Hydrogen-bonded Ring Research Articles

Network topology of deeply supercooled water

Empirical potential structure refinements have been made to recent high-energy x-ray diffraction data, providing molecular models of deeply supercooled water. The average O-O coordination number is found to drop from 5.13 at 293 K to 4.85 at 244 K, within 3.5 Å. Triplet O-O-O bond angle distributions reveal a broad peak centred at 96.4° at 293 K which shifts to 100.0° at 244 K, indicative of the local geometry becoming increasingly tetrahedral with decreasing temperature. However, although the number of non-bonded interstitial molecules between the first and second shells is depleted upon cooling, the number of interstitial molecules forming triplets that are embedded within the hydrogen bonded tetrahedral network at θOOO = 53°, remains constant. This is consistent with previous observations of an invariant O-O coordination number with temperature (4.24 out to 3.3 Å) and corresponds to non-bonded molecules positioned at close to half the ideal tetrahedral angle. Both -O-O-O- and hydrogen-bonded -O-H-O- ring length distributions show increases in 6 and 7-membered rings upon supercooling. This is concomitant with a shift and increase in intensity of peaks at r4 ∼8.7 Å and r5 ∼10.8 Å in the oxygen-oxygen pair distribution function, which in the models correspond to correlations between adjacent and next-nearest-neighbour hydrogen-bonded rings.

(3,5-Di-methyl-adamantan-1-yl)ammonium methane-sulfonate (memanti-nium mesylate): synthesis, structure and solid-state properties.

The asymmetric unit of the title compound, C12H22N+·CH3O3S-, consists of three (3,5-di-methyl-adamantan-1-yl)ammonium cations, C12H22N+, and three methane-sulfonate anions, CH3O3S-. In the crystal, the cations and anions associate via N-H⋯O hydrogen bonds into layers, parallel to the (001) plane, which include large supra-molecular hydrogen-bonded rings.

Crystal structure and energetic features of the cocrystal of carbamazepine with 3,5-dinitrobenzoic acid.

The synthesis and detailed description of the crystal structure and energetic features of the 1:1 cocrystal of carbamazepine (5H-dibenzo[b,f]azepine-5-carboxamide, CBZ) with 3,5-dinitrobenzoic acid (35DNBA), i.e. C15H12N2O·C7H4N2O6, are reported. The CBZ and 35DNBA molecules are packed in alternately arranged layers. Two characteristic R22(8) and R22(16) hydrogen-bond ring motifs have been found. The supramolecular architecture, besides the network of hydrogen bonds, is also stabilized by numerous C-H...π, C=O...π, N-O...π, N-O...C and C=O...N weak intermolecular contacts involving neighbouring molecules in the crystal network. Identified interactions have been discussed in detail on the basis of a structural and energetic analysis. The latter approach, performed using the Pixel and CrystalExplorer programs, yielded additional information about the lattice energy and energetic landscape of the respective interactions in the crystal of CBZ·3DNBA with the evaluation of electrostatic, polarization, repulsion and dispersion terms.

Three New Supramolecular Coordination Polymers Based on 1H-pyrazolo[3-b]pyridin-3-amine and 1,3-benzenedicarboxylate Derivatives.

Three new supramolecular coordination polymers, namely [Zn(1,3-BDC)(HL)]n (Polymer 1), [Zn3(1,3,5-BTC)2(HL)2(H2O)2]n (Polymer 2), and [Zn9(5-SO3-1,3-BDC)2(L)8(OH)4]n (Polymer 3), were synthesized under solvothermal conditions, based on 1H-pyrazolo[3,4-b]pyridin-3-amine (HL) along with 1,3-benzenedicarboxylate (1,3-BDC) and its derivatives, such as 1,3,5-benzenetricarboxylate (1,3,5-BTC) and 5-sulfo-1,3-benzenedicarboxylate (5-SO3-1,3-BDC). Polymers 1–3 were characterized by elemental analysis, IR spectroscopy, powder X-ray diffraction (PXRD), and single crystal X-ray diffraction analysis. Polymer 1 exhibited a two-dimensional (2D) 4-connected sql net. The neighboring 2D nets were further linked into a 3D supramolecular network by hydrogen-bonding interactions. Polymer 2 displayed a 3D (4, 4, 4)-connected network, which was further stabilized by (14) and S(9) hydrogen-bonding rings along with π–π interactions. The 2D sheet structure of Polymer 3 was constructed by novel quasi-linear nonanuclear Zn(II) units, which further extended into a 3D supramolecular structure by hydrogen-bonding interactions. The solid-state photoluminescence properties of Polymers 1–3 were also investigated.

Computational investigation of Au·H hydrogen bonds involving neutral AuI N-heterocyclic carbene complexes and amphiprotic binary hydrides.

In this computational study, we investigate the ability of various neutral R-AuI-NHC (NHC = N-heterocyclic carbene) complexes [R = H, CH3, Cl, OH] to form hydrogen bonds with the amphiprotic binary hydrides NH3, H2O and HF. Optimized geometries of the adducts calculated at various levels of theory all exhibit Au⋯HX hydrogen bonds. In adducts of complexes containing NHC ligands with α(N)H units, (NH)carbene⋯XH interactions also exist, yielding hydrogen-bonded rings with graph-set notation [Formula: see text] that correspond to pseudo chelates with κ2C,H coordination. AIM analysis at the MP2/aug-cc-pVTZ-pp level of theory indicates that the (NH)carbene⋯XH hydrogen bonds are generally stronger than the Au···HX interactions, except for those involving HF. The Au⋯HX interactions vary with the Lewis basicity of the Au(I) center as a result of the nature of the R ligand, while the (NH)carbene⋯XH hydrogen bonds are unaffected by R. Energy decomposition analysis at the BP86/TZP level of theory identifies the origin of this difference as the greater component of polarization involved in Au⋯HX interactions. Replacing the α(N)Hs with methyl groups prevents formation of a strong (NH)carbene⋯XH interaction, thus reducing the overall stabilization of the adducts. Nevertheless, the Au⋯H interactions remain largely unchanged and are strong enough to sustain the hydrogen-bonded complexes, although weak C-H⋯X interactions are often also present.

Development of Imidazo[1,2- a]pyridine Derivatives with an Intramolecular Hydrogen-Bonded Seven-Membered Ring Exhibiting Bright ESIPT Luminescence in the Solid State.

Imidazo[1,2- a]pyridine derivatives with different hydroxyaryl units (1-3), which could potentially form an intramolecular hydrogen-bonded seven-membered ring in either a planar or a twisted conformation, were newly developed, and the effect of conformation and steric repulsion on the excited-state intramolecular proton transfer (ESIPT) luminescence was evaluated. Among them, 1 and 2 formed an intramolecular hydrogen-bonded seven-membered ring in the crystalline state and exhibited efficient ESIPT luminescence in the solid state (quantum yield up to 0.45).

The Chiral Trimer and a Metastable Chiral Dimer of Achiral Hexafluoroisopropanol: A Multi-Messenger Study.

1,1,1,3,3,3-hexafluoro-propan-2-ol aggregates preferentially into an achiral dimer of achiral monomers, but the trimer is found to prefer three metastable chiral monomer units arranged into a strained OH⋅⋅⋅O hydrogen-bonded ring, which is reinforced by secondary CH⋅⋅⋅FC interactions. This is shown by a combination of infrared, microwave, and Raman spectroscopy in supersonic jet expansions and supported by high-level quantum chemical calculations. It involves an activation of the monomers by >15 kJ mol-1 , clearly driven by the much stronger hydrogen-bond interaction available to the gauche and even more to the cis monomer units.

Some Problems of Computer Simulation of Non-Bonded Interactions in DNA

Some difficulties in the application of various methods of computer modeling for the study of regularities of formation of spatial structure of DNA are analyzed. Computations of intermolecular interaction energy for all ten pairwise combinations of methylated bases (1-methylpyrimidines and 9-methylpurines) in various mutual base positions were performed due to the important role of nitrous bases. Local energy minima that correspond to different mutual positions of the molecules have been found using different molecular mechanics force fields, ab initio quantum mechanics, and density functional theory. The energy minima that correspond to three types of mutual molecule positions, namely, (1) base positions with two N–H…O and/or N–H…N hydrogen bonds; (2) nearly parallel arrangements of base ring planes, that is, base stacking; and (3) T-shaped (nearly perpendicular) base ring positions and hydrogen bond formation were extensively studied. The majority of these minima were obtained using methods of different complexities; however, the method of calculation determines which minimum is the deepest (global) for certain base combination and relative depths of various minima. Analysis of these simulations and of the computations on simple DNA fragments, as well as of extensive data from the literature suggests that there has been no method suitable for quantitative description of all the experimental data on non-bonded interactions in DNA. The comparison of energy and structure characteristics of the complexes calculated by various methods demonstrates their abilities and shortcomings. A valid description of non-bonded interactions of nucleic acids requires additional investigations of their simple fragments and the combined use of various methods.

Synergy of Water and Ammonia Hydrogen Bonding in a Gas-Phase Reaction.

We report a very significant cooperative effect of water-ammonia hydrogen bonding in their reactions with a Criegee intermediate, syn-CH3CHOO. Under near ambient conditions, we found that the reaction of syn-CH3CHOO with NH3 becomes much faster (by up to 138 times) at high humidity. Intriguingly, merely adding NH3 (or H2O) alone has almost no effect on the rate of syn-CH3CHOO decay. Quantum chemistry calculation shows that the main reaction involves a hydrogen-atom (or proton) relay in a hydrogen-bonded ring structure; on the product side, a C-N bond is formed and H2O is regenerated as a catalyst. This result demonstrates a new category of reaction in which having two types of hydrogen-bond players (NH3 and H2O) is much more effective than having only one.

Outer Coordination Sphere Proton Relay Base and Proximity Effects on Hydrogen Oxidation with Iron Electrocatalysts

The intra- and intermolecular deprotonation reactions of [(CpC5F4N)Fe(PEtNR′PEt)H]+ (PEtNR′PEt = (Et2PCH2)2NR′) complexes are rate-limiting processes in the electrocatalytic oxidation of hydrogen and can be mediated by an amine base in the outer coordination sphere (OCS) by facilitating the matching of energy of deprotonation intermediates. A series of complexes with different N-substituents (R′ = Me, Et, CH2OMe, CH2N(Ph)Me, and (CH2)nNMe2; n = 1–4) was examined computationally using density functional theory to determine the influence of the identity and proximity of the OCS base on the intramolecular deprotonation. Complexes with an OCS dimethylamino substituent were the most suitably energy matched. The number of carbon atoms between the secondary and OCS nitrogen atoms dictated the strength of the hydrogen-bonding interaction and ring strain following deprotonation of the iron hydride. The previously reported [(CpC5F4N)Fe(PEtNR′PEt)H]+ (R′ = (CH2)3NMe2) electrocatalyst was predicted to have the most f...

A stable AIEgen cis-diarylethene-based 'ESIPT' benchmark.

The one-flask synthesis of seven-membered free-base BOPYINs (NBs) using benzo indole and β-substituted pyrrole moieties has been reported. This stable cis-configuration of diarylethenes with Aggregation Induced Emission (AIE) properties was locked by the seven-membered ring hydrogen bond (HB) and steric hindrance, which made 'Excited-State Intramolecular Proton Transfer (ESIPT)' phenomena take place in this benchmark.

Conformational Analysis of n→π* Interactions in Collagen Triple Helix Models.

Ab initio calculations of three models of collagen at positions Pro-Pro-Gly (1), Pro-Gly-Pro (2), and Gly-Pro-Pro (3) were performed to assess the conformational variation of n→π* contributions to the stability of the collagen triple helix. Full conformational analyses by relaxed potential-energy scans of the Ψ dihedral angle of the central residue in models 1, 2, and 3 revealed the presence of several n→π* interactions. In model 2, with Gly as the central residue, both the Φ and Ψ dihedral angles of Gly were scanned. Most minima of each model contained one or two n→π* interactions, with pyramidalization at the π* carbon. We also observed pyramidalization at the n→π* donor amide nitrogens. Minima with hydrogen-bond or non-native n→π* interactions compete with the collagen stabilizing n→π* interactions. The collagen-like n→ re-π* conformation was found as the global minimum only in model 3. The global minimum of 1 had a 5-membered ring hydrogen bond with an additional weak n→ si-π* interaction. The global minimum of 2 was in the extended conformation. We predict that the n→π* interactions found in native collagen, while individually small, cumulatively contribute to the stability of the triple helix conformation of collagen.

Criegee Intermediate Reaction with Alcohol Is Enhanced by a Single Water Molecule.

The role of water in gas-phase reactions has gained considerable interest. Here we report a direct kinetic measurement of the reaction of syn-CH3CHOO (a Criegee intermediate or carbonyl oxide) with methanol at various relative humidity (RH = 0-80%) under near-ambient conditions (298 K, 250-755 Torr). The data indicate that a single water molecule expedites the reaction by up to a factor of three. The rate coefficient of the corresponding reaction, syn-CH3CHOO + CH3OH + H2O → products, has been determined to be (1.95 ± 0.11) × 10-32 cm6 s-1 at 298 K, with no observable pressure dependence for 250-755 Torr. Quantum chemistry calculation shows that the dominating pathway involves a hydrogen-bonded ring structure, in which methanol is donating a hydrogen atom to water, water is donating a hydrogen atom to the terminal oxygen atom of the Criegee intermediate, and, on the product side, H2O is reformed and acts as a catalyst.

High and low density patches in simulated liquid water.

We present insights into the nature of structural heterogeneities in liquid water by characterizing the empty space within the hydrogen bond network. Using molecular dynamics simulations, we show that density fluctuations create regions of empty space characterized by a diverse morphology - from spherical to fractal-like voids. These voids allow for the identification of low and high density patches of the liquid, encompassing short (0.3-0.5 nm) as well as long (1-2 nm) length-scales. In addition, we show that the formation of these patches is coupled to collective fluctuations involving the topology of hydrogen-bonded rings of water molecules. In particular, water molecules in the high density patches tend to be slightly more tetrahedral - which is consistent with the predictions of the hydrophobic effect.

Charge-assisted hydrogen bonding in three diaminobenzene salts.

Hydrogen-bonding interactions play an important role in the rational design of crystal systems with desirable architectures. The crystal structures of benzene-1,2-diaminium sulfate sesquihydrate, C6H20N22+·SO42-·1.5H2O, (1), benzene-1,3-diaminium tetrachloridozincate(II), (C6H20N2)[ZnCl4], (3), and 3-aminoanilinium perchlorate, C6H9N2+·ClO4-, (4), are reported. Hydrated salt (1) is a polymorph (space group C2/c) of a previously reported [Anderson et al. (2011). Cryst. Growth Des. 11, 4904-4919] crystalline modification of salt (2) (space group P21/c). The contents of the asymmetric unit of (2) are twice that of (1). In each, the extended structures exhibit hydrogen bonds, resulting in chains of ions and hydrogen-bonded rings with an R44(8) motif involving water molecules. Hirshfeld surface analysis shows that a significant difference between the two is the degree of C...C interaction. Salt (3) exhibits an extended structure having hydrogen-bonded rings and parallel benzene rings, with a centroid-to-centroid separation of 3.860 (2) Å. Salt (4) displays a three-dimensional superstructure that results from linked planes of ions joined by an extensive hydrogen-bonding network involving N-H...O, N-H...N and C-H...π interactions. The cation-anion and N-H...N interaction energies in (4), determined using density functional theory (DFT), show significantly stronger aminium-perchlorate than amine-perchlorate interactions.

Graph theory for automatic structural recognition in molecular dynamics simulations.

Graph theory algorithms have been proposed in order to identify, follow in time, and statistically analyze the changes in conformations that occur along molecular dynamics (MD) simulations. The atomistic granularity level of the MD simulations is maintained within the graph theoric algorithms proposed here, isomorphism is a key component together with keeping the chemical nature of the atoms. Isomorphism is used to recognize conformations and construct the graphs of transitions, and the reduction in complexity of the isomorphism has been achieved by the introduction of "orbits" and "reference snapshots." The proposed algorithms are applied to MD trajectories of gas phase molecules and clusters as well as condensed matter. The changes in conformations followed over time are hydrogen bond(s), proton transfer(s), coordination number(s), covalent bond(s), multiple fragmentation(s), and H-bonded membered rings. The algorithms provide an automatic analysis of multiple trajectories in parallel, and can be applied to ab initio and classical MD trajectories alike, and to more coarse grain representations.

Hydrazone to deprotonated azo/azo-enol transformation for isomeric pyrazolone based heterocyclic dyes via metal-ion complexation

Two pairs of isomeric heterocyclic dyes were synthesized successfully by diazotization reactions between the common 1-phenyl-3-methyl-5-pyrazolone coupling component and 2-aminobenzoic/4-aminobenzoic acid as well as 2-amino-5-nitrophenol/2-amino-3-nitrophenol. The introduction of additional carboxyl and hydroxyl groups in the phenyl ring makes them good multidentate chelating ligands in terms of coordination chemistry, and three Cu(II) and one Fe(II) dye-metal complexes were then produced showing different deprontonated states in ligands (monovalent and divalent), metal-ligand ratios (1:1 and 1:2) and structural diversity (mononuclear, dinuclear and one-dimensional chain). Red shifts of 3–6 nm in the UV–Vis spectra are observed for the ortho-COOH and ortho-NO2 dyes compared with corresponding para substituted ones, which could be supported by the formation of fused six-membered intramolecular hydrogen-bonding rings found in their single-crystal structures involving the hydrazone protons. More interesting, different from our previously reported solvent and pH induced hydrazone to azo-keto transformation, another kind of hydrazone to azo-enol transformation has been observed for our pyrazolone based dyes in addition to conventional hydrazone to deprotonated azo transformation after metal-ion complexation.

The structure of 9-(3-bromo-6-chloro-2-hy-droxy-phen-yl)-10-(2-hy-droxy-ethyl)-3,6-diphenyl-3,4,5,6,7,9-hexa-hydro-2H-acridine-1,8-dione.

In the structure of the title compound C33H29BrClNO4, (I), the hexa-hydro-2H-acridine ring system has a hy-droxy-ethyl substituent on the N atom and a 3-bromo-6-chloro-2-hy-droxy-phenyl substituent on the central C atom at the 9-position. An unusual feature of the mol-ecule is that the substituents at the 3- and 5-positions of the outer cyclo-hexenone rings are phenyl rings rather than the more common dimethyl substituents. C atoms on both of the cyclo-hexenone rings are disordered over two sites. In the crystal structure, O-H⋯O, C-H⋯O and C-H⋯π(ring) hydrogen bonds combine with an Br-O and unusual C-Br⋯π(ring) halogen bonds to generate a three dimensional network with mol-ecules stacked along the a-axis direction.

Variations of the Hydrogen Bonding and Hydrogen-Bonded Network in Ethanol-Water Mixtures on Cooling.

Molecular dynamics computer simulations have been conducted for ethanol-water liquid mixtures in the water-rich side of the composition range, with 10, 20, and 30 mol % of alcohol, at temperatures between room temperature and the experimental freezing point of the given mixture. All-atom-type (optimized potential for liquid simulations) interatomic potentials have been assumed for ethanol, in combination with two kinds of rigid water models (SPC/E and TIP4P/2005). Both combinations have provided excellent reproductions of the experimental X-ray total structure factors at each temperature; this yielded a strong basis for further structural analyses. Beyond partial radial distribution functions, various descriptors of hydrogen-bonded assemblies, as well as of the hydrogen-bonded network have been determined. A clear tendency was observed toward that an increasing proportion of water molecules participate in hydrogen bonding with exactly two donor and two acceptor sites as temperature decreases. Concerning larger assemblies held together by hydrogen bonding, the main focus was put on the properties of cyclic entities: it was found that, similarly to methanol-water mixtures, the number of hydrogen-bonded rings has increased with lowering temperature. However, for ethanol-water mixtures, the dominance of 5-fold rings, and not 6-fold rings, could be observed.

Metal-ion mediated regioselective complexation for bis(pyridine-2,6-dione) dyes with different deprotonated states

Bis(pyridine-2,6-dione) dyes with different pyridine N-tails are first used as the multidentate ligands to prepare a series of CaII, NaI, CuII and NiII complexes. 1H NMR and UV–Vis spectral as well as X-ray single-crystal analyses reveal that they have mononuclear, dinuclear and one-dimensional structures bearing bis(pyridine-2,6-dione) based ligands with more coordination sites, distinguishable coordination modes and deprotonated states. In addition, the transformations from the hydrazone form to deprotonated hydrazone form and deprotonated azo form have been observed before and after metal-ion complexation. pH-controlled syntheses and pH-induced conversion have been achieved for a pair of alkali-earth metal CaII complexes, which can be verified by (1) their different colors and crystalline forms in syntheses; (2) different chemical shifts of pyridine methyl groups in the 1H NMR spectra; (3) the presence of an isosbestic point during the pH-titration experiments; (4) comparisons on the coordination bond lengths and dihedral angles between the two pyridine rings for related complexes. It is very interesting to mention that regioselective complexation has been found for bis(pyridine-2,6-dione) based ligands, which could be explained by the competition between coordination abilities of metal ions and strength of intramolecular hydrogen-bonding ring involving the central hydrazone proton.