established by performing partial optimizations. The dimer is stabilized by the N-H...O hydrogen bonding interactions, which lead to the contractions of N-H bonds as well as the characteristic blue-shifts of the stretching vibrational frequencies nu(N-H). The NBO analysis shows that both rehybridization and electron density redistribution contribute to the large blue-shifts of the N-H stretching frequencies. A quantitative correlations of the intermolecular distance H...O (r(H...O)) with the parameters: rho at bond critical points (BCPs), s-characters of N atoms in N-H bonds, electron densities in the sigma*(N-H), the blue-shift degrees of nu(N-H) are presented. The relationship between the difference of rho (|Deltarho|) for the one hydrogen bond compared with the other one and the difference of interaction energy (DeltaE) are also illustrated. It indicates that for r(H...O) ranging from 2.05 to 2.3528 A, with increasing r(H...O), there is the descending tendency for one rho(H...O) and the ascending tendency for the other rho(H...O). r(H...O) ranging from 2.3528 to 2.85 A, there are descending tendencies for the two rho(H...O) with increasing r(H...O). On the potential energy surface of the dimer, the smaller the difference between one rho(H...O) and the other rho(H...O) is, the more stable the structure is. As r(H...O) increases, the blue-shift degrees of nu(N-H) decrease. The cooperative descending tendencies in s-characters of two N atoms with increasing r(H...O) contribute to the decreases in blue-shift degrees of nu(N-H). Ranging from 2.05 to 2.55 A, the increase of the electron density in one sigma*(N-H) with elongating r(H...O) weakens the blue-shift degrees of nu(N-H), simultaneously, the decrease of the electron density in the other sigma*(N-H) with elongating r(H...O) strengthens the blue-shift degrees of nu(N-H). Ranging from 2.55 to 2.85 A, the cooperative ascending tendencies of the electron densities in two sigma*(N-H) with increasing r(H...O) contribute to the decreases in blue-shift degrees of nu(N-H).     

取代基对N—H…O＝C氢键三聚体中氢键强度的影响

使用MP2方法研究了氢键三聚体中N-H…O=C氢键强度,探讨了氢键受体分子中不同取代基对N-H…O=C氢键强度的影响.研究表明,不同取代基对氢键三聚体中N-H…O=C氢键强度的影响是不同的:取代基为供电子基团,氢键键长r(H…O)缩短,氢键强度增强;取代基为吸电子基团,氢键键长r(H…O)伸长,氢键强度减弱.自然键轨道(NBO)分析表明,N-H…O=C氢键强度越强,氢键中氢原子的正电荷越多,氧原子的负电荷越多,质子供体和受体分子间的电荷转移越多.供电子基团使N-H…O=C氢键中氧原子的孤对电子n(O)对N-H的反键轨道σ~*(N-H)的二阶相互作用稳定化能增加,吸电子基团使这种二阶相互作用稳定化能减小.取代基对与其相近的N-H…O=C氢键影响更大.     

Supramolecular silanol chemistry in the gas phase. Topological (AIM) and population (NBO) analyses of hydrogen-bonded complexes between H3SiOH and selected O- and N-acceptor molecules

Hydrogen bonding of the type SiO-H...A (A = O, N) has been studied in the gas phase for simple H3SiOH.acceptor complexes with the acceptor molecules being O(H)SiH3, OH2, O(H)CH3, O(CH3)2, O(CH3)SiH3, O(SiH3)2, NH3, N(CH3)H2, N(CH3)2H, N(CH3)3, N(CH3)2C6H5, and NC5H5, respectively, at the B3LYP/6-311+(2d,p) level of theory, using Bader's atoms in molecules (AIM) and Weinhold's natural bond orbital (NBO) methodology. For all complexes (except H3SiOH.N(CH3)2C6H5) the complex energy Eadd. is a good estimate for the hydrogen bond energy EHB, which is generally higher in N-acceptor complexes (-5.52 to -7.17 kcal mol-1) than in O-acceptor complexes (-2.09 to -5.06 kcal mol-1). In case of H3SiOH.N(CH3)2C6H5, EHB and Eadd. differ by the energy associated with the loss of n(N)-->pi conjugation in N(CH3)2C6H5 upon complex formation. EHB shows no correlation with O...A distances and the red shifts Deltanu(OH) of the OH-stretching vibrations when different acceptors are compared, although both parameters are commonly used to estimate the strength of the hydrogen bond from spectroscopic and diffraction data. A good linear correlation of the hydrogen bond energy EHB has been established with parameters derived from the AIM and NBO analyses, namely, the electron densities rho(HA) and rho(OH) at the H...A and O-H bond critical points (BCPs) and the NLMO bond orders BONLMO(HA) of the H...A bonds of the H3SiOH.acceptor complexes as well as the change of natural charges DeltaqNPA(O) at the O-donor atom upon H3SiOH.acceptor complex formation. Hydrogen bonding of the type SiO-H...A (A = O, N) has been also studied in the related cyclic multiple H3SiOH.acceptor complexes (H3SiOH)3, (H3SiOH)2.NC5H5, and (H3SiOH)4, respectively, at the same level of theory. Cooperative hydrogen bonding is evident for all cyclic multiple H3SiOH.acceptor complexes, whereby the strongest concomitant strengthening of the hydrogen bonds is observed for (H3SiOH)4 and (H3SiOH)2.NC5H5.     

Experimental electron density study of a complex between copper(II) and the antibacterial quinolone family member ciprofloxacin

An experimental charge density study of a 1 : 1 complex of Cu-cfx (cfx = ciprofloxacin), 1 [Cu(cfx)(H(2)O)(3)]SO4.2H(2)O, has been performed using single-crystal X-ray diffraction data collected at 100 K using conventional Mo Kalpha radiation. Metal-ligand (ML) bonds and hydrogen bonds (HBs) have been analysed using topological analysis of the electron density with the atoms in molecules (AIM) approach. The copper atom binds to two oxygen atoms in one end of the zwitterionic form of the cfx molecule, in addition to forming bonds with three water molecules, forming a square pyramidal coordination geometry. AIM decomposition of the experimental electron density establishes that the copper atom binds more strongly to the cfx molecule than to the water molecules, suggesting that the latter can be detached leaving behind a reactive, water-free Cu-cfx complex available for interaction with e.g. a macromolecular site. AIM analysis of the extensive hydrogen bond pattern reveals that the positively charged N-end of the zwitterionic cfx forms a relatively strong N-H-O hydrogen bond implying that this region of cfx may play an important role in the docking process in the active site. Visualisation and statistics of selected density derived properties on the molecular surface of the isolated cfx molecule vs its metal complexed counterpart points out regions of potential reactivity. The effect of the fluorine atom is to expand the negative region of the electrostatic potential, while the nitrogen end is heavily electropositive and willingly donates to--for molecular docking purposes--relatively strong hydrogen bonding. The Cu atom is highlighted as a potentially highly reactive site which is likely to interact strongly with any given negative ligand.