Molecular structure investigation and spectroscopic studies on 2,3-difluorophenylboronic acid: a combined experimental and theoretical analysis

FT-IR, FT-raman and UV spectra and ab initio HF and DFT study of conformational analysis, molecular structure and properties of ortho- meta- and para-chlorophenylboronic acid isomers

In this study, the FT-IR, FT-Raman, and UV-Vis spectroscopic properties of three monosubstituted phenylboronic acid derivatives: ortho-chlorophenylboronic acid (o-ClPhBA), meta-chlorophenylboronic acid (m-ClPhBA) and para-chlorophenylboronic acid (p-ClPhBA) molecules are investigated both experimentally and theoretically using Density Functional Theory (B3LYP) and Hartree Fock (HF). In order to find the stable possible conformations of the compounds, the conformational analysis was carried out by running potential energy surface (PES) scan by means of rotation of two structural parameters, the dihedral angles indicated as φ2 (C6-B-O1-H1A) and φ3 (C6-B-O2-H2A), varying from -180° to 180° with an increment of 10° using B3LYP/6-31G level of theory. Also, to determinate the most stable conformer for all the molecules, potential energy curve (PEC) the stable possible conformations on PES scan were investigated as a function of φ1 (C1-C6-B-O1) dihedral angle from 0° up to 180° with an increment of 10° using B3LYP/6-311++G(d,p) and HF/6-311++G(d,p) level of theory. For all the studied compounds, two conformational structures (conformer anti-anti, syn-syn) that did not have imaginary frequency values outside the equilibrium state (conformer anti-syn) were detected theoretically at the both methods. Due to their conformational flexibility, the relative stabilities of the anti-syn, anti-anti, and syn-syn conformers of o-ClPhBA, m-ClPhBA, and p-ClPhBA are 0.0, 4.66, and 6.76 kcal/mol, respectively, at the B3LYP/6-311++G(d,p) level of theory. For the HF/6-311++G(d,p) level of theory, the relative stabilities are 0.00, 4.54, and 6.11 kcal/mol for o-ClPhBA; 0.00, 3.98, and 1.51 kcal/mol for m-ClPhBA; and 0.00, 4.10, and 1.44 kcal/mol for p-ClPhBA, respectively. Some of the determined stable conformations of these molecules are different in symmetry groups. It was observed that the increase in the symmetry was effective in the of molecular properties, especially for vibrational frequencies. The structural parameter, dipole moments (μ), vibrational frequencies, polarizability (α), hyperpolarizability (β), the highest occupied molecular orbital (HOMO), and the lowest unoccupied molecular orbital (LUMO) of the stable conformers were calculated by using Ab initio HF/6-311++G(d,p) and DFT/B3LYP/6-311++G(d,p) level of theory. The assignments of fundamental vibrational modes of the studied molecule were performed based on total energy distribution (TED) analysis.

Evaluation of experimental, computational, molecular docking and dynamic simulation of flucytosine

Flucytosine (5-fluorocytosine), a fluorine derivative of pyrimidine, has been studied both experimentally and quantum chemically. To obtain the optimized structure, vibrational frequencies and other various parameters, the B3LYP method with a 6-311++G(d,p) basis set was used. Atom-in-molecule theory was used to calculate the binding energies, ellipticity and isosurface projection by electron localization of the molecule (AIM). In addition, the computational results from IR and Raman were compared with the experimental spectra. NBO analysis was used to analyze the donor and acceptor interactions. To know the reactive region of the molecule, the molecular electrostatic potential (MEP) and Fukui functions were determined. The UV-Vis spectrum calculated by the TD-DFT/PCM method was also compared with the experimentally determined spectrum. The HOMO-LUMO energy outcomes proved that there was a good charge exchange occurring within the molecule. With DMSO and MeOH as the solvents, maps of the hole and electron density distribution (EDD and HDD) were produced in an excited state. An electrophilicity index parameter was looked at to theoretically test the bioactivity of the compound. To find the best ligand-protein interactions, molecular docking was also carried out with various receptor proteins. In order to verify the inhibitory potency for the receptor protein complex predicted by docking and molecular dynamic simulation studies, the binding free energy of the receptor protein complex was calculated. Using the MM/GBSA technique, we determined the docked complex's binding free energy. To confirm the molecule's drug similarity, a biological drug similarity investigation was also executed.Communicated by Ramaswamy H. Sarma.

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.

Dithiane Based Boronic Acid as a Carbohydrate Sensor in an Aqueous Solution at pH 7.5: Theoretical and Experimental Approach

Carbohydrate sensing in an aqueous solution remains a very challenging area of interest. Using the idea of covalent reversible interaction between boronic acids and the diol groups in carbohydrates enable us to design a carbohydrate sensor 1-thianthrenylboronic acid (1T), which has high selectivity towards fructose. To elucidate the sensing and binding properties of 1T with sugars, we have incorporated theoretical (DFT and TD-DFT) and spectroscopic techniques. For an optimized geometry, the complete vibrational assignments were done with FT-IR and FT-Raman spectra. Physiochemical parameters were obtained by implementing frontier molecular orbital (FMO) analysis. Further, excited state properties were determined by performing TD-DFT calculations in solvent and these properties were in good agreement with the experiment. The steady state fluorescence measurements with varying concentration of sugars, revealed that the fluorescence intensity of boronic acid is enhanced by studied sugars due to the structural modification. We also noticed remarkable changes in fluorescence lifetimes and quantum yield after adding sugars. The article also reports influence of pH on boronic acid's fluorescence intensity with and without sugars. The fluorescence of boronic acid increases with the increase in pH. These changes are due to acid-base equilibrium of boronic acid and led us to estimate the pKa value of 7.6. All the theoretical and experimental evidences suggested that 1T can be used as a possible fluorescent sensor for fructose. In addition, 1T showed very good affinity for Cu²⁺ ion with K_a = 150 × 10² M^-1, which suggests that 1T can also be used as a chemosensor for Cu²⁺ ions.

Experimental approach, theoretical investigation and molecular docking of 2- chloro-5-fluoro phenol antibacterial compound

The molecular structural dimerization of biologically potent 2-chloro-5-fluoro phenol (2C5FP) is optimized. A combined experimental and theoretical characteristics of vibrational spectral determinations (NMR, FT-IR and Raman) on 2-chloro-5-fluoro phenol (2C5FP) were used at DFT-B3LYP/6–31++G (d,p) level of computation. A close coherence is achieved when experimentally observed wave numbers are compared with calculated wave numbers by refinement of the scale factors. Calculated values of global chemical descriptors of the present molecule reveal significant molecular stability and chemical reactivity. Non-Linear optical (NLO) property of the present molecule is investigated by determining the second order non linear parameter of first hyperpolarizability β. Moreover, hydrogen bond and thermodynamic parameters at various temperatures are determined and discussed. Investigated compound 2C5FP possesses a better antibacterial activity against Echerichia coli, Streptococcus aureus, Pseudomonas aureus,and Staphylococcus aureus, respectively. The title molecule is subjected to molecular docking studies with two different proteins, namely Staphylococcus aureus Tyrosyl-tRNA synthetase (PDB ID: 1JIL) and human dihydroorotate dehydrogenase (hDHODH) (PDB ID: 6CJF). The results of molecular docking analysis support the antibacterial activity and demonstrate a strong interaction with the DHODH inhibitor.

Influence of fluorine substituents on the properties of phenylboronic compounds

Rapid development of research on the chemistry of boronic acids is connected with their applications in organic synthesis, analytical chemistry, materials’ chemistry, biology and medicine. In many applications Lewis acidity of boron atoms plays an important role. Special group of arylboronic acids are fluoro-substituted compounds, in which the electron withdrawing character of fluorine atoms influences their properties. The present paper deals with fluoro-substituted boronic acids and their derivatives: esters, benzoxaboroles and boroxines. Properties of these compounds, i.e. acidity, hydrolytic stability, structures in crystals and in solution as well as spectroscopic properties are discussed. In the next part examples of important applications are given.

Direct Fluorescent Detection of a Polymethoxyflavone in Cell Culture and Mouse Tissue

Convenient detection methods for bioactive food compounds and their metabolites in biological samples are needed to better understand their mechanism of actions. Herein, we developed a novel approach to directly monitor and visualize the distribution of 5,3',4'-tridemethylnobiletin (TDN), a unique polymethoxyflavone metabolite derived from citrus polymethoxyflavone, in biological samples such as cultured cells and mouse colonic tissues. Our results showed that a fluorescent conjugate could be formed between TDN and 2-aminoethyl diphenyl borate (DPBA) under simple reaction conditions, which was confirmed by both Raman spectroscopy and mass spectroscopy. We further demonstrated the application of DPBA-based conjugation reaction in the characterization of TDN in different biological samples including floating cells, adherent cells, and animal tissues. This is the first report demonstrating direct fluorescent detection of polymethoxyflavone in biological samples.

4-Mercaptophenylboronic acid: conformation, FT-IR, Raman, OH stretching and theoretical studies

4-Mercaptophenylboronic acid (4-mpba, C6H7BO2S) was investigated experimentally by vibrational spectroscopy. The molecular structure and spectroscopic parameters were studied by computational methods. The molecular dimer was investigated for intermolecular hydrogen bonding. Potential energy distribution analysis of normal modes was performed to identify characteristic frequencies. The present work provides a simple physical picture of the OH stretch vibrational spectra of 4-mpba and analogues of the compound studied. When the different computational methods are compared, there is a strong evidence of the better performance of the BLYP functional than the popular B3LYP functional to describe hydrogen bonding in the dimer. The findings of this research work should be useful to experimentalists in their quests for functionalised 4-mpba derivatives.

The spectroscopic and quantum chemical studies of 3,4-difluoroaniline

Spectroscopic and structural investigations of 3,4-difluoroaniline molecule are presented by using experimental (FT-IR, FT-Raman, (1)H and (13)C NMR, and UV-Vis) techniques and theoretical (DFT approach) calculations. FT-IR and FT-Raman spectra of 3,4-difluoroaniline molecule are recorded in the region 4000-400cm(-1) and 3500-10cm(-1) in the liquid phase, respectively. The NMR chemical shifts ((1)H and (13)C) are recorded in chloroform-d solution. The UV absorption spectra of 3,4-difluoroaniline dissolved in ethanol and water are recorded in the range of 200-400nm. Experimental results are supported with the following theoretical calculations; the optimized geometry and vibrational (FT-IR and FT-Raman) spectra are carried out by DFT (B3LYP)/6-311++G(d,p) basis set calculations. The nuclear magnetic resonance spectra ((1)H and (13)C NMR) are obtained by using the gauge-invariant atomic orbital method. Moreover, electronic characteristics, such as HOMO and LUMO energies, density of state diagrams, and molecular electrostatic potential surface are investigated. Nonlinear optical properties and thermodynamic features are also outlined theoretically. An excellent correlation of theoretical and experimental results provides a detailed description of the structural and physicochemical properties of the molecule. Thus, this work leads to a deep understanding of the characteristics of di-substituted aniline derivatives.

FT-IR, FT-Raman, NMR and UV-Vis spectra and DFT calculations of 5-bromo-2-ethoxyphenylboronic acid (monomer and dimer structures)

In this study, the Fourier Transform Infrared (FT-IR) and Fourier Transform Raman (FT-Raman) spectra of 5-bromo-2-ethoxyphenylboronic acid (5Br2EPBA) are recorded in the solid phase in the region 4000-400 cm(-1) and 3500-10 cm(-1), respectively. The (1)H, (13)C and DEPT nuclear magnetic resonance (NMR) spectra are recorded in DMSO solution. The UV-Vis absorption spectrum of 5Br2EPBA is saved in the range of 200-400 nm in ethanol and water. The following theoretical calculations for monomeric and dimeric structures are supported by experimental results. The molecular geometry and vibrational frequencies in the ground state are calculated by using DFT methods with 6-31G(d,p) and 6-311G(d,p) basis sets. There are four conformers for the present molecule. The computational results diagnose the most stable conformer of 5Br2EPBA as Trans-Cis (TC) form. The complete assignments are performed on the basis of the total energy distribution (TED) of vibrational modes, calculated with scaled quantum mechanics (SQM) method in parallel quantum solutions (PQS) program. The (1)H and (13)C NMR chemical shifts of 5Br2EPBA molecule are calculated by using the Gauge Invariant Atomic Orbital (GIAO) method in DMSO and gas phase for monomer and dimer structures of the most stable conformer. Moreover, electronic properties, such as the HOMO and LUMO energies (by TD-DFT and CIS methods) and molecular electrostatic potential surface (MEPs) are investigated. Stability of the molecule arising from hyper-conjugative interactions, charge delocalization is analyzed using natural bond orbital (NBO) analysis. Nonlinear optical (NLO) properties and thermodynamic features are presented. All calculated results are compared with the experimental data of the title molecule. The correlation of theoretical and experimental results provides a detailed description of the structural and physicochemical properties of the title molecule.

DFT calculations and experimental FT-IR, FT-Raman, NMR, UV-Vis spectral studies of 3-fluorophenylboronic acid

The spectroscopic (FT-IR, FT-Raman, (1)H and (13)C NMR, UV-Vis), structural, electronic and thermodynamical properties of 3-fluorophenylboronic acid (C6H4FB(OH)2), 3FPBA) were submitted by using both experimental techniques and theoretical methods (quantum chemical calculations) in this work. The experimental infrared and Raman spectra were obtained in the region 4000-400 cm(-1) and 3500-10 cm(-1), respectively. The equilibrium geometry and vibrational spectra were calculated by using DFT (B3LYP) with 6-311++G(d,p) basis set. The vibrational wavenumbers were also corrected with scale factor to take better results for the calculated data. The total energy distributions (TED) of the vibrational modes were performed for the assignments of the title molecule by using scaled quantum mechanics (SQM) method. The NMR chemical shifts ((1)H and (13)C) were recorded in DMSO solution. The (1)H and (13)C NMR spectra were computed by using the gauge-invariant atomic orbital (GIAO) method, showing a good agreement with the experimental ones. The last one UV-Vis absorption spectra were analyzed in two solvents (ethanol and water), saved in the range of 200-400 nm. In addition these, HOMO and LUMO energies, the excitation energies, density of states (DOS) diagrams, thermodynamical properties and molecular electrostatic potential surface (MEPs) were presented. Nonlinear optical (NLO) properties and thermodynamic features were performed. The experimental results are combined with the theoretical calculations using DFT calculations to fortification of the paper. At the end of this work, the results were proved our paper had been indispensable for the literature backing.

Experimental (FT-IR, FT-Raman, UV and NMR) and quantum chemical studies on molecular structure, spectroscopic analysis, NLO, NBO and reactivity descriptors of 3,5-Difluoroaniline

Comprehensive investigation of geometrical and electronic structure in ground as well as the first excited state of 3,5-Difluoroaniline (C6H5NF2) was carried out. The experimentally observed spectral data (FT-TR and FT-Raman) of the title compound was compared with the spectral data obtained by DFT/B3LYP method using 6-311++G(d,p) basis set. The molecular properties like dipole moment, polarizability, first static hyperpolarizability, molecular electrostatic potential surface (MEPs), and contour map were calculated to get a better insight of the properties of the title molecule. Natural bond orbital (NBO) analysis was applied to study stability of the molecule arising from charge delocalization. UV-Vis spectrum of the title compound was also recorded and the electronic properties, such as Frontier orbitals and band gap energies were measured by TD-DFT approach. Total and partial density of state (TDOS and PDOS) and also overlap population density of state (OPDOS) diagrams analysis were presented. Global and local reactivity descriptors were computed to predict reactivity and reactive sites on the molecule. (1)H and (13)C NMR spectra by using gauge including atomic orbital (GIAO) method of studied compound were compared with experimental data obtained. Moreover, the thermodynamic properties were evaluated.

Vibrational spectroscopy (FT-IR and Laser-Raman) investigation, and computational (M06-2X and B3LYP) analysis on the structure of 4-(3-fluorophenyl)-1-(propan-2-ylidene)-thiosemicarbazone

In this study, the experimental and theoretical vibrational spectral analysis of 4-(3-fluorophenyl)-1-(propan-2-ylidene)-thiosemicarbazone have been carried out. The experimental FT-IR (4000-400 cm(-1)) and Laser-Raman spectra (4000-100 cm(-1)) have been recorded for the solid state samples. The theoretical vibrational frequencies and the optimized geometric parameters (bond lengths and angles) have been calculated for gas phase using density functional theory (DFT/B3LYP: Becke, 3-parameter, Lee-Yang-Parr) and M06-2X (the highly parametrized, empirical exchange correlation function) quantum chemical methods with 6-311++G(d,p) basis set. The diversity in molecular geometry of fluorophenyl substituted thiosemicarbazones has been discussed based on the X-ray crystal structure reports and theoretical calculation results from the literature. The assignments of the vibrational frequencies have been done on the basis of potential energy distribution (PED) analysis by using VEDA4 software. A good correlation was found between the computed and experimental geometric and vibrational data. In addition, the highest occupied (HOMO) and lowest unoccupied (LUMO) molecular orbital energy levels and other related molecular energy values of the compound have been determined using the same level of theoretical calculations.

Influence of fluorine substituents on the NMR properties of phenylboronic acids

The paper presents results of a systematic NMR studies on fluorinated phenylboronic acids. All possible derivatives were studied. The experimental (1)H, (13)C, (19)F, (11)B, and (17)O spectral data were compared with the results of theoretical calculations. The relation between the calculated natural bond orbital parameters and spectral data (chemical shifts and coupling constants) is discussed. The first examples of (10)B/(11)B isotopic effect on the (19)F spectra and (4)JFO scalar coupling in organic compounds are reported.

An experimental and theoretical investigation of Acenaphthene-5-boronic acid: conformational study, NBO and NLO analysis, molecular structure and FT-IR, FT-Raman, NMR and UV spectra

The solid state Fourier transform infrared (FT-IR) and FT-Raman spectra of Acenaphthene-5-boronic acid (AN-5-BA), have been recorded in the range 4000-400cm(-1) and 4000-10cm(-1), respectively. Density functional theory (DFT), with the B3LYP functional was used for the optimization of the ground state geometry and simulation of the infrared and Raman spectra of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 09 set of quantum chemistry codes and the normal modes were assigned by a scaled quantum mechanical (SQM) force field approach. Hydrogen-bonded dimer of AN-5-BA, optimized by counterpoise correction, has also been studied by B3LYP at the 6-311++G(d,p) level and the effects of molecular association through O-H⋯O hydrogen bonding have been discussed. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by Gauge-Including Atomic Orbital (GIAO) method. Natural bond orbital (NBO) analysis has been applied to study stability of the molecule arising from charge delocalization. UV spectrum of the title compound was also recorded and the electronic properties, such as frontier orbitals, and band gap energies were measured by TD-DFT approach. The first order hyperpolarizability 〈β〉, its components and associated properties such as average polarizability and anisotropy of the polarizability (α and Δα) of AN-5-BA was calculated using the finite-field approach.