Hydrogen-bonded Dimers Research Articles

Synthesis, XRD structural analysis and theoretical studies of a potential inhibitor against rheumatoid arthritis (RA).

This work focused on analyzing the properties of N-(5-nitrothiazol-2-yl)furan-2-carboxamide (C8H5N3O4S, NTFC) as a possible inhibitor of the rheumatoid arthritis process. The synthesis of NTFC was carried out and good-quality crystals were obtained and studied by NMR (1H and 13C), DEPT 135, UV-Vis, IR, MS and single-crystal X-ray diffraction. The structure of NTFC consists of two rings, thiazole and furan, and a central C-N-C(=O)-C segment, which appears to be planar. This central amide segment forms angles of 2.61 (10) and 7.97 (11)° with the planes of the thiazole and furan rings, respectively. The crystal structure of NTFC exhibits N-H...N, N-H...O and C-H...O hydrogen bonds, and C-H...π and π-π interactions that facilitate self-assembly and the formation of hydrogen-bonded dimers, which implies the appearance of R22(8) graph-set motifs in this interaction. The stability of the dimeric unit is complemented by the formation of strong intramolecular C-S...O interactions of chalcogen character, with an S...O distance of 2.6040 (18) Å. Hirshfeld surface (HS) analysis revealed that O...H/H...O interactions were dominant, accounting for 36.8% of the total HS, and that N-H...N interactions were fundamental to the formation of the dimeric structure. The molecular electrostatic potential (MEP) map showed a maximum energy of 46.73 kcal mol-1 and a minimum of -36.06 kcal mol-1. The interaction energies of molecular pairs around NTFC are highest for those interactions linked by N-H hydrogen bonds. The properties of the NTFC ligand as a potential inhibitor of the DHODH (dihydroorotate dehydrogenase) enzyme were evaluated by molecular docking, showing coupling energies very close to those obtained with the control drug for rheumatoid arthritis, i.e. leflunomide.

Anisole-Water and Anisole-Ammonia Complexes in Ground and Excited (S1) States: A Multiconfigurational Symmetry-Adapted Perturbation Theory (SAPT) Study.

Binary complexes of anisole have long been considered paradigm systems for studying microsolvation in both the ground and electronically excited states. We report a symmetry-adapted perturbation theory (SAPT) analysis of intermolecular interactions in anisole-water and anisole-ammonia complexes within the framework of the multireference SAPT(CAS) method. Upon the S1 ← S0 electronic transition, the hydrogen bond in the anisole-water dimer is weakened, which SAPT(CAS) shows to be determined by changes in the electrostatic energy. As a result, the water complex becomes less stable in the relaxed S1 state despite decreased Pauli repulsion. Stronger binding of the anisole-ammonia complex following electronic excitation is more nuanced and results from counteracting shifts in the repulsive (exchange) and attractive (electrostatic, induction and dispersion) forces. In particular, we show that the formation of additional binding N-H···π contacts in the relaxed S1 geometry is possible due to reduced Pauli repulsion in the excited state. The SAPT(CAS) interaction energies have been validated against the coupled cluster (CC) results and experimentally determined shifts of the S1 ← S0 anisole band. While for the hydrogen-bonded anisole-water dimer SAPT(CAS) and CC shifts are in excellent agreement, for ammonia SAPT(CAS) is only qualitatively correct.

Versatile photoluminescence behavior of polycyclic hydroxybenzimidazoles driven by intermolecular hydrogen bonding

Herein, the synthesis of polycyclic hydroxybenzimidazole based on 4-hydroxyphthalimide is presented and two isomeric structures are formed. The isomeric structures are capable of forming intermolecular hydrogen-bonded molecular associates. Hydroxybenzimidazole hydrogen-bonded organic frameworks have been shown to be sensitive to different solvent polarity, particularly in proton donor media, resulting in a blue shift in emission. The role of proton donor media has been evaluated using the binary mixture of acetonitrile/water and protonation by trifluoroacetic acid. The results show that by tuning the environment, the aggregation induced emission has appeared in the blue region and larger aggregates are formed compared to the less polar aprotic solvents. Under acidic conditions, the disruption of the hydrogen-bonded dimers was estimated, resulting in deep blue emission. This provides an opportunity to control the molecular associates and tune the optical behavior.

The Aggregation Units of J-Aggregates: Transitioning from Monomers to Hydrogen-Bonded Dimers.

In recent years, J-aggregates, as supramolecular assembly structures, have increasingly attracted scientific interest. Currently, the prevailing consensus is that J-aggregates are formed through the interleaved stacking of monomers arranged in parallel. However, our findings suggest that the fundamental units constituting J-aggregates are not limited to monomers alone but also encompass molecular aggregates interconnected by noncovalent bonds, which we designate as aggregation units. We have synthesized three asymmetric pyrrolopyrrole cyanine (PPCy) dyes capable of forming hydrogen-bonded dimers and have verified that these hydrogen-bonded dimers can serve as aggregation units to generate J-aggregates. The detailed structural and optical properties revealed that the J-aggregates of these dyes exhibited a significantly red-shifted and narrowed emission in the near-infrared (NIR) fluorescence compared to the monomers.

On the shape of the simulated infrared spectral density of strongly hydrogen-bonded systems: Mapping and identification of Hadži ABC structure in phosphonic acid dimers in gas phase

Herein, we explore the origin of three-peaked structure, referred to as the Hadži ABC structure, illustrated within the absorption bands in infrared (IR) spectra of strongly H-bonded systems. The exploration is particularly elucidated for two phosphinic acid dimers (R2POOH) in gas phase, namely bis-(iodomethyl)-phosphinic acid dimer (i.e., R = CH2I) at 465 K and dibutyl-phosphinic acid dimer (i.e., R = C4H9O) at 425 K. A direct theoretical illustration of this spectral signature, related predominantly to very strongly hydrogen bonded complexes, is proposed. The spectral density, υSO−H,is determined by the aid of an approach describing the high-frequency O − H stretching modes by harmonic potentials. The intermolecular potential modes (O…O) are assumed to be of anharmonic nature. The approach is founded on the strong anharmonic coupling approximation, which prescribes a linear dependency of the O − H frequency on the O…O stretching coordinate as rationalized by the fundamental model of Maréchal and Witkowski. Both direct relaxation of the O − H vibrational mode and its homolog, indirect one, affecting the O…O stretching mode are taken into consideration. The model also considers Davydov coupling, which describes the mutual interaction that takes place in the centrosymmetric dimer between the two existent hydrogen bonds as well as Fermi resonances, which occur between the bending modes arising in- and out-of-plane of the dimer and the fundamental O − H stretching mode. Interestingly, we illustrate how the (A, B, and C) triplet detected in the IR absorption band of phosphonic acids can be generated and discuss how the ABC structure can be numerically simulated. The approach provides a direct explanation of the emergence of this unusual feature and mainly reveals that the A peak is due to the Davydov coupling mechanism, whereas the BC diad is found to be generated by Fermi resonances. This was elucidated in a distinctly different approach, rationalized by Sheppard and Claydon, affirming that the provenance of the BC diad is exclusively due to Fermi resonances mechanism. Altogether, our results highlight the congregated effects of both Fermi resonance mechanism and Davydov coupling for the formation of the ABC structure. The model paves the way for a deeper understanding of the ABC structure, characteristic of very toxic strongly hydrogen-bonded dimers. This is of capital importance as it allows one to develop a solid understanding of nerve agents, such as phosphonic acids, from theory alone, so as to avoid difficult and dangerous experiments since they are extremely toxic.

Protonation State of a Bioactive Compound Regulates Its Release from Lamellar Gel-Phase Bilayers.

Lamellar gel networks (LGNs) in personal care or pharmaceutical lotions and creams provide an opaque cream appearance and a creamy texture to these products. Within the LGNs, the lamellar gel (Lβ) phase composed of regularly spaced bilayers of surfactants and long-chain fatty alcohols is predominately responsible for the unique rheological properties of the LGNs. To extend the shelf life of LGN-containing products, bioactive compounds with antimicrobial properties are often incorporated into the formulation. However, how the protonation state of the bioactive compounds regulates their release from the Lβ-phase bilayers is currently unknown. Using molecular dynamics simulations, we found that the protonated (neutral) form of cinnamic acid, a common antimicrobial food additive, has a retention ratio higher than that of its deprotonated (charged) counterpart in the Lβ-phase bilayer. From free energy calculations, we determined that not only is the protonated molecule more stable in the hydrophobic interior of the bilayer but also the formation of hydrogen-bonded dimers significantly enhances its stability within the bilayer. Thus, the protonation state has a profound impact on bioavailability of the compounds. Our results also highlight the importance of considering possible oligomeric states of molecules when performing calculations to estimate the permeability of molecules within various bilayers.

Computational Study of Molecular Interactions in ZnCl2(urea)2 Crystals as Precursors for Deep Eutectic Solvents

Deep eutectic solvents (DESs) are now enjoying an increased scientific interest due to their interesting properties and growing range of possible applications. Computational methods are at the forefront of deciphering their structure and dynamics. Type IV DESs, composed of metal chloride and a hydrogen bond donor, are among the less studied systems when it comes to their understanding at a molecular level. An important example of such systems is the zinc chloride–urea DES, already used in chemical synthesis, among others. In this paper, the ZnCl2(urea)2 crystal is studied from the point of view of its structure, infrared spectrum, and intermolecular interactions using periodic density functional theory and non-covalent interactions analysis. The two main structural motifs found in the crystal are a strongly hydrogen-bonded urea dimer assisted by chloride anions and a tetrahedral Zn(II) coordination complex. The crystal is composed of two interlocking parallel planes connected via the zinc cations. The infrared spectrum and bond lengths suggest a partially covalent character of the Zn−Cl bonds. The present analysis has far-reaching implications for the liquid ZnCl2–urea DES, explaining its fluidity, expected microstructure, and low conductivity, among others.

Spectroscopic Evidence for Doubly Hydrogen-Bonded Cationic Dimers in the Solid, Liquid, and Gaseous Phases of Carboxyl-Functionalized Ionic Liquids.

Intermolecular interactions determine whether matter sticks together, gases condense into liquids, or liquids freeze into solids. The most prominent example is hydrogen bonding in water, responsible for the anomalous properties in the liquid phase and polymorphism in ice. The physical properties are also exceptional for ionic liquids (ILs), wherein a delicate balance of Coulomb interactions, hydrogen bonds, and dispersion interactions results in a broad liquid range and the vaporization of ILs as ion pairs. In this study, we show that strong, local, and directional hydrogen bonds govern the structures and arrangements in the solid, liquid, and gaseous phases of carboxyl-functionalized ILs. For that purpose, we explored the H-bonded motifs by X-ray diffraction and attenuated total reflection (ATR) infrared (IR) spectroscopy in the solid state, by ATR and transmission IR spectroscopy in the liquid phase, and by cryogenic ion vibrational predissociation spectroscopy (CIVPS) in the gaseous phase at low temperature. The analysis of the CO stretching bands reveals doubly hydrogen-bonded cationic dimers (c═c), resembling the archetype H-bond motif known for carboxylic acids. The like-charge doubly hydrogen-bonded ion pairs are present in the crystal structure of the IL, survive phase transition into the liquid state, and are still present in the gaseous phase even in (2,1) complexes wherein one counterion is removed and repulsive Coulomb interaction increased. The interpretation of the vibrational spectra is supported by quantum chemical methods. These observations have implications for the fundamental nature of the hydrogen bond between ions of like charge.

Dimerization and Dissociation: The Rate-Controlling steps of molecular Self-Assembly during solution nucleation determined by variation of gas media

To further probe into the link between solution chemistry and nucleation processes experimental and computational data are presented on unsaturated, saturated, and supersaturated solutions and in situ monitoring of nucleation chemistry of p-chlorobenzoic acid (PCBA), p-methoxybenzoic acid (PMBA) and p-nitrobenzoic acid (PNBA), three benzoic acid derivatives with different properties of para-substituents. By variation of the gas media, we were able to establish that hydrogen-bonded dimers (HD) are the basic building unite in solution for clusters and nucleuses despite of the gases and solvents, and there is a strong link between the supersaturated solution chemistry and the intrinsic supersaturation ratio, and the nucleation kinetics. Two different molecular self-assembly pathways and the rate-controlling steps were discussed, which paves new aspects for understanding the role of solution chemistry in directing nucleation processes.

Structural Analysis of 3,5-Bistrifluoromethylhydrocinnamic Acid

The crystal structure of 3,5-bistrifluoromethylhydrocinnamic acid [systematic name: 3-[3,5-bis(trifluoromethyl)phenyl]propanoic acid], C11H8F6O2, has been determined and described. The structure was subject to the Hirshfeld surface-analysis and CE-B3LYP interaction-energies calculations. The title compound crystallises in the monoclinic P21/c space group with one molecule in the asymmetric unit. The propanoic acid side chain of the studied molecule has a bent conformation. The key supramolecular motif in the crystal structure is a centrosymmetric O–H∙∙∙O hydrogen-bonded dimer (R22(8) in the graph set notation). According to CE-B3LYP, the molecules involved in this motif exhibit the strongest pairwise interaction total energy (Etot = −67.9 kJ/mol). On the other hand, there are seven other interacting molecular pairs with significant Etot values in the range of −17 to −28 kJ/mol. In these, the energy is dominated by the dispersive contribution. A survey of the Cambridge Structural Database revealed that in other 3-phenylpropanoic acid structures, the middle dihedral angle of the propanoic acid side chain is always in the trans conformation. This contrasts the current structure where this dihedral angle is in the gauche conformation. According to the Density Functional Theory calculations in the gas phase (at the B3LYP/aug-cc-pvDZ level), the presence of the two CF3 groups (strong electron-withdrawing character) increases the population of the gauche conformers by a substituent electronic effect, and this may be a minor factor contributing to the appearance of this conformation observed in the solid state.

Supramolecular Interactions of Teixobactin Analogues in the Crystal State.

This Note presents the X-ray crystallographic structure of the N-methylated teixobactin analogue N-Me-d-Gln4,Lys10-teixobactin (1). Eight peptide molecules comprise the asymmetric unit, with each peptide molecule binding a chloride anion through hydrogen bonding with the amide NH group of residues 7, 8, 10, and 11. The peptide molecules form hydrogen-bonded antiparallel β-sheet dimers in the crystal lattice, with residues 1-3 comprising the dimerization interface. The dimers further assemble end-to-end in the crystal lattice.

Phase transitions of choline dihydrogen phosphate: A vibrational spectroscopy and periodic DFT study.

Choline dihydrogen phosphate, [Chol][H2PO4], is a proton-conducting ionic plastic crystal exhibiting a complicated sequence of phase transitions. Here, we address the argument in the literature around the thermal properties of [Chol][H2PO4] using Raman and infrared microspectroscopy. The known structure of the low-temperature crystal, which contains the anti-conformer of [Chol]+ and hydrogen-bonded dimers of anions, was used to do periodic density functional theory calculations of the vibrational frequencies. Raman spectra indicate that the solid-solid transition at 20 °C is linked to a conformational change to the gauche [Chol] conformer with a concurrent local rearrangement of the anions. The distinct bands of lattice modes in the low-frequency range of the Raman spectra vanish at the 20 °C transition. Given the ease with which metastable crystals can be produced, Raman mappings demonstrate that a sample of [Chol][H2PO4] at ambient temperature can contain a combination of anti- and gauche conformers. Heating to 120 °C causes continuous changes in the local environment of anions rather than melting as suggested by a recent calorimetric investigation of [Chol][H2PO4]. The monotonic change in vibrational spectra is consistent with earlier observations of a very small entropy of fusion and no abrupt jump in the temperature dependence of ionic conductivity along the phase transitions of [Chol][H2PO4].

Crystal structure of anthraquinone-2-carboxylic acid, C15H8O4

The crystal structure of anthraquinone-2-carboxylic acid has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional theory techniques. Anthraquinone-2-carboxylic acid crystallizes in space group P-1 (#2) with a = 3.7942(2), b = 13.266(5), c = 22.835(15) Å, α = 73.355(30), β = 89.486(6), γ = 86.061(1)°, V = 1098.50(7) Å3, and Z = 4. The crystal structure contains two independent molecules of anthraquinone-2-carboxylic acid. Although the expected hydrogen-bonded dimers are present, the dimers are not centrosymmetric. The dimer contains one molecule of each planar low-energy conformation. The crystal structure consists of a herringbone array of centrosymmetric pairs of molecules parallel to the bc-plane. The molecules stack along the short a-axis. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™ (PDF®).

The sulfur dioxide–water complex: CCSD(T)/CBS anharmonic vibrational spectroscopy of stacked and hydrogen-bonded dimers

This study examines the structures, energies, and IR vibrational spectra of the sulfur dioxide–water SO2(H2O) complexes by employing coupled cluster theory CCSD(T) with Dunning style correlation consistent type basis sets aug-cc-pV(n+d)Z (n = D, T, Q, 5). Complete basis set (CBS) extrapolations have been carried out to predict binding energies for two isomers of the SO2(H2O) complex: a stacked global minimum (1A) structure and a hydrogen-bonded local minimum (1B) structure. The CCSD(T)/CBS extrapolation predicts an intermolecular S–O distance rS⋯O = 2.827 Å for the stacked isomer, which is in excellent agreement with an experimental measurement of 2.824 Å [K. Matsumura et al., J. Chem. Phys., 91, 5887 (1989)]. The CCSD(T)/CBS binding energy for the stacked dimer 1A and hydrogen-bonded form 1B is De = −4.37 kcal/mol and De = −2.40 kcal/mol, respectively. This study also employs anharmonic VPT2 MP2/aug-cc-pV(n+d)Z level corrections to CCSD(T)/aug-cc-pV(n+d)Z vibrational frequencies in both forms of SO2(H2O). The anharmonic CCSD(T)/aug-cc-pV(Q+d)Z OH stretching frequencies in the stacked structure 1A are 3743 cm−1 (ν3) and 3647 cm−1 (ν1), and these align well with the recorded IR spectroscopic values of 3745 and 3643 cm−1, respectively [C. Wang et al., J. Phys. Chem. Lett., 13, 5654 (2022)]. If we combine CCSD(T)/aug-cc-pV(n+d)Z De values with VPT2 vibrational frequencies, we obtain a new CCSD(T)/aug-cc-pV(Q+d)Z anharmonic dissociation energy D0 = −3.48 kcal/mol for 1A and D0 = −1.74 kcal/mol for 1B. In summary, the results presented here demonstrate that the application of CCSD(T) calculations with aug-cc-pV(n+d)Z basis sets and CBS extrapolations is critical in probing the structure and IR spectroscopic properties of the sulfur dioxide–water complex.

Multiple hydrogen-bonded dimers: are only the frontier atoms relevant?

Non-frontier atom exchanges in hydrogen-bonded aromatic dimers can induce significant interaction energy changes (up to 6.5 kcal mol-1). Our quantum-chemical analyses reveal that the relative hydrogen-bond strengths of N-edited guanine-cytosine base pair isosteres, which cannot be explained from the frontier atoms, follow from the charge accumulation in the monomers.

Facile Synthesis of Asymmetric aza-Boron Dipyrromethene Analogues Bearing Quinoxaline Moiety.

An asymmetric aza-BODIPY analogue bearing quinoxaline moiety was synthesized via a titanium tetrachloride-mediated Schiff-base-forming reaction of 6,7-dimethyl-1,4-dihydroquinoxaline-2,3-dione and benzo[d]thiazol-2-amine. This novel aza-BODIPY analogue forms a complementary hydrogen-bonded dimer due to the quinoxaline moiety in the crystal structure. It also shows intense absorption and fluorescence, with fluorescence quantum yields close to unity. The electrochemical measurements and the DFT calculations revealed the presence of the low-lying HOMO, which benefits their potential applications as an electron-transporting material.

Using Noncovalent Interactions to Test the Precision of Projector-Augmented Wave Data Sets.

The projector-augmented wave (PAW) method is one of the approaches that are widely used to approximately treat core electrons and thus to speed up plane-wave basis set electronic structure calculations. However, PAW involves approximations, and it is thus important to understand how they affect the results. Tests of the precision of PAW data sets often use the properties of isolated atoms or atomic solids. While this is sufficient to identify problematic PAW data sets, little information has been gained to understand the origins of the errors and suggest ways to correct them. Here, we show that the interaction energies of molecular dimers are very useful not only to identify problematic PAW data sets but also to uncover the origin of the errors. Using dimers from the S22 and S66 test sets and other dimers, we find that the error in the interaction energy is composed of a short-range component with an exponential decay and a long-range electrostatic part caused by an error in the total charge density. We propose and evaluate a simple improvable scheme to correct the long-range error and find that even in its simple and readily usable form, it is able to reduce the interaction energy errors to less than half on average for hydrogen-bonded dimers.

Structural characterization of a 3-hydroxychromone dye trehalose conjugate for fluorescent labelling of mycobacteria

3-Hydroxychromone (3HC) dye trehalose conjugates have previously been exploited as environment-sensitive fluorescent labels to detect mycobacteria by fluorescence microscopy. We have studied the 3HC dye 2-(6-(diethylamino)benzofuran-2-yl)-3-hydroxy-4H-chromen-4-one (3HC-2) trehalose conjugate 3HC-2-Tre by X-ray crystallography, spectroscopic methods augmented by DFT calculations and conducted preliminary labelling experiments with Mycobacterium abscessus, a non-tuberculous mycobacterium and opportunistic pathogen. In the crystal structure of 3HC-2-Tre ⋅ 3.14 H2O, the 3HC-2-Tre molecules exhibit an intramolecular OH⋅⋅⋅O hydrogen bond between the 5-hydroxy group of trehalose and the chromone carbonyl oxygen atom, and form hydrogen-bonded dimers via the trehalose units with approximate local C2 symmetry. The chromophore adopts an s-cis conformation of the chromone and benzofuran systems about its central CC bond, as previously encountered in the crystal structure of the free dye 3HC-2, and the trehalose moieties approximately retain the shape as found in the crystal structures of anhydrous trehalose and the dihydrate. Absorption spectra of 3HC-2-Tre acquired in four different solvents revealed small positive solvatochromy. Fluorescence microscopy detected M. abscessus cells treated with 3HC-2-Tre in the GFP channel.

Short chiral pitch and blue phase stability in cholesteric liquid crystal mixtures by adding achiral benzoic acid derivative

ABSTRACT Cholesteric liquid crystal (CLC) is anticipated to have applications such as blue light and ultraviolet (UV) light blocking for human skin owing to its selective wavelength reflection against incident sunlight through several hundred nanometres of a periodic helical twist structure. In this study, we investigated short chiral pitch control and enlargement of the blue phase (BP) temperature range by adding an achiral constituent of 4-n-octylbenzoic acid (8 BA) into CLC mixtures composed of three kinds of cholesteryl compounds: cholesteryl chloride, cholesteryl pelargonate and cholesteryl palmitate. Hydrogen bonding dependence of chiral pitch and BP temperature range were also investigated for achiral dopant (8 BA) and CLC mixture through temperature-dependent Fourier-transform infrared analysis. It was found that 40 wt% of 8 BA within the CLC mixture selectively reflected UV and blue light over 360–400 nm with a decrease of chiral pitch. It was also found that the BP temperature range increased by 15.6°C owing to hydrogen bond dimers composed of 8 BA molecules in the CLC mixture.

Hydrogen-Bonded Complexes in Binary Mixture of Imidazolium-Based Ionic Liquids with Organic Solvents.

Though local structures in ionic liquids are dominated by strong Coulomb forces, directional hydrogen bonds can also influence the physicochemical properties of imidazolium-based ionic liquids. In particular, the C-2 position of the imidazolium cation is acidic and can bind with suitable hydrogen bond acceptor sites of molecular solvents dissolved in imidazolium-based ionic liquids. In this report, we identify hydrogen-bonded microenvironments of the model ionic liquid, 1-ethyl-3-methylimidazolium tris(pentafluoroethyl) trifluorophosphate, and the changes that occur when molecular solvents are dissolved in it by using a C-D infrared reporter at the C-2 position of the cation. Our linear and nonlinear infrared experiments, along with computational studies, indicate that the molecular solvent dimethyl sulfoxide can form strong hydrogen-bonded dimers with the cation of the ionic liquid at the C-2 position. In contrast, acetone, which is also a hydrogen bond acceptor similar to dimethyl sulfoxide, does not show evidence of cation-solvent hydrogen-bonded conformers at the C-2 position. The outcome of our study on a broad scale strengthens the importance of cation-solute interactions in ionic liquids.