Infrared spectral density of H-bonds within the strong anharmonic coupling theory: Indirect relaxation effect

Computational and experimental insights into the spectroscopy, electronic states, and molecular docking of (2S)-2,6-diaminohexanoic acid [DAHA]

This paper presents a theoretical analysis of the L-Lysine molecule using the DFT (density functional theory) method with a 6-311+ + G(d,p) basis set, a quantum-mechanical atomistic simulation method. The research encompasses the analysis of optimized chemical structure, vibrations, FMO, ELF, NLO, RDG, etc., to study the molecule's intensive properties, stability, and other biological activities. IR and UV spectra were analysed for the spectrochemical study, and the VEDA program was used to determine the PED values. The chemical reactivity of the molecule was identified through analysis of the Frontier molecular orbitals, Fukui, and molecular electrostatic potential. The electron localization function and reduced density gradient were determined to understand bonding and electronic structure. The temperature dependence on the properties of the molecule was estimated. The optical properties of the molecule were discussed by analyzing the non-linear optical property. The feasibility of the molecule as a therapeutic drug was examined using the drug likeness concept. Molecular docking analysis was conducted to acquire the best ligand-receptor complex and to study the molecule's biological activity.

Deciphering the abnormal IR spectral density of phthalic acid dimer crystals: Unveiling the role of the dynamical effects of the Davydov coupling and the mechanisms of relaxation

To consistently determine the anomalous characteristics of phthalic acid crystal (PAC) derivatives, we performed quantum dynamics simulations of the infrared spectral density of the h6-PAC and d6-PAC isotopomers that show up in the H/D isotopic frequency domain at two different temperatures viz. 77 and 298 K. A theoretical framework explaining the dynamical cooperative interactions within the hydrogen bonds (HBs) in the PAC crystals across a simulation of IR spectral density of the stretching band was developed. The model presupposes HBs from the nearby (COOH)2 cycles to have exceptionally strong dynamical cooperative contacts. The approach precisely hinges upon on a model that consider the dimer as centrosymmetric in which the low-frequency intermonomer mode (that is, O⋯O) stretches anharmonically and committing the O-H vibrational mode, associated with the high-frequency mode, to stretch harmonically. The approach considers also the following effects: Davydov coupling arising from the interference between the two HBs in the dimer; strong anharmonic coupling between the two stretching modes within the same HB; direct relaxation mechanism of the high stretches in the HB; and indirect relaxation mechanism that is devoted to the high stretches via the slow stretches. Using this approach, the principal characteristics of the O-H(D) experimental bands of the isotopomers studied herein with their peculiarities are simulated by selecting physically sound parameters that uniquely identify the onset of the specific features of the IR spectral densities. The impacts of the important parameters, characterizing the different leading mechanisms within this approach on the spectra, are revealed. The contrast of the emerging simulated spectra with the experimental ones reveals decent agreement for the studied isotopomers. By congregating the different mechanisms employed herein within the pioneering context of the linear response theory of Kubo, the obtained results strongly demonstrate and identify the main effects responsible for the generation of the experimental O-H and O-D bands. Through an examination of the effect of each mechanism involved within the h 6-PAC and d4-PAC isotopomers, it is possible to relate the emergence of IR spectral density to an interplay between the Davydov coupling and the relaxation dynamics.

Quantum chemical treatment, electronic energy in various solvents, spectroscopic, molecular docking and dynamic simulation studies of 2-amino-N-(2-chloro-6-methylphenyl)thiazole-5-carboxamide: A core of anticancer drug

The titled molecule 2-Amino-N-(2-chloro-6-methylphenyl)thiazole-5-carboxamide (ANMC) is a core of anticancer drug dasatinib (leukemia). Its derivatives exhibited bioactivity against breast cancer. Experimentally, the titled compound was described using NMR (1H NMR and 13C NMR), FTIR and UV-visible spectroscopy. The results were compared with the theoretical predictions, showing good agreement such as theoretical NH vibrations showed symmetric stretching and asymmetric stretching at 3429 and 3440 cm-1 respectively, λmax values appear at 305 nm for experimental and 307.75 nm for theoretical observations in acetone medium. Hirshfeld surface analysis well described the secondary internal and external interactions obtained like dnorm and di ranges -1.8551 to 1.4590 and 0.0918 to 2.6756 respectively. Comparing UV-visible spectra obtained in various solvents with the calculated TD-DFT results revealed minimal solvent effects. Molecular electrostatic potential (MEP) map and Fukui functions were employed, which indicated reactive sites of the molecule and the obtained order of nucleophilic reactivity was C16 > C2 > C8 > Cl1 > C22 > C21. The bioactivity profile probability of ANMC was theoretically explored by calculation of electrophilicity index and drug-likeness. Molecular docking of the ANMC molecule was performed with ten receptors to obtain the best ligand-protein interaction and the minimum binding energy obtained was -8.0 kcal/mol. Biomolecular stability of ANMC was investigated by Molecular Dynamic Simulation (MDS). And also the analysis of free energies showed strong interactions between the ligand and the protein.

Coating based on chitosan/vancomycin nanoparticles: Patterns of formation in a water-carbon dioxide biphase system and in vivo stability

The patterns of formation of chitosan nanoparticles doped with vancomycin and coatings based on them in carbonate solutions have been investigated for the first time in this study. Using a technique of radioactive indicators, it was found that at a CO2 pressure of 30 MPa, the yield of the nanoparticles was ∼85 %, and a maximum antibiotic encapsulation efficiency of ∼30 % was achieved. By spectrophotometric and high-resolution microscopy, it was found that the coating of stabilized xenopericardial tissue of bioprosthetic heart valve, based on chitosan nanoparticles doped with vancomycin with a zeta potential |ζ| ∼20 mV completely covers collagen fibers by depositing about 60 nm nanoparticles onto them under direct deposition from carbonic acid at a pressure of 30 MPa CO2. The coating preserves the mechanical strength characteristics of collagen tissue and completely suppresses the growth of S. aureus pathogenic biofilm. This is consistent with the observed increase in antibiotic release of 15 % when the medium was acidified. Histological study demonstrated that the structure of pericardial tissues was not significantly altered by the deposition nanoparticles from carbonic acid. It was found that the rate of biodegradation of polymers and vancomycin in the coating differs by half (16 weeks for the rat model). A significantly lower degradation rate of antibiotics (∼50 % of vancomycin total remaining mass and ∼25 % of chitosan) was associated with its reliable encapsulation into nanoparticles.

Synthesis, growth, optical, mechanical, thermal, dielectric, and SHG properties of Triethylaminium picrate (TEAP) single crystal for nonlinear optical applications

Triethylaminium picrate (TEAP) crystals were grown using the slow evaporation solution growth method at ambient (35 °C) temperature. Salt was synthesized from Picric acid, and Triethylamine and methanol was used as solvents. The solution was mixed at a 1:1 ratio and evaporated slowly, produced yellow colour single crystal of TEAP with an average dimension of 19 × 8 × 5 mm3. The structure of the compound was determined by single-crystal X-ray diffraction (SCXRD) study, which confirms that the crystal is belongs to Orthorhombic crystal system, and its crystallinity was confirmed by the Bragg peak in the powder X-ray diffraction pattern. The superamolecular characteristic of the TEAP was confirmed by the Hirshfield analysis. CHN elemental analysis confirmed the stoichiometry and chemical composition of the synthesized complex salts. FT-IR and Polarized Raman spectral analyses confirmed the presence of different functional groups in the complex. UV-vis-NIR study identified the optical transmission window and the lower (TEAP) cut-off wavelength. Vickers' microhardness analysis determined the mechanical stability of the grown crystal. Studies of dielectric and AC conductivity were analyzed as a function of frequency. The thermogravimetry (TG) and differential thermal analysis (DTA) techniques were used to investigate the thermal behaviour of the material. The Kurtz-Perry powder technique was used to analyze the crystal's nonlinear optical properties (NLO) and found that its SHG efficiency was 1.5 times higher than that of potassium dihydrogen phosphate (KDP). The results from the obtained characterizations conclude that the TEAP crystal could be useful for NLO applications.

Bonding and noncovalent interactions effects in 2,6-dimethylpiperazine-1,4-diium oxalate oxalic acid: DFT calculation, topological analysis, NMR and molecular docking studies

The pharmaceutical proprieties of the 2,6-dimethylpiperazine-1,4-diium oxalate oxalic acid compound have been studied and the relevant drug design has been considered. The investigated organic compound with formula (2,6-(CH3)C4H10N2)2(C2O4)2·H2C2O4 (2DPOA) has been synthesized by slow evaporation technique at room temperature of a molar ratio 3:2 mix of oxalic acid and 2,6-dimethylpiperazine. Then 2DPOA has been characterized by IR, 13C NMR, UV–visible and the DFT calculation at the B3LYP level of theory has been made. The molecular structure and parameters (bond angles and lengths) of the molecule have been optimized using the Gaussian 09 software and compared with the XRD data. The atoms-in-molecules (AIM), electron localization function (ELF), and localized orbital locator (LOL) methods have been utilized to determine the types and nature of noncovalent interactions present within the 2DPOA molecule. These methods offer insights into the characteristics and behavior of these interactions. Furthermore, the presence of these interactions has been confirmed through the Hirshfeld Surface (HS) and reduced density gradient (RDG) analysis. The NBO analysis is employed to assess the charge exchange occurring within the studied compound. The molecular reactive sites have been examined using the molecular potential surface and Mulliken atomic charges. The energy gap between HOMO–LUMO and chemical properties of 2DPOA have been determined within the frontier molecular orbital theory. The UV–Vis spectrum of the 2DPOA molecule has been recorded and examined. The calculated and experimental infrared absorption and nuclear magnetic resonance spectra of 2DPOA molecule have been investigated. Finally, the molecular docking simulation has been used to find novel inhibitors and drugs for the cancer and epilepsy disease treatment.

Computational modeling of imines based anti-oxidant and anti-esterases compounds: Synthesis, single crystal and In-vitro assessment

Molecular modeling strategy was adopted to check the biological potential of the imine based molecules against free radical, acetylcholine esterase and butyrylcholine esterase. Three Schiff based compounds as (E)-2-(((4-bromophenyl)imino)methyl)-4-methylphenol (1), (E)-2-(((3-fluorophenyl)imino)methyl)-4-methylphenol (2) and (2E,2E)-2-(2-(2-hydroxy-5-methylbenzylidene)hydrazono)-1,2-diphenylethanone (3) were synthesized with high yield. The synthesized compounds were characterized with the help of modern techniques such as UV, FTIR and NMR while exact structure was depicted with Single Crystal X-Ray diffraction technique which disclosed that compound 1 is orthorhombic, while 2 and 3 are monoclinic. A hybrid functional (B3LYP) method with general basis set of 6-31 G(d,p) were applied to optimize synthesized Schiff bases. The contribution of in-between molecular contacts within a crystalline assembly of compounds were studied using Hirshfeld surface analysis (HS). In order to check the ability of the synthesized compounds toward free radical and enzyme inhibition, in vitro models were used to assess the radical scavenging and enzyme inhibition potential which depicted that compound 3 showed highest potential (57.43 ± 1.0%; DPPH, 75.09 ± 1.0%; AChE and 64.47 ± 1.0%; BChE). The ADMET assessments suggested the drug like properties of the synthesized compounds. It was concluded from results (in vitro and in silico) that synthesized compound have ability to cure the disorder related to free radical and enzyme inhibition. Compound 3 was shown to be the most active compared to other compounds.

17-β-Estradiol-β-Cyclodextrin Complex as Solid: Synthesis, Structural and Physicochemical Characterization

17-β-estradiol (EST) is the most potent form of naturally occurring estrogens; therefore, it has found a wide pharmaceutical application. The major problem associated with the use of EST is its very low water solubility, resulting in poor oral bioavailability. To overcome this drawback, a complexation with cyclodextrins (CD) has been suggested as a solution. In this work, the host-guest inclusion complex between the ß-CD and EST has been prepared using four different methods. The obtained samples have been deeply characterized using ¹³C CP MAS solid state NMR, PXRD, FT-IR, TGA, DSC, and SEM. Using SCXRD, the crystal structure of the complex has been determined, being to the best of our knowledge the first solved crystal structure of an estrogen/CD complex. The periodic DFT calculations of NMR properties using GIPAW were found to be particularly helpful in the analysis of disorder in the solid state and interpretation of experimental NMR results. This work highlights the importance of a combined ssNMR/SCXRD approach to studying the structure of the inclusion complexes formed by cyclodextrins.

Insight into the release mechanisms of diflunisal and salicylic acid from poly(vinyl alcohol). The role of hydrogen bonding interactions

Diflunisal (5-(2,4-Difluorophenyl)salicylic acid, DIF), salicylic acid (SAL) derivative, which, on the one hand, is active pharmaceutical ingredient, on the other hand, belongs to the compounds exhibiting excited-state intramolecular proton transfer (ESIPT) behaviour was used to study the drug interactions with poly(vinyl alcohol) (PVA) matrix. For clarifying the nature and mechanisms of the drug-matrix interactions the salicylic acid (SAL) molecule was selected as the model active ESIPT compound, whose physicochemical properties in different media are well understood. The solute-solvent interactions (non-specific (dipole-dipole) versus specific (hydrogen bonding)) of DIF and SAL with different neat solvents were investigated using the steady-state spectroscopic technique. The solvent effect on spectral behaviours of DIF and SAL was analyzed based on the parametric solvent scales. In order to identify functional groups in the PVA matrices, determine the structure present in the studied molecule-PVA system and thus obtain information about the potential interactions between PVA and the studied molecules, the Raman spectra of pure PVA, SAL-PVA and DIF-PVA systems were measured. It has been shown that the molecular structure of the active substance entrapped in the polymer matrix affects the structure of the polymer, i.e., isotactic (SAL-PVA) versus syndiotactic (DIF-PVA) structure. The analysis of drug release kinetics revealed that the DIF is more strongly bound to PVA in comparison to SAL, which confirms conclusions drawn from the analysis of the Raman spectra i.e., the isotactic structure of SAL-PVA material results in a faster initial release process of weakly bound, located on the surface of the polymer SAL molecules.

Theoretical Study on Spectrum and Luminescence Mechanism of Indocyanine Green Dye Based on Density Functional Theory (DFT)

Indocyanine green is a great near-infrared fluorescence with good luminescent properties and important medical applications. In this paper, the theoretical spectrum and orbital model of its molecular level are established. The two most probable conformations were studied, and their energies, vibrational spectra, UV-Vis absorption spectra, frontier molecular orbitals (HOMO and LUMO), and energy gaps were obtained by density functional theory (DFT) calculations, respectively. This provides a theoretical and design basis for the development of novel dyes similar to indocyanine green dyes and a reference case for improved application methods and synthetic predesign of novel fluorescent dyes.

Crystal Structure, Topology, DFT and Hirshfeld Surface Analysis of a Novel Charge Transfer Complex (L3) of Anthraquinone and 4-{[(Anthracen-9-yl)meth­yl] Amino}­Benzoic Acid (L2) Exhibiting Photocatalytic Properties: An Experimental and Theoretical Approach

Here, we report a facile route to the synthesizing of a new donor–acceptor complex, L3, using 4-{[(anthracen-9-yl)meth-yl] amino}-benzoic acid, L2, as donor moiety with anthraquinone as an acceptor moiety. The formation of donor–acceptor complex L3 was facilitated via H-bonding and characterized by single-crystal X-ray diffraction. The X-ray diffraction results confirmed the synthesized donor–acceptor complex L3 crystal belongs to the triclinic system possessing the P-1 space group. The complex L3 was also characterized by other spectral techniques, viz., FTIR and UV absorption spectroscopy, which confirmed the formation of new bonds between donor L2 moiety and acceptor anthraquinone molecule. The crystallinity and thermal stability of the newly synthesized complex L3 was confirmed by powdered XRD and TGA analysis and theoretical studies; Hirshfeld surface analysis was performed to define the type of interactions occurring in the complex L3. Interestingly, theoretical results were successfully corroborated with experimental results of FTIR and UV absorption. The density functional theory (DFT) calculations were employed for HOMO to LUMO; the energy gap (∆E) was calculated to be 3.6463 eV. The complex L3 was employed as a photocatalyst for the degradation of MB dye and was found to be quite efficient. The results showed MB dye degraded about 90% in 200 min and followed the pseudo-first-order kinetic with rate constant k = 0.0111 min⁻¹ and R² = 0.9596. Additionally, molecular docking reveals that the lowest binding energy was −10.8 Kcal/mol which indicates that the L3 complex may be further studied for its biological applications.

Towards accurate infrared spectral density of weak H-bonds in absence of relaxation mechanisms

Following the previous theoretical developments to completely reproduce the IR spectra of weak hydrogen bond complexes within the framework of the linear response theory (LRT), the quantum theory of the high stretching mode spectral density (SD) of weak H-bonds is reconsidered. Within the LRT theory, the SD is the one sided Fourier transform of the autocorrelation function (ACF) of the high stretching mode dipole moment operator. In order to provide more accurate theoretical bandshapes, we have explored the equivalence between the SDs given in previous studies with respect to a new quantum one, and revealed that in place of the basic equations used in the precedent works for which the SD I_Old(ω)=2Re∫₀^∞G_Old(t)e^-iωtdt where the ACF G_Old(t) = ⟨μ(0)μ(t)⁺⟩ = tr {ρ {μ(0)} {μ(t)}⁺}, one can use a new expression for the SD, given by I_New(ω)=2ωRe∫₀^∞G_New(t)e^-iωtdt where G_New(t)=μ(0)μ(t)⁺=1βtrρ_B∫₀^βμ(0)μ(t+iλℏ)⁺dλ. Here ρ_B is the Boltzmann density operator, μ(0) the dipole moment operator at initial time and μ(t) the dipole moment operator at time t in the Heisenberg picture, ℏ is the Planck constant, β is the inverse of the Boltzmann factor k_BT where T is the absolute temperature and k_B the Boltzmann constant. Using this formalism, we demonstrated that the new quantum approach gives the same final SD as used by previous models, and reduces to the Franck-Condon progression appearing in the Maréchal and Witkowski's pioneering approach when the relaxation mechanisms are ignored. Results of this approach shed light on the equivalence between the quantum and classical IR SD approaches for weak H-bonds in absence of medium surroundings effect, which has been a subject of debate for decades.

Equivalence between the Classical and Quantum IR Spectral Density Approaches of Weak H-Bonds in the Absence of Damping

The aim of this paper is to overhaul the quantum elucidation of the spectral density (SD) of weak H-bonds treated without taking into account any of the damping mechanisms. The reconsideration of the SD is performed within the framework the linear response theory. Working in the setting of the strong anharmonic coupling theory and the adiabatic approximation, the simplified expression of the classical SD, in the absence of dampings, is equated to be I_Cl(ω) = Re[∫₀^∞G_Cl(t)e^-iΩt dt] in which the classical-like autocorrelation function (ACF), G_Cl(t), is given by G_Cl(t) = tr{ρ(β){μ(0)}{μ(t)}^†}. With this consideration, we have shown that the classical SD is equivalent to the line shape obtained by F(ω) = ΩI_Cl(ω), which in turn is equivalent to the quantum SD given by I_Qu(ω) = Re[∫₀^∞G_Qu(t)e^-iΩt dt], where G_Qu(t) is the corresponding quantum ACF having for expression G_Qu(t) = (1/β) tr{ρ∫₀^β[μ(0)}{μ(t + iλℏ)}^† dλ}. Thus, we have shown that for weak H-bonds dealt without dampings, the SDs obtained by the quantum approaches are equivalent to the SDs geted by the classical approach in which the incepation ACF is, however, of quantum nature and where the line shape is the Fourier transform of the ACF times the angular frequency. It is further shown that the classical approach dealing with the SD of weak H-bonds leads identically to the result found by Maréchal and Witkowski in their pioneering quantum treatment where they ignored the linear response theory and dampings.