Molecular orbital theory applied to the study of nonsteroidal anti-inflammatory drug efficiency.

Using a simple quantum mechanical method, we calculated the energy of the highest-occupied molecular orbital (E(HOMO)) of three groups of anti-inflammatory compounds, and we have found correlations between E(HOMO) of these molecules and experimental data previously reported on (1) inhibition of sheep-vesicular-gland prostaglandin cyclooxygenase by phenolic compounds, (2) inhibition of prostaglandin cyclooxygenase in mouse macrophages by salicylates, benzoates and phenols, and (3) peroxyl-radical scavenging and radioprotection of a bacterial virus by NSAID drugs, including metiazinic acid, sulindac, D-penicillamine, piroxicam, indomethacin, benoxaprofen, and aspirin. Our correlations using a systematic evaluation of the HOMO energies can be of predictive value in the search for new anti-inflammatory drugs as well as for new radioprotectors.     

Mechanism of action in a 4,5-diarylpyrrole series of selective cyclo-oxygenase-2 inhibitors

Using semi-empirical AM1 calculation and 6.31G* basis sets, we have calculated the energy of the highest-occupied molecular orbital (E(HOMO)) for anti-inflammatory 4,5-diarylpyrroles which have been shown to have inhibitory activity on cyclooxygenase COX-2, an inducible enzyme expressed during inflammation. We have found a correlation between the E(HOMO) of a molecule and its COX-2 inhibition. However, no correlation was observed between E(HOMO) and the inhibition efficiency of cyclooxygenase-1 (COX-1), the constitutively expressed enzyme, protective to the organism. This result suggests that the inhibitions of the two isoforms follow different molecular mechanisms.     

Molecular orbital theory on cellulolytic reactivity between pNP-cellooligosccharides and beta-glucosidase from Cellulomonas uda CS1-1

A beta-glucosidase with the molecular mass of 160,000 Da was purified to homogeneity from cell extract of a cellulolytic bacterium, Cellulomonas uda CS1-1. The kinetic parameters (Km and Vmax) of the enzyme were determined with pNP-cellooligosccharides (DP 1-5) and cellobiose. The molecular orbital theoretical studies on the cellulolytic reactivity between the pNP-cellooligosaccharides as substrate (S) molecules and the purified beta-glucosidase (E) were conducted by applying the frontier molecular orbital (FMO) interaction theory. The results of the FMO interaction between E and S molecules verified that the first stage of the reaction was induced by exocyclic cleavage, which occurred in an electrophilic reaction based on a strong charge-controlled reaction between the highest occupied molecular orbital (HOMO) energy of the S molecule and the lowest occupied molecular orbital (LUMO) energy of the hydronium ion (H3O+), more than endocyclic cleavage, whereas a nucleophilic substitution reaction was induced by an orbital-controlled reaction between the LUMO energy of the oxonium ion (SH+) protonated to the S molecule and the HOMO energy of the H2O2 molecule. A hypothetic reaction route was proposed with the experimental results in which the enzymatic acid-catalyst hydrolysis reaction of E and S molecules would be progressed via SN1 and SN2 reactions. In addition, the quantitative structure-activity relationships (QSARs) between these kinetic parameters showed that Km has a significant correlation with hydrophobicity (logP), and specific activity has with dipole moment, respectively.     

Understanding the substituent effect on the acidity of alcohols and para-substituted phenols

We carried out Hartree–Fock (HF) and density functional theory calculations on the conjugated bases of phenols and alcohols for 23 compounds and analysed their acid–base behaviour using molecular orbital (MO) energies and their dependence on solvent effects. Despite the well-known correlation between highest-occupied MO (HOMO) energies and proton affinity (PA), we observed that HOMO energies are inadequate to describe the acid–base behaviour of these compounds. Therefore, we established a criterion to identify the best frontier MO for describing PA values and also to understand why the HOMO approach fails. The MO that fits our criterion provided very good correlations with PA values, much better than those obtained by the HOMO energies. Since the frontier MOs are those which drive the acid–base reactions in each compound, they were called frontier effective-for-reaction MOs, or FERMOs. By using the FERMO concept, the reactions that are HOMO driven, and those that are not, can be better explained, independent of the calculation method used, since both HF and Kohn–Sham methodologies lead to the same FERMO.     

Theoretical study of the infrared spectrum of 5-phenyl-1,3,4-oxadiazole-2-thiol by using DFT calculations

We have carried out a structural and vibrational study for 5-phenyl-1,3,4-oxadiazole-2-thiol by using the infrared (IR) spectrum and theoretical calculations. For a complete assignment of the compound IR spectrum, density functional theory calculations were combined with Pulay's scaled quantum mechanical force field methodology in order to fit the theoretical wavenumber values to the experimental ones. An agreement between theoretical and available experimental results was found. The theoretical vibrational calculations allowed us to obtain a set of scaled force constants fitting the observed wavenumbers. The results were then used to predict the Raman spectra, for which there are no experimental data. The nature of the benzyl and oxadiazole rings was studied by means of natural bond order and atoms in molecules theory calculations. In addition, the frontier molecular (highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO)) orbitals were analysed and compared with those calculated for the oxadiazole molecule.     

Molecular orbital studies of the action of thyroid hormone analogs: Effects on oxygen consumption of mitochondria and horseradish peroxidase-catalyzed NADH oxidation

The electronic structure of thyroxine and related compounds were calculated by semiempirical molecular orbital methods. When the quantum chemical indices obtained were compared with the structure-activity relationship obtained so far byin vivo andin vitro assays, it was found that HOMO (highest occupied molecular orbital) energy levels of thyroxine and its analogs are well correlated with the increase in oxygen consumption of rat kidney mitochondria determined byin vitro assay. This finding permits the hypothesis that these compounds may play a role in activating the electron transport system of mitochondria by mediating the oxidation-reduction of cytochromes. Furthermore, HOMO energy levels of thyroxine and phenol derivatives were found to correlate well with the stimulation of horseradish peroxidase-catalyzed oxidation of NADH. This suggests that the step of electron removal from these compounds by the enzyme system may be a rate-limiting step, confirming the view that phenoxy-radicals meditate the whole reaction.     

Why are cyclodisilazane rings more stable than cyclodisiloxanes? A qualitative molecular orbital approach to the bonding in cyclodisilazanes and cyclodisiloxanes

The approximate molecular orbitals of cyclic Si₂E₂ (E=nitrogen or oxygen) rings are discussed. It is shown that, due to high silicon 3p_z orbital contribution to the siloxane HOMO, the 3d orbitals can not strenghten the silicon-oxygen bond. In contrast, in the silazane ring considerable Si(3d_π)N(2pπ) bonding may occur. These additional π bonds are responsible for the relative stability of cyclodisilazane rings as compared with the isoelectronic cyclodisiloxane rings.     

Kinetic and molecular orbital studies on the rate of oxidation of monosubstituted phenols and anilines by horseradish peroxidase compound II

The second-order rate constant (k4) for the oxidation of a series of aromatic donor molecules (monosubstituted phenols and anilines) by horseradish peroxidase (HRP) compound II was examined with a stopped-flow apparatus. The electronic states of these substrates were calculated by an ab initio molecular orbital method. It was found that in both phenols and anilines log k4 values correlate well with the highest occupied molecular orbital (HOMO) energy level and the lowest unoccupied molecular orbital (LUMO) energy level, but not with the net charge or frontier electron density on atoms of these molecules. The HOMO and LUMO energy levels of phenols and anilines further showed linear relationships with Hammett's sigma values with negative slopes. Similar results were obtained in the oxidation of substrates by HRP compound I, except that the rate of reaction was much higher than in the case of HRP compound II. In addition, the rates of oxidation of phenols by compound I or II were found to be about 1000 times higher than those of anilines with similar HOMO energy levels. On the basis of these results, the mechanism of electron transfer from the substrate to the heme iron of HRP compound II is discussed.     

Chemical kinetics and interactions involved in horseradish peroxidase-mediated oxidative polymerization of phenolic compounds

The primary objective of this research was to evaluate various factors that affect the reaction rate of oxidative coupling (OXC) reaction of phenolic estrogens catalyzed by horseradish peroxidase (HRP). Kinetic parameters were obtained for the conversion of phenol as well as natural and synthetic estrogens estrone (E(1)), 17β-estradiol (E(2)), estriol (E(3)), and 17α-ethinylestradiol (EE(2)). Molecular orbital theory and Autodock software were employed to analyze chemical properties and substrate binding characteristics. Reactions were first order with respect to phenolic concentration and reaction rate constants (k(r)) were determined for phenol, E(3), E(1), E(2) and EE(2) (in increasing order). Oxidative coupling was controlled by enzyme-substrate interactions, not collision frequency. Docking simulations show that higher binding energy and a shorter binding distance both promote more favorable kinetics. This research is the first to show that the OXC of phenolics is an entropy-driven and enthalpy-retarded process.     

A theoretical model of the catalytic mechanism of the Delta5-3-ketosteroid isomerase reaction

The present paper describes a theoretical approach to the catalytic reaction mechanism involved in the conversion of 5-androstene-3,17-dione to 4-androstene-3,17-dione. The model incorporates the side chains of the residues tyrosine (Tyr(14)), aspartate (Asp(38)) and aspartic acid (Asp(99)) of the enzyme Delta(5)-3-ketosteroid isomerase (KSI; EC 5.3.3.1). The reaction involves two steps: first, Asp(38) acts as a base, abstracting the 4beta-H atom (proton) from C-4 of the steroid to form a dienolate as the intermediate; next, the intermediate is reketonized by proton transfer to the 6beta-position. Each step goes through its own transition state. Functional groups of the Tyr(14) and Asp(99) side chains act as hydrogen bond donors to the O1 atom of the steroid, providing stability along the reaction coordinate. Calculations were assessed at high level Hartree-Fock theory, using the 6-31G(*) basis set and the most important physicochemical properties involved in each step of the reaction, such as total energy, hardness, and dipole moment. Likewise, to explain the mechanism of reaction, highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO), atomic orbital contributions to frontier orbitals formation, encoded electrostatic potentials, and atomic charges were used. Energy minima and transition state geometries were confirmed by vibrational frequency analysis. The mechanism described herein accounts for all of the properties, as well as the flow of atomic charges, explaining both catalytic mechanism and proficiency of KSI.     

Evaluation of the energetic position of the lowest excited singlet state of beta-carotene by NEXAFS and photoemission spectroscopy.

In carotenoids the lowest energetic optical transition belonging to the pi-electron system is forbidden by symmetry, therefore the energetic position of the S(1) (2(1)A(g)) level can hardly be assessed by optical spectroscopy. We introduce a novel experimental approach: For molecules with pi-electron systems the transition C1s-->2p(pi*) from inner-atomic to the lowest unoccupied molecular orbital (LUMO) appears in X-ray absorption near edge spectra (NEXAFS) as an intense, sharp peak a few eV below the carbon K-edge. Whereas the peak position reflects the energy of the first excited singlet state in relation to the ionization potential of the molecule, intensity and width of the transition depend on hybridization and bonding partners of the selected atom. Complementary information can be obtained from ultraviolet photoelectron spectroscopy (UPS): At the low binding energy site of the spectrum a peak related to the highest occupied molecular orbital (HOMO) appears. We have measured NEXAFS and UPS of beta-carotene. Based on these measurements and quantum chemical calculations the HOMO and LUMO energies can be derived.     

对氨基苯甲酸酯同系物形成细胞色素P_（450）代谢中间体络合物的定量结构与活性关系

细胞色素Ｐ４５０（Ｐ４５０,Ｅｃ１．１４．１４．１）是一种十分重要的催化氧化反应的酶。本文测定了１２个对氨基苯甲酸酯同系物与Ｐ４５０相互作用而形成Ｐ４５０代谢中间体络合物的活性,用半经验分子轨道法ＭＮＤＯ－ＰＭ３计算得到了这些同系物的分子轨道指数,并用逐步多元回归分析法导出了活性与分子轨道指数及正辛醇／水分配系数的对数值（ＬｏｇＰ）之间的定量结构与活性关系（ＱＳＡＲ）。结果表明：对氨基苯甲酸脂同系物形成Ｐ４５０代谢中间体络合物的活性与原子净电荷的绝对值之和（∑Ｑ）和ＬｏｇＰ均具有很好的抛物线型相务性,同时,ＬｏｇＰ与∑Ｑ之间也存在相当好的相关性。     

Computational strategies for understanding the nature of interaction in dioxin imprinted nanoporous trappers

A new computational model capable of understanding the nature of interactions in signature complexes formed between the template (2,3,7,8‐tetrachlorodibenzo‐p dioxin (TCDD)) and the functional monomers (methacrylic acid (MAA)) using density functional theory (DFT) has been designed. The polymer precursors were optimized for geometries in polymerization media, computing the interaction energies between template molecules and functional monomers of transient pre‐polymerized complexes (PPC), and structural and vibrational properties reference to theoretical infrared spectra were computed using DFT of B3LYP/6 311+G(d,p) hybrid functional method. Atom in molecule theory was used to analyze the hydrogen‐bonding characteristics of PPC of MAA–TCDD. Considering the theoretical titrations conducted in a virtual solvent box, it was found that the 1:4 molar ratio was required to form the most stable PPC in a given solvent system. The electron density plots indicate strong hydrogen bonding as shown by the 2pz dominant highest occupied molecular orbital (HOMO) character that could be the preferable sites of binding for target molecule, TCDD. Considering HOMO approach, the active adsorption sites in molecularly imprinted polymer was modeled to get insight on molecular recognition property for targeted molecule, TCDD. The proposed computational protocol is simple, accurate, and novel to design the polymer and is useful to predict the properties of polymer systems than the conventional theoretical analysis of template–monomer interactions. Copyright © 2015 John Wiley & Sons, Ltd.     

The interaction of a homologous series of hydrocarbons with hepatic cytochrome P-450. Molecular orbital-derived electronic and structural parameters influencing the haemoprotein spin state

The spectral interaction of a homologous series of alkyl-substituted benzenes and related compounds with purified mammalian cytochrome P-450 has been investigated. Each of the 10 hydrocarbons produced a Type I spectral change, indicative of a low to high spin transition of the haem iron of cytochrome P-450. The extent of perturbation of the cytochrome P-450 spin equilibrium varied for each compound and was used to quantify the spin shifts of the haemoprotein and consequently the substrate-bound spin equilibrium constant, K2. Molecular orbital calculations were utilised to determine the electronic structural parameters of the 10 hydrocarbons investigated, including the electrophilic and nucleophilic super-delocalizabilities summed over all atoms (sigma SE and sigma SN, respectively), the sum of the absolute values of net atomic charge (sigma QT) and the energy levels of both the highest occupied and lowest unoccupied molecular orbitals (E (HOMO) and E (LUMO) respectively). Multiple regression analyses were then utilized to generate quantitative structure-activity relationships between the above structural parameters and the substrate-bound spin equilibrium constant, K2. Good correlations were observed between sigma SE, sigma SN and sigma QT, indicating the importance of hydrophobicity and steric factors in the perturbation of the haemoprotein spin equilibrium. In addition, the electron-accepting potential of the hydrocarbons was an important structural feature and exhibited better correlations with K2 than the electron donating parameter. Taken collectively, our data show the importance of the hydrophobic and charge transfer characteristics of hydrocarbon substrates in dictating the position of the cytochrome P-450 spin equilibrium, and as such, provides a rational molecular explanation based on sound chemical principles for the differential interaction of hydrocarbons with cytochrome P-450.     

Photosensitized oxidation of phenyl and tert-butyl sulfides.

The photosensitized oxygenation of diphenyl (1), di-tert-butyl (2) and phenyl tert-butyl sulfide (3) was studied. Bimolecular rate constants of singlet oxygen quenching are low (1 to 5 x 10(4) M(-1)s(-1)) since the sulfides are poor nucleophiles due to sterical hindrance (2, 3) or the HOMO on the sulfur atom being a less accessible p(z) orbital (1). The quenching is mainly physical, but chemical reaction leading to sulfoxides also takes place in methanol and, to a lower degree, in acetonitrile. Catalysis by carboxylic acids considerably enhances the rate of sulfoxidation. Inefficiency in the chemical reaction is again due to the poor nucleophilicity of the sulfides, which limits oxygen transfer by electrophilic intermediates such as the protonated persulfoxide.     

Quantitative structure-activity relationship analysis of phenolic antioxidants

In this report, the quantitative structure-activity relationship (QSAR) analyses of substituted phenols, vitamin E derivatives and flavonoids are presented. Two models have been derived using calculated parameters such as the heat of formation (H_f), the energy of the lowest unoccupied molecular orbital of radicals (E_lumo-r), the energy of the highest occupied molecular orbital of the parent compounds (E_homo) and the number of hydroxyl groups (OH). These models can be used to estimate the redox potentials or antioxidant activities of new substituted phenolic compounds or vitamin E derivatives. The Trolox equivalent antioxidant capacities (TEACs) of 42 different flavonoids are found to be mainly governed by the number and location of hydroxyl groups on the flavonoid ring system.     

Kinetic and molecular orbital studies on the rate of oxidation of monosubstituted phenols and anilines by lactoperoxidase compound II in comparison with the case of horseradish peroxidase

The second-order rate constant (k4) for the oxidation of monosubstituted phenols and anilines by lactoperoxidase compound II was examined by Chance's method [B. Chance, Arch. Biochem. Biophys. 71 (1957), 130–136]. When the electronic states of these substrates were calculated by an ab initio molecular orbital method, it was found that the log k4 value correlates well with the highest occupied molecular orbital (HOMO) energy level but not with the net charge or frontier electron density. These results are essentially similar to those reported previously in the case of horseradish peroxidase [J. Sakurada, R. Sekiguchi, K. Sato, and T. Hosoya, Biochemistry 29 (1990), 4093–4098], showing some dissimilar features which are considered to reflect the structural difference between the two enzymes.Abbreviations HOMO highest occupied molecular orbital - HRP horseradish peroxidase - LPO lactoperoxidase (EC 1.11.1.7) - LUMO lowest unoccupied molecular orbital     

Structure-activity relationships for halobenzene induced cytotoxicity in rat and human hepatocytes

Halobenzenes are ubiquitous environmental contaminants, which are hepatotoxic in both rodents and humans. The molecular mechanism of halobenzene hepatotoxicity was investigated using Quantitative structure-activity relationships (QSAR) and accelerated cytotoxicity mechanism screening (ACMS) techniques in rat and human hepatocytes. The usefulness of isolated hepatocytes for prediciting in vivo xenobiotic toxicity was reassessed by correlating the LC(50) of 12 halobenzene congeners in phenobarbital (PB) induced rat hepatocytes in vitro determined by ACMS to the hepatotoxicities reported in vivo in PB-induced male Sprague-Dawely (SD) rats. A high correlation (r(2)=0.90) confirmed the application of hepatocytes as a "gold standard" for toxicity testing in vitro. QSARs were derived to determine the physico-chemcial variables that govern halobenzene toxicity in PB-induced rat, normal rat and human hepatocytes. We found that toxicity in normal rat and normal human hepatocytes both strongly correlate with hydrophobicity (logP), ease of oxidation (E(HOMO), energy of the highest molecular orbital) and on the asymmetric charge distribution according to arrangement of halogen substituents (dipole moment, mu). This suggests that halobenzene interaction with cytochrome P450 for oxidation is the metabolic activating path for toxicity and is similar in both species. In PB-induced rat hepatocytes the QSAR derivation is changed, where halobenzene toxicity strongly correlates to logP and dipole moment, but not E(HOMO). The changed QSAR suggests that oxidation is no longer the rate-limiting step in the cytotoxic mechanism when CYP2B/3A levels are increased, confirming CYP450 oxidation as the metabolic activating step under normal conditions.