The effect of intermolecular hydrogen bonding on the planarity of amides

First mesomorphic and DFT characterizations for 3- (or 4-) n-alkanoyloxy benzoic acids and their optical applications

New liquid crystalline hydrogen bonded 3- (or 4)-n-alkanoyloxy benzoic acids were synthesized and probed theoretically and experimentally. The molecular structures of these compounds were elucidated by proton NMR, carbon-13 NMR and elemental analyses. Differential scanning calorimetry (DSC) was used to investigate the thermal and mesomorphic properties of all the symmetrical dimers that bearing identical alkanoyloxy chains. Moreover, polarized optical microscopy (POM) was used to determine their mesophases. The findings show that all the designed symmetrical dimers exhibit the smectic mesophase with relative thermal stability that depends on the length of their terminal side chain. Additionally, the experimental findings of the mesomorphic behavior are further supported by DFT calculations. The alkanoyloxy benzoic acid para-derivatives (In) were shown to be more stable than their meta-substituted (IIn) analogues due to stronger hydrogen bonding interactions. The computed reactivity parameters showed that the position of ester moiety has a significant impact on the acids reactivity. The absorbance spectra of both the 3- (or 4)-n-alkanoyloxy benzoic acids revealed a blue shift with the increment of the of alkyl chain size; however, the energy band gaps of 3-n-alkanoyloxy benzoic derivatives were found to be slightly higher than those of the 4-n-alkanoyloxy benzoic acids. Moreover, the photoluminescence spectrum of the prepared materials is rather broad, and exhibited a red shift as the alkyl chain length increases. The fluorescence lifetime shown to rise as alkyl chain length grows longer, and 3-n-alkanoyloxy benzoic acids have slightly longer lifetime compared to their 4-n-alkanoyloxy benzoic analogues.

Liquid Structure of Single and Mixed Cation Alkylammonium Bromide Urea Deep Eutectic Solvents

The liquid structures of three alkyl ammonium bromide and urea DESs, ethylammonium bromide:urea (1:1), butylammonium bromide:urea (1:1), and ethylammonium bromide/butylammonium bromide:urea (0.5:0.5:1), have been studied using small-angle neutron diffraction with H/D substituted sample contrasts. The diffraction data was fit using empirical potential structure refinement (EPSR). An amphiphilic nanostructure was found in all DESs due to cation alkyl chains being solvophobically excluded from charged domains, and due to clustering together. The polar domain was continuous in all three DESs, whereas the apolar domain was continuous for the butylammonium DES and in the mixed DES, but not the ethylammonium DES. This is attributed to solvophobic interactions being weaker for the short ethyl chain. Surprisingly, the urea also forms large clusters in all three DESs. In ethylammonium bromide:urea (1:1), urea-urea orientations are mainly perpendicular, but in butylammonium bromide:urea (1:1) and the mixed system in-plane and perpendicular arrangements are found. The liquid nanostructures found in this work, especially for the ethylammonium DES, are different from those found previously for the corresponding DESs formed using glycerol, revealing that the DES amphiphilic nanostructure is sensitive to the nature of the HBD (hydrogen bond donor).

Investigation of the Anticancer Activity of Coordination-Driven Self-AssembledTwo-Dimensional Ruthenium Metalla-Rectangle

Coordination-driven self-assembly is an effective synthetic tool for the construction of spatially and electronically tunable supramolecular coordination complexes (SCCs), which are useful in various applications. Herein, we report the synthesis of a two-dimensional discrete metalla-rectangle [(η6-p-cymene)4Ru4(C6H2O4)2(2)2](CF3SO3)4 (3) by the reaction of a dinuclear half-sandwich ruthenium (II) complex [Ru2(η6-p-cymene)2(C6H2O4)Cl2] (1) and bis-pyridyl amide linker (2) in the presence of AgO3SCF3. This cationic ruthenium metalla-rectangle (3) has been isolated as its triflate salt and characterized by analytical techniques including elemental analysis, Fourier-transform infrared spectroscopy (FT-IR), proton nuclear magnetic resonance spectroscopy (1H-NMR), carbon nuclear magnetic resonance spectroscopy (13C-NMR), 1H-1H correlation spectroscopy (COSY), 1H-1H nuclear Overhauser effect spectroscopy (NOESY), diffusion ordered spectroscopy (DOSY), and high-resolution electrospray ionization mass spectrometry (HR-ESI-MS). Significantly, the 2D cationic ruthenium metalla-rectangle showed better anticancer activity towards three different cell lines (A549, Caki-1 and Lovo) as compared with the parent ruthenium complex (1) and the commercially used drug, cisplatin.

Theoretical investigation on the mechanism of the OH-initiated degradation process of reactive red 2 azo dye

The dual descriptor (Δf) data of azo form (a, RR2) and hydrazone form (b, HRR2) of RR2 dianion. For Δf> 0 (green), the site is favorable for nucleophilic attack, for Δf< 0 (blue), the site is favorable for electrophilic attack. Key bond lengths in Å.

Inelastic neutron scattering study of reline: shedding light on the hydrogen bonding network of deep eutectic solvents

Goldilocks conditions of hydrogen bond strength on the basis of deep eutectic behavior.

Diffusional behavior and guest conformational analysis of hexadecane-1,16-diol and hexadecane in urea crystal model via molecular dynamics simulation approach

Diffusion at the atomic or molecular level is a source of many physical, chemical, and biological processes taking place in plentiful materials. This work is an endeavor toward investigating the diffusional behavior of two different type of guests, hexadecane-1,16-diol and hexadecane enclathration in urea tunnel architecture, whereby the correlation of the diffusion mechanism with the guest's structural and conformational properties is explored. To carry out this study, molecular dynamics simulation approach is adopted. It is found that hexadecane-1,16-diol exhibit slower diffusion with an average diffusion coefficient value [Formula: see text], where hexadecane diffuse more rapidly with an average diffusion coefficient value [Formula: see text]. It is also observed that the structural properties influence the guest's travel distance and torsion angle distribution of the trans and gauche conformational proportion. Furthermore, the observed high energy barrier accounted for hexadecane-1,16-diol and low energy barrier for hexadecane along urea tunnel systems was analyzed. The comparison of our obtained results are in close agreement with the available experimental measurements, i.e., gauche proportion properties between two different guest molecules correlate well with Raman spectroscopy investigation on α,ω-dihalogenoalkane/urea inclusion compounds. Our calculations also successfully endorse the structure-property relation between the two systems.

Doubly ionic hydrogen bond interactions within the choline chloride–urea deep eutectic solvent

Computational analysis indicates flexibility and diversity in the hydrogen bonding, but limited charge delocalisation, within the choline chloride–urea eutectic.

Gas-Phase Thermal Tautomerization of Imidazole-Acetic Acid: Theoretical and Computational Investigations

The gas-phase thermal tautomerization reaction between imidazole-4-acetic (I) and imidazole-5-acetic (II) acids was monitored using the traditional hybrid functional (B3LYP) and the long-range corrected functionals (CAM-B3LYP and ωB97XD) with 6-311++G** and aug-cc-pvdz basis sets. The roles of the long-range and dispersion corrections on their geometrical parameters, thermodynamic functions, kinetics, dipole moments, Highest Occupied Molecular Orbital-Lowest Unoccupied Molecular Orbital (HOMO-LUMO) energy gaps and total hyperpolarizability were investigated. All tested levels of theory predicted the preference of I over II by 0.750-0.877 kcal/mol. The origin of predilection of I is assigned to the H-bonding interaction (nN8→σ*O14-H15). This interaction stabilized I by 15.07 kcal/mol. The gas-phase interconversion between the two tautomers assumed a 1,2-proton shift mechanism, with two transition states (TS), TS1 and TS2, having energy barriers of 47.67-49.92 and 49.55-52.69 kcal/mol, respectively, and an sp³-type intermediate. A water-assisted 1,3-proton shift route brought the barrier height down to less than 20 kcal/mol in gas-phase and less than 12 kcal/mol in solution. The relatively high values of total hyperpolarizability of I compared to II were interpreted and discussed.

Conformational behavior of polyalanine peptides with and without protecting groups of varying chain lengths: population of PP-II structure!

Oculopharyngeal muscular dystrophy (OPMD), a polyalanine myopathy, occurs due to expansion of homo-polyalanine stretch in normal polyadenylating binding protein nuclear 1 (PABPN1) protein from Ala10 to Ala11-17. Therefore, the conformational behavior of polyalanine peptides with n = 10-17, with and without terminal protecting groups, have been investigated with different starting geometries in water by molecular dynamics simulation studies. Alanine peptides are shown to give rise to unordered structure irrespective of starting geometry and not more than two residues at a stretch have the same/similar set of φ, ψ values. However, the final structure with terminal protecting groups look like β-strand. Unprotected poly-Ala peptides adopt twisted β-hairpin/multi hairpin like structure with increasing chain length. The number of residues having φ, ψ values in collagen region is found to be less in peptides with unprotected termini as compared to peptides with protected termini of same chain length. The results have been supported by recent synchrotron radiation circular dichroism spectroscopy of polyproline II and unordered secondary structures. Opening of the helical structure in poly-Ala peptides with protecting groups has been shown to take place from C-terminal and in peptides without protecting groups opening of helix starts from both terminals. Further, opening of helix takes more time in poly-Ala peptides without terminal protecting groups. The deviations in amide bond planarity have been discussed and compared with available experimental and computational results.

Investigation of steric influences on hydrogen-bonding motifs in cyclic ureas by using X-ray, neutron, and computational methods

A series of urea-derived heterocycles, 5N-substituted hexahydro-1,3,5-triazin-2-ones, has been prepared and their structures have been determined for the first time. This family of compounds only differ in their substituent at the 5-position (which is derived from the corresponding primary amine), that is, methyl (1), ethyl (2), isopropyl (3), tert-butyl (4), benzyl (5), N,N-(diethyl)ethylamine (6), and 2-hydroxyethyl (7). The common heterocyclic core of these molecules is a cyclic urea, which has the potential to form a hydrogen-bonding tape motif that consists of self-associative R₂²(8) dimers. The results from X-ray crystallography and, where possible, Laue neutron crystallography show that the hydrogen-bonding motifs that are observed and the planarity of the hydrogen bonds appear to depend on the steric hindrance at the α-carbon atom of the N substituent. With the less-hindered substituents, methyl and ethyl, the anticipated tape motif is observed. When additional methyl groups are added onto the α-carbon atom, as in the isopropyl and tert-butyl derivatives, a different 2D hydrogen-bonding motif is observed. Despite the bulkiness of the substituents, the benzyl and N,N-(diethyl)ethylamine derivatives have methylene units at the α-carbon atom and, therefore, display the tape motif. The introduction of a competing hydrogen-bond donor/acceptor in the 2-hydroxyethyl derivative disrupts the tape motif, with a hydroxy group interrupting the N-H···O=C interactions. The geometry around the hydrogen-bearing nitrogen atoms, whether planar or non-planar, has been confirmed for compounds 2 and 5 by using Laue neutron diffraction and rationalized by using computational methods, thus demonstrating that distortion of O-C-N-H torsion angles occurs to maintain almost-linear hydrogen-bonding interactions.