Strength Of Intermolecular Hydrogen Bonds Research Articles

Structural Characterization, Spectroscopic Profile, Molecular Docking, ADMET Properties, Molecular Dynamics Simulation Studies, and Molecular Mechanics Generalized Born Surface Area Analysis of 5-(Adamantan-1-yl)-4-butyl-2,4-dihydro-3H-1,2,4-triazole-3-thione as a Potential COX Inhibitor.

Employing a synergistic combination of theoretical density functional theory (DFT) and experimental techniques, we conducted a comprehensive analysis elucidating the structural and pharmacological attributes of 5-(adamantan-1-yl)-4-butyl-2,4-dihydro-3H-1,2,4-triazole-3-thione (5A4BT) as a potent COX inhibitor. The X-ray crystallographic data of 5A4BT showed the pivotal role played by weak interactions, notably π-π and C-H-π interactions, alongside hydrogen bonding, in orchestrating the intricate supramolecular architectures within the crystalline lattice. A quantitative analysis of the arrangement of the crystal structure, as well as both inter- and intramolecular interactions, was conducted using Hirshfeld surfaces and 2D fingerprint plots. Additionally, a comprehensive examination of the IR spectra was undertaken, employing both experimental methods and theoretical DFT techniques, to elucidate the vibrational characteristics of the compound. The strength of intermolecular N-H···S hydrogen bonding and charge transfer within the system was assessed through natural bonding orbital analysis. Moreover, Bader's atoms in molecules theory was employed to estimate the strength of intermolecular hydrogen bonds, revealing strong interactions within the 5A4BT dimer. The title compound exhibited binding affinities of -6.4 and -6.5 kcal/mol for COX1 (PDB 3KK6) and COX2 (1CX2) target proteins, respectively. For the first time, predictions regarding ADMET properties, drug-likeness, and toxicity, including favorable bioavailability, along with 100 ns molecular dynamics simulations, binding free energy, and energy decomposition per residue in the binding cavity of the protein from molecular mechanics generalized born surface area approach, collectively indicate the potential of 5A4BT as a nonselective COX inhibitor.

Spectroscopic investigations and electronic transitions, topology studies, and biological assay of a potent antimicrobial compound: 2-amino-pyrimidine benzoic acid

The derivatives of benzoic acid, a claimed anti-fungal agent, are physiologically active components of vitamin B-complex. Signals in a heavily deshielded area is found using nuclear magnetic resonance analysis. In optimized geometry, the result reveals that nitrogen and oxygen are responsible for transfer of charge within the ring system wherein increases the bond length. Broadening and red shifting, which result from vibrational assignments, show the strength of intermolecular hydrogen bonds. Topological analysis like atoms in molecules, reduced density gradient graph that demonstrates favorable findings The electron localized function and localized orbital locator analysis are helpful when a site displays a strong distribution of electrons as a result of having the presence of a covalent bond, a lone pair of electrons, or a nuclear shell there. Findings of in vitro tests for antimicrobial activity clearly show that all two strains’ activity and inhibition both rise as compound concentrations climb. The title chemical may be verified to block antimicrobial activity and be a pesticide using molecular docking, in vitro antimicrobial activity, and qualities of a drug’s resemblance.

Ortho-pyridinyl anilines: A class of fluorescent chemoprobes for quantitatively visualizing proton donating ability

Proton donating ability is known to be a key factor during most chemical, physical, and biological processes; therefore, quantifying such an ability visibly is crucial for further research. However, there has long been a lack of excellent models to fulfil such a quantitative visualization. Here, we designed and synthesized a series of fluorescent chemoprobes based on ortho-pyridinyl anilines, whose fluorescence signal showed a quantitative relationship with its intermolecular hydrogen bond strength. On this basis, the proton donating ability of the external proton donors through competitive hydrogen bond formation could be shown quantitatively by virtue of the changes of the fluorescence.

Geometrical and temperature impact on elucidation of intermolecular interactions for the binary mixtures of morpholine with aliphatic esters by thermodynamic, FTIR and DFT study

Abstract In this investigation, the binary solutions of morpholine (MP) with tert-butyl acetate (TBA), iso-butyl acetate (IBA), butyl acetate (BA) and butyl acrylate (BAC) were prepared for the densities (ρ) and speeds of sound (u) measurements at T = (303.15, 308.15, 313.15 and 318.15) K over the entire composition range and at atmospheric pressure (P = 0.1 MPa). From these data, excess thermodynamic properties such as excess molar volume ( V m E ${V}_{m}^{E}$ ), excess isentropic compressibility ( κ S E ${\kappa }_{S}^{E}$ ) and excess speeds of sound ( u E ${u}^{E}$ ) were calculated to elucidate the strength and types of intermolecular interactions between the component molecules. Redlich-Kister (RK) equation and Prigogine–Flory–Patterson (PFP) theory was applied to correlate the excess parameters and excess volumes, respectively. Further, intermolecular free length theory and collision frequency theory were used to correlate the speed of sound data. Shifting of bands (δν), bond length and hydrogen bond strength between the atoms were calculated from the experimental FTIR and DFT theoretical studies. The systematic increasing order of the intermolecular hydrogen bond strength between the two atoms in the studied binary systems as follows: TBA > IBA > BA > BAC.

Short-side-chain regulation of colorless and transparent polyamide-imides for flexible transparent displays

Improving the heat resistance, dimensional stability and mechanical properties of colorless and transparent polyimides remains a popular and promising topic as it is considered to be the basis for their application in next-generation flexible displays. However, enhancing these properties without sacrificing optical transparency is challenging. Although recent research has revealed that hydrogen bonding is a potential route to balance optical and other physical properties, no systematic studies or comparisons have been performed. Here, we synthesized five amide-containing diamines with different substituents and prepared the corresponding polyamide-imides (CPAIs). Short-chain substituents were introduced to regulate the conformation between benzene and imide rings, as well as the ability of amide hydrogen bond formation. The effects of the position and number of –CH3 and/or -CF3 substituents on blocking the formation of charge-transfer complexes and on the strength of intermolecular hydrogen bonds, which affect CPAI transparency and other properties, were investigated. The results demonstrated that the combination of the twisted conformation from ortho-methyl groups and hydrogen bonds from the amide promoted the optical, thermal and mechanical properties of the CPAIs. In particular, CPAI-7 exhibited a high optical transmittance at 400 nm of up to 86 %, a Tg as high as 402 °C, a low thermal expansion coefficient of 17 ppm K−1 and an extremely high tensile modulus of 5.2 GPa. The excellent and comprehensive performance of the CPAI films illustrates their potential application in the field of flexible displays.

The investigation of the ultrafast excited state deactivation mechanisms for coumarin 307 in different solvents.

The intramolecular charge transfer (ICT) and twisted intramolecular charge transfer (TICT) processes of coumarin 307 (C307) in different solvents were investigated by performing steady-state/time-resolved transient absorption spectroscopic and steady-state photoluminescence spectroscopic characterizations in combination with time-dependent density functional theoretical calculation (TDDFT). The study unveiled the remarkable influence of solvent polarity and the strength of intermolecular hydrogen bonds formed between the solutes and solvents on the relaxation dynamics of the electronic excited state. Significantly, the emergence of the TICT state was observed in polar solvents, specifically dimethylformamide (DMF) and dimethyl sulfoxidemethanol (DMSO), owing to their inherent polarity as well as the enhanced intermolecular hydrogen bonding interactions. Interestingly, even in a weak polar solvent such as methanol (MeOH), the TICT state was also observed due to the intensified hydrogen bonding effects. Conversely, nonpolar solvents, exemplified by 1,4-dioxane (Diox), resulted in the stabilization of the ICT state due to the augmented N-H⋯O hydrogen bonding interactions. The experimental findings were corroborated by the computational calculations, thus ensuring the reliability of the conclusions drawn. Furthermore, schematic diagrams were presented to illustrate the mechanisms underlying the excited-state deactivation. Overall, this investigation contributes valuable mechanistic insights and provides a comprehensive understanding of the photochemical and photophysical properties exhibited by coumarin dyes.

Thermal induced crystalline transition of bio-based polyamide 56

Thermal induced crystalline transition of polyamide 56 (PA56) was investigated by DSC, in-situ WAXD, and in-situ FTIR spectroscopy. The PA56 α-like phase, crystallized from formic acid solution, showed a Brill transition that completed at 200 °C (TB) and only γ phase crystallites were mainly obtained when cooling the PA56 samples to room temperature from molten state. The characteristic absorbance bands of PA56 α-like and γ phases on FTIR spectra were assigned. The strength of the hydrogen bonds in PA56 γ phase was stronger than those in α-like phase, which could be the main reason for the irreversible Brill transition behavior of the PA56 α-like phase. In-situ FTIR results indicated that the intermolecular hydrogen bond strength of α-like phase reduced during Brill transition before 200 °C upon heating. During the melting process, the intermolecular hydrogen bond strength first enhanced and then reduced. The Brill transition of PA56 upon heating was further confirmed by the decrease and increase in the intensity of the band at 1631 cm−1 and 1637 cm−1, corresponding to the vibration band (amide I) of CO group of α-like and γ phases of PA56, respectively. FTIR results also confirmed the deformation, twisting, and rocking vibrations of CH2 groups were enhanced during the Brill transition procedure.

Examination of proline, hydroxyproline and pyroglutamic acid with different polar groups by terahertz spectroscopy

Hydroxyproline (HYP) and pyroglutamic acid (PGA), as amino acid derivatives, are highly similar in structure to proline (Pro). However, their low-frequency vibrations show significant differences in the range of 0.25–2.6 THz. Therefore, this study investigated the reasons for the differences combined with terahertz time domain spectroscopy (THz-TDS) and density functional theory (DFT). The results show that HYP and PGA have stronger absorption of terahertz waves due to the existence of polar substituents. Furthermore, the absorption peaks of HYP and PGA are significant red shifted and blue shifted, respectively. We believe that this is caused by the change in the strength of intermolecular hydrogen bonds. Our findings demonstrate that dipole and hydrogen bond effects play a significant role in low-frequency vibrations.

Structural Variations of Wheat Proteins under ultrasound treatment

The present work investigated the effects of ultrasound on the hydrogen-bond strength, the secondary and network structures, granule size and microstructures of gluten, glutenin and gliadin, in order to explicate the possible mechanisms of ultrasound-assisted dough processing. The results showed that ultrasound weakened the intermolecular hydrogen-bond strength of protein. After sonication, the contents of β-turns and β-sheets decreased and increased, respectively, which was especially evident under medium-intensity sonication (23.08 W/L; 30 min) among low-, medium- and high-intensity. This implied that ultrasonic treatment facilitated the conversion of β-turns into β-sheets. Sonicated gluten proteins have uniform sizes and exhibit a flocculent, rough, fluffy and relatively dispersed structure with loosely distributed particles. Sonicated glutenin has a complete network structure with more ordered crosslinks between molecules. For sonicated gliadin, small pores can be observed on the surface and its overall structure appears fluffy and enlarged. Generally, ultrasound could affect the protein structure by hydrogen-bonding interactions, as well as the molecular crosslink, granule size and distribution, mechanical properties and air chamber structure.

Experimental and correlated solid–liquid equilibrium data of quizalofop-p-ethyl + CH3OH + H2O and quizalofop-p-ethyl + CH3CH2OH + H2O

Quizalofop-p-ethyl (C19H17ClN2O4) is a widely used herbicide for controlling annual and perennial grass weeds in broad-leaved agricultural crops. The solid–liquid phase equilibrium of quizalofop-p-ethyl in binary solvents (methanol + water and ethanol + water) was measured by using a gravimetric method from (293 to 322) K at atmospheric pressure. The results indicated that the solubility of quizalofop-p-ethyl increases with increasing temperature and decreases with increasing mass fraction of water in binary solvents. Solubility of quizalofop-p-ethyl in methanol + water and ethanol + water range from 0.0000158 to 0.0113177 and 0.000285–0.0157060 in rang of 293 to 322 K at mass fraction of water 0.10–0.60, respectively. The modified Apelblat model, λh model and Jouyban-Acree model were applied to correlate the experimental data. The strength of intermolecular hydrogen bonds were calculated by optimizing the complexes between quizalofop-p-ethyl and solvents with the B3LYP theoretic method and the 6–31 + G(d,p) basis set, which showed the bent OH···O and OH···N was −31471.040 and −33892.903 kJ·mol−1, respectively. The calculated dissolution enthalpy and entropy of quizalofop-p-ethyl in the binary solvents were positive, which indicated that the process is endothermic and increased randomness.

Noncovalent functionalization of graphene through physisorption of 1,1-diamino-2,2-dinitroethene: Impacts of and cooperativity between hydrogen bond and π···π interaction

The rich π-electrons region of graphene enables it to be a good material which can interact with many organic molecules. As a low-sensitivity and high-energy explosive, 1,1-diamino-2,2-dinitroethene and its dimer possess unique characters including hydrogen bonds and π bond which can adsorb on graphene through physisorption. The results suggest that the adsorption energies have a very small difference on the different adsorption sites. Due to the physisorption, the geometrical and electronic properties of 1,1-diamino-2,2-dinitroethene and its dimer vary significantly. The intramolecular as well as intermolecular hydrogen bond strengths are considerably affected due to the π···π interaction of 1,1-diamino-2,2-dinitroethene or its dimer with graphene. The cooperativity between intermolecular hydrogen bonds and π···π interactions is observed which causes wax of intermolecular hydrogen bonds and wane of π···π interactions. The physisorption of 1,1-diamino-2,2-dinitroethene or its dimer also leads to the variation of electronic property of graphene.

The anomalous behaviour of aliphatic fatty diamides: Chain length and hydrogen bonding interactions

A series of five linear aliphatic diamides were synthesised via facile direct coupling of stearic acid (C18) with diamines of varying carbon number (18-n-18, n = 2, 4, 6, 8 and 10) in a catalyst-free neat reaction. The compounds were investigated as potential renewable phase change materials (PCMs) for latent heat thermal energy storage. The thermal properties of the diamides were predictably related to the diamine chain length. TGA measurements indicated that the diamides evaporated before decomposition, with evaporation onsets increasing from 325 °C for 18-2-18 to plateau at 337 °C for the longer-chain diamides. The diamides display negligible supercooling and melt and crystallize at 140 °C–150 °C within a narrow transition span (<5 °C). Notably, both their melting and crystallization temperatures versus n present a maximum at n = 4, explained by peak hydrogen bonding and chain length considerations. As the distance between the amide groups increases, the transition temperatures decrease exponentially owing to the subsequent decrease in intermolecular hydrogen bond strength. The latent heat of the diamides presented a sharp increase from 165 J/g for 18-2-18 to plateau at ~210 J/g for the other amides (n ≥ 4). XRD measurements support the thermal transition behaviour; it shows that all the diamides crystallize from the melt into the β-phase, except for 18-2-18 in which the β-phase co-existed with the less stable β′-phase. Overall, the study shows that the diamides are suitable alternatives to classical petrochemical derived PCMs, expanding the currently limited library of organic PCMs.

Experimental and theoretical DFT (B3LYP, X3LYP, CAM-B3LYP and M06-2X) study on electronic structure, spectral features, hydrogen bonding and solvent effects of 4-methylthiadiazole-5-carboxylic acid

ABSTRACTDetailed structural, electronic and spectroscopic study of 4-methylthiadiazole-5-carboxylic acid, one of the simplest 1,2,3-thiadiazole derivatives has been performed using density functional theory at four different functionals (B3LYP, X3LYP, CAM-B3LYP and M06-2X). The two possible conformers and their dimeric forms have been investigated for the stability and hence for the calculation of molecular properties of the title compound. Vibrational analysis has been performed with the help of experimental FT-IR and FT-Raman spectra. NBO analysis has been performed to estimate the N–H—O=C hydrogen bond strength and to evaluate the intra and inter molecular charge transfer in the system. Intermolecular hydrogen-bond strength has also been computed using Atoms in Molecules (AIM) theory. To visualise spatial domain, key sites of electron transitions and electron density difference between ground as well as excited states, and their 2D and 3D plots have been computed. Solvent effect on the intermolecular hydrogen bonding have also been investigated using solvents of different polarities. Non-linear optical properties, molecular electrostatic potential surface map (MESP), thermodynamic potentials at different temperatures have also been computed and plotted.

Why does β-cyclodextrin prefer to bind nucleotides with an adenine base rather than other 2'-deoxyribonucleoside 5'-monophosphates?

β-Cyclodextrin (β-CD), which resides in the α-hemolysin (αHL) protein pore, can act as a molecular adapter in single-molecule exonuclease DNA sequencing approaches, where the different nucleotide binding behavior of β-CD is crucial for base discrimination. In the present contribution, the inclusion modes of β-CD towards four 2'-deoxyribonucleoside 5'-monophosphates (dNMPs) were investigated using quantum mechanics (QM) calculations. The calculated binding energy suggests that the binding affinity of dAMP to β-CD are highest among all the dNMPs in solution, in agreement with experimental results. Geometry analysis shows that β-CD in the dAMP complex undergoes a small conformational change, and weak interaction analysis indicates that there are small steric repulsion regions in β-CD. These results suggest that β-CD has lower geometric deformation energy in complexation with dAMP. Furthermore, topological analysis and weak interaction analysis suggest that the number and strength of intermolecular hydrogen bonds and van der Waals interactions are critical to dAMP binding, and they both make favorable contributions to the lower interaction energy. This work reveals the reason why β-CD prefers to bind dAMP rather than other dNMPs, while opening exciting perspectives for the design of novel β-CD-based molecular adapters in the single-molecule exonuclease method of sequencing DNA. Graphical Abstract The binding affinity of β-cyclodextrin towards four 2'-deoxyribonucleoside 5'-monophosphates was investigated using quantum mechanics calculations.

IR spectroscopy and single crystal X-ray diffraction study of 1,2-bis(2-aminophenoxy)-ethane, 1,5-bis(2-aminophenoxy)-3-oxapentane, and 1,8-bis(2-aminophenoxy)-3,6-dioxaoctane

Vibrational spectra of 1,2-bis(2-aminophenoxy)-ethane, 1,5-bis(2-aminophenoxy)-3-oxapentane, and 1,8-bis(2-aminophenoxy)-3,6-dioxaoctane–podands, different in the length of oxyethylene fragments, are measured and their single crystal X-ray diffraction analysis is performed. It is demonstrated that the strength of intermolecular hydrogen bonds (IMHB) with the participation of NH groups increases with the elongation of the oxyethylene spacer. According to the XRD data for 1,2-bis(2-aminophenoxy)-ethane, the weakest hydrogen bonds are characteristic. From the IR spectra, important intermolecular hydrogen bonds are typical of 1,8-bis(2-aminophenoxy)-3,6-dioxaoctane having the longest oxyethylene fragment.

Computational Analysis of Sugar Alcohols as Phase-Change Material: Insight into the Molecular Mechanism of Thermal Energy Storage

Sugar alcohols are one promising candidate for phase-change materials (PCMs) in energy industrial societies because of their large thermal storage capacity. In this paper, we investigate the melting point and enthalpy of fusion related to the thermal storage of six-carbon sugar alcohols (galactitol, mannitol, sorbitol, and iditol) by molecular dynamics simulations and elucidate physical principles required for new PCM design. The computational melting points and enthalpies of fusion reproduce the experimental trend qualitatively. On the basis of the energy decomposition analysis we find that their enthalpies of fusion originate mainly from the decrease in the number and strength of intermolecular hydrogen bonds upon melting. Furthermore, we examine the origin of the difference of enthalpy of fusion between the four isomers. The results show that the larger enthalpy of fusion of galactitol and mannitol comes from their stable solid phases associated with the absence of notable repulsive electrostatic inter...

Hydrogen bonds of sodium alginate/Antarctic krill protein composite material

Sodium alginate/Antarctic krill protein composite material (SA/AKP) was successfully obtained by blending method. The hydrogen bonds of SA/AKP composite material were analyzed by Fourier transform infrared spectroscopy (FT-IR) and Nuclear magnetic resonance hydrogen spectrum (HNMR). Experiment manifested the existence of intermolecular and intramolecular hydrogen bonds in SA/AKP system; strength of intermolecular hydrogen bond enhanced with the increase of AKP in the composite material and the interaction strength of hydrogen bonding followed the order: OH…Ether O>OH…π>OH…N. The percentage of intermolecular hydrogen bond decreased with increase of pH. At the same time, the effect of hydrogen bonds on properties of the composite material was discussed. The increase of intermolecular hydrogen bonding led to the decrease of crystallinity, increase of apparent viscosity and surface tension, as well as obvious decrease of heat resistance of SA/AKP composite material. SA/AKP fiber SEM images and energy spectrum showed that crystallized salt was separated from the fiber, which possibly led to the fibrillation of the composite fibers.

Studying the geometric parameters, stability of isomer and IR frequencies in enaminone compounds with the DFT and HF methods: A theoretical study

Enaminones are the large category of chemical compounds that their numerous applications caused to be interested by researchers and scientists in two important experimental and theoretical forms. Calculating chemistry as one of the vital field for the chemistry can help us to investigate of enaminone structures. Our three isomers of the compounds are enaminone. In this research, Sustainability and inter-molecular hydrogen bond strength of each isomer is investigated. Four methods HF, B3LYP, B3P86, B3PW91 and two basis set 6-311G**, 6-311++G** were used in order to making calculation. The results of calculations in geometry parameters indicated that in our parameters, B3P86 method and 6-311++G** basis set have considerable preference than other methods and basis sets. In regarding to this method and basis set, hydrogen bonding was investigated and the third isomer (III) showed the strongest hydrogen bond achieved. Finally theoretical vibrational frequencies, in B3P86/6-311++G** basis set was investigated.

Terahertz spectroscopy and computational investigation of the flufenamic acid/nicotinamide cocrystal.

Terahertz spectroscopy probes the low-frequency vibrations that are sensitive to both the intermolecular and intramolecular interactions of molecules in the solid state. Thus, terahertz spectroscopy can be a useful tool in the investigation of crystalline pharmaceutical compounds, where slight changes in the packing arrangement can modify the overall effectiveness of a drug formulation. This is especially true for cases of polymorphic systems, hydrates/solvates, and cocrystals. In this work, the cocrystal of flufenamic acid with nicotinamide was investigated using terahertz spectroscopy and solid-state density functional theory. The solid-state simulations enable understanding of the low-frequency vibrations seen in the terahertz spectra, while also providing insight into the energetics involved in the formation of the cocrystal. The comparison of the cocrystal to the pure forms of the molecular components reveals that the cocrystal has better overall binding energy, driven by increased intermolecular hydrogen bond strength and greater London dispersion forces and that the trifluoromethyl torsional potential is significantly different between the studied solids.

Synthesis and mesomorphic behaviour of hexacatenar di-hydrazine derivatives

A new series of hydrazide derivatives of N,N-bis(3,4,5-tris(heptyloxy)benzoyl) (T7 series) were designed and synthesised. Investigations on the liquid crystalline properties by differential scanning calorimetry (DSC), wide-angle X-ray diffraction (WAXD) and polarising optical microscopy (POM) showed that the di-hydrazine derivatives exhibited different mesophases, which were ascribed to the different structure of T7 series. The rectangular columnar mesophases of T7-ben remained stable down to room temperature during cooling, T7-fuma was decomposed at 259°C in the first heating, while T7-mal showed simple cubic mesophase and crystalline phase at room temperature during cooling. Comparing Fourier-transformed infrared (FTIR) at room temperature of T7 series, some differences were found in the N–H stretching vibration and C = O stretching vibration bands, indicating that T7 series had some differences in intermolecular hydrogen bond strength, which were caused by the different linking unit of T7 series. Intermolecular hydrogen bonding between –C = O and –N–H groups in crystalline and liquid crystalline phases was confirmed by temperature FTIR spectroscopy and temperature 1H NMR spectroscopy.