Hydrogen-bonding Associations Research Articles

Tetraaquabis(5-carboxy-2-nitrobenzoato-κO)manganese(II) dihydrate: a metal–water chain complex containing cyclic water tetramers

In the title complex, [Mn(C(8)H(4)NO(6))(2)(H(2)O)(4)] x 2H(2)O, cyclic water tetramers forming one-dimensional metal-water chains have been observed. The water clusters are trapped by the co-operative association of coordination interactions and hydrogen bonds. The Mn(II) ion resides on a center of symmetry and is in an octahedral coordination environment comprising two O atoms from two 5-carboxy-2-nitrobenzoate ligands and four O atoms from water molecules.

3,5-Dinitrosalicylic Acid in Molecular Assembly. III. Proton-Transfer Compounds of 3,5-Dinitrosalicylic Acid with Polycyclic Aromatic and Heteroaromatic Amines, and Overall Series Structural Systematics

The crystal structures of the 1:1 proton-transfer compounds of 3,5-dinitrosalicylic acid (dnsa) with a series of common polycyclic aromatic and heteroaromatic amines (quinoline, 1-naphthylamine, 1,2,3,4-tetrahydroquinoline, quinaldic acid, benzimidazole, 1,10-phenanthroline, and 2,2′-bipyridine) have been determined and the hydrogen-bonding associations in each analyzed. The compounds are [(C9H8N)+(dnsa)–] 1, [(C10H10N)+(dnsa)–] 2, [(C9H12N)+(dnsa)–] 3, [(C10H8NO2)+(dnsa)–] 4, [(C7H7N2)+(dnsa)–] 5, [(C12H9N2)+(dnsa)–] 6, and [(C10H9N2)+(dnsa)–] 7. In all compounds, protonation of either the substituent amino group or the hetero-N of the Lewis base occurs, with subsequent hydrogen bonding via this and other hydrogen donors variously to the carboxylate, phenate, and nitro oxygen acceptors of the dnsa anions. The result is the formation of primary N+–H···O associations which with secondary peripheral interactions, which within this set of compounds includes an increased incidence of aromatic C–H···O associations, give framework polymer structures. In three of the compounds [1, 4, and 6], cation–anion π–π interactions are also found. The completion of this series of compounds has now allowed the categorization of the molecular assembly modes in the proton-transfer compounds of 3,5-dinitrosalicylic acid.

Competing hydrogen-bonding patterns and phase transitions of 1,2-diaminoethane at varied temperature and pressure

1,2-diaminoethane has been in-situ pressure- and temperature-frozen; apart from two known low-temperature phases, Ialpha and II, three new phases, Ibeta, Igamma and III, have been observed and their structures determined by X-ray diffraction. The measurements at 0.1 MPa were carried out at 274, 243 and 224 K, and 296 K measurements were made at 0.15 GPa (phase Ialpha), at 0.3 and 1.1 GPa (phase Ibeta), at 1.5 GPa (phase Igamma), and at 0.2, 0.3 and 0.5 GPa (phase III). All these phases are monoclinic, space group P2(1)/c, but the unit-cell dimension of phases Ialpha and III are very different at 296 K: aIalpha=5.078 (5), bIalpha=7.204 (8), cIalpha=5.528 (20) A, betaIalpha=115.2 (2) degrees at 0.15 GPa, and aIII=5.10 (3), bIII=5.212 (2), cIII=7.262 (12) A, betaIII=111.6 (4) degrees at 0.2 GPa, respectively; in both phases Z=2. An ambient-pressure low-temperature phase II has been observed below 189 K. Discontinuities in the unit-cell dimensions and in the N...N distance mark the isostructural transition between phases Ialpha and Ibeta at 0.2 GPa, which can be attributed to a damping process of the NH2 group rotations. In phase Igamma the unit-cell parameter a doubles and Z increases to 4. The molecule has inversion symmetry in all the structures determined. 1,2-Diaminoethane can be considered as a simple structural ice analogue, but with NH...N hydrogen bonds and with the H-atom donors (four in one molecule) in excess over H-atom acceptors (two per molecule). Thus, the transformations of 1,2-diaminoethane phases involving the conformational dynamics affect the hydrogen-bonding geometry and molecular association in the crystal. The 1,2-diaminoethane:1,2-dihydroxyethane mixture has been separated by pressure-freezing, and a solid 1,2-diaminoethane crystal in liquid 1,2-dihyroxyethane has been obtained.

Processes of molecular association and excimeric emission in protonated N, N-dimethylformamide

Formation of associates of N, N-dimethylformamide (DMF) molecules was studied to clarify their role in photoluminescent activity of protonated DMF solutions. The association of DMF molecules was observed in dilute aqueous solutions at concentrations of DMF above ∼4x10 −2 M. The association is enhanced when the C O bond of the DMF molecule is activated by protonation with hydrochloric acid, which leads to appearance of an excimeric emission at ∼530 nm. The excitation spectrum of the excimeric emission showed the excitation maximum in the region of the absorption of DMF associates, which is a first evidence of a more complex mechanism of excimer formation originating from excitation of associated rather than monomeric molecules in the ground state. A simple approach was provided to evaluate a number of molecules in the excimer structure. An original theory has been developed, and it was calculated that the DMF excimer has a dimeric nature. A model of the excimer formation was proposed, which suggests that a hydrogen-bonded associate is an intermediate form leading to the excimeric structure upon excitation. It was observed that DMF possesses also a monomeric emission with the emission maximum at ∼385 nm, which was attributed to the intramolecular charge-transfer process. It has been found that the change in structure of the DMF associates via the liquid–solid phase transition affects both excitation and emission bands of excimers, so that the excimeric emission shifts to the blue region and intermixes with the emission of DMF monomers.

Intermolecular and Intramolecular Forces: A General Chemistry Laboratory Comparison of Hydrogen Bonding in Maleic and Fumaric Acids

This article presents a simple laboratory experiment that is designed to enhance students' understanding of inter- and intramolecular hydrogen bonding by demonstrating the comparative effect of these phenomena on some chemical and physical properties. Ball-and-stick molecular models are built and used for the consideration of hydrogen bonding possibilities in cis-1,2-dicarboxyethene (maleic acid) and trans-1,2-dicarboxyethene (fumaric acid). On the basis of the expected relative strengths of inter- and intramolecular hydrogen bond associations, students predict which of the two compounds has the higher melting point, higher first acid ionization constant, and higher second acid ionization constant. Appropriate measurements are then performed and used to identify which of a pair of compounds is maleic acid. Students are given standard enthalpies of sublimation, formation, combustion, and hydrogenation and asked to consider their relative values based on intra- and intermolecular hydrogen bonding.

The β-form of trans-3-(2-nitrophenyl)prop-2-enoic acid at 130 K

The crystal structure of a non-centrosymmetric polymorphic modification of the title compound, C9H7NO4, determined at 130 K, shows the presence of 21 screw-generated one-dimensional zigzag chains formed through catemeric C(4) syn–anti carboxylic acid hydrogen-bonding associations.

Two pseudopolymorphic hydrates of brucine: brucine–water (1/4) and brucine–water (1/5.25) at 130 K

The structures of two pseudopolymorphic hydrates of brucine, C23H26N2O4·4H2O, (I), and C23H26N2O4·5.25H2O, (II), have been determined at 130 K. In both (I) and (II) (which has two independent brucine mol­ecules together with 10.5 water mol­ecules of solvation in the asymmetric unit), the brucine mol­ecules form head-to-tail sheet substructures, which associate with the water mol­ecules in the inter­stitial cavities through hydrogen-bonding associations and, together with water–water associations, give three-dimensional framework structures.

DFT analysis of diclofenac activity and cation type influence on the theoretical parameters of some diclofenac complexes

The twisted structure of diclofenac sodium that is behind the excessively remarkable reactivity of this drug, was investigated by DFT calculations at the B3LYP/6-311G (d) level of theory. The repulsion forces, existing within the molecule because of the simultaneous presence of the acetate moiety as well as the two Cl atoms, created a twisted (74°) diphenylamine structure to yield a preferred orientation. B3LYP/ 6-311G (d) calculations of diclofenac and its complexes, ML 2 (L=Ca, Mg, Zn), showed that distortions of the geometric parameters were due to the differing hybridizations depending on the cation type in question. The energy gap values, Δ E, increased in the order Mg>Zn>Ca, pointing out that the energy associated with electron pairing is greatest in the Mg 2+ complex, due to the [Ne]3s 2 configuration and large charge to radius ratio (3.3) of the metal. The charge density contour plots of the complexes showed the negative charge as condensed around the N atom, indicating a very highly polarized M–N coordinate bond. Both the acid form and sodium salt displayed the typical weak N–H⋯O hydrogen bond association which is absent in the Mg, Ca and Zn complexes. The distance between H and O in all three (3.837 Mg, 3.307 Ca and 4.277 Zn Å) exceeded the possible limit of 3.0 Å.

FT-IR and Raman spectroscopic study of di-urea cross-linked poly(oxyethylene)/siloxane ormolytes doped with Zn 2+ ions

The interactions occurring in di-urea ( NHC( O)NH ) cross-linked poly(oxyethylene) (POE)/siloxane hybrids (di-ureasils) doped with zinc triflate (Zn(CF 3SO 3) 2) were investigated by Fourier Transform infrared (FT-IR) and Raman (FT-Raman) spectroscopies. Bonding of the Zn 2+ ions to the urea carbonyl oxygen atoms occurs in the entire range of compositions studied (∞ > n ≥ 1, where n, salt content, is the molar ratio of oxyethylene moieties per Zn 2+ ion). At n > 20 the incorporation of the guest cations progressively reduces the number of free C O groups. At n = 20 the saturation of the urea cross-links is attained and the Zn 2+ ions start to coordinate to the POE chains giving rise to the formation of a crystalline POE/Zn(CF 3SO 3) 2 complex. The latter process occurs at the expense of the destruction of the hydrogen-bonded POE/urea structures of the host di-ureasil structure. New hydrogen-bonded associations, more ordered than the urea–urea aggregates present in the non-doped matrix and including Zn 2+⋯O C coordination, emerge in parallel. “Free” and weakly coordinated CF 3SO 3 − ions, present in all the xerogels studied, appear to be the main charge carriers of the conductivity maximum of this family of ormolytes located at n = 60 at 30 °C. In materials with n ≤ 20 contact ion pairs, “cross-link separated” ions pairs and higher ionic aggregates appear. The data reported demonstrate that the behaviour of the di-ureasils doped with triflate salts depends on the type of cation.

Temperature-dependent FTIR spectroscopic and thermoanalytic studies of hydrogen bonding of hydroxyl (phenolic group) terminated hyperbranched aromatic polyesters

The formation and modification of inter- and intramolecular hydrogen bonds of hydroxyl (phenolic group) terminated hyperbranched aromatic polyesters (HBP-OH) have been studied by temperature-dependent Fourier transform infrared (FTIR) spectroscopy. Three ‘heating–annealing–cooling’ (HAC) cycles starting from room temperature to 235 °C were measured. The IR spectroscopic results indicate different types of hydrogen bond association. The weakening and breaking of hydrogen bonds with increasing temperature was observed. Additionally, a curve fitting procedure of the hydroxyl and carbonyl vibration regions has been done to gather additional information of the hydrogen bond association. On the basis of the band shifts and the changes of the normalised integral band intensity (NIBI) and halfwidth of a band (HWB), the formation of a network of hydrogen bonds was proposed. Four different interactions regarding hydroxyl (phenolic) groups association were detected. Several types of associated carbonyl groups existing within HBP-OH were revealed. The spectra and curve fitting results indicate the relative stability of formed bond structures with participation of the ester groups of the HBP rigid segments in the studied temperature region. Differential scanning calorimetry (DSC) was applied to reveal changes in thermal behaviour after the first, the second and the third HAC cycle. As expected, the aromatic ester backbone structure strongly influences the glass transition. Therefore, the performed measurements did not show any changes in glass transition related to the rearrangements in the hydrogen bonded network.

Syntheses, π-stacking interactions and base-pairings of uracil pyridinium salts and uracilyl betaines with nucleobases

Reaction of 6-chlorouracil with 4-(dimethylamino)pyridine, 4-methylpyridine, and pyridin-4-yl-morpholine yielded pyridinium-substituted uracils as chlorides which were converted into pyridinium uracilates by deprotonation. These heterocyclic mesomeric betaines are cross-conjugated and thus possess separate cationic (pyridinium) and anionic (uracilate) moieties. Calculations and X-ray single crystal analyses were performed in order to characterize these systems and to compare the salts with the betaines. (1)H NMR experiments in D(2)O proved pi-interactions between the uracilyl betaines and adenine, adenosine, as well as adeninium. No pi-stacking interactions were detected between the betaines and guanosine. The acidic N8-H group of the uracil pyridinium salts caused acid-base reactions which were observed in parallel to pi-stacking interactions. Self-complementarity of the modified uracils was detected by (1)H NMR experiments in DMSO-d(6) and electrospray ionisation mass spectrometry (ESIMS). Ab initio calculations predicted base-pairings of the modified uracils with adeninium, cytosine, and guanine. Several geometries of hydrogen-bonded associates were calculated. Hoogsteen pairings between the uracil-4-(dimethylamino)pyridinium salt and adeninium, as well as associates between the corresponding betaine plus cytosine, and the betaine plus guanine were calculated, and the most stable conformations were determined. In the ESI mass spectra, prominent peaks of associates between the modified uracils and adeninium, cytosine, cytidine, guanosine and d(CpGp) were detected.

Molecular Recognition in Proton-Transfer Compounds of Brucine with Achiral Substituted Salicylic Acid Analogues

The 1:1 proton-transfer brucinium compounds from the reaction of the alkaloid brucine with 5-nitrosalicylic acid, 3,5-dinitrosalicylic acid, and 5-sulfosalicylic acid, namely anhydrous brucinium 5-nitrosalicylate (1), brucinium 3,5-dinitrosalicylate monohydrate (2), and brucinium 5-sulfosalicylate trihydrate (3) have been prepared and their crystal structures determined by X-ray crystallography. All structures further demonstrate the selectivity of brucine for meta-substituted benzoic acids and comprise three-dimensional hydrogen-bonded framework polymers. Two of the compounds (1 and 3) have the previously described undulating brucine sheet host-substructures which incorporate interstitially hydrogen-bonded salicylate anion guest species and additionally in 3 the water molecules of solvation. The structure of 2 differs in having a three-centre brucinium–salicylate anion bidentate N+–H···O(carboxyl) hydrogen-bonding association linking the species through interstitial associations involving also the water molecules of solvation. A review of the crystallographic structural literature on strychnine and brucine is also given.

Synthesis and characterization of a proton-transfer complex of 1,2,4,5-benzenetetracarboxylic acid with 1, 10-phenanthroline

A proton-transfer complex of 1,2,4,5-benzenetetracarboxylic acid (H4BTC) with 1,10-phenanthroline (phen), [(H2BTC)2−·2(Hphen)+·(H4BTC)] was synthesized and characterized by IR, UV-Vis spectra and luminescence. The structure was determined by X-ray single crystal diffraction. It crystallizes in the triclinic system, space group P-1 with a=7.3767(15), b=10.704(2), c=12.890(3) A, α=102.96(3), β=105.71(3), γ=99.68(3)o, V=926.0(3) A3, Dc=1.558 g/cm3, Z=2, μ(Mo-Kα)=0.121 mm−1 and F(000)=448. The final R=0.0401 and wR=0.0862 for 2983 observe reflections with [1>2σ(1)]. It is composed of discrete H4BTC molecules, H2BTC2− anions and, [Hphen]+ cations. The extensive hydrogen-bonding associations formed between the H4BTC molecules and H2BTC2− anions result in the formation of a two-dimensional layer, to which the [Hphen]+ cations are attached through the hydrogen bonds formed between the carboxyl groups of H4BTC and the NH groups of [Hphen]+. Under the excitation of UV light, it emits an intense blue luminescence.

Local Structure and Near-Infrared Emission Features of Neodymium-Based Amine Functionalized Organic/Inorganic Hybrids

Nd(3+)-based organic/inorganic hybrids have potential application in the field of integrated optics. Attractive sol-gel derived di-urea and di-urethane cross-linked poly(oxyethylene) (POE)/siloxane hybrids (di-ureasils and di-urethanesils, respectively) doped with neodymium triflate (Nd(CF(3)SO(3))(3)) were examined by Fourier transform mid-infrared (FT-IR), Raman (FT-Raman), (29)Si magic-angle spinning (MAS) nuclear magnetic resonance (NMR) and photoluminescence spectroscopies, and small-angle X-ray scattering (SAXS). The goals of this work were to determine which cation coordinating site of the host matrix (ether oxygen atoms or carbonyl oxygen atoms) is active in each of the materials analyzed, its influence on the nanostructure of the samples and its relation with the photoluminescence properties. The main conclusion derived from this study is that the hydrogen-bonded associations formed throughout the materials play a major role in the hybrids nanostructure and photoluminescence properties.

Hydrogen bonding patterns in pyrazole Pt(II- and IV) chloride complexes

The solid-state packing arrays of the platinum(II) trans- and cis-[PtCl 2(PzH) 2] ( 1 and 2) and platinum(IV) trans- and cis-[PtCl 4(PzH) 2] ( 3 and 4) complexes have been examined and the occurrence of N–H ⋯ Cl hydrogen-bonding associations in those structures has been discussed. Although different packing motifs are observed, in all cases molecules are interacting mostly via NH ⋯ Cl and CH ⋯ Cl associations. The square planar 1 and 2 form stacked arrays of PtCl 2(PzH) 2, which are supported by NH ⋯ Cl and CH ⋯ Cl hydrogen bonding. The isomeric structure of the complexes and orientation of the PzH rings determine NH ⋯ Cl bonding mode (intermolecular or intramolecular) and also the extent of the platinum–platinum interaction. The synthetic procedures for the preparation of 1– 4 along with elemental and X-ray analyses, TG/DTA, FAB +-MS, IR, and 1H and 13C{ 1H} NMR data are also given in this article.

Dynamic NMR studies of base-catalyzed intramolecular single vs. intermolecular double proton transfer of 1,3-bis(4-fluorophenyl)triazene

In this paper, we explore the mechanisms of degenerate base-catalyzed intra- and intermolecular proton transfer using dynamic liquid state NMR. For this purpose, the model compound 1,3-bis(4-fluorophenyl)[1,3- 15N 2]triazene ( 1) was studied with and without the presence of dimethylamine ( 2), trimethylamine ( 3) and water, using tetrahydrofuran- d 8 and methylethylether- d 8 as solvents, down to 130 K. Compound 1 represents an analog of carboxylic acids and of diarylamidines forming cyclic dimers in which a fast double proton transfer takes place. By contrast, the structure of 1 was chosen in such a way that this double proton transfer is suppressed, thus revealing the base catalyzed transfer by dynamic 1H and 19F NMR. Surprisingly, both 2 and 3 can pick up the mobile proton of 1 at one nitrogen atom and carry it to the other nitrogen atom of 1, resulting in an intramolecular transfer process catalyzed each time by a different base molecule. Even more surprising is that the intramolecular transfer catalyzed by 2 is faster than the superimposed intermolecular double proton transfer. In the absence of added bases, a 1 is subject to a slow proton exchange with 2-amino-5,4′-difluoro-diphenyl-diazene ( 4) which is formed in small quantities from 1 in the presence of acid impurities. This process can be minimized by a proper sample preparation technique. The kinetic H/D isotope effects are small, especially in the catalysis by 2, indicating a major heavy atom rearrangement and absence of tunneling. Semi-empirical PM3 and ab initio DFT calculations indicate a reaction pathway via a hydrogen bond switch of the protonated amine representing the transition state. The Arrhenius curves of all processes exhibit strong convex curvatures. This phenomenon is explained in terms of the hydrogen bond association of 1 with the added bases, preceding the proton transfer. At low temperatures, all catalysts are in a hydrogen bonded reactive complex with 1, and the rate constants observed equal to those of the reacting complex. However, at high temperatures, dissociation of the complex occurs, and the temperature dependence of the observed rate constants is affected also by the enthalpy of the hydrogen bond association. Finally, implications of this study for the mechanisms of enzyme proton transfers are discussed.

Brucinium toluene-4-sulfonate trihydrate at 130 K

The low-temperature (130 K) structure of the 1:1 proton-transfer compound of brucine with toluene-4-sulfonic acid (systematic name: 2,3-dimeth­oxy-10-oxostrychnidinium toluene-4-sulfonate trihydrate), C23H27N2O4+·C7H7O3S−·3H2O, has been determined. The asymmetric unit contains two cations, two anions and six molecules of water. Brucinium cations form the familiar undulating head-to-tail ribbon structures, which associate with the toluene-4-sulfonate anions and the water mol­ecules in the inter­stitial cavities through hydrogen-bonding associations involving all available donor and acceptor atoms on all species. The result is a framework polymer structure.

Influence of Random Branching on Multiple Hydrogen Bonding in Poly(alkyl methacrylate)s

A series of linear and randomly branched poly(alkyl methacrylate)s with pendant 2-ureido-4[1H]-pyrimidone (UPy) groups, which form quadruple hydrogen bonds, were synthesized, and the role of molecular topology on intermolecular hydrogen bonding was investigated. In solution rheological studies of poly(methyl methacrylate-co-UPy methacrylate) (PMMA-co-UPyMA) copolymers, a branched copolymer in the nonassociated state displayed a larger entanglement concentration (Ce) than a linear copolymer of equal molar mass. However, Ce of the branched copolymer approached the Ce of the linear analogue as the degree of hydrogen bond associations increased in solution, which suggested the reduced chain dimensions of the branched structure were overcome upon intermolecular association of the UPy groups. A series of linear and branched poly(2-ethylhexyl methacrylate-co-UPy methacrylate) (PEHMA-co-UPyMA) copolymers with 0−10 mol % UPy were utilized for melt rheological studies. A decrease in zero shear viscosity (η0) and re...

Diethylaminium 3,5-dinitrosalicylate at 130 K

The low-temperature (130 K) crystal structure of the 1:1 proton-transfer compound of 3,5-dinitro­salicylic acid (DNSA) with diethyl­amine, viz. diethyl­aminium 3,5-dinitro­salicylate, C4H12N+·C7H3N2O7−, shows the presence of conformationally extended diethyl­aminium cations in which both H atoms of the aminium centres participate in three-centre hydrogen-bonding associations [one R12(4) and the other R12(6)] with carbox­yl, phenol and nitro O-atom acceptors of two separate DNSA anion species [N⋯O = 2.813 (3)–3.320 (3) A]. These result in 12-membered cyclic R64(12) associations linking the two sets of hetero-species into discrete centrosymmetric tetra­mers which have no significant peripheral extensions.

Hydrogen bonding dynamics and two‐dimensional vibrational spectroscopy: N‐methylacetamide in liquid methanol

AbstractThe distribution of the fluctuating amide I mode frequency of N‐methylacetamide (NMA)–methanol solution at room temperature was recently found to be non‐Gaussian and can be decomposed into two Gaussians that are associated with two different solvation structures. In the present paper we discuss the temperature dependences of hydrogen bonding dynamics and their influences on one‐ and two‐dimensional vibrational spectra by carrying out molecular dynamics simulations of the same solution at five temperatures from 230 to 310 K. The radial distributions reveal the detailed solvent configuration around the NMA. The two‐species model where conformational transitions between the two distinct solvation structures are treated as a reversible reaction and the Onsager regression hypothesis was used to estimate the hydrogen bond association and dissociation rates and to study thermodynamic properties. By using the time evolution of the amide I mode frequency fluctuation, both IR absorption and two‐dimensional IR photon echo spectra were numerically simulated and compared with approximate two‐species model results. An approximation method that can be used to extract kinetic information of the hydrogen bonding dynamics from the spectra is briefly discussed. Copyright © 2005 John Wiley & Sons, Ltd.