密度泛函活性理论中的Rényi熵, Tsallis熵和Onicescu信息能

根据密度泛函理论,分子的电子密度确定了该体系基态下的所有性质,其中包括结构和反应活性.如何运用电子密度泛函有效地预测分子反应活性仍然是一个有待解决的难题.密度泛函活性理论(DFRT)倾力打造这样一个理论和概念架构,使得运用电子密度以及相关变量准确地预测分子的反应特性成为可能.信息理论方法的香农熵和费舍尔信息就是这样的密度泛函,研究表明,它们均可作为反应活性的有效描述符.本文将在DFRT框架中介绍和引进三个密切相关的描述符, Rényi熵、Tsallis熵和Onicescu信息能.我们准确地计算了它们在一些中性原子和分子中的数值并讨论了它们随电子数量和电子总能量的变化规律.此外,以第二阶Onicescu信息能为例,在分子和分子中的原子两个层面上,系统地考察了其随乙烷二面角旋转的变化模式.这些新慨念的引入将为我们深入洞察和预测分子的结构和反应活性提供额外的描述工具.     

蛋白质分子的电学性质、结构与生物活性*

在生命体内,蛋白质通常固着在膜载体上与其它分子相互作用而参与生命活动,所以承受各向异性压力的蛋白质是其存在和功能化的基本形式。设计和研究蛋白质分子在各向异性压力下的分子结构、力学性质和电学/电化学性质不仅对深入理解蛋白质的生物活性至关重要,而且有助于促进蛋白质分子在分子电子器件中的应用。本文综述了利用导电原子力显微镜对蛋白质分子的电学性质的研究进展。在不同的探针压力下,蛋白质分子发生不同程度的形变,表现了不同的电子输运机理。由此可以进一步推测蛋白质分子的生物活性。     

Effect of green solvents physical,chemical, biological and bonding nature on 5-acetyl-thiophene-2-carboxylic acid by DFT and TD-DFT approach – An antiviral agent

The density functional theory (DFT) is applied to 5-acetyl-thiophene-2-carboxylic acid (5AT2CA). To determine the optimal structure and different physical, chemical, and biological characteristics, the B3LYP technique and 6–311++G(d,p) basis set are employed. The binding energies and ellipticity are determined using the atoms in molecules theory (AIM). NBO analysis is used to study the exchanges between the contributor and receiver by energies. By utilizing HOMO-LUMO values and important electronic parameters, stability is determined. The molecular electrostatic potential (MEP) and Fukui function from Mulliken charges are used to determine the reactive regions of the molecule. The TD-DFT technique obtains the electronic transition using UV–Vis spectrum with various solvents. NLO studies were carried out on this molecule. Studies of temperature effect on 5AT2CA are done by thermodynamic parameters. Drug-likeness and molecular docking tests are used to evaluate the bioactivity and antiviral properties.     

Electronic and optical properties of edge modified peritetracene: a DFT study

Peritetracene (PTA) molecules have promising applications in organic electronics and organic light-emitting diodes, but the major constraints come from their poor stability with higher energy gap. We have investigated the stability, electronic, and optical properties of different electron-donating- and electron-withdrawing-substituted PTA molecule groups using density functional theory (DFT) and time-dependent density functional theory (TDDFT) methods. On substituting suitable electron donor and acceptor groups, the energy gap of PTA molecules reduces up to 0.37 eV with an increase in their stability. The stabilities of considered PTA molecules have been investigated using the distribution pattern of frontier molecular orbital energies. The charge transfer properties with smaller ionization potential and larger electron affinity for PTA molecule have been evaluated using Koopmans’ theorem. Enhancement in dipole moment, polarizability, and hyperpolarizability of PTA substituted with electron-donating groups shows the presence of NLO properties. Also, we have investigated the spectroscopic properties of different electron-donating- and electron-withdrawing-substituted PTA molecule groups. Our spectroscopic properties show the bathochromic shift and small hypsochromic shifts in wavelengths of PTA with substituents groups. It is therefore concluded that the –NCH₃ and –NO₂ substituent groups on PTA are observed to have the strongest and highest stability than the other substituent groups considered.

     

Quantum chemical calculation,topological analysis,biological evaluation and molecular docking of allo-ocimenol against breast cancer

The main aim of this study is to identify the structural stability of allo-ocimenol and its molecular reactivity against breast cancer-associated proteins to confirm its anti-cancer capability using density function theory and molecular docking analysis. The structural optimization was carried out via the DFT/B3LYP technique with a 6-311++G (d,p) basis set. The molecular geometry and vibrational assignments of the Allo-Ocimenol molecule were analyzed through density functional theory (DFT). Through optimized molecular structure, the vibrational frequencies (FT-IR and FT-Raman) were assigned and related with experimentally observed vibrational frequencies and the UV spectrum was computed and experimentally confirmed. The allo-ocimenol's reactive activity was further analyzed through a computed molecular electrostatic potential surface. Utilizing the HOMO-LUMO energies and molecular electrostatic potential energy gap, the reactivity and molecular stability of the allo-ocimenol molecule was calculated. Mulliken and natural population analyses were used to determine the charge distribution across the allo-ocimenol atoms. The natural bond orbitals were used to demonstrate the bioactivity of the titled molecule. RDG evaluation was used to examine the weak interactions of the allo-ocimenol molecule. ELF and LOL analyses were utilized to investigate the topology of the allo-ocimenol molecule. Thermodynamic evaluation has been utilized to acquire values and asses the thermodynamic parameters that reveal the thermal stability of the title molecule. Allo-Ocimenol's anti-microbial activity was assessed through an in-vitro disc diffusion method, and its tumor inhibitory and pharmacokinetic properties were evaluated through an in-silico approach using molecular docking and ADMET investigation. Zones of clearance were seen in anti-microbial analyses at various concentrations, and the breast cancer target protein NAMPT established the greatest binding potential, with a docking value of −7.4 Kcal mol⁻¹.     

氢键对分子器件电学特性的影响

利用密度泛函理论和弹性散射格林函数方法,研究了被不同官能团取代后的联苯分子的电输运特性.计算结果表明,由于氢键的影响,使得分子的电子结构发生了变化,特别是对电子在分子结内的跃迁几率影响较大,从而直接影响了分子器件的伏安特性.     

DFT,ADMET and Molecular Docking Investigations for the Antimicrobial Activity of 6,6′-Diamino-1,1′,3,3′-tetramethyl-5,5′-(4-chlorobenzylidene)bis[pyrimidine-2,4(1H,3H)-dione]

Heterocyclic compounds, including pyrimidine derivatives, exhibit a broad variety of biological and pharmacological activities. In this paper, a previously synthesized novel pyrimidine molecule is proposed, and its pharmaceutical properties are investigated. Computational techniques such as the density functional theory, ADMET evaluation, and molecular docking were applied to elucidate the chemical nature, drug likeness and antibacterial function of molecule. The viewpoint of quantum chemical computations revealed that the molecule was relatively stable and has a high electrophilic nature. The contour maps of HOMO-LUMO and molecular electrostatic potential were analyzed to illustrate the charge density distributions that could be associated with the biological activity. Natural bond orbital (NBO) analysis revealed details about the interaction between donor and acceptor within the bond. Drug likeness and ADMET analysis showed that the molecule possesses the agents of safety and the effective combination therapy as pharmaceutical drug. The antimicrobial activity was investigated using molecular docking. The investigated molecule demonstrated a high affinity for binding within the active sites of antibacterial and antimalarial proteins. The high affinity of the antibacterial protein was proved by its low binding energy (−7.97 kcal/mol) and a low inhibition constant value (1.43 µM). The formation of four conventional hydrogen bonds in ligand–protein interactions confirmed the high stability of the resulting complexes. When compared to known standard drugs, the studied molecule displayed a remarkable antimalarial activity, as indicated by higher binding affinity (B.E. −5.86 kcal/mol & Ki = 50.23 M). The pre-selected molecule could be presented as a promising drug candidate for the development of novel antimicrobial agents.     

Structural and charge‐transfer properties of indolylfulgides

The structural and electronic properties of a photochromic molecule dictate their potential photochemical activity. To gain insight into these influences, the ground‐state structure and excited state properties of six indolylgulgides were calculated using several time dependent‐density functional theory (DFT) (TD‐DFT)//DFT methods, second‐order M?ller–Plesset (MP2), and CIS(D). These methods simulated the charge‐transfer properties and the conformation of the ground‐state structure for each molecule. Generally, TD‐DFT accurately simulated the expected charge‐transfer state. The degree of spatial overlap of the occupied and virtual molecular orbitals involved in the S₁ transition of indolylfulgides quantitatively assessed their charge‐transfer character and was qualitatively useful in assessing their photochromic activity. The M06, M06‐2X, and M11 structures were quite similar to those calculated by MP2. Structural differences, similarities, and functional trends are compared and discussed. © 2013 Wiley Periodicals, Inc.     

Study of the Chemical Space of Selected Bacteriostatic Sulfonamides from an Information Theory Point of View

The relative structural location of a selected group of 27 sulfonamide‐like molecules in a chemical space defined by three information theory quantities (Shannon entropy, Fisher information, and disequilibrium) is discussed. This group is composed of 15 active bacteriostatic molecules, 11 theoretically designed ones, and para‐aminobenzoic acid. This endeavor allows molecules that share common chemical properties through the molecular backbone, but with significant differences in the identity of the chemical substituents, which might result in bacteriostatic activity, to be structurally classified and characterized. This is performed by quantifying the structural changes on the electron density distribution due to different functional groups and number of electrons. The macroscopic molecular features are described by means of the entropy‐like notions of spatial electronic delocalization, order, and uniformity. Hence, an information theory three‐dimensional space (IT‐3D) emerges that allows molecules with common properties to be gathered. This space witnesses the biological activity of the sulfonamides. Some structural aspects and information theory properties can be associated, as a result of the IT‐3D chemical space, with the bacteriostatic activity of these molecules. Most interesting is that the active bacteriostatic molecules are more similar to para‐aminobenzoic acid than to the theoretically designed analogues.     

Molecular structure and microbiological activity of alkali metal 3,4-dihydroxyphenylacetates

The changes in physical, chemical and biological properties of chemical compounds decide about their biological activity. In this paper the molecular structure of alkali metal 3,4-dihydroxyphenylacetates is studied in comparison to 3,4-dihydroxyphenylacetic acid (3,4-DHPAA) using FT-IR, FT-Raman and UV–Vis spectroscopy as well as density functional theory (DFT) calculations. The B3LYP/6-311++G⁷ method is used to calculate optimized geometrical structures of studied compounds, atomic charges (Mulliken, APT, NBO), dipole moments, energies as well as the wavenumbers and intensities of the bands in vibrational spectra. Theoretical parameters are compared to the experimental data. The relationship between spectroscopic parameters of studied compounds and their biological activity is analyzed. Antioxidant activity is studied using FRAP and DPPH methods. IC₅₀ parameter is also calculated. Bacillus subtilis, Pseudomonas aeruginosa, Escherichia coli and Klebsiella oxytoca are used in microbiological analysis of 3,4-DHPAA as well as its sodium and potassium salts.     

FT-IR and FT-Raman, UV spectroscopic investigation of 1-bromo-3-fluorobenzene using DFT (B3LYP, B3PW91 and MPW91PW91) calculations

The FT-IR and FT-Raman spectra of 1-bromo-3-fluorobenzene (C₆H₄FBr) molecule have been recorded using Bruker IFS 66 V spectrometer in the range of 4000–100 cm⁻¹. The molecular geometry and vibrational frequencies in the ground state are calculated using the DFT (B3LYP, B3PW91 and MPW91PW91) methods with 6-31++G(d,p) and 6-311++G(d,p) basis sets. The computed values of frequencies are scaled using a suitable scale factor to yield good coherence with the observed values. The isotropic DFT (B3LYP, B3PW91 and MPW1PW91) analysis showed good agreement with the experimental observations. Comparison of the fundamental vibrational frequencies with calculated results by B3LYP methods. The complete data of this molecule provide the information for future development of substituted benzene. The influence of bromine and fluorine atom on the geometry of benzene and its normal modes of vibrations has also been discussed. A study on the electronic properties, such as absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies, was performed by time dependent DFT (TD-DFT) approach. The electronic structure and the assignment of the absorption bands in the electronic spectra of steady compounds were discussed. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. On the basis of the thermodynamic properties of the title compound at different temperatures have been calculated in gas phase, revealing the correlations between standard heat capacities (C) standard entropies (S), standard enthalpy changes (H) and temperatures.     

DFT study of the dissociative adsorption of HF on an AlN nanotube

We have investigated the adsorption of hydrogen fluoride (HF) on the AlN nanotube surface using density functional theory in terms of energetic, structural and electronic properties. By overcoming energy barriers of 27.90–52.30 kcal/mol, HF molecule is dissociated into H and F species on the tube surface and its molecular structure is not preserved after the adsorption process. Dissociation energies have been calculated to be −52.57 and −70.10 kcal/mol. The process has negligible effect on the electronic and field emission properties of the AlN nanotube. This process may increase the solubility of AlN nanotubes.     

Paracetamol adsorption on C60 fullerene and its derivatives: In silico insights

Fullerene-C₆₀ and its heteroatom decorated forms have been widely investigated as drug delivery vehicles and for sensor applications. Further, in the literature carboxylated or carboxylic derivatives of fullerenes have found a special place for biological applications due to their promising water-soluble properties. In the scope of this study, we examined the interaction between paracetamol (acetaminophen) which is a widely prescribed drug to manage acute and chronic pain conditions and C₆₀, silicon doped fullerene (SiC₅₉) and (1,2-methanofullerene C₆₀)-61-carboxylic acid (C₆₀-CH-COOH) using density functional theory calculations. Stability evaluations, electronic and structural properties were carried out by analyzing binding energies, frontier molecular orbitals and natural bond orbitals. It was found that silicon doping on the surface of C₆₀ enhanced the adsorption strength of paracetamol and SiC₅₉ is quite sensitive to the presence of paracetamol drug molecule.     

Synthesis,antioxidant, antibacterial,and DFT study on a coumarin based salen-type Schiff base and its copper complex

Synthesis of new efficient compounds is becoming urgent due to the resistance of organisms to drugs. Salen derivatives have interesting therapeutic and industrial applications. A coumarin based derivative of salen, 7-hydroxy-8-((E)-((2-((E)-((7-hydroxy-5-methyl-2-oxo-3,8a-dihydro-2Hchromen-8-yl)methylene)amino)-4-methylphenyl)imino)methyl)-5-methyl-2H-chromen-2-one (L), and its copper complex, CuL, have been synthesized and characterized. Antibacterial and antioxidant activity of these compounds have been evaluated and electronic, optical and molecular properties have been calculated using density functional theory (DFT) with B3LYP. The results were correlated with the biological activity and reactivity of the compounds. Experimental and theoretical calculations indicate that the studied copper complex has the potential to function as a drug.     

Modeling of the electronic,optoelectronics, photonic and thermodynamics properties of 1,4-bis(3-carboxyl-3-oxo-prop-1-enyl) benzene molecule

The modeling of the molecule 1,4-bis(3-carboxyl-3-oxo-prop-1-enyl) benzene has been carried out to study the electronic, optoelectronics, photonic and thermodynamics properties using Hartree–Fock, density functional theory (B3LYP) and MP2 (Möller–Plesset perturbation theory second-order) with the 6-31G and 6-31+G** basis sets. The dipole moment (µ), polarizability (〈α〉), first hyperpolarizability (β _mol), dielectric constant (ε), electric susceptibility (χ), refractive index (η) and thermodynamics properties of this molecule have been calculated using the same level of theory. The small values of ε, and LUMO–HOMO energy gap, and the high values of χ, η, MR, 〈α〉 and (β _mol) show that the molecule has very good electronic, optoelectronic and photonic applications. The results of this study show that this molecule is an interesting pi-conjugated molecule whose electronic structure and properties can be regulated over a wide range by variation in backbone structure, by side group substitution, and through intramolecular hydrogen bonding.     

Complementary molecular orbital investigations on the conformation of choline derivatives

Quantum-mechanical computations by the PCILO method, applied previously to the study of the conformational properties of acetylcholine and its derivatives modified in the central part of this molecule, are extended to modifications involving its cationic head and its ester terminal. The replacement of the methyl groups of the cationic head by hydrogens or ethyl groups leads to a steep decline in parasympathomimetic activity. It is shown that the triethyl derivative conserves the gauche form as the most stable one. The redistribution of the electronic charges at the onium group implies, however, a transition from an ionic to a hydrophobic binding. The replacement of the methyls by two or three hydrogens leads to a different preferred gauche-gauche conformation. The replacement of the methyl group at the ester terminal by a phenyl ring enables a comparison with the conformational properties of local anesthetics. The study brings about evidence, substantiated by NMR spectroscopy, that acetylcholine analogs and protonated local anesthetics are conformationally similar. Choline ethers also show a general preference for a gauche conformation. Nevertheless, biological studies do not indicate a constant correlation between conformation and biological potency. Conformational analogies or discrepancies alone cannot thus account for the fine details of the biological activity which must depend also on the electronic structure.This work was supported by the A.T.P. N A 655-2303 of the C.N.R.S.     

Theoretical investigation on the structures,densities, and detonation properties of polynitrotetraazaoctahydroanthracenes

The polynitrotetraazaoctahydroanthracenes were optimized to obtain their molecular geometries and electronic structures at density functional theory–B3LYP/6‐31+G(d) level. Detonation velocities (D) and detonation pressures (P) were estimated for this nitramine compounds using Kamlet‐Jacobs equations, based on the theoretical densities (ρ) and heats of formation. It is found that there are good linear relationships between volume, density, detonation velocity, detonation pressure and the number of nitro group. Thermal stability of the compounds was investigated by calculating the bond dissociation energies and energy gap (ΔE_LUMO–HOMO). The simulation results reveal that molecule H performs similarly to famous explosive RDX. These results provide basic information for molecular design of novel high energetic density compounds. © 2011 Wiley Periodicals, Inc.     

Insight into crucial inhibitor–enzyme interaction of arylamides as novel direct inhibitors of the enoyl ACP reductase (InhA) from Mycobacterium tuberculosis: computer-aided molecular design

Abstract  

The enoyl ACP reductase enzyme (InhA) involved in the type II fatty acid biosynthesis pathway of Mycobacterium tuberculosis is an attractive target enzyme for antitubercular drug development. Arylamide derivatives are a novel class of InhA inhibitors used to overcome the drug-resistance problem of isoniazid, the frontline drug for tuberculosis treatment. Their remarkable property of inhibiting the InhA enzyme directly without requiring any coenzyme, makes them especially appropriate for the design of new antibacterials. In order to find a sound binding conformation for the different arylamide analogs, molecular docking experiments were performed with subsequent QSAR investigations. The X-ray conformation of one arylamide within its cocrystallized complex with InhA was used as a starting conformation for the docking experiments. The results thus obtained are perfectly consistent (rmsd = 0.73 ?) with the results from X-ray analysis. A thorough investigation of the arylamide binding modes with InhA provided ample information about structural requirements for appropriate inhibitor–enzyme interactions. Three different QSAR models were established using two three-dimensional (CoMFA and CoMSIA) and one two-dimensional (HQSAR) techniques. With statistically ensured models, the QSAR results obtained had high correlation coefficients between molecular structure properties of 28 arylamide derivatives and their biological activity. Molecular fragment contributions to the biological activity of arylamides could be obtained from the HQSAR model. Finally, a graphic interpretation designed in different contour maps provided coincident information about the ligand–receptor interaction thus offering guidelines for syntheses of novel analogs with enhanced biological activity.