An experimental and theoretical approach to 5alpha-cholestan-6-spiro-1',2',4'-triazolidine-3'-one

The 5alpha-cholestan-6-one semicarbazone (1) on reaction with hydrogen peroxide at 0 degrees C affords selectively 5alpha-cholestan-6-spiro-1',2',4'-triazolidine-3'-one. (2) The structural assignment of the product was confirmed on the basis of its elemental, analytical and spectral analysis. The Hartree-Fock method using 6-31G* basis set was employed in order to explore the reaction mechanism. The results of the computational study show that the reaction proceeds through two radical intermediates formation. The different characteristics involved during the reaction were explained, firstly, the lower energy conformation of each molecule using total energy, hardness and dipole moment, and secondly, the explanation of the free radical mechanism, using frontier molecular orbital (FMO) theory, encoded electrostatic potential, spin electronic density and atomic charges. The localization of highest occupied molecular orbital (HOMO) or alpha-HOMO, lowest unoccupied molecular orbital (LUMO) or alpha-LUMO and the flow of atomic charges are in good agreement to support the present mechanism of the reaction. Stability and feasibility of all the optimized structures were supported by their respective fundamental frequencies and energy minima.     

The reaction of 5alpha-cholestan-6alpha-ol with phosphorus pentachloride and with thionyl chloride.

GC analysis of the reaction product of 5alpha-cholestan-6alpha-ol and phosphorus pentachloride indicated the presence of 6alpha-chloro-5alpha-cholestane, 6beta-chloro-5alpha-cholestane, 5,6beta-dichloro-5alpha-cholestane, and traces of cholest-5-ene; a computerised GC-MS system furnished visual reproductions of the gas chromatograms, but failed to yield corresponding mass chromatograms because of decomposition of the chlorides in the molecular separator. GC analysis of the reaction product of 5alpha-cholestan-6alpha-ol and thionyl chloride showed the formation of 6alpha-chloro-5alpha-cholestane, cholest-5-ene, 5-chloro-5alpha-cholestane, and traces of four unidentified substances, whilst the GC-MS system furnished visual reproductions of the gas chromatograms, but again failed to yield corresponding mass chromatograms.     

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.     

基于密度泛函叶绿素a分子活性的量子化学计算

在液相环境下,根据量子化学密度泛函(DFT)的B3LYP泛函在6-31G基组水平的计算结果,从叶绿素a分子的光谱特性、特征基团对前线轨道能量贡献率、激发态、Mulliken电荷分布等量化参数分析比较了其各特征基团的生物活性及吸收波长。结果表明:叶绿素a分子中的5个活性基团中,C(33)、O(34)所组成的酮羰基活性最强,卟啉环的活性次之,C(36)位置上的酯羰基和C(13)位置上的酯羰基及共轭碳碳双键的活性较弱;在发生HOMO→LUMO跃迁后,卟啉环转移的电荷变化总量为0.00012。而酮羰基得到的电荷变化,总量为-0.00062。     

Theoretical investigation of cyromazine tautomerism using density functional theory and Møller–Plesset perturbation theory methods

A computational chemistry analysis of six unique tautomers of cyromazine, a pesticide used for fly control, was performed with density functional theory (DFT) and canonical second-order Møller–Plesset perturbation theory (MP2) methods to gain insight into the contributions of molecular structure to detection properties. Full geometry optimisation using the 6-311++G** basis set provided energetic properties, natural charges, frontier orbitals and vibrational modes. Excitation energies were obtained using time-dependent DFT. Hydrogen location and bond order contribute significantly to the electronic properties. The common cyromazine tautomer possesses the lowest energy, highest band gap energy and highest excitation energy. B3LYP/6-31G** dynamics simulations indicate each tautomer possesses a stable structure with limited rotation about the single bonds. Tautomerisation involving intramolecular hydrogen transfer influences the natural charges of neighbouring atoms and the frontier orbital properties. The excitation energies are highly correlated with band gap energies of the frontier orbitals. The calculated infrared and Raman spectra are suitable for vibrational assignments associated with the chemical structure. The tautomeric forms of cyromazine possess similar spatial properties and significant variation in electronic properties.     

Importance of substrate and cofactor polarization in the active site of dihydrofolate reductase

By using a combined quantum-mechanical and molecular-mechanical potential in molecular dynamics simulations, we have investigated the effects of the enzyme electric field of dihydrofolate reductase on the electronic polarization of its 5-protonated dihydrofolate substrate at various stages of the catalyzed hydride transfer reaction. Energy decomposition of the total electrostatic interaction energy between the ligands and the enzyme shows that the polarization effect is 4% of the total electrostatic interaction energy, and, significantly, it accounts for 9kcal/mol of transition state stabilization relative to the reactant state. Therefore it is essential to take account of substrate polarization for quantitative interpretation of enzymatic function and for calculation of binding free energies of inhibitors to a protein. Atomic polarizations are calculated as the differences in the average atomic charges on the atoms in gas phase and in molecular simulations of the enzyme; this analysis shows that the glutamate tail and the pterin ring are the highly polarized regions of the substrate. Electron density difference plots of the reactant and product complexes at instantaneous configurations in the enzyme active center confirm the inferences made on the basis of partial atomic charges.     

Multiple subunit fitting into a low-resolution density map of a macromolecular complex using a gaussian mixture model

Recently, electron microscopy measurement of single particles has enabled us to reconstruct a low-resolution 3D density map of large biomolecular complexes. If structures of the complex subunits can be solved by x-ray crystallography at atomic resolution, fitting these models into the 3D density map can generate an atomic resolution model of the entire large complex. The fitting of multiple subunits, however, generally requires large computational costs; therefore, development of an efficient algorithm is required. We developed a fast fitting program, “gmfit”, which employs a Gaussian mixture model (GMM) to represent approximated shapes of the 3D density map and the atomic models. A GMM is a distribution function composed by adding together several 3D Gaussian density functions. Because our model analytically provides an integral of a product of two distribution functions, it enables us to quickly calculate the fitness of the density map and the atomic models. Using the integral, two types of potential energy function are introduced: the attraction potential energy between a 3D density map and each subunit, and the repulsion potential energy between subunits. The restraint energy for symmetry is also employed to build symmetrical origomeric complexes. To find the optimal configuration of subunits, we randomly generated initial configurations of subunit models, and performed a steepest-descent method using forces and torques of the three potential energies. Comparison between an original density map and its GMM showed that the required number of Gaussian distribution functions for a given accuracy depended on both resolution and molecular size. We then performed test fitting calculations for simulated low-resolution density maps of atomic models of homodimer, trimer, and hexamer, using different search parameters. The results indicated that our method was able to rebuild atomic models of a complex even for maps of 30 Å resolution if sufficient numbers (eight or more) of Gaussian distribution functions were employed for each subunit, and the symmetric restraints were assigned for complexes with more than three subunits. As a more realistic test, we tried to build an atomic model of the GroEL/ES complex by fitting 21-subunit atomic models into the 3D density map obtained by cryoelectron microscopy using the C7 symmetric restraints. A model with low root mean-square deviations (14.7 Å) was obtained as the lowest-energy model, showing that our fitting method was reasonably accurate. Inclusion of other restraints from biological and biochemical experiments could further enhance the accuracy.     

Biosynthesis of cholestanol: 5-alpha-cholestan-3-one reductase of rat liver

The 3-beta-hydroxysteroid dehydrogenase of rat liver which catalyzes the conversion of 5alpha-cholestan-3-one to 5alpha-cholestan-3beta-ol is localized mainly in the microsomal fraction. The enzyme required NADPH as hydrogen donor and differed from the known 3-beta-hydroxysteroid dehydrogenases of the C(19) series in being inactive in the presence of NADH. The microsomal preparations did not reduce the 3-keto groups of cholest-4-en-3-one, cholest-5-en-3-one, or 5beta-cholestan-3-one to the corresponding 3beta-hydroxy compounds. The conversion of 5alpha-cholestan-3-one to 5alpha-cholestan-3beta-ol was only slightly inhibited by the reaction product or by other monohydroxy steroids, but a strong inhibitory effect was noted with cholest-5-en-3-one, 5alpha-cholestane-3beta, 7alpha-diol and 5alpha-cholestan-7-on-3beta-ol. The microsomes, but not high speed supernatant solution, catalyzed the reverse of the cholestanone reductase reaction, namely the conversion of 5alpha-cholestan-3beta-ol to 5alpha-cholestan-3-one in the presence of oxygen and an NADP-generating system. The action of the microsomal preparations upon 5alpha-cholestan-3-one produced 5alpha-cholestan-3alpha-ol in addition to the 3beta-epimer. The 3-alpha-hydroxysteroid dehydrogenase involved functioned with either NADH or NADPH as hydrogen donor. The ratio of 5alpha-cholestan-3beta-ol to 5alpha-cholestan-3alpha-ol formed from 5alpha-cholestan-3-one was approximately 10:1 and was independent of the sex of the animal from which the microsomes were prepared.     

Syntheses and biologic studies of steroidal methyl sulfides and sulfones.

Reactions of cholest-5-ene (I) and its 3 beta-chloro (II) and 3 beta-acetoxy (III) analogs with trimethylchlorosilane-dimethyl sulfoxide in dry acetonitrile furnish cholest-4-en-6 beta-yl methyl sulfide (IV) and its 3 beta-chloro (V) and 3 beta-acetoxy (VI) analogs. Oxidation of (IV) with m-chloroperbenzoic acid affords cholest-4-en-6 beta-yl methyl sulfone (VII) and 4 alpha, 5-epoxy-5 alpha-cholestan-6 beta-yl methyl sulfone (VIII). Under similar reaction conditions, V furnishes 3 beta-chlorocholest-4-en-6 beta-yl methyl sulfone (IX), while VI gives 3 beta-acetoxycholest-4-en-6 beta-yl methyl sulfone (X) and 3 beta-acetoxy-4 alpha, 5-epoxy-5 alpha-cholestan-6 beta-yl methyl sulfone (XI). The structures of these compounds were established on the basis of analytic and spectral data. Some of these compounds have been evaluated for their possible biologic activities.     

Computer studies on the stereostructure and quantum chemical properties of 6-pyruvoyl tetrahydropterin, the key intermediate of tetrahydrobiopterin biosynthesis

The optimized geometry of the conformation of atoms constituting the 6-pyruvoyl tetrahydropterin molecule, the labile key intermediate of tetrahydrobiopterin biosynthesis, was obtained by molecular orbital calculations within the MINDO/3 framework. The stereostructure of the molecule showing the preferred mode for binding to sepiapterin reductase or pyruvoyl tetrahydropterin reductase was drawn in perspective. The resulting structure with the equatorial staggered configuration of the 6-1',2'-dioxopropyl (pyruvoyl) side chain indicated that O(1') and H(6) were located in the trans position around the C(6)-C(1') bond and that the two vicinal carbonyls in the side chain were fixed in the incomplete trans form. The calculation of atomic charges and LUMO coefficients of these carbonyls suggests that the C2'-carbonyl may be more reactive toward NADPH than the C1'-carbonyl in the enzymatic reaction.     

Density functional computational studies on (E)-2-[(2-Hydroxy-5-nitrophenyl)-iminiomethyl]-4-nitrophenolate

Density functional calculations of the structure, atomic charges, molecular electrostatic potential and thermodynamic functions have been performed at B3LYP/6-31G(d,p) level of theory for the title compound (E)-2-[(2-hydroxy-5-nitrophenyl)-iminiomethyl]-4-nitrophenolate. The results show that the phenolate oxygen atom and all of the nitro group oxygen atoms have bigger negative charges, and the coordination ability of these atoms differs in different solvents. The energetic behavior of the title compound in solvent media has been examined using B3LYP method with the 6-31G(d,p) basis set by applying the Onsager method and the isodensity polarized continuum model (IPCM). The results obtained with these methods reveal that the IPCM method yielded a more stable structure than Onsager’s method. In addition, natural bond orbital and frontier molecular orbital analysis of the title compound were performed using the B3LYP/6-31G(d,p) method.     

Experimental and theoretical investigation of the molecular and electronic structure of 5-(4-aminophenyl)-4-(3-methyl-3-phenylcyclobutyl)thiazol-2-amine

The title molecule, 5-(4-aminophenyl)-4-(3-methyl-3-phenylcyclobutyl)thiazol-2-amine (C₂₀H₂₁N₃S), was prepared and characterized by ¹H-NMR, ¹³C-NMR, IR and single-crystal X-ray diffraction. The compound crystallizes in the monoclinic space group P2₁/c with a?=?9.4350(5) Å, b?=?11.2796(6) Å, c?=?18.4170(8) Å and β?=?113.378(3)°. In addition to the molecular geometry from X-ray experiment, the molecular geometry, vibrational frequencies, gauge including atomic orbital (GIAO) ¹H- and ¹³C-NMR chemical shift values and atomic charges distribution of the title compound in the ground state have been calculated using the Hartree–Fock (HF) and density functional method (DFT) (B3LYP) with 6-31G(d) basis set. To determine conformational flexibility, molecular energy profile of the title compound was obtained by semi-empirical (AM1) calculations with respect to two selected degrees of torsional freedom, which were varied from ?180° to +180° in steps of 10°. Besides, frontier molecular orbitals (FMO) analysis was performed by the B3LYP/6-31G(d) method.     

Theoretical mechanism of the formation of cholesteryl chloride from cholesterol and thionyl chloride

This work describes a theoretical approach to the substitution reaction mechanism involving the conversion of cholesterol to cholesteryl chloride. Two chlorosulfite ester molecules were formed as intermediates. An iso-steroid was found as the transition state. The final product was cholesteryl chloride and the side products were HCl and SO₂. Calculations were carried out at high level Hartree–Fock theory, using the 6–31G* basis set. From the electronic structure of the reactants, the most important physicochemical properties involved in the reaction pathway were used. Thus, to determine the participation of each molecule and to explain the mechanism of reaction; the total energy, HOMO and LUMO, atomic orbital contribution to frontier orbitals formation, electrostatic potentials, atomic charges, hardness and dipole moment were used. Characterization of intermediates and transition state was supported by their respective energy minima, fundamental frequencies and equilibrium geometry.Figure Synopsis of the reaction pathway. The reaction starts when the lone pair of the Ch oxygen interacts with the sulfur atom, releasing a chloride ion. As a result, the first intermediate is formed. Next, in the first intermediate the nucleophilic chloride ion bonds the electrophilic hydrogen atom, releasing HCl and yielding the second intermediate. In the second intermediate, the electrophilic H-atom from HCl bonds with the lone pair of the Cl atom adjacent to the sulfur atom, restoring HCl. Concurrently, SO₂ is liberated and causes the formation of the C3-C5 partial bond and breaking of the C5-C6 -bond leading to the transition state. In the transition state, the electrophilic H from HCl bonds with the Cl lone pair at C6-Cl, forming HCl again and leaving the C6 atom electron-deficient, which restores the C5-C6 -bond and breaks the C3-C5 partial bond. Finally, the electrophilic C3 atom and the nucleophilic Cl atom form a bond, yielding cholesteryl chloride. HCl and SO₂ are also formed as side products. The arrows show the rearrangement of electrons.     

Hybridization-displaced charges for amino-acids: a new model using two point charges per atom along with bond-center charges

A new charge distribution is proposed for the amino acids where each atom is associated with two point charges while each bond center is associated with one point charge. Centroids of charges arising due to atomic orbital hybridization called hybridization-displaced charges (HDC) and those located at the atomic sites and bond centers obtained by a modified form of the Mulliken scheme were combined. The density matrix calculations required for this analysis were performed at the B3LYP/6-31G** level of density functional theory. The combination of HDC centroids with the modified Mulliken charges was found to yield dipole moments and surface molecular electrostatic potentials (MEP) of the amino acids in good agreement with those obtained by rigorous DFT calculations or those obtained using the MEP-fitted CHelpG charges. This study shows that the combination of HDC centroids with the modified Mulliken charges is significantly superior to the conventional Mulliken charges.     

Chemical bonding in carborane/aromatic co-polymers: a first-principles analysis of experimental photoemission spectra

First-principles density functional theory calculations have been used to study the relative stability and analyse the chemical bonding of novel cross-linked carborane polymers. Atomic charges with several population analysis methods based on fully relaxed structures were calculated to interpret the chemical binding energy shifts of XPS spectra of these boron carbide polymers. The results indicate that a base structure with one aromatic linking unit with carborane is energetically favoured. The linear relationship between experimental core-level photoemission binding energies and computational partial atomic charges from four population analysis methods (Mulliken, Hirshfeld, atoms-in-molecules (AIM) and natural bond order (NBO)) were analysed and the results indicate that cross-linking occurs at icosahedral B sites non-adjacent to icosahedral carbon sites, in agreement with recently reported experimental results. The role of basis set size in determining partial atomic charges was found to vary with population analysis method. Best linear correlations were identified with the more robust population analysis methods (Hirshfeld, AIM and NBO) with the AIM methods noted as being particularly sensitive to basis set size.     

Crystallographic study of the complex between sulfite and bakers' yeast flavocytochrome b2

The complex between Saccharomyces cerevisiae flavocytochrome b2 and the sulfite anion has been analyzed by x-ray diffraction. A map of the difference in electron density between the complex and the native protein has been computed. One positive peak of electron density is visible at the active site of each of the two subunits in the asymmetric unit, very close to the N-5 of the flavin. The molecular fragment SO3(2-) can account for the shape of this difference in electron density. A third peak is visible in the subunit containing pyruvate, the reaction product. It is a peak of negative electron density localized at the position where the pyruvate usually is in the native form. These results are interpreted on the basis of the mechanism defined in solution for the reaction between flavins and sulfite.     

Catalytic mechanism of the inverting N-acetylglucosaminyltransferase I: DFT quantum mechanical model of the reaction pathway and determination of the transition state structure

The complex N-glycan structures on glycoproteins play important roles in cell adhesion and recognition events in metazoan organisms. A critical step in the biosynthetic pathway leading from high mannose to these complex structures includes the transfer of N-acetylglucosamine (GlcNAc) to a mannose residue by the inverting N-acetylglucosaminyltransferase I (GnT-I). The catalytic mechanism of this enzymatic reaction is explored herein using DFT quantum chemical methods. The computational model used to follow the reaction is based on the X-ray crystallographic structure of GnT-I and contains 127 atoms that represent fragments of residues critical for the substrate binding and catalysis. The mechanism of the catalytic reaction was monitored by means of a 2D potential energy map calculated as a function of predefined reaction coordinates at the B3LYP/6-31G** level. This potential energy surface revealed one transition state associated with a reaction pathway following a concerted mechanism. The reaction barrier was estimated, and the structure of the transition state was characterized at the B3LYP/6-311++G**// B3LYP/6-31G** level.     

YUP.SCX: coaxing atomic models into medium resolution electron density maps

The structures of large macromolecular complexes in different functional states can be determined by cryo-electron microscopy, which yields electron density maps of low to intermediate resolutions. The maps can be combined with high-resolution atomic structures of components of the complex, to produce a model for the complex that is more accurate than the formal resolution of the map. To this end, methods have been developed to dock atomic models into density maps rigidly or flexibly, and to refine a docked model so as to optimize the fit of the atomic model into the map. We have developed a new refinement method called YUP.SCX. The electron density map is converted into a component of the potential energy function to which terms for stereochemical restraints and volume exclusion are added. The potential energy function is then minimized (using simulated annealing) to yield a stereochemically-restrained atomic structure that fits into the electron density map optimally. We used this procedure to construct an atomic model of the 70S ribosome in the pre-accommodation state. Although some atoms are displaced by as much as 33 Å, they divide themselves into nearly rigid fragments along natural boundaries with smooth transitions between the fragments.     

Modeling the interaction of seven bisphosphonates with the hydroxyapatite(100) face

The interaction of seven pamidronate bisphosphonate (Pami-BPs) and its analogs with the hydroxyapatite (HAP) (100) surface was studied using density functional theory (DFT) and molecular dynamic (MD) methods. Partial Mulliken oxygen atomic charges in protonated structures were calculated at the level of B3LYP/6-31G*. The MD simulation was performed using the Discover module of Material Studio by compass force field. The results indicate the abilities of donating electrons of the oxygen atoms of the phosphate groups that are closely associated with the antiresorptive potency. The binding energies, including vdw and electrostatic, are used to discuss the mechanism of antiresorption. The results of calculations show that the strength of interaction of the HAP (100) face with the bisphosphonates is N(4)?>?N(6)?>?N(7)?>?N(5)?>?N(3)?>?N(2)?>?N(1) according to their experimental pIC(50) values.     

鸟嘌呤碱基与羟基自由基反应的密度泛函理论

羟基自由基 (·OH)进攻嘌呤碱基是破坏核酸造成DNA断链损伤的重要原因之一 .采用密度泛函 (DFT)理论中B3LYP方法在 6— 31G基组水平上对鸟嘌呤 (G)受羟基自由基进攻形成的各种可能产物自由基进行几何全优化 .根据总能量、键长和自旋密度的计算结果 ,从理论上确认了C 5和C 8位加成机制 .得产物自由基G5OH·、G8OH· ,且G5OH·易与N 11位H脱水得一个更稳定的产物自由基 ,而G8OH·不易发生开环反应 ,得到与实验一致的结论 .这些稳定自由基的形成造成DNA断链损伤