Anharmonic effects on theoretical IR line shapes of medium strong H(D) bonds

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.

DFT studies of solvent effect in hydrogen abstraction reactions from different allyl-type monomers with benzoyl radical

Inert allyl-type monomers have been widely documented due to reduce degradation chain transfer. Recently, we and others discovered that the [3 + 2] cyclization reaction process by a photo-driven radical reaction, which can accelerate the polymerization. It was discovered that allyl ether monomers had much higher reactivity than other allyl monomers in the suspension photopolymerization initiated by Type I photoinitiator. Since the hydrogen abstraction reaction (HAR) is the initial step of cyclization, and in order to clarify the influence of solvents effect, three allyl-type monomers were employed, containing "O", "N" and "S" atom as hydrogen donors. The benzoyl radical obtained from cleavage of photoinitiator was chosen as hydrogen acceptors. We explored the hydrogen abstraction reaction in different solvents (methanol, water and DMSO) by quantum chemistry for geometry and energy. An investigation was undertaken regarding the structural orbital by electrostatic potential (ESP) and topological analysis (ELF and LOL). The findings were also combined with the distortion model and transition state theory. We obtained the molecular interactions used independent gradient method in the Hirshfeld molecular density partition (IGMH). The Eckart's correction allowed to examine the driving factors of the hydrogen abstraction reaction tunnels and these reactions constant rates are determined in the range of 500-2500 K depending on the modified Arrhenius form in different solvents effect. Our results can provide an answer for the different reactivities.

Studies on crystal growth, experimental, structural, DFT, optical, thermal and biological studies of 3-hydroxy-4-methoxybenzaldehyde single crystals

The organic 3-hydroxy-4-methoxybenzaldehyde single crystal has been grown by the slow evaporation technique. Single crystal X-ray diffraction (XRD) study shows that the grown crystal belongs to a monoclinic crystal system with centrosymmetric space group P2₁/c. The spectral analysis of 3-hydroxy-4-methoxybenzaldehyde calculations was performed with the help of DFT at the B3LYP/6-311 + G(d,p) level of theory. The experimental results of FTIR and FT-Raman were compared with the computational results. Detailed interpretations of the vibrational spectra were carried out with the aid of vibrational energy distribution analysis using potential energy distribution (PED) analysis and vibrational wavenumber scaled by the WLS (Wavenumber Linear Scaling) method. The natural bond orbital (NBO) analysis was carried out to identify intramolecular hydrogen bonding. The optical properties of the grown crystal were analyzed by UV-Visible studies. Photoluminescence studies show that the high-intensity peak observed around 410 nm. The laser damage threshold value of the grown crystal has been determined using an Nd:YAG laser operating at 1064 nm. The HOMO (Highest Occupied Molecular Orbital) - LUMO (Lowest Unoccupied Molecular Orbital) was used to identify the energy gap. Hirshfeld Surface (HS) analysis was used to determine the intermolecular interactions. The thermal properties of the grown crystal were performed by Thermogravimetric (TG) and Differential thermal analyses (DTA). The kinetic and thermodynamic parameters were calculated. The surface morphology of the grown crystal was studied by using Scanning Electron Microscopy (SEM) analysis. The antibacterial and antifungal studies were analyzed.

Molecular Structure, Spectral Analysis, Molecular Docking and Physicochemical Studies of 3-Bromo-2-hydroxypyridine Monomer and Dimer as Bromodomain Inhibitors

In this paper, both methods (DFT and HF) were used in a theoretical investigation of 3-bromo-2-Hydroxypyridine (3-Br-2HyP) molecules where the molecular structures of the title compound have been optimized. Molecular electrostatic potential (MEP) was computed using the B3LYP/6-311++G(d,p) level of theory. The time-dependent density functional theory (TD-DFT) approach was used to simulate the HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital) on the one hand to achieve the frontier orbital gap and on the other hand to calculate the UV–visible spectrum of the compound in gas phase and for different solvents. In addition, electronic localization function and Fukui functions were carried out. Intermolecular interactions were discussed by the topological AIM (atoms in molecules) approach. The thermodynamic functions have been reported with the help of spectroscopic data using statistical methods revealing the correlations between these functions and temperature. To describe the non-covalent interactions, the reduced density gradient (RDG) analysis is performed. To study the biological activity of the compound of the molecule, molecular docking studies were executed on the active sites of BRD2 inhibitors and to explore the hydrogen bond interaction, minimum binding energies with targeted receptors such as PDB ID: 5IBN, 3U5K, 6CD5 were calculated.

Sulfation of Wheat Straw Soda Lignin with Sulfamic Acid over Solid Catalysts

Soda lignin is a by-product of the soda process for producing cellulose from grassy raw materials. Since a method for the industrial processing of lignin of this type is still lacking, several research teams have been working on solving this problem. We first propose a modification of soda lignin with sulfamic acid over solid catalysts. As solid catalysts for lignin sulfation, modified carbon catalysts (with acid sites) and titanium and aluminum oxides have been used. In the elemental analysis, it is shown that the maximum sulfur content (16.5 wt%) was obtained with the Sibunit-4® catalyst oxidized at 400 °C. The incorporation of a sulfate group has been proven by the elemental analysis and Fourier-transform infrared spectroscopy. The molecular weight distribution has been examined by gel permeation chromatography. It has been demonstrated that the solid catalysts used in the sulfation process causes hydrolysis reactions and reduces the molecular weight and polydispersity index. It has been established by the thermal analysis that sulfated lignin is thermally stabile at temperatures of up to 200 °C. According to the atomic force microscopy data, the surface of the investigated film consists of particles with an average size of 50 nm. The characteristics of the initial and sulfated β-O-4 lignin model compounds have been calculated and recorded using the density functional theory.

Sulfation of Wheat Straw Soda Lignin with Sulfamic Acid over Solid Catalysts

Soda lignin is a by-product of the soda process for producing cellulose from grassy raw materials. Since a method for the industrial processing of lignin of this type is still lacking, several research teams have been working on solving this problem. We first propose a modification of soda lignin with sulfamic acid over solid catalysts. As solid catalysts for lignin sulfation, modified carbon catalysts (with acid sites) and titanium and aluminum oxides have been used. In the elemental analysis, it is shown that the maximum sulfur content (16.5 wt%) was obtained with the Sibunit-4^® catalyst oxidized at 400 °C. The incorporation of a sulfate group has been proven by the elemental analysis and Fourier-transform infrared spectroscopy. The molecular weight distribution has been examined by gel permeation chromatography. It has been demonstrated that the solid catalysts used in the sulfation process causes hydrolysis reactions and reduces the molecular weight and polydispersity index. It has been established by the thermal analysis that sulfated lignin is thermally stabile at temperatures of up to 200 °C. According to the atomic force microscopy data, the surface of the investigated film consists of particles with an average size of 50 nm. The characteristics of the initial and sulfated β-O-4 lignin model compounds have been calculated and recorded using the density functional theory.

Catalytic Sulfation of Betulin with Sulfamic Acid: Experiment and DFT Calculation

Betulin is an important triterpenoid substance isolated from birch bark, which, together with its sulfates, exhibits important bioactive properties. We report on a newly developed method of betulin sulfation with sulfamic acid in pyridine in the presence of an Amberlyst®15 solid acid catalyst. It has been shown that this catalyst remains stable when being repeatedly (up to four cycles) used and ensures obtaining of sulfated betulin with a sulfur content of ~10%. The introduction of the sulfate group into the betulin molecule has been proven by Fourier-transform infrared, ultraviolet-visible, and nuclear magnetic resonance spectroscopy. The Fourier-transform infrared (FTIR) spectra contain absorption bands at 1249 and 835–841 cm−1; in the UV spectra, the peak intensity decreases; and, in the nuclear magnetic resonance (NMR) spectra, of betulin disulfate, carbons С3 and С28 are completely shifted to the weak-field region (to 88.21 and 67.32 ppm, respectively) with respect to betulin. Using the potentiometric titration method, the product of acidity constants K1 and K2 of a solution of the betulin disulfate H+ form has been found to be 3.86 × 10–6 ± 0.004. It has been demonstrated by the thermal analysis that betulin and the betulin disulfate sodium salt are stable at temperatures of up to 240 and 220 °C, respectively. The density functional theory method has been used to obtain data on the most stable conformations, molecular electrostatic potential, frontier molecular orbitals, and mulliken atomic charges of betulin and betulin disulfate and to calculate the spectral characteristics of initial and sulfated betulin, which agree well with the experimental data.

Catalytic Sulfation of Betulin with Sulfamic Acid: Experiment and DFT Calculation

Betulin is an important triterpenoid substance isolated from birch bark, which, together with its sulfates, exhibits important bioactive properties. We report on a newly developed method of betulin sulfation with sulfamic acid in pyridine in the presence of an Amberlyst®15 solid acid catalyst. It has been shown that this catalyst remains stable when being repeatedly (up to four cycles) used and ensures obtaining of sulfated betulin with a sulfur content of ~10%. The introduction of the sulfate group into the betulin molecule has been proven by Fourier-transform infrared, ultraviolet-visible, and nuclear magnetic resonance spectroscopy. The Fourier-transform infrared (FTIR) spectra contain absorption bands at 1249 and 835-841 cm-1; in the UV spectra, the peak intensity decreases; and, in the nuclear magnetic resonance (NMR) spectra, of betulin disulfate, carbons С3 and С28 are completely shifted to the weak-field region (to 88.21 and 67.32 ppm, respectively) with respect to betulin. Using the potentiometric titration method, the product of acidity constants K1 and K2 of a solution of the betulin disulfate H+ form has been found to be 3.86 × 10-6 ± 0.004. It has been demonstrated by the thermal analysis that betulin and the betulin disulfate sodium salt are stable at temperatures of up to 240 and 220 °C, respectively. The density functional theory method has been used to obtain data on the most stable conformations, molecular electrostatic potential, frontier molecular orbitals, and mulliken atomic charges of betulin and betulin disulfate and to calculate the spectral characteristics of initial and sulfated betulin, which agree well with the experimental data.

Wojcik M. Impact of non-covalent interactions on FT-IR spectrum and properties of 4-methylbenzylammonium nitrate. A DFT and molecular docking study

In this research, the impact of non-covalent interactions on the FT-IR spectrum and structural, electronic, topological and vibrational properties of hybrid 4-methylbenzylammonium nitrate (4MBN) have been studied combining B3LYP/CC-PVTZ calculations with molecular docking. 4MBN was synthesized and characterized by using the FT-IR spectrum while the optimized structures in gas phase and in ethanol and aqueous solutions have evidenced monodentate coordination between the nitrate and methylbenzylammonium groups, in agreement with that experimental determined for this species by X-ray diffraction. Here, non-covalent interactions were deeply analyzed in terms of topological parameters (AIM), electron localization function (ELF), localized orbital locator (LOL), Hirshfeld surface and reduced density gradient (RDG) method. Weak interactions such as H-bonds, VDW and steric effect in 4MBN were visualized and quantified by the independent gradient density (IGM) based on the promolecular density. The hyper-conjugative and the delocalization of charge in 4MBN have been elucidated by natural bonding orbital (NBO) while its chemical reactivity was studied and discussed by using molecular electrostatic potential surface (MESP), frontier molecular orbital (FMOs), density of state (DOS) and partial density of state (PDOS). The complete vibrational assignments of 69 vibration modes expected for 4MBN are reported together with the scaled force constants while the electronic transitions were evaluated by TD-DFT calculations in ethanol solution. Thermal analysis (DTA and DSC) was also determined. Molecular docking calculations have suggested that 4MBN presents biological activity and could act as a good inhibitor against schizophrenia disease.

5-((1H-imidazol-1-yl)methyl)quinolin-8-ol as potential antiviral SARS-CoV-2 candidate: Synthesis, crystal structure, Hirshfeld surface analysis, DFT and molecular docking studies

A potential new drug to treat SARS-CoV-2 infections and chloroquine analogue, 5-((1H-imidazol-1-yl)methyl)quinolin-8-ol (DD1) has been here synthesized and characterized by FT-IR, 1H-NMR, 13C-NMR, ultraviolet-visible, ESI-MS and single-crystal X-ray diffraction. DD1 was optimized in gas phase, aqueous and DMSO solutions using hybrid B3LYP/6-311++G(d,p) method. Comparisons between experimental and theoretical infrared spectra, 1H and 13C NMR chemical shifts and electronic spectrum in DMSO solution evidence good concordances. Higher solvation energy was observed in aqueous solution than in DMSO, showing in aqueous solution a higher value than antiviral brincidofovir and chloroquine. on Bond orders, atomic charges and topological studies suggest that imidazole ring play a very important role in the properties of DD1. NBO and AIM analyses support the intra-molecular O15-H16•••N17 bonds of DD1 in the three media. Low gap value supports the higher reactivity of DD1 than chloroquine justified by the higher electrophilicity and low nucleophilicity. Complete vibrational assignments of DD1 in gas phase and aqueous solution are reported together with the scaled force constants. In addition, better intermolecular interactions were observed by Hirshfeld surface analysis. Finally, the molecular docking mechanism between DD1 ligand and COVID-19/6WCF and COVID-19/6Y84 receptors were studied to explore the binding modes of these compounds at the active sites. Molecular docking results have shown that the DD1 molecule can be considered as a potential agent against COVID-19/6Y84-6WCF receptors.

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.