Vibrational spectra and normal coordinate analysis of 2-hydroxy-3-(2-methoxyphenoxy) propyl carbamate

Quantum Computational, Spectroscopic (FT-IR, FT-Raman, NMR, and UV-Vis) Hirshfeld Surface and Molecular Docking-Dynamics Studies on 5-Hydroxymethyluracil (Monomer and Trimer)

For many decades, uracil has been an antineoplastic agent used in combination with tegafur to treat various human cancers, including breast, prostate, and liver cancer. Therefore, it is necessary to explore the molecular features of uracil and its derivatives. Herein, the molecule's 5-hydroxymethyluracil has been thoroughly characterized by NMR, UV-Vis, and FT-IR spectroscopy by means of experimental and theoretical analysis. Density functional theory (DFT) using the B3LYP method at 6-311++G(d,p) was computed to achieve the optimized geometric parameters of the molecule in the ground state. For further investigation and computation of the NLO, NBO, NHO analysis, and FMO, the improved geometrical parameters were utilized. The potential energy distribution was used to allocate the vibrational frequencies using the VEDA 4 program. The NBO study determined the relationship between the donor and acceptor. The molecule's charge distribution and reactive regions were highlighted using the MEP and Fukui functions. Maps of the hole and electron density distribution in the excited state were generated using the TD-DFT method and PCM solvent model in order to reveal electronic characteristics. The energies and diagrams for the lowest unoccupied molecular orbital (LUMO) and the highest occupied molecular orbital (HOMO) were also provided. The HOMO-LUMO band gap estimated the charge transport within the molecule. When examining the intermolecular interactions in 5-HMU, Hirshfeld surface analysis was used, and fingerprint plots were also produced. The molecular docking investigation involved docking 5-HMU with six different protein receptors. Molecular dynamic simulation has given a better idea of the binding of the ligand with protein.

Comprehensive Study of the Ammonium Sulfamate-Urea Binary System

The physicochemical properties of binary systems are of great importance for the application of the latter. We report on the investigation of an ammonium sulfamate-urea binary system with different component ratios using a combination of experimental (FTIR, XRD, TGA/DSC, and melting point) and theoretical (DFT, QTAIM, ELF, RDG, ADMP, etc.) techniques. It is shown that, at a temperature of 100 °C, the system under study remains thermally and chemically stable for up to 30 min. It was established using X-ray diffraction analysis that the heating time barely affects the X-ray characteristics of the system. Data on the aggregate states in specified temperature ranges were obtained with thermal analysis and determination of the melting point. The structures of the ammonium sulfamate-urea system with different component ratios were optimized within the density functional theory. The atom-centered density matrix propagation calculation of the ammonium sulfamate-urea system with different component ratios was performed at temperatures of 100, 300, and 500 K. Regardless of the component ratio, a regular increase in the potential energy variation (curve amplitude) with an increase in temperature from 100 to 500 K was found.

A Comprehensive Study of N-Butyl-1H-Benzimidazole

Imidazole derivatives have found wide application in organic and medicinal chemistry. In particular, benzimidazoles have proven biological activity as antiviral, antimicrobial, and antitumor agents. In this work, we experimentally and theoretically investigated N-Butyl-1H-benzimidazole. It has been shown that the presence of a butyl substituent in the N position does not significantly affect the conjugation and structural organization of benzimidazole. The optimized molecular parameters were performed by the DFT/B3LYP method with 6-311++G(d,p) basis set. This level of theory shows excellent concurrence with the experimental data. The non-covalent interactions that existed within our compound N-Butyl-1H-benzimidazole were also analyzed by the AIM, RDG, ELF, and LOL topological methods. The color shades of the ELF and LOL maps confirm the presence of bonding and non-bonding electrons in N-Butyl-1H-benzimidazole. From DFT calculations, various methods such as molecular electrostatic potential (MEP), Fukui functions, Mulliken atomic charges, and frontier molecular orbital (HOMO-LUMO) were characterized. Furthermore, UV-Vis absorption and natural bond orbital (NBO) analysis were calculated. It is shown that the experimental and theoretical spectra of N-Butyl-1H-benzimidazole have a peak at 248 nm; in addition, the experimental spectrum has a peak near 295 nm. The NBO method shows that the delocalization of the aσ-electron from σ (C1-C2) is distributed into antibonding σ* (C1-C6), σ* (C1-N26), and σ* (C6-H11), which leads to stabilization energies of 4.63, 0.86, and 2.42 KJ/mol, respectively. Spectroscopic investigations of N-Butyl-1H-benzimidazole were carried out experimentally and theoretically to find FTIR vibrational spectra.

Structural and Vibrational Investigation of Benzil-(1,2-Diphenylethane-1,2-Dione): Experimental and Theoretical Studies

Single crystals of benzil commonly known as 1,2-diphenylethane-1,2-dione are grown by the slow evaporation method at room temperature. Gaussian 09 program is applied for theoretical calculations with B3LYP/6-311++G(d,p) basis set. The structure is optimized, and the energy, structural parameters, vibrational frequencies, IR, and Raman intensities are determined. Complete natural bonding orbital (NBO) analysis is carried out to analyze the intramolecular electronic interactions and their stabilization energies. From the second-order perturbation theory analysis of the benzil molecule, it is observed that there exists a hyperconjugative intramolecular stabilization energy between 17.45 and 22.76 KJmol-1. HOMO-LUMO analysis has been performed to identify the charges transferred within the molecule. The energy gap is calculated to be 2.919 eV and thus establishes the soft nature of the molecule. The molecular electrostatic potential (MEP) of the grown crystal was analyzed using the B3LYP method with 6-311++G(d,p) basis set. First-order hyperpolarizability calculations reveal the nonlinear optical microscopic behavior of the benzil molecule with nonzero values. The total value of the first-order hyperpolarizability ( ${\beta }_{\text{tot}}$ ) is of the order of $41.5246\times {10}^{-31}\text{esu}$ , which is found to be 11.135 times that of urea. Hence, benzil can be referred to as a good material for nonlinear optical applications.

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.

Food Xanthan Polysaccharide Sulfation Process with Sulfamic Acid

Xanthan is an important polysaccharide with many beneficial properties. Sulfated xanthan derivatives have anticoagulant and antithrombotic activity. This work proposes a new method for the synthesis of xanthan sulfates using sulfamic acid. Various N-substituted ureas have been investigated as process activators. It was found that urea has the greatest activating ability. BBD of xanthan sulfation process with sulfamic acid in 1,4-dioxane has been carried out. It was shown that the optimal conditions for the sulfation of xanthan (13.1 wt% sulfur content) are: the amount of sulfating complex per 1 g of xanthan is 3.5 mmol, temperature 90 °C, duration 2.3 h. Sulfated xanthan with the maximum sulfur content was analyzed by physicochemical methods. Thus, in the FTIR spectrum of xanthan sulfate, in comparison with the initial xanthanum, absorption bands appear at 1247 cm-1, which corresponds to the vibrations of the sulfate group. It was shown by GPC chromatography that the starting xanthan gum has a bimodal molecular weight distribution of particles, including a high molecular weight fraction with Mw > 1000 kDa and an LMW fraction with Mw < 600 kDa. It was found that the Mw of sulfated xanthan gum has a lower value (~612 kDa) in comparison with the original xanthan gum, and a narrower molecular weight distribution and is characterized by lower PD values. It was shown by thermal analysis that the main decomposition of xanthan sulfate, in contrast to the initial xanthan, occurs in two stages. The DTG curve has two pronounced peaks, with maxima at 226 and 286 °C.

Anticancer activity of indapamide adsorbed on gold nanoparticles: DFT, in-silico, and in-vitro analysis

The adsorption properties of the lung cancer agent indapamide (IND) on gold nanoparticles (AuNPs), were studied with the help of surface-enhanced Raman scattering techniques. The structure-activity of the IND and INDA molecule has been studied using DFT/B3LYP methodology. NBO analysis reveals that, both the molecules are stabilized by a C─H^… O intramolecular hydrogen bonding, apart from the conjugative and intramolecular charge transfer interactions. The analysis of the electron density of frontier molecular orbital analysis gives a comparative idea of the reactivity, the low kinetic stability, and low value of energy gap indicating the electron transport in the molecule and thereby its bioactivity. The molecular electrostatic potential, local and global reactivity indicators predict the reactive site of the molecules. FT-IR, FT-Raman, and surface-enhanced Raman scattering have been investigated and compared with the theoretical prediction. Effective in-silico (molecular docking) biological activity screening of the molecules was checked on lung cancer cells. In-vitro (surface-enhanced Raman scattering techniques and MTT assay) analysis confirms the results from the in-silico analysis. This study promotes the potential of SERS agents for targeted drug delivery and photothermal therapy and the novelty of the IND and INDA molecule against lung cancer activity.

Quantum chemical studies on molecular structure, AIM, ELF, RDG and antiviral activities of hybrid hydroxychloroquine in the treatment of COVID-19: Molecular docking and DFT calculations

Structure-activity relationships for hydroxychloroquine compound and its derivatives resulted in a potent antiviral activity. Where hydroxychloroquine derivatives showed an apparent efficacy against coronavirus related pneumonia. For this reason, the current study is focused on the structural properties of hydroxychloroquine and hydroxychloroquine sulfate. Optimized structures of these molecules have been reported by using DFT method at B3LYP/6-31G* level of theory. The geometric were determined and compared with the experimental crystal structure. The intra and intermolecular interactions which exist within these compounds are analyzed by different methods namely the topological analysis AIM, ELF and the reduced gradient of the density. These approaches make it possible in particular to study the properties of hydrogen bonds. The highest occupied molecular orbital and the lowest unoccupied molecular orbital energy levels are constructed and the corresponding frontier energy gaps are determined to realize the charge transfer within the molecule. The densities of state diagrams were determined to calculate contributions to the molecular orbitals. The molecular electrostatic potential surfaces are determined to give a visual representation of charge distribution of these ligands and to provide information linked to electrophilic and nucleophilic sites localization. Finally, these derivatives were evaluated for the inhibition of COVID-19 activity by using the molecular docking method.

Single-crystal X-ray structural characterization, Hirshfeld surface analysis, electronic properties, NBO, and NLO calculations and vibrational analysis of the monomeric and dimeric forms of 5-nitro-2-oxindole

The information of interactions is given by RDG versus sign(λ₂)ρ product of the sign of the second largest eigenvalue of electron density Hessian matrix and electron density) investigated by RDG surface analysis.

Spectroscopic and quantum computational study on naproxen sodium

The spectroscopic (FT-IR, FT-Raman, NMR), electronic (UV--Vis.), structural and thermodynamical properties of an anti-inflammatory analgesic called Naproxen Sodium, (s)-6-methoxy-α-methyl-2-naphthaleneacetic acid sodium salt are submitted by using both experimental techniques and theoretical methods as quantum chemical calculations in this work. The equilibrium geometry and vibrational spectra are calculated by using DFT (B3LYP) with 6-311++G (d,p) basis set using GAUSSIAN 09. The vibrational wavenumbers are also corrected with scale factor to take better results for the calculated data. The HOMO-LUMO calculations are carried out on the title compound. The theoretical and experimental NMR peaks were found to be in good agreement. In addition, the detailed study on the Non-Bonding Orbitals, the excitation energies, AIM charges, condensed fukui calculations, thermodynamical properties, Localized Orbital Locator (LOL) and Electron Localization Function (ELF) are also performed. Furthermore, the study is extended to calculate the first order hyperpolarizability and to predict its NLO properties. The docking studies details helped on predicting the binding with different proteins.

A detailed computational investigation on the structural and spectroscopic properties of propolisbenzofuran B

This investigation deals with some structural and spectroscopic aspects of propolisbenzofuran B molecule as one of the most important bioactive molecules which exists in the bee propolis composition. FT-IR vibrational analysis carried-out at B3LYP/6-311++G(d,p) level of the theory. ¹H and ¹³C NMR chemical shift have been predicted with GIAO method. TD- DFT calculations have been established to predict the UV- Vis spectral analysis for propolisbenzofuran B molecule. The detailed structural analysis such as electronic characterization, HOMO and LUMO, DOS plot, Molecular Electronic Potential (MEP), Natural Bond Orbital (NBO) are performed and discussed for studied molecule.

Quantum mechanical and spectroscopic (FT-IR, FT-Raman) study, NBO analysis, HOMO-LUMO, first order hyperpolarizability and molecular docking study of methyl[(3R)-3-(2-methylphenoxy)-3-phenylpropyl]amine by density functional method

Quantum chemical techniques such as density functional theory (DFT) have become a powerful tool in the investigation of the molecular structure and vibrational spectrum and are finding increasing use in application related to biological systems. The Fourier transform infrared (FT-IR) and Fourier transform Raman (FT-Raman) techniques are employed to characterize the title compound. The vibrational frequencies were obtained by DFT/B3LYP calculations with 6-31G(d,p) and 6-311++G(d,p) as basis sets. The geometry of the title compound was optimized. The vibrational assignments and the calculation of Potential Energy Distribution (PED) were carried out using the Vibrational Energy Distribution Analysis (VEDA) software. Molecular electrostatic potential was calculated for the title compound to predict the reactive sites for electrophilic and nucleophilic attack. In addition, the first-order hyperpolarizability, HOMO and LUMO energies, Fukui function and NBO were computed. The thermodynamic properties of the title compound were calculated at different temperatures, revealing the correlations between heat capacity (C), entropy (S) and enthalpy changes (H) with temperatures. Molecular docking studies were also conducted as part of this study. The paper further explains the experimental results which are in line with the theoretical calculations and provide optimistic evidence through molecular docking that the title compound can act as a good antidepressant. It also provides sufficient justification for the title compound to be selected as a good candidate for further studies related to NLO properties.