Hydrogen-bonded Dimers Research Articles

Flexing of a Metal–Organic Framework upon Hydrocarbon Adsorption: Atomic Level Insights from Neutron Scattering

Metal–organic frameworks (MOFs) offer considerable opportunities for gas uptake, storage, and separation due to their porosity, chemical tunability, and flexibility. Flexible MOFs undergo reversible structural transformations triggered by external stimuli such as adsorption of specific guest molecules. The MUF-16 family of materials has exceptional gas adsorption properties including selective uptake of carbon dioxide over other gases. We observed one member of this family, MUF-16(Mn), to be flexible upon the adsorption of hydrocarbon gases. We used a combination of in situ synchrotron X-ray and neutron diffraction to identify the framework–gas interactions that underlie the structural flexibility. Inelastic neutron scattering, along with calculations, also enables an understanding of the dynamics of the flexibility. In essence, C3 hydrocarbons effectively bridge across hydrogen-bonded carboxyl dimers in the framework, triggering pore expansion and inhibiting certain types of motion in the framework.

DIMERIZATION AND HYDRATION OF GLYOXYLIC ACID: A COMPUTATIONAL STUDY

The hydrogen-bonded dimers and 1:1 complexes formed between glyoxylic acid (GA) and H2O have been investigated employing computational techniques like Natural Bond Orbital (NBO) analysis and Atoms in Molecules (AIM) etc. All calculations are carried at B3LYP/6-311++G** level. Seven dimers and four monohydrates are located on the potential energy surface (PES) each for intramolecular hydrogen bonding (IHB) stabilized G3 and non-IHB stabilized rotamer G1. The most stable dimer and hydrate are formed by non-IHB stabilized rotamer G1. In the most stable dimer, two GA units interact in a duo of C=O…H-O hydrogen bonds forming an eight-membered ring structure. In most stable hydrate, H2O acts as a hydrogen bond acceptor and GA acts as an HB donor. The stabilization energies are calculated and the effect of basis set superposition errors (BSSE) is also considered. A good correlation is found between S.E. and the sum of AIM electron densities at bond critical points for both dimers and hydrates. The gas phase hydration and clustering of GA drive new particle formation for atmospheric aerosols, which affect climate, weather, and human health, hence the study has a significant environmental concern.

Graphene Oxide Induced Sub-structures of Bi-tilted Smectic CG in Dimer Liquid Crystals

A nanocomposite built of the hydrogen-bonded (HB) dimer liquid crystal 4-heptyloxybenzoic acid (7OBA) and Graphene oxide (GO) exhibiting a cascade of phase transitions and phases not typical for pristine 7OBA, was investigated by optical polarization microtexture analysis and Raman spectroscopy. We use the 7OBA/GO nanocomposite beacause of the effective functionalizing properties of GO to study the generation and development of the ferroelectric smectic CG phase in its bi-tilted configuration. For the appearance of the CG phase with its substructures we propose an explanation based on the HB formation between 7OBA dimers in closed and open conformations and the GO sheets, aided by the π–π interaction with graphene hexagons which are free from functional groups. We propose molecular and macroscopic models for the substructures CGcl and CGln and indicate their triclinic C1 symmetry, characterized by a polar vector directed oblique to the layers. This confirms that the bi-tilted CG and its substructures are ferroelectric in the bulk similarly to solid ferroelectrics, thus showing potential as material for controllable photonic functional devices.

COCRYSTAL PREDICTION OF THE SALICYLIC ACIDNICOTINAMIDE

Salicylic acid-nicotinamide was used as a prediction model in the hydrogen bond interactions dominating a cocrystal structure. The combined conformation of the two molecules was analyzed at the B3LYP-D3BJ and WB97M-D3BJ theoretical level. The existing hydrogen bond dimer conformations were compared with putative conformations to determine the bond energy and stability. Some parameters were assessed for predictive descriptors, such as geometric parameters, total energy, interaction energy, single hydrogen bond energy, HOMO-LUMO gap, Laplacian Bond Order, and Natural Bond Orbital. An existing conformation, SACNIC1, produced intermolecular hydrogen bond energy which was quite higher than the other conformations, including the pure homomolecular conformations of either salicylic acid or nicotinamide. The cocrystal packing formation seems to be initiated with SACNIC1 as the basic structure conformation. Furthermore, the presence of the strongest intermolecular hydrogen bond energy in SACNIC1 suggests its potential utility as a predictive descriptor.

From bonds to interactions: comprehensive molecular characterization via polarizable bond-dipole approach.

Accurately characterizing molecular interactions stands as a pivotal requirement for ensuring the reliability of molecular dynamics simulations. In line with our bond-dipole-based interaction model proposed by Gao et al. [X.-C. Gao, Q. Hao and C.-S. Wang, J. Chem. Theory Comput., 2017, 13, 2730-2741.], we have implemented an efficient and concise approach to compute electrostatic potential. This methodology capitalizes on the polarizable nature of chemical bond dipoles, resulting in a model of remarkable simplicity. In this study, we have revised the polarizable bond-dipole-based force field (PBFF) through the meticulous curation of quantum chemical data sets. These data sets encompass a comprehensive collection of 40 000 conformations, including those of water, methylamine, methanol, and N-methylacetamide. Additionally, we incorporate 520 hydrogen-bonded dimers into our data sets. In pursuit of enhanced accuracy in molecular dynamics simulations and a more faithful representation of potential energy landscapes, we undertook the re-optimization of the nonbonded parameters within the PBFF framework. Concurrently, we intricately fine-tuned the bonded parameters. The results of our comprehensive evaluation denote that this newly optimized force field method adeptly and efficiently computes structural characteristics, harmonic frequencies, and interaction energies. Overall, this study provides further validation for the applicability of PBFF in molecular dynamics simulations.

Direct Detection of Hydrogen Bonds in Supramolecular Systems Using 1H-15N Heteronuclear Multiple Quantum Coherence Spectroscopy.

Hydrogen-bonded supramolecular systems are usually characterized in solution through analysis of NMR data such as complexation-induced shifts and nuclear Overhauser effects (nOe). Routine direct detection of hydrogen bonding particularly in multicomponent mixtures, even with the aid of 2D NMR experiments for full assignment, is more challenging. We describe an elementary rapid 1H-15N HMQC NMR experiment which addresses these challenges without the need for complex pulse sequences. Under readily accessible conditions (243/263 K, 50 mM solutions) and natural 15N abundance, unambiguous assignment of 15N resonances facilitates direct detection of intra- and intermolecular hydrogen bonds in mechanically interlocked structures and quadruply hydrogen-bonded dimers─of dialkylaminoureidopyrimidinones, ureidopyrimidinones, and diamidonaphthyridines─in single or multicomponent mixtures to establish tautomeric configuration, conformation, and, to resolve self-sorted speciation.

Cyclic Dimers of 4-n-Propyloxybenzoic Acid with Hydrogen Bonds in the Gaseous State.

A comprehensive study of saturated vapors of 4-n-propyloxybenzoic acid (POBA) by gas electron diffraction (GED) and mass spectrometric (MS) methods supplemented by quantum chemical (QC) calculations was carried out for the first time. An attempt was made to detect dimeric forms of the acid in the gaseous state. It has been established that at the temperature of GED experiment, vapor over a solid sample contains up to 20 mol.% of cyclic dimers with two O-H...O hydrogen bonds. The main geometrical parameters of gaseous monomers and dimers of POBA are obtained. The distance r(O…O) = 2.574(12) Å in the cyclic fragment of the gaseous dimer is close to that in the crystal structure (2.611 Å). In the mass spectrum of the POBA recorded the ions of low intensity with a mass exceeding the molecular mass of the monomer were detected. The presence of ions, whose elemental composition corresponds to the dissociative ionization of the dimer, confirms the results of the GED experiment on the presence of POBA dimers in the gas state. The results of GED studies of acetic acid, benzoic acid, and POBA were compared. It is shown that the COOH fragment saves its geometric structure in monomers, as well as the COOH...HOOC fragment with two hydrogen bonds in dimers of different acids. The intermolecular interaction energy in considered acid dimers was estimated using QC calculations (B97D/6-311++G **). The significant value of last (>84 kJ/mol) is the reason for the noticeable presence of dimers in the gas phase.

The Structure of Liquid and Glassy Carbamazepine.

To enhance the solubility of orally administered pharmaceuticals, liquid capsules or amorphous tablets are often preferred over crystalline drug products. However, little is known regarding the variation in bonding mechanisms between pharmaceutical molecules in their different disordered forms. In this study, liquid and melt-quenched glassy carbamazepine have been studied using high energy X-ray diffraction and modeled using Empirical Potential Structure Refinement. The results show significant structural differences between the liquid and glassy states. The liquid shows a wide range of structures; from isolated molecules, to aromatic ring correlations and NH-O hydrogen bonding. Upon quenching from the liquid to the glass the number of hydrogen bonds per molecule increases by ~50% at the expense of a ~30% decrease in the close contact (non-bonded) carbon-carbon interactions between aromatic rings. During the cooling process, there is an increase in both singly and doubly hydrogen-bonded adjacent molecules. Although hydrogen-bonded dimers found in the crystalline states persist in the glassy state, the absence of a crystalline lattice also allows small, hydrogen-bonded NH-O trimers and tetramers to form. This proposed model for the structure of glassy carbamazepine is consistent with the results from vibrational spectroscopy and nuclear magnetic resonance.

N-Benzyl-N-(2-hydroxyethyl)-2-(oxazolidin-2-on-3-yl)-2-phenylacetamide

The title compound, obtained by base-induced dimerization of 3-benzyloxazolidin-2-one, has been prepared and fully characterised. Its X-ray structure features hydrogen-bonded dimers involving the hydroxyl OH and amide carbonyl, forming a 14-membered ring.

Gold nanoclusters-loaded hydrogel formed by dimeric hydrogen bonds crosslinking: A novel strategy for multidrug-resistant bacteria-infected wound healing.

Restoring skin integrity after wound infection remains a tougher health challenge due to the uncontrolled antibiotic-resistant pathogens caused by antibiotic abuse. Herein, an injectable hydrogel with dual antibacterial and anti-inflammatory activities composed of gold nanoclusters (GNCs) and carbomer (CBM) is developed for wound dressing to overcome multidrug-resistant infection. Firstly, both experimental investigations and molecular dynamics simulation validate the protonation state of 6-mercaptohexanoic acid (MHA) ligands play an important role in its antibacterial action of GNCs. The self-organizing GNCs-CBM composite hydrogel is then spontaneously cross-linked by the dimeric hydrogen bonds (H-bonds) between the MHA ligands and the acrylic acid groups of CBM. Benefitting from the dimeric H-bonds, the hydrogel becomes thickening enough as an ideal wound dressing and the GNCs exist in the hydrogel with a high protonation level that contributes to the enhanced bactericidal function. In all, by combining bactericidal and immunomodulatory actions, the GNCs-CBM hydrogel demonstrated excellent synergy in accelerating wound healing in animal infection models. Hence, the dimeric H-bonds strengthening strategy makes the GNCs-CBM hydrogel hold great potential as a safe and effective dressing for treating infected wounds.

Field-Induced Single Molecule Magnetic Behavior of Mononuclear Cobalt(II) Schiff Base Complex Derived from 5-Bromo Vanillin

A mononuclear Co(II) complex of a Schiff base ligand derived from 5-Bromo-vanillin and 4-aminoantipyrine, that has a compressed tetragonal bipyramidal geometry and exhibiting field-induced slow magnetic relaxation, has been synthesized and characterized by single crystal X-ray diffraction, elemental analysis and molecular spectroscopy. In the crystal packing, a hydrogen-bonded dimer structural topology has been observed with two distinct metal centers having slightly different bond parameters. The complex has been further investigated for its magnetic nature on a SQUID magnetometer. The DC magnetic data confirm that the complex behaves as a typical S = 3/2 spin system with a sizable axial zero-field splitting parameter D/hc = 38 cm−1. The AC susceptibility data reveal that the relaxation time for the single-mode relaxation process is τ = 0.16(1) ms at T = 2.0 K and BDC = 0.12 T.

Geometrically Mismatched Hydrogen-bonded Framework Composed of Tetratopic Carboxylic Acid.

Porous organic frameworks possessing interactive free sites in the pore have attracted much attention due to their potential to show the site-originated specific functionalities. Herein, we demonstrate that such a framework could be constructed using a concept of geometrically mismatched frameworks composed of phenanthroline-based tetratopic carboxylic acid CP-Phen. Simple recrystallization of CP-Phen yielded a solvent included porous framework CP-Phen-1, in which three of four carboxy groups form hydrogen-bonded dimer to form a ladder-shaped framework, while the remained one does not participate in framework formation due to geometrical mismatch and interacts with solvent molecules through weak hydrogen-bonding. This result implies that our proposed strategy is effective to provide free interactive sites in porous frameworks. Although CP-Phen-1 undergoes two-step structural transformation presumably accompanied by hydrogen-bond rearrangements upon loss of solvent molecules, the activate framework shows good thermal stability up to 360 °C and selective CO2 adsorption.

From ACQ to AIE: The CN(π)-(π)Ar interaction driven structural and photophysical properties of aromatic ring conjugated novel diaminomaleonitrile derivatives

Studying solid and solution state photoluminescence properties are exclusive to understanding Aggregation Caused Quenching (ACQ) and Aggregation Induced Emission (AIE) behaviour of organic molecules to explore the mechanism of molecular luminescence in greater detail. A unique hydrogen-bonded dimer with imperative interaction (CN)π---π(Ar) was designed and synthesized by selecting diaminomaleonitrile (DMN) as stator and decorated with different aromatic rotors (phenyl to pyrene). Depending on the intermolecular interaction present in the molecular system, (AIE) or (ACQ) has been observed and found to be tunable. The single-crystal x-ray diffraction analysis of these derivatives shows that AIE characteristics could be seen where to (CN)π---π(Ar) intermolecular interactions between the aromatic rotors and stator, coupled with NH–-–NC intermolecular hydrogen bonding is present, while the absence of these interaction reflected in ACQ observation. The significant impacts of steric, conjugation and electronic effects on the ACQ / AIE properties are presented based on crystallography analysis, optical spectra measurements and theoretical calculations.

Anti-electrostatic hydrogen-bonded tellurate dimers captured and stabilized by crystallization of a bis-iminoguanidinium salt

Anionic Te2O6(OH)44– dimers have been captured by crystallization of a hydrated salt of glyoxal-bis-iminoguanidinium (GBIG), and structurally characterized by single-crystal X-ray diffraction and vibrational spectroscopy. The crystal structure reveals anti-electrostatic hydrogen-bonded chains of Te2O6(OH)44– dimers, consisting of edge-sharing TeO6 octahedra, stabilized by hydrogen bonding from the GBIG cations and the water molecules included in the crystal. FTIR spectroscopy confirms the presence of TeO6 octahedra with characteristic Te–O stretching modes at 755 cm−1 and 689 cm−1, while the observed stretching mode at 3459 cm−1 confirms the presence of axially-bonded hydroxyl groups. Raman spectroscopy and DFT calculations confirm the presence of the Te2O6(OH)44– dimers in the crystalline phase and of the TeO(OH)5– monomers in solution.

A quantum chemical study of the interaction of carboxylic acids with DMSO

Quantum chemical computational methods, which use quantum mechanics and molecular dynamics theory, have developed rapidly in the past few decades, and quantum chemical computation has penetrated almost all fields of chemistry. Hydrogen bonds are ubiquitously common weak intermolecular interactions. Moreover, the bonding mechanism of hydrogen bonds is considered to be different from that of chemical bonding. Because of the difficulty of experimental studies, a more accurate calculation of hydrogen bonding from theory is a more convenient and direct method to understand hydrogen bonding. Density functional theory (DFT) is the most widely used general function in quantum chemical calculations, giving accurate results for most chemical systems. In this paper, the geometries of the hydrogen-bonded dimer complex of acetic acid and DMSO was structurally optimized and potential energy surface was determined. The geometries of four related hydrogen-bonded dimer complexes were fully optimized using the M06-2X/6-311++G (3d, 2p) exchange-correlation functional with DFT-D3(BJ) empirical dispersion correction. We found that hydrogen bonding is a mixture of electrostatic interactions and covalent bonding, and that hydrogen bonding is a kind of force with different percentages of electrostatic and covalent character, rather than a special force independent of chemical bonding. Thus, more clearly defining our inherent classification of forces between substances provides a new perspective for our future study of weak interactions such as hydrogen bonding.

Intermolecular Hydrogen Bond in Tertiary Butyl Alcohol and Its Solutions. Raman Scattering Spectra

It is found that the 750 cm–1 band in pure tertiary butyl alcohol shows attributes of a complex structure that can be interpreted as a result of the superposition of several closely located lines belonging to different aggregates of alcoholmolecules. As the alcohol is diluted with neutral solvents, the width of this band passes through a maximum that corresponds to the concentration of the mixture with comparable contents of various most stable aggregates in the solution. The performed quantum-chemical calculations confirm the complexity of the 750-cm–1 band of pure alcohol caused by the aggregation of molecules by means of hydrogen bonds. The calculated energy gain due to the formation of a hydrogen bond (dimer) amounts to 19.7 kJ/mole, and the length of the hydrogen bridge equals 2.068 Å.

Directing Crystallization Outcomes of Conformationally Flexible Molecules: Polymorphs, Solvates, and Desolvation Pathways of Fluconazole.

Control over polymorphism and solvatomorphism in API assisted by structural information, e.g., molecular conformation or associations via hydrogen bonds, is crucial for the industrial development of new drugs, as the crystallization products differ in solubility, dissolution profile, compressibility, or melting temperature. The stability of the final formulation and technological factors of the pharmaceutical powders further emphasize the importance of precise crystallization protocols. This is particularly important when working with highly flexible molecules with considerable conformational freedom and a large number of hydrogen bond donors or acceptors (e.g., fluconazole, FLU). Here, cooling and suspension crystallization were applied to access polymorphs and solvates of FLU, a widely used azole antifungal agent with high molecular flexibility and several reported polymorphs. Each of four polymorphic forms, FLU I, II, III, or IV, can be obtained from the same set of alcohols (MeOH, EtOH, isPrOH) and DMF via careful control of the crystallization conditions. For the first time, two types of isostructural channel solvates of FLU were obtained (nine new structures). Type I solvates were prepared by cooling crystallization in Tol, ACN, DMSO, BuOH, and BuON. Type II solvates formed in DCM, ACN, nPrOH, and BuOH during suspension experiments. We propose desolvation pathways for both types of solvates based on the structural analysis of the newly obtained solvates and their desolvation products. Type I solvates desolvate to FLU form I by hydrogen-bonded chain rearrangements. Type II solvates desolvation leads first to an isomorphic desolvate, followed by a phase transition to FLU form II through hydrogen-bonded dimer rearrangement. Combining solvent-mediated phase transformations with structural analysis and solid-state NMR, supported by periodic electronic structure calculations, allowed us to elucidate the interrelations and transformation pathways of FLU.

Thermodynamically Stable Cationic Dimers in Carboxyl-Functionalized Ionic Liquids: The Paradoxical Case of "Anti-Electrostatic" Hydrogen Bonding.

We show that carboxyl-functionalized ionic liquids (ILs) form doubly hydrogen-bonded cationic dimers (c+=c+) despite the repulsive forces between ions of like charge and competing hydrogen bonds between cation and anion (c+–a−). This structural motif as known for formic acid, the archetype of double hydrogen bridges, is present in the solid state of the IL 1−(carboxymethyl)pyridinium bis(trifluoromethylsulfonyl)imide [HOOC−CH2−py][NTf2]. By means of quantum chemical calculations, we explored different hydrogen-bonded isomers of neutral (HOOC–(CH2)n–py+)2(NTf2−)2, single-charged (HOOC–(CH2)n–py+)2(NTf2−), and double-charged (HOOC– (CH2)n−py+)2 complexes for demonstrating the paradoxical case of “anti-electrostatic” hydrogen bonding (AEHB) between ions of like charge. For the pure doubly hydrogen-bonded cationic dimers (HOOC– (CH2)n−py+)2, we report robust kinetic stability for n = 1–4. At n = 5, hydrogen bonding and dispersion fully compensate for the repulsive Coulomb forces between the cations, allowing for the quantification of the two equivalent hydrogen bonds and dispersion interaction in the order of 58.5 and 11 kJmol−1, respectively. For n = 6–8, we calculated negative free energies for temperatures below 47, 80, and 114 K, respectively. Quantum cluster equilibrium (QCE) theory predicts the equilibria between cationic monomers and dimers by considering the intermolecular interaction between the species, leading to thermodynamic stability at even higher temperatures. We rationalize the H-bond characteristics of the cationic dimers by the natural bond orbital (NBO) approach, emphasizing the strong correlation between NBO-based and spectroscopic descriptors, such as NMR chemical shifts and vibrational frequencies.

Hydrogen-bonded dimers of mono-alkylated diketopyrrolopyrroles and their physical properties

Judicious utilization of hydrogen bonding in diketopyrrolopyrroles (DPPs) could allow smooth carrier transfer when applied to organic semiconducting materials. In this study, we determined the association constants of dimerization by hydrogen bonding for a mono-alkylated DPP in the solution state to obtain basic insights that could aid in the utilization of hydrogen bonding. The IR spectroscopy, thermal analysis, and X-ray diffractometry results demonstrate that the hydrogen-bonded dimer structure was preferentially formed in the solid state. Electron transporting properties was only observed in the DPP derivatives, forming the hydrogen-bonded dimer structure, indicating the formation of a film morphology suitable for carrier-transport pathway.

2,2,3,3,3-Pentafluoro-1-propanol and its dimer: structural diversity, conformational conversion, and tunnelling motion.

Rotational spectra of 2,2,3,3,3-pentafluoro-1-propanol (PFP) were measured using cavity and chirped pulse Fourier transform microwave spectrometers. Of the nine possible PFP configurations which include four mirror-imaged pairs and an achiral conformer, the two most stable monomeric PFP imaged pairs, i.e., PFPG+g+/G-g- and PFPTg+/Tg- were observed and assigned, along with the 13C, 18O and deuterated isotopologues of PFPG+g+/G-g-. The rotational transitions of PFPTg+/Tg- exhibit large tunnelling splittings and were analyzed in detail. CREST, a recently developed conformational search tool that was used for systematic conformational searches of possible binary PFP conformers and the subsequent DFT calculations at the B3LYP-D3(BJ)/def2-QZVP level produced nearly 80 stable, binary PFP geometries, where ten of them are within a narrow energy window of ∼1 kJ mol-1, highlighting the structural diversity of the system. Rotational spectra of five (PFP)2 conformers were assigned and were identified as the five most stable binary conformers predicted. A closer examination reveals that the assigned binary conformers are made exclusively of the two most stable PFP monomeric subunits observed experimentally. A combined kinetic and thermodynamic model was proposed to explain the observation or non-observation of low energy conformers, and the analysis was further verified by the 'argon test'. The non-covalent intermolecular interactions of PFP and its binary conformers are also discussed with the aid of quantum theory of atoms in molecules (QTAIM) and non-covalent interaction (NCI) analyses, as well as the effects of fluorination by comparing with 1-propanol and its dimers.