Investigation of spectroscopic studies and DFT calculations on glucofuranose derivatives of dithiophosphonates

Abstract

2,4-Bis(4-methoxyphenyl)-1,3,2,4-dithiadiphosphetane-2,4-disulfide (Lawesson’s reagent: LR) was reacted with 1,2:5,6-di-O-cyclohexylidene-α-D-glucofuranose and 1,2:5,6-di-O-isopropylidene-α-D-glucofuranose in toluene and gave rise to crude dithiophosphonic acids. The crude dithiophosphonic acids were treated with excess triethylamine and the triethylammonium salts of dithiophosphonic acids (1) and (2) were isolated by crystallization method. Compounds 1 and 2 were characterized by elemental analysis, IR, and NMR (¹H-, ¹³C- and ³¹P-) spectroscopies and mass spectrometry. In addition, NMR spectra, the electronic properties (the electronic chemical potential, electronegativity, chemical hardness and the global electrophilicity index) and NBO analysis of compound 2 have been calculated by using the Gaussian 16?W program. The electronic properties were calculated using Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO) energies by density functional method (DFT/B3LYP) at 6-31G(d,p) level. The HOMO and LUMO energies are ?5.9 and ?0.72?eV, respectively. The HOMO–LUMO energy difference is 5.18?eV and this value shows that compound 2 has a high stability and low reactivity.     

Quantum parameters based study of some heterocycles using density functional theory method: A comparative theoretical study

Density functional theory can envisage a vast assortment of molecular possessions such as molecular structures, vibrational frequencies, molecular energies, ionization energies, polar, electric and magnetic properties etc. The efficacy of this method relies on the study of electronic parameters to categorize the reactive sites to comprehend the plausible action of these scaffolds. Further it also facilitates the correlation between the structural characteristics of drug and their inhibition efficiency against infectious microorganisms. In light of the above facts, we have studied the structural parameters such as energy (total), variation of electron density over highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO), charge distribution, absolute electronegativity (χ), softness/hardness (σ/ɳ) and fraction of electron transfer (ΔN) of some previously synthesized heterocycles.     

Theoretical and experimental investigations of complexation with BF3.Et2O effects on electronic structures,energies and photophysical properties of Anil and tetraphenyl (hydroxyl) imidazol

The novel compounds (E)‐2‐(((4‐hydroxyphenyl)imino)methyl)phenol, Tetraphenyl (hydroxyl) imidazole and their corresponding Boron difluoride complexes were synthesized and characterized by spectroscopic techniques. Density functional theory calculations at B3LYP‐D3/6–311++G (d, p) level of theory were performed for the geometric parameters. The MEP surface studies were used to understand the behavior of molecules in terms of charge transfer and to determine how these molecules interact. We used the GIAO and the B3LYP‐D3 with a 6–311++ G (d, p) basis set to simulate the (¹H‐NMR and ¹⁹F‐NMR) and the IR spectra, respectively. The corresponding calculated results are in good agreement with the experimental data. The stability of the molecule arising from hyperconjugation interaction and charge delocalization were analyzed using NBO analysis. FMOs revealed the occurrence of charge transfer within the molecule. The complexation using BF₃.Et₂O was also found to have remarkable effects on the electrochemical properties of the studied molecules, where (b) and (d) present lower chemical stability, higher reactivity and higher polarizability than (a) and (c), respectively. Moreover, the energy gap of (a) and (c) decreased after complexation using BF₃.Et₂O, indicating the reliability of the electrochemical evaluation of LUMO and HOMO energy levels. These values are the factors explaining the possible charge transfer interaction within the molecule. The absorption and emission spectra of the model compound were also simulated and compared to experimental observations in the DMF solvent. The results of DFT calculations supported the structural and spectroscopic data and confirmed the structure modification of frontier molecular orbitals for BF₂ complexes as well as tunable potentials and energy levels.     

Electronic structure and quantum chemical analysis of the corrosion inhibition efficiency of quinoxalines

A theoretical investigation of the corrosion inhibition effectiveness of 1-[4-acetyl-2-(4-chlorophenyl) quinoxalin-1(4H)-yl] acetone (Q1), 2-(4-(2-ethoxy-2-oxoethyl)-2-p-tolylquinoxalin-1(4H)-yl) acetate (Q2) and 2-(4-methylphenyl)-1,4-dihydroquinoxaline (Q3) was evaluated by using quantum chemical parameters from density functional theory (DFT) with 6–311++ G (d, p) basis set at B3LYP level. Several quantum chemical parameters were determined to evaluate the array of selected molecules such as (E_LUMO), energy gap (ΔE), (E_HOMO), hardness, ionization potential, electronegativity, dipole moment (μ), the fraction of the electrons transferred from the inhibitor to the metal surface (ΔN), the softness (σ) and the total energy (TE). Theoretical data were found to confirm experimental results. By using these different quantitative chemical parameters to determine corrosion inhibition efficiency, we compare the results of the recent corrosion investigation of these inhibitors.     

Quantum chemical studies on para-substituted styrenyl fullerene. Study of substitution effects on structural and electronic properties

Quantum chemical investigations on para-substituted styrenyl fullerene derivatives with substituents linked to para position of styrenyl group have been carried out. The density functional theory (DFT) have been used in this study with B3LYP functional and the modest 3-21G* basis sets. The substituents were variable donating and withdrawing to study the effect of such structural change on the structural and electronic properties of the studied molecules.     

Theoretical and experimental studies on solubility and reactivity behavior of lysergol,elymoclavine, and dihydrolysergol

Lysergol, elymoclavine (Δ^9,10 and Δ^8,9 regioisomers), and dihydrolysergol are important members of ergolines. The present work reports their comparative study in gas and solvent phase (water) that has been performed both experimentally and theoretically. Theortical calculations have been carried within the density functional theory formalism to analyze the structural and electronic properties of these molecules with B3LYP hybrid exchange–correlational fuctional in conjunction with 6‐311++G (d,p) basis set. Hessian calculations are performed at B3LYP/6‐31G (d,p) level of theory in gas phase as well as other solvent phases. Solvent phase calculations are performed using Onsager reaction field model as implemented in Gaussian 03. A good agreement has been found between experimental and theoretical infrared and nuclear magnetic resonance (NMR) spectra. The calculated NMR data has been analyzed statistically. Stability of these regioisomers has been analyzed in terms of the energy gap between highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO–LUMO gap). Calculations for lysergol and elymoclavine in water as solvent were carried to examine the effect of solvent on the HOMO–LUMO levels and energy of these molecules. © 2012 Wiley Periodicals, Inc.     

Structural, electronic, and optical properties of 9-heterofluorenes: a quantum chemical study

Density-functional theory studies were applied to investigate the structural, electronic, and optical properties of 9-heterofluorenes achieved by substituting the carbon at 9 position of fluorene with silicon, germanium, nitrogen, phosphor, oxygen, sulfur, selenium, or boron. These heterofluorenes and their oligomers up to pentamers are highly aromatic and electrooptically active. The alkyl and aryl substituents of the heteroatom have limited influence, but the oxidation of the atom has significant influence on their molecular structures and properties. The highest occupied molecular orbital (HOMO)-lowest occupied molecular orbital (LUMO) interaction theory was successfully applied to analyze the energy levels and the frontier wave functions of these heterofluorenes. Most heterofluorenes belong to type B of interaction with low-lying LUMO and have the second kind of wave function. Carbazole and selenafluorene have type C of interaction with high-lying HOMO and the third kind of wave function. Types C and D of heterofluorenes, such as carbazole, oxygafluorene, sulfurafluorene, and selenafluorene also have high triplet state energies. The extrapolated HOMO and LUMO for polyheterofluorenes indicate that polyselenonafluorene has the lowest LUMO; polycarbazole has the highest HOMO; polyselenafluorene has the highest bandgap (E(g)); and polyborafluorene has the lowest E(g). Heterofluorenes and their oligomers and polymers are of great experimental interests, especially those having extraordinary properties revealed in this study.     

Conformational and structural study of N-nicotinyl N′, N″-bis(diisobutyl amine)phosphoric triamide

Single crystals of C5H4NC(O)NHP(O)[N(i-C4H9)2]2 were prepared and investigated by X-ray crystallography. Interestingly, four symmetrically independent conformers were detected in the structure of this compound by X-ray crystallography. The greatest difference in these conformers was different torsion angles. In all conformers, the phosphoryl and carbonyl groups showed anti-configurations, and the two terminal CH3 groups of each alkyl chain in amine parts have different spatial orientations due to their connection to a prochiral carbon atom. The diastereotopic protons of every CH2 moiety in amine groups also have different spatial orientations. Every conformer forms a centrosymmetric dimer with its own symmetrically generated analog via a hydrogen bond. The first conformer connects to others (A, B, and C) via electrostatic interactions and forms a tetramer. All hydrogen bonds and electrostatic interactions result in the formation of a three-dimensional polymeric network in the crystalline lattice of compound. To find the most stable conformer, density functional theory (DFT) calculations were performed. The computationally optimized geometric parameters are in good agreement with the experimental results. According to DFT calculations, B is the most stable conformer with energy of ?987714.07 kcal/mol. In all conformers the electron density of HOMO is localized on P=O and C=O oxygen atoms and some parts of amine groups, while LUMO is localized on the nicotinamide part of the molecule.     

Investigation of the New Inhibitors by Sulfadiazine and Modified Derivatives of α-D-glucopyranoside for White Spot Syndrome Virus Disease of Shrimp by In Silico: Quantum Calculations,Molecular Docking,ADMET and Molecular Dynamics Study

The α-D-glucopyranoside and its derivatives were as the cardinal investigation for developing an effective medication to treat the highest deadly white spot syndrome virus (WSSV) diseases in Shrimp. In our forthcoming work, both computational tools, such as molecular docking, quantum calculations, pharmaceutical kinetics, ADMET, and their molecular dynamics, as well as the experimental trial against WSSV, were executed to develop novel inhibitors. In the beginning, molecular docking was carried out to determine inhibitors of the four targeted proteins of WSSV (PDB ID: 2ED6, 2GJ2, 2GJI, and 2EDM), and to determine the binding energies and interactions of ligands and proteins after docking. The range of binding affinity was found to be between −5.40 and −7.00 kcal/mol for the protein 2DEM, from −5.10 to 6.90 kcal/mol for the protein 2GJ2, from −4.70 to −6.2 kcal/mol against 2GJI, and from −5.5 kcal/mol to −6.6 kcal/mol for the evolved protein 2ED6 whereas the L01 and L03 display the highest binding energy in the protein 2EDM. After that, the top-ranked compounds (L01, L02, L03, L04, and L05), based on their high binding energies, were tested for molecular dynamics (MD) simulations of 100 ns to verify the docking validation and stability of the docked complex by calculating the root mean square deviation (RMSD) and root mean square fluctuation (RMSF). The molecules with the highest binding energy were then picked and compared to the standard drugs that were been applied to fish experimentally to evaluate the treatment at various doses. Consequently, approximately 40–45% cure rate was obtained by applying the dose of oxytetracycline (OTC) 50% with vitamin C with the 10.0 g/kg feed for 10 days. These drugs (L09 to L12) have also been executed for molecular docking to compare with α-D-glucopyranoside and its derivatives (L01 to L08). Next, the evaluation of pharmacokinetic parameters, such as drug-likeness and Lipinski’s principles; absorption; distribution; metabolism; excretion; and toxicity (ADMET) factors, were employed gradually to further evaluate their suitability as inhibitors. It was discovered that all ligands (L01 to L12) were devoid of hepatotoxicity, and the AMES toxicity excluded L05. Additionally, all of the compounds convey a significant aqueous solubility and cannot permeate the blood-brain barrier. Moreover, quantum calculations based on density functional theory (DFT) provide the most solid evidence and testimony regarding their chemical stability, chemical reactivity, biological relevance, reactive nature and specific part of reactivity. The computational and virtual screenings for in silico study reveals that these chosen compounds (L01 to L08) have conducted the inhibitory effect to convey as a possible medication against the WSSV than existing drugs (L09, L10, L11 and L12) in the market. Next the drugs (L09, L10, L11 and L12) have been used in trials.     

A computational investigation on core-expanded subphthalocyanines

Subazaphenalenephthalocyanines are the derivatives of boron subphthalocyanine chloride with a core-expanded six-membered ring, which have a wide absorption range in the visible region and seem to have great potential to be new photo-electro materials. However, it is still an open question how the core expansion influences the electronic and optical properties of boron subphthalocyanine chloride. In the present work, three subazaphenalenephthalocyanine molecules, having one, two, and three six-membered rings, are explored by using density functional theory. The relaxation energy, electronic structures, UV-Vis spectra, and exciton binding energy of three molecules are calculated, and the open circuit voltages of subazaphenalenephthalocyanine/C60 solar cells are roughly predicted using an empirical equation. The results show that the planarity, the wavelength of absorption peaks, and HOMO energy increase gradually along with the increasing number of expanded rings, while the trends of open circuit voltage and relaxation energy are opposite. We find that the subazaphenalenephthalocyanine molecule with three six-membered rings seems to have great potential to be a new donor material of organic solar cell because it has the smallest exciton binding energy and relaxation energy, and strong absorption strength in the visible region.     

Molecular structure, vibrational spectra and HOMO, LUMO analysis of yohimbine hydrochloride by density functional theory and ab initio Hartree-Fock calculations

Yohimbine hydrochloride (YHCl) is an aphrodisiac and promoted for erectile dysfunction, weight loss and depression. The optimized geometry, total energy, potential energy surface and vibrational wavenumbers of yohimbine hydrochloride have been determined using ab initio, Hartree–Fock (HF) and density functional theory (DFT/B3LYP) method with 6-311++G(d,p) basis set. A complete vibrational assignment is provided for the observed Raman and IR spectra of YHCl. The UV absorption spectrum was examined in ethanol solvent and compared with the calculated one in gas phase as well as in solvent environment (polarizable continuum model, PCM) using TD-DFT/6-31G basis set. These methods are proposed as a tool to be applied in the structural characterization of YHCl. The calculated highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) with frontier orbital gap are presented.     

2|4-二氯-5-硝基嘧啶甲胺化的ab initio研究

2，4-二氯-5-硝基嘧啶的甲胺化反应是制备鸟嘌呤衍生物中间体的重要反应[1]，实验发现该反应主要有三种产物：究竟哪种产物占优势？主要由反应物（Ⅰ）和甲胺分子的电子结构性质决定，本文对反应物（Ⅰ）和甲胺的电子结构性质进行了abinitio研究．采用RHF能量梯度法，在DZ基组水平上对反应物（Ⅰ）和甲胺分子进行全分子几何优化，梯度模收敛指标控制为0刀003·对得到的平衡几何进行市居数分析和静电势研究．计算采用Tulbomole程序［到在SGI图形工作站上完成．反应物（I）分子的平衡几何如图1所示．从优化后的结构可知，硝基和南吠环不在…     

Molecular structure, spectroscopic studies and first-order molecular hyperpolarizabilities of ferulic acid by density functional study

Quantum chemical calculations of energies, geometrical structure and vibrational wavenumbers of ferulic acid (FA) (4-hydroxy-3-methoxycinnamic acid) were carried out by using density functional (DFT/B3LYP/BLYP) method with 6-31G(d,p) as basis set. The optimized geometrical parameters obtained by DFT calculations are in good agreement with single crystal XRD data. The vibrational spectral data obtained from solid phase FT-IR and FT-Raman spectra are assigned based on the results of the theoretical calculations. The observed spectra are found to be in good agreement with calculated values. The electric dipole moment (μ) and the first hyperpolarizability (β) values of the investigated molecule have been computed using ab initio quantum mechanical calculations. The calculation results also show that the FA molecule might have microscopic nonlinear optical (NLO) behavior with non-zero values. A detailed interpretation of the infrared and Raman spectra of FA was also reported. The energy and oscillator strength calculated by time-dependent density functional theory (TD-DFT) results complements with the experimental findings. The calculated HOMO and LUMO energies shows that charge transfer occur within the molecule. The theoretical FT-IR and FT-Raman spectra for the title molecule have been constructed.     

Stability,Spectroscopic Investigation (Experimental and Theoretical), Electronic,and Molecular Docking of Anesthetic Agent: Propofol

In this paper, a complete quantum chemical study of propofol molecule has been done by using DFT-B3LYP/6-311G (d, p) method. The equilibrium geometry, HOMO–LUMO gap, NBO calculation, and DOS have been studied with the help of density functional theory (DFT) employing 6–311G (d, p) as the basis set. A good correlation is observed between experimental and calculated vibrational frequencies. Its molecular docking with 1B4N receptor shows that propofol can bind and inhibit the receptor enzymes therefore can act as an effective drug. NLO calculation shows that the molecule is good non-linear optical candidate in future due to its more ICT moment of π–electron. Study shows that title molecule binds well with 1B4N protein.     

A DFT study of determination of the reactive sites of the acetylcholine and its agonists: In the gas phase and dielectric medium

The reactive behavior of acetylcholine and its agonist molecules have been investigated using B3LYP hybrid density functional method at the 6‐311++G** basis set level, in the gas phase and aqueous phase. The calculations have been performed to obtain optimized geometries, relative reactivities, net atomic charges, HOMO, and LUMO energies. The solvent effect has been analyzed by using the continuum model (IPCM) and, the obtained results have shown that the all molecules have been stabilized more by solvent dielectric constant. For Ach and its analogues, it has been very well known that esteratic site and quaternary ammonium group which have reflected the difference in biological activity have been the two of the most important active site for interactions between molecule and its receptor. The structures of these analogues have provided an essential foundation for subsequent structure‐activity analysis of ligand binding at acetylcholine receptors, neuronal uptake inhibitors and transporters. Molecular modeling predictions will be important initial steps toward the development of novel pharmaceuticals in the fight acetylcholine‐related neurological disorders. This work is therefore expected to facilitate the design and development of new biologically active Ach analogues to treat Ach‐related neurological disorders and, specially is used to qualitative understanding of the reactivity and related properties and, so on can be used to a preselection of new ligands which at the moment is taken essentially from empirical knowledge. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Effect of Frontier Orbital on Aggregation Behavior of Barbituric Acid Derivatives

IntroductionA greatdeal of organic compounds with a D-π-A structure have been synthesized and theirphotophysical and photochemical properties havebeen extensively studied due to their potentialapplication in nonlinear optics,opto- electricalconversion and light- harvesting systems etc[1,2 ] .Tofabricate useful devices,itis necessary to assemblethose functional molecules into the organizedsupramolecular assemblies[3— 5] . Barbituric acidderivatives have been widely employed to fabricatenanos…     

A combined semiempirical-DFT study of oligomers within the finite-chain approximation, evolution from oligomers to polymers

A computationally cheap approach combining time-independent density functional theory (TIDFT) and semiempirical methods with an appropriate extrapolation procedure is proposed to accurately estimate geometrical and electronic properties of conjugated polymers using just a small set of oligomers. The highest occupied molecular orbital-lowest unoccupied molecular orbital gap (HLG) obtained at a TIDFT level (B3PW91) for two polymers, trans-polyacetylene--the simplest conjugated polymer, and a much larger poly(2-methoxy-5-(2,9-ethyl-hexyloxy)-1,4-phenylenevinylene (MEH-PPV) polymer converge to virtually the same asymptotic value than the excitation energy obtained with time-dependent DFT (TDDFT) calculations using the same functional. For TIDFT geometries, the HLG is found to converge to a value within the experimentally accepted range for the band gap of these polymers, when an exponential extrapolation is used; however if semiempirical geometries are used, a linear fit of the HLG versus 1/n is found to produce the best results. Geometrical parameters are observed to reach a saturation value in good agreement with experimental information, within the length of oligomers calculated here and no extrapolation was considered necessary. Finally, the performance of three different semiempirical methods (AM1, PM3, and MNDO) and for the TIDFT calculations, the performance of 7 different full electron basis sets (6-311+G**, 6-31+ +G**, 6-311+ +G**, 6-31+G**, 6-31G**, 6-31+G*, and 6-31G) is compared and it is determined that the choice of semiempirical method or the basis set does not significantly affect the results.     

Frontier molecular orbital analysis for determining the equilibrium geometries of atmospheric prenucleation complexes

A systematic characterization of the frontier molecular orbitals (FMO) of gas-phase prenucleation complexes between H₂SO₄ and other molecules present in the atmosphere (NH₃, H₂O, (CH₃)OH, HF, (CH₃)₂PH, (CH₃)SH) is carried out using the ωB97X-D/6-311++(2d,2p) method at the density functional theory level of theory. The FMO theory principles are taken into account to gain insight into the nature of intermolecular interactions. The results show that the highest occupied molecular orbital/lowest unoccupied molecular orbital molecular system characterization can be adopted as a complementary tool of analysis in supporting the study of atmospheric prenucleation processes. It is shown that the stability and the spatial arrangement of molecular systems can be also thought in terms of inter- and intra-molecular energy gaps ΔE_HL that play an important role in the development of association processes.