6-31G Basis Research Articles

Theoretical Study of the Structural and Electronic Properties of NIPAM Polymer Dosimetry Gel

Background: Gel dosimeters consist of two types: Frick and Polymer, with compounds that are highly reactive to radiation. Objective: The difference in energy between the Highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) was investigated. Methods: An examination of the structure of a dosimetry gel polymer of type N- sopropylacrylamide (NIPAM) was carried out with the assistance of the Gaussian 09 software, the Fourier Transform Infrared Spectrometer (FTIR), the proton and carbon nuclear magnetic resonance (H NMR-C NMR), and the ultraviolet-visible spectroscopy (UV-vis) approach were used. The molecular geometry was determined using density functional theory (DFT) (B3LYP) and computational means. Subsequently, this molecule’s vibrational frequencies and electrical characteristics were examined, with the ground state represented by the 6-31G basis. The computations of the structure, as well as the vibrational frequencies and chemical shift, demonstrated a satisfactory theoretical approximation. Results: Based on the findings, it has been shown that NIPAM has a high-water solubility and is of great assistance in the process of introducing a powerful polar amide group into a hydrophobic polymer via the use of suspension or emulsion polymerization, and strong coupling effect (interaction of magnetic fields) between the hydrogen atoms and the deformation. Conclusions: The atoms within the structure, the molecule is highly reactive, the computed results demonstrated the accuracy of the theoretical approximation despite these discrepancies.

The influence of basis sets and ansatze building to quantum computing in chemistry.

Quantum computing is an exciting area, which has grown at an astonishing rate in the last decade. It is especially promising for the computational and theoretical chemistry area. One algorithm has received a lot of attention lately, the variational quantum eigensolver (VQE). It is used to solve electronic structure problems and it is suitable to the noisy intermediate-scale quantum (NISQ) hardware. VQE calculations require ansatze and one of the most known is the unitary coupled cluster (UCC). It uses the chosen basis set to generate a quantum computing circuit which will be iteratively minimized. The present work investigates the circuit depth and the number of gates as a function of basis sets and molecular size. It has been shown that for the current quantum devices, only the smallest molecules and basis sets are tractable. The H molecule with the cc-pVTZ and aug-cc-pVTZ basis sets have circuit depths in the order of 10 to 10 gates and the C H molecule with 3-21G basis set has a circuit depth of gates. At the same time the analysis demonstrates that the H molecule with STO-3G basis set, requires at least 500 shots to reduce the error and that, although error mitigation schemes can diminish the error, they were not able to completely negate it. The quantum computing and electronic structure calculations were performed using the Qiskit package from IBM and the PySCF package, respectively. The ansatze were generated using the UCCSD method as implemented in Qiskit, using the basis sets STO-3G, 3-21G, 6-311G(d,p), def2-TZVP, cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, and aug-cc-pVTZ. The operators and the Hamiltonian were mapped using the Jordan-Wigner scheme. The classical optimizer chosen was the simultaneous perturbation stochastic approximation (SPSA). The quantum computers used were the Nairobi and Osaka, with 7 and 127 qubits respectively.

In Silico Coformer Screening for Mefenamic Acid Cocrystallization

Cocrystallization is a widely used approach to enhance the solubility and dissolution characteristics of poorly soluble drugs. A pharmaceutical cocrystal is a multicomponent system composed of a solid active pharmaceutical ingredient (API) and a coformer, governed by non-covalent interactions. Screening for suitable coformers is essential to obtain an optimal cocrystal for specific drugs. This study aims to determine the drug-coformer interactions to select the most suitable coformer for cocrystal formation using the molecular docking method. Mefenamic acid, classified as a class II drug in the biopharmaceutical classification system (BCS), was used as the model drug. Two-dimensional structures of mefenamic acid (PubChem CID: 4044) and potential coformers were sourced from PubChem. Geometric optimization of all compounds was performed using GaussView 5.0.8 and Gaussian09 with the 3-21G basis set and Density Functional Theory (DFT) B3LYP method. The optimized compounds were prepared by adding hydrogen atoms and calculating Kollman partial charges using AutoDock 4.2. A grid box of size 40 Å × 40 Å × 40 Å was generated, with a maximum radius of 0.375 Å set as the surface distance in each simulation. A hundred conformations were run using the Lamarckian Genetic Algorithm. Interaction types and binding energies were analyzed using VMD 1.9.2 and BIOVIA Discovery Studio 2020 to compare interactions between mefenamic acid and each coformer. The results revealed that most coformer compounds formed interactions with mefenamic acid via hydrogen bonding and π–interactions. Saccharin demonstrated the most optimal interaction with mefenamic acid, with a binding free energy of –3.1 kcal/mol. Saccharin was identified as the most suitable coformer for mefenamic acid cocrystal formation based on the molecular docking study. Further experimental validation of saccharin is recommended to confirm its effectiveness in cocrystallization with mefenamic acid.

Band Gap Energy of Periodic Anatase TiO2 System Evaluated with the B2PLYP Double Hybrid Functional

The electronic properties of anatase titanium dioxide (TiO2) materials are of paramount importance for photocatalytic application. Ab initio calculation is performed on anatase TiO2 with various cluster sizes and shape, using Gaussian 09 program employing the standard 6-311G(d) and 3-21G basis set. Hartree-Fock (HF) theory, exchange-functional of density functional theory including hybrid (B3LYP, B3PW91, PBE1PBE and PBEh1PBE) and double-hybrid (B2PLYP), together with 2nd order Møller-Plesset perturbation theory are used to predict the band gap energy of anatase TiO2. With the inclusion of long-range HF exchange, double hybrid B2PLYP functional is able to predict band gap energy value (3.06 eV) which as compared to the experimental value (3.20 eV). Besides, this double hybrid exchange-correlation functional shows good compromise by obtaining an accurate description for cohesive energy of anatase TiO2. Thus, double-hybrid B2PLYP functional is suggested to be a practical choice for predicting the electronic properties for anatase TiO2.

Study of A Ferroelectric Liquid Crystal Mesogen by Geometrical Optimization and Electro-Optic Characterization

In the present work one biphenyl benzoate cored liquid crystal was characterized using geometrical optimization and electro-optic study. Geometry of the molecule was optimized using Hartree-Fock method with 3-21G basis. The simulated value of molecular length and dipole moment was reported. The Infrared (IR) spectra were also simulated and analyzed. The energy gap between highest occupied molecular orbit (HOMO) and lowest unoccupied molecular orbit (LUMO) was calculated. The phase transition temperatures and phase sequences were identified by observing the topological defects in the optical textures at different temperatures under polarizing microscope. It exhibited ferroelectric smectics C* (SmC*) phase for a wide range of temperature and then directly melted into isotropic phase. The optical tilt angle of the compound was measured in SmC* phase and was fitted with mean field model to explore the nature of phase transition. The applicability of the compound for display applications were judged based on the parameters measured.

Combined Experimental and Theoretical Insights: Spectroscopic and Molecular Investigation of Polyphenols from Fagonia indica via DFT, UV-vis, and FT-IR Approaches.

This review deals with computational study of polyphenolic compounds of medicinal importance and interest for drug development. Herein, four polyphenolic compounds comprising catechol (1), caffeic acid (II), gallic acid (III), and pyrogallol (IV) have been isolated from a medicinal specie, Fagonia indica, by applying silica gel column chromatography. These compounds were identified by using gas chromatography-mass spectrometry (GC-MS) analysis and confirmed by geometric computational analysis. According to computational results, caffeic acid has shown the highest biological activation due to higher chemical softness, electronegativity (χ (eV) = -648.644), and electrostatic potential value (-8.424 × 10-2 to +8.424 × 10-2), while smaller values of chemical potential (-0.269), ELUMO (-0.080), and energy gap (ΔE = 0.149). The Mulliken atomic charges were calculated by using DFT/B3LYP with basis set 6-311G for the determination of active sites. The oxygen atom of catechol showed highest nucleophilic characteristic with a more negative charge (08 = -0.695), and pyrogallol indicated a strong electrophilic center at C14 = 0.415 with a higher positive charge. Moreover, UV-visible absorption spectra and a detailed study of vibrational frequencies for all phenolic compounds by employing the DFT approach with 3-21G, 6-31G, and 6-311G basis sets at the ground-state level showed the great agreement with experimental results. ANOVA has been applied to validate the theoretical data. Results suggest that compounds I-IV are suitable in diverse fields.

DFT Study of a Series of Nicotinic Acid Benzylidenehydrazide Derivatives: Structure, Stability and Reactivity

Hydrazones especially nicotinic acid benzylidenehydrazide derivatives constitute an important class of compounds that has received much interest in recent years, due to their diverse biological characteristics, such as antimicrobial, anticonvulsant, analgesic, anti-inflammatory, antiplatelet, antituberculous and antitumor activities. These compounds have donor sites such as N and O which have non-bonding doublets which allow them to coordinate with metal ions. For this purpose, ten hydrazones structures were optimized in the DFT method, using the B3LYP functional, with the basis 6-31G** for all atoms, in the gas phase using the Gaussian 09 program. The structural, energetic (energies, EHOMO-LUMO gaps), electronic (dipolar moments, atomic charges) parameters were determined. A study of the stability of the ligands was carried out based on the relative energies to study the chemical reactivity of the optimized structures, we calculated the global reactivity parameters (ionization potential, electronic affinity, electronic chemical potential, absolute hardness, overall softness and overall electrophilicity). The results obtained show that All the systems considered are stabilized by two types of electronic effect. Either; an inductive attractor effect, with a coexistence of mesomeric effects. Analysis of chemical hardness values indicates that the most stable isomers found are the hardest, with larger HOMO/LUMO gaps, and therefore less reactive. As a result, charge transfer will be predominant. The most nucleophilic systems are also determined based on the calculation of the eletrophicity and nucleophilicity indices.

Investigation of thermoelectric properties of cadmium selenide CdnSen (n= 7, 11, 13) molecular junctions: a DFT study.

The thermoelectric properties of cadmium selenide (CdnSen) molecular junctions (n = 7, 11, 13) were investigated before and after adding hydrogen atoms. The effects of hydrogen passivation on the transmission and thermopower curves were analyzed. CdSe-diamantane (Cd7Se7) and CdSe-tetramantane (Cd11Se11) junctions exhibited the best thermoelectric performance due to their low surface reconstruction energy, which is attributed to the number of dangling and unsaturated bonds. This study guides the design of new molecular junctions with desired thermoelectric properties. The electrical and thermal properties of cadmium selenide (CdnSen) molecular junctions (n = 7, 11, 13) were investigated using a ballistic quantum transport method based on the non-equilibrium Green's function (NEGF) approach. Thermoelectric properties were calculated for the molecular junctions with different structures before and after hydrogen passivation. Density functional theory (DFT) calculations were performed at the B3LYP level with the 3-21G basis set for the Cd atoms and the 6-31G** basis set for the Se atoms. The SIESTA and GOLLUM codes were used to study the effect of changing the shape and size of each structure on its electrical and thermal characteristics.

Density Functional Theory Calculations of Electronic Properties ,IR and UV-Vis Spectrum , Dipoles Moments ,and Atomic Charge Distribution of Mg 1-X Zn XFe2O4 Ferrite

Theoretical study using (Density Functional Theory) DFT method with B3LYP functional and the 3-21G(d,p) basis set had been implemented of calculating molecular structure properties of Magnesium – Zinc spinel ferrite having the chemical formula (Mg1-xZnxFe2O4). DFT had been used to optimize molecular structure, electronic state (HOMO-LUMO) , and electronic properties ( ionization potential, electronegativity, electron affinity, electrophilic, hardness, and softness) are calculated. Theoretical electronic IR spectrum were computed and plotted . UV-Vis spectrum calculated and plotted of this molecule. Dipole, Quadrupole, and Traceless Quadrupole moments were calculated. The Mullikan and Natural Bond Orbital (NBO) distribution of Mg1-xZnxFe2O4 compound are also computed by DFT. All these properties had been calculated using Gaussian09 program with Gauss view 5.08 program by using (Density Functional Theory) DFT method with 3-21G(d,p) basis set.

STUDYING DFT ANALYSIS OF VARIOUS FORMS OF GLUTAMINE

This paper presents the results of DFTanalysis and electron-structural and coordination properties, boundary molecular orbitals and descriptors of global reactivity of various forms of glutamine, using quantum-chemical calculation.For glutamine, the MEP was calculated using the DFT/B3LYP program, the basis 6-311G++(d,p) and the surface of the molecular electrostatic potential was constructed

ИЗУЧЕНИЕ DFT АНАЛИЗА РАЗЛИЧНЫХ ФОРМ ГЛЮТАМИНА

В данной работе приведены результаты DFT анализа и электронно-структурных и координационных свойств, граничные молекулярные орбитали и дескрипторы глобальной реактивности различных форм глютамина, с применением кватово-химического расчета. Для глутамина МЭП был рассчитан с помощью программы DFT/B3LYP базис 6-311G++(d,p) и построена поверхность молекулярного электростатистического потенциала.

Functionality of Covalent Organic Framework (COF) in Gas Storage Application: First Principal Study

Industrial growth in recent years led to air pollution and an increase in concentration of hazardous gases such as O3 and NO. Developing new materials is important to detect and reduce air pollutants. While catalytic decomposition and zeolites are traditional ways used to reduce the amount of these gases. We need to develop and explore new promising materials. Covalent organic framework (COF) has become an attractive platform for researcher due to its extended robust covalent bonds, porosity, and crystallinity. In this study, first principal calculations were performed for gases adsorption using COFs containing nitrogen and π-bonds. Different building blocks (BBs) and linkers (LINKs/LINK1 & LINK2) were investigated by means of density functional theory (DFT) calculations with B3LYP and 3-21G basis sets to calculate the binding energies of gases @COF systems. Electrostatic potential maps (ESPM), Mulliken charges and non-covalent interaction (NCI) are used to understand the type of interactions between gas and COFs fragments. O3 was found to bind strongly with COF system in comparison with NO which could make COF a useful selective material for mixed gases environment for sensing and removal application.

Density Functional Theory Investigation For Ni6, Co5, Au12, Y5 and Ni6Li, Co5Li, Au12Li, Y5Na Interactions

Geometry optimization for pure transition metals structures Ni6 , Co5 , Au12 , Y5 and alkali-transition metals structures Ni6Li , Co5Li , Au12Li , Y5Na at B3LYP level, 3-21G and LaNL2DZ basis sets has been investigated by using Density Functional Theory (DFT) throughout Gaussian09 package. Electrostatic potential,contours, infrared spectra, symmetry, energy gap has been studied for all structures. Total energy for pure transition metals structures is greater than the total energy for alkali-transition metals structures, One can say that the orbitals that generate between Lithium and atoms of pure Nickel structure will be from anti-bonding type. Dipole moment for some pure Nickel structure has zero value because it is homostructure, the other pure transition structures has nonzero values although they are homostructures this is result because of the geometry structures, but the dipole moment for all alkali-transition structures has nonzero numerical values because it is hetrostructures. Energy gap for Y5Na is the smallest value of energy gaps of the structures under study, it approaches to the energy gap of GaAs, this property is very useful in electronic applications such as manufacturing of processors of laptops, Eg of Y5Na = 0.95 eV, Eg of GaAs = 0.8 eV.

Structural, Characterization, Biological Activity, and DFT Studies on some Novel Ruthenium 2-Aminomethyl Benzimidazole Complexes

Novel 2-aminomethyl benzimidazole (AMBI) ruthenium complexes were synthesized and thoroughly characterized by elemental analysis, spectroscopy (FTIR, 1HNMR, UV–Vis), magnetic measurements, molar conductivity, and thermal analysis techniques. According to analytical data, all complexes demonstrated a 1:1 metal-to-ligand ratio with an octahedral shape. Thermal analysis showed that the complexes have acceptable thermal stability. Cyclic voltammetry was also used to observe their redox actions, and it was found that all of the complexes had electrochemical activity. Using GAUSSIAN 09 W software, the density functional theory (DFT) method and the 3-21G basis set, optimized structures (HOMO & LUMO) of ruthenium complexes (1-4) were carried out. Additionally, the selected quantum and geometric parameters of bond lengths and angles have been determined. The antimicrobial activity of ligand and ruthenium complexes has been evaluated against bacteria (Escherichia coli, Staphylococcus aureus) and fungi (Candida albicans). Two human cancers, HePG-2(hepatocellular carcinoma) and MCF-7 (Michigan Cancer Foundation-7), were tested for cytotoxic activity of complexes. Using the ABTS technique, the antioxidant function of complexes was evaluated. Using a high-affinity Fab sandwich and a specific PCa antibody, molecular docking was utilized to anticipate how the ligand would bind to a human prostate-specific antigen (PSA) immune system receptor (3qum).

Synthesis, Characterization, Biological Activities and Ab-initio Study of Transition Metal Complexes of [Methyl 2-((4-chlorophenyl)(hydroxy)methyle) Acrylate

Taking cognizance of the medicinal significance and diverse functions of synthetic Morita-Baylis-Hillman adducts (MBHA), the title ligand was synthesized and purified through column chromatography. Cr+3, Mn+2, Co+3, Ni+2, Cu+2 complexes of the ligand were synthesized under basic conditions, subjected to characterization through spectral analyses and verified with the IR spectrum that was generated computationally by the DFT B3LYP method, with 6-311++ G (d,p) basis set and Hartree Fock (HF) B3LYP method in conjunction with 3-21G(d,p) basis set. Powder XRD helped to testify crystals of the complexes. Moreover, the antibacterial, and antioxidant characteristics of MBHA and its complexes were also established. All of them were found to be active antioxidants. The antibacterial activities, examined against S. aureus, E. coli, B. pumilis and S. typhi have revealed that its Cobalt complex has an excellent potential to act against all of them. Hence, these compounds maybe having potentialities for the discovery of new, cheaper and efficient drugs against various infectious diseases. The study also uncovers the first example of utilization of MBHA towards metal complex formation.

Reactivity of 4,5-Dichlorophthalic Anhydride towards Thiosemicarbazide and Amines: Synthesis, Spectroscopic Analysis, and DFT Study.

The cyclic anhydrides are broadly employed in several fields, such as the chemical, plastic, agrochemical, and pharmaceutical industries. This study describes the chemical reactivity of 4,5-dichlorophthalic anhydride towards several nucleophiles, including thiosemicarbazide and different amines, to produce the carboxylic acid derivatives resulting from anhydride’s opening, namely, phthalimide and dicarboxylic acid (1–12) products. Their chemical structures are confirmed by NMR, IR and MS spectra analyses. Density–functional theory (DFT) studies are performed using (DFT/B3LYP) with the 6-311G(d, p) basis sets to recognize different chemical and physical features of the target compounds.

Robustness of hydrogen bonding in the construction of supramolecular architectures in protonated perchlorate salts

Five new multicomponent salts of perchloric acid with a series of substituted anilines and N-heterocyclic amines namely Diphenylaminium perchlorate (DPAPC) (1), 2, 5-dichloroanilinium perchlorate (25DAP) hydrate (2), 4-Methylanilinium perchlorate (4MAPC) (3), 4-diamino-6-methyl-1, 3, 5-triazin-1-ium hydrogen perchlorate (24DAMTHP) (4), and 8-hydroxyquinolinium hydrogen perchlorate (8HQP) (5) were prepared and structurally characterized. The entire complexes were subjected to FTIR and elemental analysis. A vast family of intermolecular contacts N-H…O, O-H…O, N-H…N, and C-H…O was observed, which are key ingredient in the generation of privileged supramolecular self-assemblies appeared as one-dimensional chain, two-dimensional ladder, and helix. Cambridge Structural Database (CSD) analysis of 52 hits revealed the perchloric acid display higher propensity of ladder architectures. Molecular stability of the complexes was studied by quantum chemical calculations using DFT/B3LYP method with 6-31G(d,p) basis set. Furthermore, their relative charge distributions were identified using molecular electrostatic potential map. The use of Hirshfeld surfaces in combination with fingerprint plots was visualized in order to study the closer contacts within the molecule. The relative contribution of the whole percentage of interactions associated is highlighted.

Fourier transform infrared and Raman spectra of the complex cation diethyldithiocarbamate Cr(III) Di-hydrate, [Cr(DDTC)2(OH2)2]+. UV-Vis spectrum, DFT:B3LYP/6-311G(d, p) structural determination, vibrational and natural bond orbital analysis

Diethyldithiocarbamate Cr(III) di-hydrate, [Cr(DDTC)2(OH2)2]+ was synthesized and the analysis of its structure was performed. The calculations as well as its infrared and Raman spectra interpretation were based on the DFT/B3LYP method. The vibrational spectra show a blue shift of the bands in the high energy region (C-H stretching of the -CH3 and -CH2 groups), a result corroborated by the calculated spectra. Besides, the blue shift of the C-H bands of the CH3 and CH2 groups of the complex was interpreted by means of the intermediate hybridization between the sp3 and sp2 orbitals of the carbon atoms whose bonds increased the force constants, shifting the position of the CH bands to the blue. The geometry of the complex produced wave numbers with excellent agreement with the experimental ones, thus indicating that the proposed geometry is correct. Electronic transitions spin allowed (ν1, ν2 and ν3) according to the time-dependent process using the B3LYP functional with basis 6-311G(d,p), and according to the TS diagram they were assigned as: ν12T1g(G)←4A2g (Bu), ν24T2g(F)←4A2g(Ag). ν34T1g(F)←4A2g(Ag). The agreement between the two procedures that led to the assignment was excellent. Natural bond orbital analysis was also carried out as a way to find the hybridization of the carbon atoms of the –CH3 and –CH2 groups. Koopmans’ energy (eV), Mulliken population analysis and assignment for the frontier orbitals of [Cr(DDTC)2 (OH2)2]+, with the B3LYP method, were also performed.

Hirshfeld surface analysis and quantum chemical study of molecular structure of phosphate

ABSTRACT. In this present study, Density fuctional theoretical computations are performed at (B3LYP, PBEPBE), HF and MP2 level with 3-21G basis sets to derive optimized geometry and bonding features. The calculated geometrical parameters have been compared with experimental data. The intermolecular O–H…O and N–H…O hydrogen bonds are involved in crystal structure stabilization. An intramolecular O–H…N hydrogen bond is observed between the phosphate OH group and the N atom. Further, the molecular Hirshfeld surface analysis was carried out to reveal the nature of intermolecular contacts and the fingerprint plot provides the information about the percentage contribution and reveals that the O…H (44.1%) interactions have the major contribution to form the crystal. The Mulliken population analysis and the HOMO-LUMO energy gaps show that the molecule has a good stability and from the calculation, we conclude that the molecule is really hard materials.
 
 KEY WORDS: Energy gaps, Hydrogen bonds, Hirshfeld surface, Mulliken population, Phosphate
 
 Bull. Chem. Soc. Ethiop. 2021, 35(3), 625-638.
 DOI: https://dx.doi.org/10.4314/bcse.v35i3.13

Exploring Molecular and Electronic Property Predictions of Reduced Graphene Oxide Nanoflakes via Density Functional Theory.

In this research, we perform a theoretical interpretation of molecular and electronic properties of reduced graphene oxide (rGO) nanoflakes through the density functional theory. Here, two pristine graphene nanoflake systems were passivated by hydrogen atoms at their edges, armchair (C58H20) and zigzag (C54H20); besides, we implemented 12 rGO systems with a range of low oxide coverage (1, 3, and 4%). Computational calculations were carried out employing the functional hybrid B3LYP and the basis 6-31G(d, p) and 6-311G(d, p) levels of theory. We brought the proposed molecular structures to a stable minimum. We determined the global reactivity descriptors through chemical potential, hardness, softness, and index of electrophilicity. Besides, the maps of electrostatic potential were generated. We found that the hydroxyl and epoxy functional groups dope the graphene molecule in p-type and n-type forms, respectively. In addition, we could attribute the increases of the oxide coverage and the chemical potential to the softness of the molecule. These results suggest that structures with this type of doping can help in developing advanced electronics of sensors and devices.