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

An atomistic scale simulation study of structural properties in the silk-fibrohexamerin complex

The use of Bombyx mori silk fibroin in composite materials has been extensively explored in many studies, owing to its remarkable mechanical properties. Recently, the N-glycan-engineered P25 protein was utilized to improve the mechanical properties of silk. However, the mechanism by which N-glycan-engineered P25 protein enhances the mechanical properties of silk remains unclear. This study analyzed the interaction between the P25 protein and silkworm silk using quantum mechanics/molecular mechanics multiscale simulations and discovered stronger hydrogen bonding between the amorphous domain and the P25 protein. The results confirmed that glycoengineering of the mannose molecule in N-glycan in orders of three, five, and seven increased the hydrogen bonding of the amorphous structures. However, P25 has fewer binding interactions with the crystalline domain. Silk amino acids and mannose molecules were analyzed using QM simulations, and hydroxyl and charged amino acids in the amorphous domains were found to have relatively higher reactivity with mannose molecules in N-glycans than basic and aliphatic amino acids in the crystalline domain. This study demonstrates how the N-glycan-engineered P25 protein can improve the mechanical properties of silk fibroin and identifies a key factor for N-glycan-engineered proteins.

Spectroscopic profiling, DFT computations, molecular docking and molecular dynamic simulation of biologically active 5-isoquinolinesulfonic acid

The title compound 5-isoquinolinesulfonic acid (5IQSA) is characterized using the FT-IR, FT-Raman, NMR and UV-Vis spectra. The optimized molecular geometry, vibrational assignments, infrared intensities and Raman scattering are precisely calculated using Density Functional Theory (DFT) with the B3LYP/6-311++G(d,p) basis set. The ¹H and ¹³C NMR chemical shifts are computed and compared with the experimental data. The TD-DFT/M062X/6-311++G(d,p) method is used to compute UV-Vis for different solvents, and the results are compared to UV-Vis spectra obtained experimentally. The HOMO-LUMO band gap energy is calculated for various solvents and compared to the band gap of UV-Vis spectra. Molecular dynamics simulations are used to investigate the biomolecular stability. Non-Linear Optical (NLO) behaviour has been illustrated using hyperpolarizability calculations. Topological studies such as Reduced Gradient Density (RDG), Electron Localization Function (ELF) and Localized Orbital Locator (LOL) are performed. The Molecular Electrostatic Potential (MEP), Natural Bond Orbital (NBO) analysis, Fukui functions and thermodynamic properties were analysed. To explore the biological behaviour of the examined compound, molecular docking was performed to evaluate the hydrogen bond distance and binding energies with (2XA4) kinase inhibitor protein.Communicated by Ramaswamy H. Sarma.

Germanium-based superatom clusters as excess electron compounds with significant static and dynamic NLO response; a DFT study

Herein, the geometric, electronic, and nonlinear optical properties of excess electron zintl clusters Ge₅AM₃, Ge₉AM₅, and Ge₁₀AM₃ (AM = Li, Na, and K) are investigated. The clusters under consideration demonstrate considerable electronic stability as well as superalkali characteristics. The NBO charge is transferred from the alkali metal to the Ge-atoms. The FMO analysis shows fabulous conductive properties with a significant reduction in SOMO-LUMO gaps (0.79-4.04 eV) as compared with undoped systems. The designed clusters are completely transparent in the deep UV-region and show absorption in the visible and near-IR region. Being excess electron compounds these clusters exhibit remarkable hyperpolarizability response up to 8.99 × 10^-26 esu, where a static second hyperpolarizability (γ _o) value of up to 2.15 × 10^-30 esu was recorded for Ge₉Na₅ superatom clusters. The excitation energy is the main controlling factor for hyperpolarizability as revealed from the two-level model study. The electro-optical Pockel's effect and the second harmonic generation phenomenon (SHG) are used to investigate dynamic nonlinear optical features. At a lower applied frequency (=532 nm), the dynamic hyperpolarizability and second hyperpolarizability values are significantly higher for the studied clusters. Furthermore, for the Ge₉K₅ cluster, the hyper Rayleigh scattering (HRS) increases to 5.03 × 10^-26 esu.

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.

Spectroscopic elucidation (FT-IR, FT-Raman and UV-visible) with NBO, NLO, ELF, LOL, drug likeness and molecular docking analysis on 1-(2-ethylsulfonylethyl)-2-methyl-5-nitro-imidazole: An antiprotozoal agent

1-(2-ethylsulfonylethyl)-2-methyl-5-nitro-imidazole (1EMI) C₈H₁₃N₃O₄S also known as Tinidazole, selected for its antiprotozoal property is extensively used for spectroscopic elucidations and computational aspects using density functional methods. Along with spectral conclusions, further investigations on fundamental reactive properties such as electrical, optical, nonlinear combined with DFT simulations were performed. Molecular docking procedure supports the results of chosen appropriate antiprotozoal agent based on ligand-protein interactions. Experimental and simulated (B3LYP/6-311++G (d,p)) IR and Raman spectra showed concurrence. NLO analysis through first order hyperpolarizability parameter helps in finding the potential of 1EMI as a good NLO candidate. Charge delocalization and the stability of the compound were discussed using natural bond orbital (NBO) analysis. Furthermore, Electron localization function (ELF), local orbital locator (LOL), and Frontier molecular orbitals (FMO) were studied. Besides, Mulliken population analysis on atomic charges, Energy gap, chemical potential, global hardness, softness, ionization potential, electronegativity, electrophilicity index along thermodynamic parameters (enthalpy, entropy and heat capacity) have been calculated. Drug likeness parameters and molecular docking approach enabled to check pharmaceutical potential and biological activity of 1EMI. The biological activity of 1EMI through ligand and protein interactions have been confirmed theoretically for the treatment of Malaria, Invasive aspergillosis and Mycobacterium tuberculosis with respect to chosen proteins. Three different activity targets and protein interactions are quite successful revealing the bond distances, intermolecular energy, binding energy and inhibition constant. 2D interaction profile image of the two maximum interacted proteins and also Ramachandran plot used to show stereochemistry of selected protein. The activities of 1EMI were studied in accordance with literature survey and the results were presented.

Molecular docking, quantum chemical computational and vibrational studies on bicyclic heterocycle "6-nitro-2,3-dihydro-1,4-benzodioxine": Anti-cancer agent

The heterocyclic aromatic compounds are primarily used to make pharmaceutical and agrochemicals. In addition, these compounds can be chosen as antioxidants, corrosion inhibitors, electro and opto-electronic devices, polymer material, dye stuff, developers, etc. On the account of this, the heterocyclic aromatic 6-nitro-2,3-dihydro-1,4-benzodioxine (6N3DB) was chosen and the structure is optimized to predict the important properties of it. The structural parameters such as bond length and bond angle have been obtained by DFT/B3LYP/6-311++G(d,p) basis set to know the geometry and orientation of 6N3DB. The molecule has been characterized by FT-IR and FT-Raman spectroscopic techniques to predict the functional groups, vibrational modes and aromatic nature of 6N3DB. The chemical shifts of ¹H and ¹³C have been obtained experimentally and compared with the theoretical data. The parameters such as the band gap between HOMO-LUMO orbitals, λ_max, and electron transition probability in frontier orbitals have been estimated to know the NLO and corrosion inhibition activity. HOMO-LUMO orbital diagram has been obtained for different energy levels and their band gap energies have been compared with UV-vis band gap values. The chemical significance of the molecule has been explained using ELF, LOL, and RDG. The binding energy and intermolecular energy values indicate that the title compound possesses anti-cancer property through hydrolase inhibition activity.

Quantum chemical determination of molecular geometries and spectral investigation of 4-ethoxy-2, 3-difluoro benzamide

The present work reports the application of density functional theory (DFT) at B3LYP with various basis sets which provide the relationship between the structural and spectral properties of 4-ethoxy-2, 3-difluoro benzamide (4EDFB). A Complete vibrational analysis has been performed at the density functional theory (DFT) method with various basis sets in the ground state. The results of vibrational wave numbers are in good agreement with the experimental spectra (Infrared and Raman). Energy gap of the molecule is evaluated using frontier molecular orbital energies (HOMO-LUMO). The frontier energy gap value reveals the chemical reactivity and intermolecular charge transfer occur within the molecule. Global chemical descriptors provide the local and global softness and local reactivity parameters used to identify the nucleophilic and electrophilic behavior of a specific site within the compound. The dimer structure is performed to evaluate the intermolecular hydrogen bond (O-H-O). The title molecule is capable of receiving second harmonic generation (SHG) is due to high value of hyperpolarizability indicates the NLO activity of the molecule. Apart from NLO entities, aromaticity and the molecular electrostatic potential surface (MEP) explain the hydrogen bonding and provide the reactive behavior of the molecule. The Mulliken population analysis leads to redistribution of electron density in the ring.

A molecular approach on the ability of functionalized single walled carbon nanotube for cathinone sensing

In this article, single walled carbon nanotube functionalized with COOH (NT1) and CONHCH₃ (NT2) groups were used for detection of the cathinone (CT) molecule in the gas phase and the liquid phase from the theoretical point of view. Density functional theory (DFT) calculations indicate that the NT2 nanostructure is more sensitive to the cathinone molecule than to the NT1 nanostructure. Compared to the gas phase, in the liquid phase water increases the sensitivity of the nanostructures toward the cathinone molecules. DFT results show that the polarity of the solvent increases the stability of the complexes. Donor–acceptor orbital interactions reveal that the cathinone molecule has a more effective orbital interaction with the NT2 nanostructure, especially in a water solvent. Also, molecular dynamic (MD) simulations confirm that the interactions between the cathinone molecule and the nanostructures increase in the water solvent. Therefore, NT nanostructures are more sensitive toward the CT molecule in a water solvent.

In this article, single walled carbon nanotube functionalized with COOH (NT1) and CONHCH₃ (NT2) groups were used for detection of the cathinone (CT) molecule in the gas phase and the liquid phase from the theoretical point of view.

Density Functional Theory Study on the Complexation of NOTA as a Bifunctional Chelator with Radiometal Ions

1,4,7-Triazacyclononane-1,4,7-triacetic acid (NOTA) is a key bifunctional chelator utilized for the complexation of metal ions in radiopharmaceutical applications; the ability of these chelators depends on the strength of their binding with ions. The focus of the present work is to evaluate the complexation of Cu²⁺, Ga³⁺, Sc³⁺, and In³⁺ radiometal ions with NOTA using density functional theory (B3LYP functional) and 6-311+G(2d,2p)/DGDZVP basis sets. The significant role of ion-water interactions in the chelation interaction energies in solution reflects the competition between ion-water and NOTA-ion interaction in the chelation process. There is reasonable agreement between experimental and theoretical binding constants, geometries, and ¹H NMR chemical shifts. Chelation interaction energies, Gibbs free energies, and entropies in solution show that the NOTA-Ga³⁺ and NOTA-Cu²⁺ are the most and least stable complexes, respectively. The natural atomic charges and second order perturbation analysis reveal charge transfer between NOTA and radiometal ions. The theoretical ¹H NMR chemical shifts of NOTA are in good agreement with experiment; these values are influenced by the presence of the ions, which have a deshielding effect on the protons of NOTA. Global scalar properties such as E_HOMO/E_LUMO, ΔE_LUMO-HOMO, and chemical hardness/softness confirm that the NOTA-Cu²⁺ complex, which has a singly occupied molecular orbital, has the lowest ΔE_LUMO-HOMO value, the least chemical hardness, and the highest chemical softness. The significant variation of the hardness and ΔE_LUMO-HOMO values of the complexes can be attributed to the different positions of the metal ions on the periodic table. This study affirms that, among the radiometal ions, Ga³⁺ can be used to effectively radiolabel NOTA chelator for radiopharmaceutical usage as it binds most stably with NOTA.

DFT study of the interaction between DOTA chelator and competitive alkali metal ions

1, 4, 7, 10-tetraazacyclododecane-1, 4, 7, 10-tetracetic acid (DOTA) is an important chelator for radiolabeling of pharmaceuticals. The ability of alkali metals found in the body to complex with DOTA and compete with radio metal ions can alter the radiolabeling process. Non-covalent interactions between DOTA complexed with alkali metals Li⁺, Na⁺, K⁺ and Rb⁺, are investigated with density functional theory using B3LYP and ωB97XD functionals. Conformational possibilities of DOTA were explored with a varying number of carboxylic pendant arms of DOTA in close proximity to the ions. It is found that the case in which four arms of DOTA are interacting with ions is more stable than other conformations. The objective of this study is to explore the electronic structure properties upon complexation of alkali metals Li⁺ Na⁺, K⁺ and Rb⁺ with a DOTA chelator. Interaction energies, relaxation energies, entropies, Gibbs free energies and enthalpies show that the stability of DOTA, complexed with alkali metals decreases down the group of the periodic table. Implicit water solvation affects the complexation of DOTA-ions leading to decreases in the stability of the complexes. NBO analysis through the natural population charges and the second order perturbation theory, revealed a charge transfer between DOTA and alkali metals. Conceptual DFT-based properties such as HOMO/LUMO energies, ΔE_HOMO-LUMO and chemical hardness and softness indicated a decrease in the chemical stability of DOTA-alkali metal complexes down the alkali metal series. This study serves as a guide to researchers in the field of organometallic chelators, particularly, radiopharmaceuticals in finding the efficient optimal match between chelators and various metal ions.

Density functional theory study of the substituent effect on the structure, conformation and vibrational spectra in halosubstituted anilines

A comparative density functional theory (DFT) study exploring the structural and spectroscopic properties of the complete set of halosubstituted anilines with the halogens being F, Cl and Br was carried out.

The interaction of NOTA as a bifunctional chelator with competitive alkali metal ions: a DFT study

This work investigates NOTA–alkali metal (Li⁺, Na⁺ and K⁺ and Rb⁺) complexation using density functional theory.

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.

A Combined theoretical and experimental study of conformational and spectroscopic profile of 2-acetamido-5-aminopyridine

Present work aims at identifying the conformational and spectroscopic profile of 2-acetamido-5-aminopyridine compound by means of experimental and computational methods. To achieve this, three-dimensional potential energy scan (PES) was performed by varying the selected dihedral angles at B3LYP/6-31+G(d,p) level of theory and thus stable conformers of the title compound were determined. The most stable conformer was further optimized at higher level and vibrational wavenumbers were calculated. Experimentally, vibrational features of title compound were determined by FT-IR and FT-Raman spectroscopic methods in the solid phase while the electronic absorption spectrum was recorded in methanol solution. On the basis of these investigations, the conformational and spectroscopic attributes of 2-acetamido-5-aminopyridine were interpreted.

Vibrational studies (FTIR and Raman), conformational analysis, NBO, HOMO-LUMO and reactivity descriptors of S-methyl thiobutanoate, CH3CH2CH2C(O)SCH3

In the present article, the molecular structure of S-methyl thiobutanoate, CH3CH2CH2C(O)SCH3 was determined by ab initio (MP2) and DFT calculations using different basis sets. The infrared and Raman spectra for the liquid phase were also recorded and the bands observed were assigned to the vibrational normal modes. The experimental and calculations confirm the presence of two most stable conformers, one with pseudo anti-syn conformation and another with gauche-syn conformation. The study was completed using natural bond orbital (NBO) and AIM analysis. The molecular properties like dipole moment, molecular electrostatic potential surface (MEP) and HOMO-LUMO molecular orbitals were calculated to get a better insight of the properties of the title molecule. Global and local reactivity descriptors were computed in order to predict reactivity and reactive sites on the molecule for nucleophilic, electrophilic and radical attacks.

Spectroscopic investigation, natural bond orbital analysis, HOMO-LUMO and thermodynamic functions of 2-tert-butyl-5-methyl anisole using DFT (B3LYP) calculations

The optimized molecular structure and corresponding vibrational assignments of 2-tert-butyl-5-methyl anisole (TBMA) have been investigated using density functional theory (DFT)/B3LYP with 6-31G(d,p) and 6-311++G(d,p) basis sets investigation of the relative orientation of the methoxy group has shown two conformers (O-cis) and (O-trans) exist. The vibrational analysis of the stable conformer of the title compound is performed by means of infrared absorption and Raman spectroscopy in combination with theoretical simultaneously. The natural bond orbital (NBO) analysis is useful to understand the intra-molecular hyper conjugative interaction lone pair and π(∗)(C-C), σ(∗)(C-H) bond orbital. HOMO and LUMO energies show that charge transfer occurs in the molecule, therefore; HOMO, LUMO and molecular electrostatic potential (MEP) were calculated and analyzed. (1)H and (13)C NMR spectra by using gauge including atomic orbital (GIAO) method of studied compound were compared with experimental data. The thermodynamic functions of TBMA were calculated by B3LYP/6-311+G(d,p) basis set.