Intramolecular Hydrogen-bonding Interactions Research Articles

Single crystal structure features, optimization of ultrasonic conditions, density functional theory studies, and antibacterial activity of a new organic compound

The synthesis of a novel water-soluble organic compound, N’-acetyl-4-nitrobenzohydrazide, was successfully achieved using hydrothermal and sonochemical methods. The resulting products, denoted as 1 and 2, were obtained as single crystals and powder, respectively. Characterization of the crystals through single-crystal X-ray diffraction (SC-XRD) indicated a monoclinic system with space group -P 2yn. Elemental analysis (CHN), energy-dispersive X-ray spectrometer (EDS), Fourier transform infrared spectroscopy (FT-IR), thermal analysis (TGA/DTA), and powder X-ray diffraction pattern (PXRD), were utilized to analyze the molecular structure of 1 and 2, confirming their identical nature. Furthermore, scanning electron microscopy (SEM) was employed to examine the surface morphology of compounds 1 and 2, revealing distinct morphological features and varying particle dimensions. The impact of time, temperature, and ultrasonic energy was examined to optimize the morphology and particle size of compound 2. A density functional theory (DFT) study was performed to find the role of intramolecular hydrogen bond (IHB) interactions on the capability of the different tautomers of newly synthesized organic compounds. Various properties such as total energies of tautomers, energies of the most important molecular orbitals, electronegativity, thermodynamic functions, molecular electrostatic potential (MEP) maps, electron charge densities, and aromaticity were computed. The antimicrobial activity of 1, and 2 have been evaluated against one Gram-positive (Staphylococcus aureus, ATCC 25,923) and one Gram-negative (Escherichia coli, ATCC 25,922) using the disc diffusion method. The analysis of the inhibition zones revealed that 2 exhibit enhanced antibacterial efficacy compared to 1. This observation suggests that particle size reduction may contribute to increased antibacterial activity, potentially due to enhanced interaction with bacterial targets.

Simple synthesis of monocyclic pyrimidine-based energetic molecule with “amino–nitro–hydrazino” arrangement

With the constant development of energetic materials, numerous explosive molecules have been synthesized, some of which feature competitive performances. However, energetic materials are directly oriented to application requirements. Therefore, more emphasis is gradually placed on route simplification and cost reduction while designing novel energetic molecules. In this work, monocyclic energetic compound 2,4-diamino-6-hydrazineyl-5-nitropyrimidine (3) was successfully obtained. This compound exhibits an alternating “amino–nitro–hydrazino” arrangement, featuring strong intramolecular hydrogen-bonding interaction. With cheap raw material, the whole reaction comprised only two steps, and exhibited simple post processing, only filtration. This novel energetic molecule possesses excellent mechanical security (IS > 40 J, FS > 360 N), acceptable thermal stability (Td = 225 °C), and good detonation parameters (Dv = 8470 m/s, P = 24.9 GPa), indicating that compound 3 may act as a candidate of insensitive explosives.

Crystal structure and Hirshfeld surface analysis of tri-chlorido-(1,10-phenanthroline-κ2 N,N')phenyltin(IV).

The title compound, [Sn(C6H5)Cl3(C12H8N2)], which was obtained by the reaction between 1,10-phenanthroline and phenyl-tin trichloride in methanol, exhibits intra-molecular hydrogen-bonding inter-actions involving the chlorine and hydrogen atoms. Crystal cohesion is ensured by inter-molecular C-H⋯Cl hydrogen bonds, as well as Y-X⋯π and π-stacking inter-actions involving three different aromatic rings with centroid-centroid distances of 3.6605 (13), 3.9327 (14) and 3.6938 (12) Å]. Hirshfeld surface analysis and the associated two-dimensional fingerprint plots reveal significant contributions from H⋯H (30.7%), Cl⋯H/H⋯Cl (32.4%), and C⋯H/H⋯C (24.0%) contacts to the crystal packing while the C⋯C (6.2%), C⋯Cl/Cl⋯C (4.1%), and N⋯H/H⋯N (1.7%) inter-actions make smaller contributions.

Programming Hydrogen Bonds for Reversible Elastic-Plastic Phase Transition in a Conductive Stretchable Hydrogel Actuator with Rapid Ultra-High-Density Energy Conversion and Multiple Sensory Properties.

Smart hydrogels have recently garnered significant attention in the fields of actuators, human-machine interaction, and soft robotics. However, when constructing large-scale actuated systems, they usually exhibit limited actuation forces (≈2kPa) and actuation speeds. Drawing inspiration from hairspring energy conversion mechanism, an elasticity-plasticity-controllable composite hydrogel (PCTA) with robust contraction capabilities is developed. By precisely manipulating intermolecular and intramolecular hydrogen-bonding interactions, the material's elasticity and plasticity can be programmed to facilitate efficient energy storage and release. The proposed mechanism enables rapid generation of high contraction forces (900kPa) at ultra-high working densities (0.96MJm-3). Molecular dynamics simulations reveal that modifications in the number and nature of hydrogen bonds lead to a distinct elastic-plastic transition in hydrogels. Furthermore, the conductive PCTA hydrogel exhibits multimodal sensing capabilities including stretchable strain sensing with a wide sensing range (1-200%), fast response time (180ms), and excellent linearity of the output signal. Moreover, it demonstrates exceptional temperature and humidity sensing capabilities with high detection accuracy. The strong actuation power and real-time sensory feedback from the composite hydrogels are expected to inspire novel flexible driving materials and intelligent sensing systems.

Crystal structure of a tris(2-amino-eth-yl)methane capped carbamoyl-methyl-phosphine oxide compound.

The mol-ecular structure of the tripodal carbamoyl-methyl-phosphine oxide compound diethyl {[(5-[2-(di-eth-oxy-phosphor-yl)acetamido]-3-{2-[2-(di-eth-oxy-phos-phor-yl)acetamido]-eth-yl}pent-yl)carbamo-yl]meth-yl}phospho-nate, C25H52N3O12P3, features six intra-molecular hydrogen-bonding inter-actions. The phospho-nate groups have key bond lengths ranging from 1.4696 (12) to 1.4729 (12) Å (P=O), 1.5681 (11) to 1.5811 (12) Å (P-O) and 1.7881 (16) to 1.7936 (16) Å (P-C). Each amide group adopts a nearly perfect trans geometry, and the geometry around each phophorus atom resembles a slightly distorted tetra-hedron.

Exploring the Supramolecular Features, Computational Studies, and Molecular Docking Studies of a Carbamate Schiff Base

Abstract: In the carbamate Schiff base compound, the molecule is stabilized by intramolecular hydrogen bonding interactions along with π···π stacking and C–H···π contacts that lead to the molecule generating diverse supramolecular architecture. The fingerprint plots associated with Hirshfeld surface analysis indicate that the most important contributions for the crystal packing are from H⋯H/H⋯H (81.8%), H⋯O/O⋯H (7.5%), and H⋯N/N⋯H (1.9%) interactions. Furthermore, a computational study is performed to find the interaction energy between molecular pairs, and a description of the active site of the compound has been included. The study inferred the role of various types of interaction energies in stabilizing the molecular pair. Additionally, the carbamate Schiff base compound was tested as a possible inhibitor for a group of the SARS-CoV-2 proteins employing a molecular docking approach. Papain-like protease (PLpro) was shown to have the highest binding affinities. The carbamate Schiff base compound with PLpro’s docking score falls within the acceptable levels for a hit compound.

Ligand Isomerization Driven Electrocatalytic Switching.

The prevailing view about molecular catalysts is that the central metal ion is responsible for the reaction mechanism and selectivity, whereas the ligands mainly affect the reaction kinetics. Here, we question this paradigm and show that ligands have a dramatic influence on the selectivity of the product. We show how even a seemingly small change in ligand isomerization sharply alters the selectivity of the well-researched oxygen reduction reaction (ORR) Co phthalocyanine catalyst from an indirect 2e- to a direct 4e- pathway. Detailed analysis reveals that intramolecular hydrogen-bond interactions in the ligand activate the catalytic Co, directing the oxygen binding and thus deciding the final product. The resulting catalyst is the first example of a Co-based molecular catalyst catalyzing a direct 4e- ORR via ligand isomerization, for which it shows an activity close to the benchmark Pt in an actual H2-O2 fuel cell. The effect of the ligand isomerism is demonstrated with different central metal ions, thus highlighting the generalizability of the findings and their potential to open new possibilities in the design of molecular catalysts.

Supramolecular Annihilator with DPA Parallelly Arranged by Multiple Hydrogen-Bonding Interactions for Enhanced Triplet-Triplet Annihilation Upconversion.

The triplet annihilator is a critical component for triplet-triplet annihilation upconversion (TTA-UC); both the photophysical properties of the annihilator and the intermolecular orientation have pivotal effects on the overall efficiency of TTA-UC. Herein, we synthesized two supramolecular annihilators A-1 and A-2 by grafting 9,10-diphenylanthracene (DPA) fragments, which have been widely used as triplet annihilators for TTA-UC, on a macrocyclic host-pillar[5]arenes. In A-1, the orientation of the two DPA units was random, while, in A-2, the two DPA units were pushed to a parallel arrangement by intramolecular hydrogen-bonding interactions. The two compounds showed very similar photophysical properties and host-guest binding affinities toward electron-deficient guests, but showed totally different TTA-UC emissions. The UC quantum yield of A-2 could be optimized to 13.7% when an alkyl ammonia chain-attaching sensitizer S-2 was used, while, for A-1, only 5.1% was achieved. Destroying the hydrogen-bonding interactions by adding MeOH to A-2 significantly decreased the UC emissions, demonstrating that the parallel orientations of the two DPA units contributed greatly to the TTA-UC emissions. These results should be beneficial for annihilator designs and provide a new promising strategy for enhancing TTA-UC emissions.

Synergetic effects of inter- and intramolecular hydrogen bonding interactions in XC5H3HC = Y···HO···H2O2 complexes (X = N, P, As and Sb; Y = O, S and NH): the role of aromaticity and exchange interactions

ABSTRACT Intramolecular hydrogen bonding (IHB) interactions were considered in XC5H3HC = Y···HO molecules which include OH···Y unit (Y = O, S and NH) and heteroatom X (X = N, P, As and Sb). Alteration of heteroatoms X in para position causes a change of properties of electron charge densities on these molecules and influences on strength of the IHB interactions. The aromaticity of the ring A (involving IHB interaction) and ring B (involving heteroatoms X) of XC5H3HC = Y···HO molecules was calculated using para-delocalisation index (PDI). Results reveal that the change of X from N to Sb is followed by the decrease in aromaticity of the mentioned rings. However, the strength of the IHB interactions increases during the change of X. Moreover, IHB energies were estimated using some computational methods and a viewpoint based on the properties of ring critical points (RCPs). The IHB energies obtained using a viewpoint based on the properties of RCPs have a better relationship with hydrogen bonding descriptors. Also, intermolecular hydrogen bond (HB) interactions of hydrogen peroxide with the close and open forms of the XC5H3HC = Y···HO molecules were considered. Cooperative effects of the HB and IHB interactions are revealed. Moreover, energy decomposition analysis (EDA) highlights the role of exchange interactions on the stability of the XC5H3HC = Y···HO···H2O2 complexes.

Regioselective amination of 4-methylene-5,7-dinitroquinazoline: a mechanistic consideration on non-conventional N-H—π interactions between amine and ethylene moiety

ABSTRACT Pi (π) interactions originating from the N-H bond of amine and ethylene moiety have been explored on the mechanism of aromatic nucleophilic substitution (ArSN) of the nitro group of 4-methylene-5,7-dinitroquinazoline with methylamine in the gas phase and solvent media within DFT framework. The free energy profiles confirmed that the amination should take place at peri-position and calculations support the one-step mechanism through a transition state with no intermediate in the reaction route. Stabilisation of peri-transition state by intramolecular weak interaction akin to hydrogen bonding N-H—CH2 = C leads to the regioselective amination at peri-position of 4-methylene-5,7-dinitroquinazoline. The intramolecular hydrogen bond interactions at N-H—CH2 = C in the peri-transition state are strongly supported by a red shift in N-H stretching vibrations in simulated IR spectra and are confirmed by studying energetics of amination of structural/electronic analogues of 4-methylene-5,7-dinitroquinazoline. The present study established that ethylene plays an important role as an efficient H-bond acceptor in fixing the regioselectivity at peri-position in the amination of 4-methylene-5,7-dinitroquinazoline. This is the first-ever report for the exploration of the role of ethylene moiety as a hydrogen bond acceptor in mediating the regioselectivity of organic reactions.

Molecular Structure of Salicylic Acid and Its Hydrates: A Rotational Spectroscopy Study.

We present a study of salicylic acid and its hydrates, with up to four water molecules, done by employing chirped-pulse Fourier transform microwave spectroscopy. We employed the spectral data set of the parent, 13C, and 2H isotopologues to determine the molecular structure and characterize the intra- and intermolecular interactions of salicylic acid and its monohydrate. Complementary theoretical calculations were done to support the analysis of the experimental results. For the monomer, we analyzed structural properties, such as the angular-group-induced bond alternation (AGIBA) effect. In the microsolvates, we analyzed their main structural features dominated by the interaction of water with the carboxylic acid group. This work contributes to seeding information on how water molecules accumulate around this group. Moreover, we discussed the role of cooperative effects further stabilizing the observed inter- and intramolecular hydrogen bond interactions.

Investigating the role of thymol as a promising inhibitor of pyruvate dehydrogenase kinase 3 for targeted cancer therapy

Protein kinases have emerged as major contributors to various diseases. They are currently exploited as a potential target in drug discovery because they play crucial roles in cell signaling, growth, and regulation. Their dysregulation is associated with inflammatory disorders, cancer, and neurodegenerative diseases. Pyruvate dehydrogenase kinase 3 (PDK3) has become an attractive drug target in cancer therapeutics. In the present study, we investigated the effective role of thymol in PDK3 inhibition due to the high affinity predicted through molecular docking studies. Hence, to better understand this inhibition mechanism, we carried out a 100 ns molecular dynamics (MD) simulation to analyse the dynamics and stability of the PDK3-thymol complex. The PDK3-thymol complex was stable and energetically favourable, with many intramolecular hydrogen bond interactions in the PDK3-thymol complex. Enzyme inhibition assay showed significant inhibition of PDK3 by thymol, revealing potential inhibitory action of thymol towards PDK3 (IC50 = 2.66 μM). In summary, we established thymol as one of the potential inhibitors of PDK3, proposing promising therapeutic implications for severe diseases associated with PDK3 dysregulation. This study further advances our understanding of thymol's therapeutic capabilities and potential role in cancer treatment.

Fabrication and characterization of polyvinyl alcohol/sodium alginate loaded carvacrol/silica hollow microspheres composite hydrogel as a colourimetric freshness indicator

A hybrid hydrogel consisting of anthocyanin (ATH), sodium alginate (SA), polyvinyl alcohol (PVA) and carvacrol (CA) loaded silica hollow microspheres (SC) was designed and fabricated as a colorimetric freshness indicator with antibacterial activity for monitoring meat spoilage. The microstructure and physicochemical properties of the hybrid hydrogels were investigated. The carvacrol could be loaded into silica microspheres, and the maximum degradation temperature raised to 179.6 °C due to the formation of hydrogen bonds between carvacrol and SiO2 microspheres. ATH and SC composite were well compatible with PVA/SA hydrogel with intramolecular hydrogen bond interactions. The three-dimensional network structure of the PVA/SA hydrogel was disrupted with increasing SC content, resulting in a gradual decrease in thermal stability, swelling capacity and tensile strength of the hydrogel. The SC-PVA/SA-ATH hydrogels exhibited satisfactory antibacterial ability against E. coli and S. aureus due to the effective release of CA from the hybrid hydrogel, and the inhibition ratio of SC3-PVA/SA-ATH was over 95%. The meat preservation experiment revealed that the hydrogel indicators exhibited distinctive color changes during the process of meat spoilage quality changes, indicating its promising application prospect in food preservation packaging.

Macrocyclization-induce emission enhancement characteristics of benzothiadiazole-based macrocycles: A theoretical study

We present a comprehensive investigation into the molecular structures in the ground state and the first singlet excited state, intramolecular and intermolecular interactions, as well as the emission properties of monomers, dimers and macrocycles using density functional theory and time-dependent density functional theory. Our study aims to unveil the macrocyclization-induce emission enhancement principle for benzothiadiazole-based macrocycles. Compared with the typical π-π stacking of monomers, macrocycles exhibit the tighter stacking arrangement due to the presence of strong intramolecular and intermolecular hydrogen bond interactions and the rigid triangular geometry of macrocycle, which is conducive to the enhancement of emissions efficiency. The calculated oscillator strength of macrocycles in the first excited state is much higher than that of dimers composed of two monomers. Meanwhile, the large transition electric dipole moment is beneficial for enhancing the emission efficiency. Additionally, our study reveals an emission wavelength red-shift for macrocycles after “CH”/N substitution in the acceptor moiety, and the transition mode from LUMO to HOMO can be mainly attributed to intramolecular charge transition characters from acceptor to donor fragments. Our theoretical study might provide valuable insights for the design of innovative luminescent macrocycles with high emission efficiency.

Evolution of molecular structure of TATB under shock loading from transient Raman spectroscopic technique

By combination of the transient Raman spectroscopic measurement and the density functional theoretical calculations, the structural evolution and stability of TATB under shock compression was investigated. Due to the improvement in synchronization control between two-stage light gas gun and the transient Raman spectra acquisition, as well as the sample preparation, the Raman peak of the N–O mode of TATB was firstly observed under shock pressure up to 13.6 GPa, noticeably higher than the upper limit of 8.5 GPa reported in available literatures. By taking into account of the continuous shift of the main peak and other observed Raman peaks, we did not distinguish any structural transition or any new species. Moreover, both the present Raman spectra and the time-resolved radiation of TATB during shock loading showed that TATB exhibits higher chemical stability than previous declaration. To reveal the detailed structural response and evolution of TATB under compression, the density functional theoretical calculations were conducted, and it was found that the pressure make N–O bond lengths shorter, nitro bond angles larger, and intermolecular and intra-molecular hydrogen bond interactions enhanced. The observed red shift of Raman peak was ascribed to the abnormal enhancement of H-bound effect on the scissor vibration mode of the nitro group.

Rational design of hybridized local and charge-transfer (HLCT) emitters towards blue OLEDs with high luminance and low efficiency roll-off

Organic blue emitters have been get more and more attention by scientists and industries in the field of organic light-emitting diodes (OLEDs). The design of efficient blue emitters, especially deep-blue ones, is still a challenge because of their intrinsic wide band-gaps and unbalanced carrier mobilities. Herein, two donor‒π‒acceptor (D‒π‒A) type molecules with phenanthro[9,10-d]imidazole (PI) as A and pyridinyl as π-bridge were designed and synthesized by fine-turning the D moieties, namely mPTPA and mP3PCZ, respectively. Theoretical calculation and single-crystal analysis showed that there exist intramolecular hydrogen bond (IHB) interactions inducing small torsion angles between pyridinyl and adjacent phenyls. The rigid 9-phenyl-9H-carbazole (PCZ) and IHB interactions makes mP3PCZ exhibiting planar configuration along the long-axis of the molecule, which could increase the orbital overlap and oscillator strength (fos). The solvatochromic effect manifested that both two emitters have hybridized local and charge-transfer (HLCT) characteristics, and the excited state of mP3PCZ exhibited LE-dominated HLCT state which is beneficial for high photoluminescence efficiency. Ultimately, the non-doped devices based on mPTPA and mP3PCZ achieved maximum luminance larger than 12000 cd m−2. Furthermore, the doped device based on mP3PCZ exhibited maximum external quantum efficiency of 5.14% with low efficiency roll-off, and with the corresponding deep-blue Commission international de l’éclairage (CIE) coordinate of (0.166, 0.085).

Theoretical study on the excited state mechanism of the fluorescent probe for detecting HOCl

The abnormal level of hypochlorous acid (HOCl) in the human body will cause a series of diseases, and it is of great importance for designing and developing efficient fluorescent probes to detect HOCl. In this work, the fluorescence mechanism of BTMSP, a ratiometric fluorescent probe for detecting HOCl based on the sulfide oxidation reaction, has been studied through theoretical calculations. The optimized geometric configuration and infrared spectroscopy analysis of BTMSP and BTMTP at the ground state and excited state demonstrate that the intramolecular hydrogen bond interaction (O − H···N) strengthened, which will facilitate the proton transfer at the excited state. The potential energy curves for BTMSP and BTMTP at the S0, S1 state along the increasing in bond length of O–H were scanned. The frontier molecular orbitals (MOs) and charge density difference (CDD) map, the distribution of electrons and holes were discussed to investigate the charge transfer process. In addition, the calculated emission spectra demonstrates a significant blue shift in the wavelength occurred when BTMSP was oxidized by HOCl, which is consistent with the experimental results. All of the above calculated results indicate the excited state intramolecular proton transfer (ESIPT) process of BTMTP are remain existed, rather than as reported that the ESIPT had been canceled due to the stronger electron-withdrawing of sulfoxide group.

Dynamics simulation of excited-state proton transfer reactions of 8-hydroxyquinoline with water clusters: A TD-DFT study

Detailed pictures of the excited-state proton transfer reactions of 8-hydroxyquinoline (8HQ) and its small clusters of water have been systematically investigated using density functional theory (DFT) and time-dependent DFT (TD-DFT) methods at B3LYP/TZVP and TD-B3LYP/TZVP level of theory, respectively. Intramolecular hydrogen bond (intraHB) and intermolecular hydrogen bond (interHB) interactions between 8HQ and water cluster become stronger in the first excited state (S1), confirmed by hydrogen bond distances and topological analysis. In addition, TD-B3LYP dynamics simulations have been elucidated and revealed that excited-state intramolecular proton transfer (ESIntraPT) and multiply excited-state intermolecular proton transfer (ESInterPT) reactions of these complexes can take place in the ultrafast time scale of femtoseconds. Increasing the number of water molecules may give rise to a barrier energy that is anti-correlated to the probability of tautomer species from phototautomerization, especially in 8HQ-W1 and 8HQ-W1+1. Moreover, water molecules initiate multiple proton transfer occurring through two- and three-step ESInterPT namely excited-state double proton transfer (ESDPT) and excited-state triple proton transfer (ESTPT) in which the interHBs are formed by rearrangement of water molecules of 8HQ-W2. This circumstance takes a longer time (up to 470 fs) compared to that of ESIntraPT. Thus, the simulated results from this study could provide insight into ESIntraPT and ESInterPT of phototautomerization and the significant photodynamics which could not be found from the experimental aspects of 8HQ and its solvent clusters.

Breaking the DFT Energy Bias Caused by Intramolecular Hydrogen-Bonding Interactions with MESSI, a Structural Elucidation Method Inspired by Wisdom of the Crowd Theory.

The use of quantum-based NMR methods to complement and guide the connectivity and stereochemical assignment of natural and unnatural products has grown enormously. One of the unsolved problems is related to the improper calculation of the conformational landscape of flexible molecules that have functional groups capable of generating a complex network of intramolecular H-bonding (IHB) interactions. Here we present MESSI (Multi-Ensemble Strategy for Structural Identification), a method inspired by the wisdom of the crowd theory that breaks with the traditional mono-ensemble approach. By including independent mappings of selected artificially manipulated ensembles, MESSI greatly improves the sense of the assignment by neutralizing potential energy biases.

Sustainable, Insoluble, and Photonic Cellulose Nanocrystal Patches for Calcium Ion Sensing in Sweat.

Self-assembly of cellulose nanocrystals (CNCs) is invaluable for the development of sustainable optics and photonics. However, the functional failure of CNC-derived materials in humid or liquid environments inevitably impairs their development in biomedicine, membrane separation, environmental monitoring, and wearable devices. Here, a facile and robust method to fabricate insoluble hydrogels in a self-assembled CNC-polyvinyl alcohol (PVA) system is reported. Due to the reconstruction of inter- or intra-molecular hydrogen bond interactions, thermal dehydration makes an optimized CNC/PVA photonic film form a stable hydrogel network in an aqueous solution rather than dissolve. Notably, the resulting hydrogel exhibits superb mechanical performance (stress up to 3.3 Mpa and tough up to 0.73MJm-3 ) and reversible conversion between dry and wet states, enabling it convenient for specific functionalization. Sodium alginate (SA) can be adsorbed into the CNC photonic structure by swelling dry CNC/PVA film in a SA solution. The prepared hydrogel showcases the comprehensive properties of freezing resistance (-20°C), strong adhesion, satisfactory biocompatibility, and highly sensitive and selective Ca2+ sensing. The material could act as a portable wearable patch on the skin for the continuous analysis of calcium trends during different physical exercises, facilitating their development in precision nutrition and health monitoring.