Hydrogen-bonded Dimers Research Articles

N-Tosyl-L-proline benzene hemisolvate: a rare example of a hydrogen-bonded carboxylic acid dimer with symmetrically disordered H atoms.

The carboxylic acid group is an example of a functional group which possess a good hydrogen-bond donor (-OH) and acceptor (C=O). For this reason, carboxylic acids have a tendency to self-assembly by the formation of hydrogen bonds between the donor and acceptor sites. We present here the crystal structure of N-tosyl-L-proline (TPOH) benzene hemisolvate {systematic name: (2S)-1-[(4-methylbenzene)sulfonyl]pyrrolidine-2-carboxylic acid benzene hemisolvate}, C12H15NO4S·0.5C6H6, (I), in which a cyclic R22(8) hydrogen-bonded carboxylic acid dimer with a strong O-(1/2H)...(1/2H)-O hydrogen bond is observed. The compound was characterized by single-crystal X-ray diffraction and NMR spectroscopy, and crystallizes in the space group I2 with half a benzene molecule and one TPOH molecule in the asymmetric unit. The H atom of the carboxyl OH group is disordered over a twofold axis. An analysis of the intermolecular interactions using the noncovalent interaction (NCI) index showed that the TPOH molecules form dimers due to the strong O-(1/2H)...(1/2H)-O hydrogen bond, while the packing of the benzene solvent molecules is governed by weak dispersive interactions. A search of the Cambridge Structural Database revealed that the disordered dimeric motif observed in (I) was found previously only in six crystal structures.

Sulphonamide chalcones: Conformationally diverse yet optically similar

In this paper, we present the synthesis of three chalcone analogues and their spectroscopic, structural and optical characterization. The influence of the different substituents on the crystalline structure and on their optical properties was evaluated. The effects of derivatization on the chalcones, both at the molecular and supramolecular levels, were evaluated. Also, the molar absorptivity, the first hyperpolarizability β and the two-photon absorption cross-section σ2PA were obtained. The extended structures in each compound are stabilized by hydrogen-bonded dimers and by a pseudo-ring formed from an intramolecular H-bond. It was observed that more voluminous substituents, such as chlorine, contribute to the deviation from planarity. Although many effects were observed in molecular structures of these analogues when in solid form, experimental results of linear and nonlinear optical (NLO) properties showed that the optical properties were not as much influenced in solution. In addition, and to support some experimental results, the theoretical first hyperpolarizability was calculated and showed good agreement with experimental results, which are approximately 10×10−30cm5/esu.

Electronic and Infrared Spectroscopy of Benzene-(H2S)n (n = 1 and 2): The Prototype of the SH-π Interaction.

Benzene-(H2S)n (n = 1 and 2) clusters are the simplest prototype exemplifying the SH-π interaction. Electronic and infrared spectroscopies were applied to the benzene-(H2S)n clusters under the molecular beam condition. The S1-S0 electronic spectrum was observed by one-color resonant two-photon ionization combined with mass spectrometry. Ionization depletion infrared spectra were also observed in the CH and SH stretch regions. The isomer-selective infrared spectra demonstrated that at least two isomers of n = 1 coexist under the present beam condition, and both of them have the SH-π bound structures. One isomer showed a red-shift in the S1-S0 electronic transition relative to that of bare benzene, while the electronic transition of another isomer was slightly blue-shifted. For n = 2, we confirmed a structure, in which hydrogen-bonded H2S dimer is located on top of the aromatic ring.

Conformational Mobility and Proton Transfer in Hydrogen-Bonded Dimers and Trimers of Phosphinic and Phosphoric Acids.

The monomers, H-bonded cyclic dimers, and trimers of five acids were studied by density functional theory calculations, such as hypophosphorous acid (H2POOH, 1), dimethylphosphinic acid (Me2POOH, 2), phenylphosphinic acid (PhHPOOH, 3), dimethylphosphoric acid ((MeO)2POOH, 4), and diphenylphosphoric acid ((PhO)2POOH, 5). Particular attention was paid to the conformational manifold existing due to the internal degrees of freedom: proton transfer (PT), puckering ("twist") within the ring of H-bonds, and mobility of the substituents (namely, -Ph, -OMe, and -OPh rotations). For acid 3, the number of conformers is additionally increased because of the varying relative orientation of nonequivalent substituents in cyclic complexes. We show that 31P NMR chemical shifts (δP) are very sensitive to the details of the conformation, spanning ranges from ca. 1 ppm (for trimers of acids 1 and 2) to ca. 12 ppm (for trimers of 4). The energy barriers for the transitions between conformers are rather low (<6 kcal/mol for PTs, <2.5 kcal/mol for puckerings, and ca. <3 kcal/mol for rotations of substituents), such that the fast exchange regime in the NMR timescale and subsequent δP averaging are expected. Correlations are proposed linking the change of average δP with the H-bond energy, showing the slope of ca. 4 ppm per kcal/mol. The sensitivity of δP to the OPO angle and the OPOH dihedral angle and the geometries of both H-bonds formed by the POOH moiety are analyzed.

Studying the Effect of Temperature on the Formation of Hydrogen Bond Dimers: A FTIR and Computational Chemistry Lab for Undergraduate Students

This laboratory experiment allows one to study the effect of temperature in the process of formation of hydrogen bound cyclic dimers of benzoic acid (BA). The implementation of the proposed methodology, which comprises the use of FTIR spectroscopy and quantum chemistry calculations, enables the obtaining of the thermodynamic parameters of the dimerization reaction and their subsequent validation by computational chemistry calculations. Hence, the students are involved in a practical learning scheme focused in the study of a central topic in chemistry, such as hydrogen bonding, with the final purpose being to train chemistry students in applying theoretical-experimental approaches to extract meaningful data and valuable information for explaining experimental observables.

Ultrafast Dynamics of Tripyrrindiones in Solution Mediated by Hydrogen-Bonding Interactions.

The optical properties and ultrafast dynamics of hexaethyl tripyrrin-1,14-dione (H3TD1) are tuned by hydrogen-bonding interactions between the solute and the solvent. In solvents with low hydrogen-bonding affinity, H3TD1 preferentially forms hydrogen-bonded dimers, whereas in solvents that can either donate or accept hydrogen bonds H3TD1 is present as a monomer. The distinction between dimer and monomer determines the dynamics of the system, with faster internal conversion observed in the dimer form. The ultrafast dynamics were characterized using time-correlated single photon counting, fluorescence upconversion, and transient absorption measurements. The time-resolved dynamics of both the monomer and dimer in solution were modeled using a Pauli master equation treatment for a three level system. The solvent-dependent optical properties were measured using steady-state absorption and fluorescence. This data was then used to calculate the quantum yield and extinction coefficients.

Facile Production of Hydrogen‐bonded Dimeric Fragments from Collision‐induced Dissociation of Na+‐bound G‐Tetrads Predicted by Thermochemistry

Facile evaporation of neutral hydrogen-bonded dimers from G-tetrads.

2-Amino-5,5-dimethylthiazol-4(5H)-one

Our work exploring the synthesis and optimization of increasingly hindered thiols led to the synthesis and crystal structure determination of the title compound, C5H8N2OS, a dimethly-substituted 4-thiazolidinone. The molecular packing exhibits a herringbone pattern with the zigzag running along the b-axis direction; the compound crystallizes as chains of hydrogen-bonded dimers formed by N—H...N hydrogen bonds, which build centrosymmetric R 2 2(8) ring motifs in the crystal.

Toward Accurate Hydrogen Bonds by Scalable Quantum Monte Carlo.

Single-determinant (SD) fixed-node diffusion Monte Carlo (FNDMC) gains popularity as a benchmark method scalable to large noncovalent systems, although its accuracy limits are not yet fully mapped out. We report on an interesting example of significant SD FNDMC accuracy variations in middle-sized hydrogen-bonded dimer complexes, formic acid (FA) vs methanediol (MD), distinct by the maximum bond order (2 vs 1). While the traditional SD FNDMC schemes based on bias cancellation are capable of achieving benchmark (2%) accuracy for MD, this has not been the case for FA. We identify the leading systematic error source in energy differences and show that suitably designed Jastrow factors enable SD FNDMC to reach the reference accuracy for FA. This work clearly illustrates the varying accuracy of the present-day SD FNDMC at the 0.1 kcal/mol scale for a particular set of systems but also points out promising routes toward alleviation of these shortcomings, still within the single-reference framework.

Structure and Properties of 1,3-Phenylenediboronic Acid: Combined Experimental and Theoretical Investigations

The structure and properties of 1,3-phenylenediboronic acid are reported. Molecular and crystal structures were determined by single crystal as well as by powder X-ray diffraction methods. Acidity constant, thermal behavior, and NMR characterization of the title compound were also investigated. In addition to the experimental data, calculations of rotational barrier and intermolecular interaction energies were performed. The compound reveals a two-step acid–base equilibrium with different pKa values. TGA and DSC measurements show a typical dehydration reaction with formation of boroxine. In crystals, hydrogen-bonded dimers with syn-anti conformation of hydroxyl groups form large numbers of ribbon motifs. The 2D potential energy surface scan of rotation of two boronic groups with respect to phenyl ring reveals that the rotation barrier is close to 37 kJ⋅mol−1, which is higher than the double value for the rotation of the boronic group in phenylboronic acid. This effect was ascribed to intermolecular interaction with C–H hydrogen atom located between boronic groups. Furthermore, the molecules in the crystal lattice adopt a less stable molecular conformation most likely resulting from intermolecular forces. These were further investigated by periodic DFT calculations supported by an estimation of dimer interaction energy, and also by topological analysis of electron density in the framework of AIM theory.

Comparative study of hydrogen-bonding interactions between cis-proline analogs and solvents

Only a small amount of peptide bonds exists in the cis conformation, however, they play an important role in the functioning of proteins. Herein, 2-pyrrolidinone (C4H7NO) was used as a cis-proline analog to study the hydrogen bonds between cis-proline and different solvents (CCl4, DMSO, and H2O). Interestingly, with the addition of solvents, the hydrogen-bonding interactions that involved NH in the C4H7NO–CCl4 system are strengthened, while those in the C4H7NO–DMSO system are weakened, which is beyond our imagination. Combined with quantum chemical calculation and excess spectra, we find that it is due to the existence of the C4H7NO doubly hydrogen-bonded dimer, which is the most stable structure in the self-aggregation. During the dilution process, CCl4 hardly breaks double hydrogen bonds, DMSO only weakens the strong hydrogen bonds, and water thoroughly breaks the double hydrogen bonds. Several complexes, such as, doubly/singly hydrogen-bonded dimers, oligomers, monomers and their complexes with solvents, are identified in those three systems, which allow the dynamic changes in the solution structures of mixtures can be obtained. In addition, the band of singly hydrogen-bonded dimers is observed for the first time, thus reflecting the superiority of the excess spectra in improving the resolution. The findings of this work provide precious structural information on C4H7NO–solvents systems, reveal the effects of the solvents on cis-proline, and may inspire the understanding of the cis-proline and some biochemical processes.

Proton-Transfer-Induced Fluorescence in Self-Assembled Short Peptides.

We employ molecular dynamics (MD) and time-dependent density functional theory (TDDFT) to explore the fluorescence of hydrogen-bonded dimer and trimer structures of cyclic FF (Phe-Phe) molecules. We show that in some of these configurations a photon can induce either an intra-molecular proton transfer, or an inter-molecular proton transfer that can occur in the excited S1 and S2 states. This proton transfer, taking place within the hydrogen bond, leads to a significant red-shift that can explain the experimentally observed visible fluorescence in biological and bioinspired peptide nanostructures with a β-sheet biomolecular arrangement. Finally, we also show that such proton transfer is highly sensitive to the geometrical bonding of the dimers and trimers and that it occurs only in specific configurations allowed by the formation of hydrogen bonds.

CO2 Capture via Crystalline Hydrogen-Bonded Bicarbonate Dimers

Summary Limiting global temperature rises is increasingly dependent on the development of energy-efficient carbon-capture methods. Here, we report a simple CO2-separation cycle using an aqueous bis(iminoguanidine) (BIG) sorbent that reacts with CO2 and crystallizes into an insoluble bicarbonate salt. X-ray diffraction analysis of the bicarbonate crystals revealed “anti-electrostatic” hydrogen-bonded (HCO3−)2 dimers, stabilized by guanidinium cations and water. Mild heating of the crystals releases the CO2 and regenerates the BIG sorbent quantitatively, thereby closing the CO2-separation cycle. Experimental and computational investigations support a CO2-release mechanism consisting of surface-initiated low-barrier proton transfer from guanidinium groups to bicarbonate anions with the formation of carbonic acid dimers, followed by CO2 and H2O release in the rate-limiting step, with a measured activation energy of 102 ± 12 kJ/mol. The minimum energy required for sorbent regeneration is 151.5 kJ/mol CO2, which is 24% lower than the regeneration energy of monoethanolamine, a benchmark industrial sorbent.

Theoretical Investigations of Hydrogen Bonding Interactions of (E)-1-(1H-Benzo[d]imidazol-2-yl)-3-Phenylprop-2-en-1-one Momoners and Dimers: NBO, QTAIM and NCI Study

Hydrogen bonding is an essential interaction in nature and plays a crucial role in many formations of materials and biological processes, requiring a deeper understanding of its formation. Benzimidazole is an important structural unit found in a large number of natural and pharmacologically active molecules. In the present work, the electronic structures and properties and relatives stabilities of a series of (E)-1-(1H-benzo[d]imidazol-2-yl)-3-phenylprop-2-en-1-one monomers and dimers have been studied by density functional theory using B3LYP 6-31+G (d, p) calculation level. the strengths of the noncovalent interactions have been analyzed in terms of the QTAIM analysis, NCI analysis and natural bond orbital approaches. It was found that the dimers are formed by double N-H⋯O hydrogen bond. QTAIM analysis proved the presence of intramolecular hydrogen bond in monomers and coexistence of intramolecular and intermolecular hydrogen bond in dimers. Frequency analysis show that intermolecular N-H⋯O interactions are proper hydrogen bond while intramolecular C-H⋯N, C-H⋯O, C-H⋯H-C interactions are improper hydrogen bond. NBO and NCI analyses confirm the existence of hydrogen bonds in the studied monomers and dimers. The presence of weakly electron acceptor group on benzene ring favor the total interaction energy of dimerization.

Novel Dual-Action Plant Fertilizer and Urease Inhibitor: Urea·Catechol Cocrystal. Characterization and Environmental Reactivity

The mechanochemical reaction of urea and catechol affords the quantitative formation of a 1:1 urea·catechol (URCAT) cocrystal that can act simultaneously as a urease inhibitor and as a soil fertilizer. The novel compound has been characterized using solid-state methods, and its environmental activity has been assessed using the inhibition of Canavalia ensiformis urease and water vapor sorption experiments at room temperature. The urea molecules within the cocrystal were organized in hydrogen-bonded dimers bridged by two catechol molecules, with the OH groups interacting via hydrogen bonds with the urea carbonyl groups. The inhibition of jack bean urease enzyme by URCAT led to the complete loss of urease activity after a 20 min incubation period. A large difference of water vapor adsorption was observed between urea and URCAT, with the latter adsorbing 3.5 times less water than urea. Our results suggested that cocrystal engineering strategies can be successfully applied to tackle sustainability problems at the food–energy–water nexus.

New Lamellar Silver Thiolate Coordination Polymers with Tunable Photoluminescence Energies by Metal Substitution

The structures of two lamellar silver thiolate coordination polymers [Ag( p-SPhCO2H)] n (1) and [Ag( p-SPhCO2Me)] n (2) are described for the first time. Their inorganic part is composed of distorted Ag3S3 honeycomb networks separated by noninterpenetrated thiolate ligands. The main difference between the two compounds arises from dimeric hydrogen bonds present for the carboxylic acids. Indepth photophysical studies show that the silver thiolates exhibit multiemission properties, implying luminescence thermochromism. More interestingly, the synthesis of a heterometallic lamellar compound, [Ag0.85Cu0.15( p-SPhCO2H)] n (3), allows to obtain mixed metal thiolate coordination polymers and to tune the photophysical properties with the excitation wavelengths from a green vibronic luminescence to a single red emission band.

Structures and properties of trifluoromethylphenylboronic acids

Three isomers of trifluoromethylphenylboronic acids were synthesized and characterized by 1H, 13C, 11B and 19F NMR. The investigated compounds exhibit high resistance to protodeboronation reaction. Molecular and crystal structure of these compounds was determined by single crystal XRD method. The compounds form typical hydrogen-bonded dimers with the syn-anti conformation. CF3 substituent does not interact with boronic moiety neither as hydrogen bond acceptor nor a lone-electron pair donor. pKa values of the isomers have been determined by spectrophotometric and potentiometric method. Introduction of the CF3 group increases the acidity for meta and para isomers in comparison to the phenylboronic acid, while for the ortho isomer the acidity is reduced due to the steric hindrance.

Hydrogen-bonding chain and dimer motifs in pyridinium and morpholinium hydrogen oxalate salts.

We present here three compounds consisting of pyridinium or morpholinium hydrogen oxalates, each displaying different hydrogen-bonding motifs, resulting in chains for 4-(di-methyl-amino)-pyridinium hydrogen oxalate 0.22-hydrate, C7H11N2 +·C2HO4 -·0.22H2O (1), dimers for 4-tert-butyl-pyridinium hydrogen oxalate, C9H14N+·C2HO4 - (2), and chains for morpholin-ium hydrogen oxalate, C4H10NO+·C2HO4 - (3).

Molecular Dynamics Investigations of Dibutyl-phosphoric Acid-Parameterization and Dimerization.

A reparameterized molecular dynamics force field for dibutyl-phosphoric acid (HDBP) has been developed. Parameterization was done using the general Amber force field, as a starting point. The density and dipole moment of bulk phase simulations compare well to that of known experimental values, and the heat of vaporization is comparable to an estimated empirical value. All values have been optimized to within 4%. The newly optimized force field was validated against the self-diffusion coefficient, matching experimental data to within 18%, which is a significant improvement compared to the nonoptimized force field. Further, a potential of mean force study was carried out to understand the behavior of hydrogen bonds in HDBP dimers. This required the determination of hydrogen bonding criteria that captures the behavior of the HDBP dimer and is reported in this work as well.

1-Methyl-4-thiocarbamoylpyridin-1-ium iodide

In the title compound, C7H9N2S+·I−, the thioamide moiety is twisted out of the aromatic plane by 38.98 (4)° and forms N—H...I hydrogen bonds. In the crystal, hydrogen-bonded centrosymmetric dimers [C7H9N2S+·I−]2 are linked via additional short contacts from an aromatic CH group to the iodide anion into ribbons parallel to the (010) plane.