Synthesis,characterization, pharmacological,molecular modeling and antimicrobial activity evaluation of novel isomer quinoline derivatives

The structural and spectroscopic characteristics of the synthesized structurally novel compound 4-chloro-6-methylquinoline-2(1H)-one (4C6MQ) and its isomer 4-chloro-8-methylquinoline-2(1H)-one (4C8MQ) have been examined by means of experimental and computational quantum chemical methods like density functional theory (DFT). The crystal structure of the 4C6MQ compound has been brought to light by single-crystal x-ray diffraction (SCXRD) method which consists of two independent molecules (A and B) in the asymmetric unit with similar conformations. Both the isomer compounds are characterized spectroscopically by FTIR, FT-Raman, UV-Vis, and NMR spectrum and compared with DFT results. The geometries of the isomer compounds have been optimized by using DFT/B3LYP method with the 6-311G++(d,p) basis sets. From the optimized geometry of the compounds, geometric parameters (bond lengths, bond angles, and torsion angles); vibrational analysis; chemical shifts; and electronic absorption of the isomer compounds have been computed and compared with the experimental result. The detailed assignments of vibrational wave numbers have been prepared based on potential energy distribution (PED) which was carried out in the VEDA4 program. In addition, natural bonding orbital analysis, frontier molecular orbital, and molecular electrostatic potential have been explained theoretically. The in silico (absorption, distribution, metabolism, excretion and toxicity) studies were analyzed to identify the potential drug likeliness of the isomer compounds. The implications of the inhibitory activity of isomer compounds against DNA gyrase and lanosterol 14 α-demethylase enzyme by molecular docking are discussed. Further, the isomer compounds were screened for their antibacterial and antifungal activities.     

An electron diffraction determination of the molecular structures of silyl- and germyl-manganese pentacarbonyl in the gas phase

The molecular structures of the title compounds have been determined by gas phase electron diffraction methods. The SiMn and GeMn bond lengths are 240.7 ? 0.5 and 248.7 ? 0.2 pm respectively and the CMnC angles in the silyl and germyl cases are 94.5 ± 2° and 97 ± 2° respectively. Comparisons are made with the reported structure of CH₃Mn(CO)₅ and He^I photoelectron spectra of these compounds in an attempt to determine the extent of d → d π-bonding in the SiMn or GeMn bonds.     

硝酸酯分子几何构型的量子化学研究

运用MINDO / 3、MNDO 和AM1 三种半经验分子轨道(MO)方法, 通过SCF计算, 首次系统地获得了32个硝酸酯化合物分子的全优化几何构型。三种方法的计算结果与已报道的四个化合物(硝酸甲酯、吉纳、硝化甘油和太安)的实验结果相比, AM1法较好。所有硝酸酯的酯基(-ONO~2)具有近似不变的几何参数。直链烷基硝酸酯的键长和键角极为相近, 全部重原子均共平面。二元直链和四元硝酸酯具有对称的分子构型。     

Structures of Nickel(II) and Copper(II) Complexes of 14-Membered Macrocyclic Quadridentate Ligands

The structures of 41 Ni(II) and 17 Cu(II) complexes of macrocyclic quadridentate ligands have been analyzed, and are discussed about bond lengths, bond angles, conformations, and configurations, upon which many conclusions are formed. The inter- or intra-molecular hydrogen bonds exist among ligands and hydrates in many compounds and play an important role in the structures. There are exhibited two distinct peaks on the histogram of the average Ni-N distances, corresponding to four coordination and six coordination; these average Ni-N distances are 1.95(4) Å and 2.10(5) Å, respectively. The most probable structures of Ni(II) macrocyclic compounds have coordination number six for the metal ion, chair forms for six-membered rings, planar structure for the metal ion and the four donor atoms of the quadridentate ligand and an inversion center at the central metal ion.     

Conformational study of halogen- and hydrogen-substituted polythionylphosphazenes using density functional theory method

The structure and conformational stability of polythionylphosphazenes is investigated by modeling single polymer chains with small mimics. The model compounds are composed of repeat units of the corresponding polythionylphosphazenes. Two of the model compounds have hydrogens and two have chlorines as substituents on phosphorus atoms. The substituents on sulfur may be either fluorine or chlorine. Fully geometry-optimized structures and energies of the stable conformations involving rotations around the P? N bond near the sulfur are obtained using the density functional theory method. The structural and conformational analyses indicate that the rotation around the N? P bond leads to variations in the bond lengths, the SNP bond angle openings, as well as couplings between dihedral angles in different conformations in all model compounds. In addition, the conformational analysis suggests that the minima on the conformational potential energy surface in these compounds may be located in the vicinity of the following values of the NP? NS dihedral angle: -50°, 90° (or 60°), 180°, and 240°. It was found that the values of the conformational energy differences range between less than 1 to 5 kcal/mol. A comparison is made between the structural results obtained using the density functional theory and the ab initio molecular orbital theory for the global minimum structures. © 1995 John Wiley & Sons, Inc.     

Molecular simulation of the comparative flexibility of bridging linkages in poly(aryl ether sulfone)s and poly(aryl ether ketone)s from a study of isolated oligomers

Atomistic molecular modelling of the bridging linkages in poly(aryl ether sulfone)s and poly(aryl ether ketone)s have been studied in vacuo. The results of these simulations indicate that models that have bond lengths and angles that agree with X-ray data are produced from the energy minimised structures and additionally that conformational analysis of these linkages produces low energy conformers that are also accessible in the X-ray data. The results of these simulations provide confidence in the modelling techniques used and indicate the potential for these models in further simulation of the bulk amorphous state.     

A density functional theory investigation of Fe-N-O bonding in heme proteins and model systems

We report the results of a series of density functional theory (DFT) calculations of the M?ssbauer quadrupole splittings and isomer shifts in NO heme model compounds, together with the results of calculations of the M?ssbauer quadrupole splittings, isomer shifts, and electron paramagnetic resonance hyperfine coupling constants in a model Fe(II)(NO)(imidazole) complex as a function of Fe-NO bond length and Fe-N-O bond angle. The results of the M?ssbauer quadrupole splitting and isomer shift calculations on the NO heme model compounds show good accord between theory and experiment, with the largest errors being observed for structures having the largest crystallographic R(1) values. The results of the property surface calculations were then used to calculate Fe-NO bond length and Fe-N-O bond angle probability surfaces (Z-surfaces) for a nitrosyl hemoglobin, using, in addition, an energy filter. The results obtained yielded a most probable Fe-NO bond length (r) of 1.79 A and an Fe-N-O bond angle (beta) of 136 degrees -137 degrees. This bond length is somewhat longer than those observed in most model compounds but may be due, at least in part, to hydrogen bond formation with the distal His residue. Bond elongation was also observed in a geometry optimized Fe(II)(NO)(imidazole) complex hydrogen bonded to an imidazole residue, in which we find r = 1.76-1.78 A and beta = 137 degrees -138 degrees. The computed bond angles are close to the canonical approximately 140 degrees value found in most model systems. Highly bent Fe-N-O bond angles or very long Fe-NO bond lengths seem unlikely to occur in proteins, due to their high energies. We also investigated the molecular orbitals and spin densities in each of the six coordinate systems investigated and found the orbitals and spin densities to be generally similar those described previously for five coordinate systems. Taken together, these results show that M?ssbauer quadrupole splittings and isomer shifts, in addition to electron paramagnetic resonance hyperfine coupling constants, can now be calculated for nitrosyl heme systems with relatively good accuracy and that the results so obtained can be used to determine Fe-N-O geometries in metalloproteins. The Z-surface approach is thus applicable to both diamagnetic (CO) and paramagnetic (NO) heme proteins with in both cases the metal-ligand binding geometries found in the proteins being very close to those seen in model systems.     

Crystal and molecular structures of diastereomeric 2-phosphoryl-, 2-thiophosphoryl-, and 2-selenophosphoryl-substituted 1,3-dithianes

The crystal and molecular structures of five pairs of diastereomeric cis- and trans-2-phosphoryl-, 2-thiophosphoryl-, and 2-selenophosphoryl-5-t-butyl-1,3-dithianes have been determined. For all the examined compounds, all of the basic geometrical parameters, such as bond lengths, bond and torsion angles, and the deformation of a chair conformation of the six-membered heterocyclic rings, have been established. The differences in corresponding bond lengths and valence angles in diastereomeric cis- and trans-2-P-substituted 1,3-dithianes are discussed.     

X-ray structural study of 3β-acetoxy-(25R)-5α-spirostan-12-one

An x-ray structural study has been made of a compound with the composition C₂₉H₄₄·O₅. The bond lengths and valence angles are the usual ones for compounds of this type. All the six-membered rings (A, B, C, and F) have the chair conformation. The five-membered rings D and E have the form of 14α- and 22α-envelopes, respectively. Rings A, B, C, and D are trans-linked, and D and E cis-linked.     

镧系金属有机配合物的研究,XL.双(2-甲氧乙基环戊二烯基)钇和镱的硼氢配合物的合成及晶体结构

双(2-甲氧乙基环戊二烯基)氯化钇和镱, 在THF中, 室温与硼氢化钠发生置换反应, 生成双(2-甲氧乙基环戊二烯基)硼氢化钇(1)和镱(2), 产率分别为70和59%。它们都经红外光谱, 质谱, ^1HNMR和元素分析鉴定。将1和2在THF-己烷中重结晶,得到适用于X射线衍射分析的单品。1的空间群为Pna2~1, 晶胞参数:a=1.2390(3),b=1.1339(2), c=1.1919(2)nm, 晶胞体积,1.6745(6)nm^3,D~c=1.39g.cm^-3, z=4, R=0.061;2的空间群为Pna2~1, 晶胞参数:a=1.2399(6),b=1.1371(5),c=1.1897(2)nm, 晶胞体积, 1.6773(1)nm^3,Dc=1.72g.cm^-3, z=4, R=0.038, 1与2都是含有两个配位键(Ln-O)的双型的单体结构。     

The MM3 force field for amides,polypeptides and proteins

The potential functions for simple amides, several peptides and a small protein have been worked out for the MM3 force field. Structures and energies were fit as previously with MM2, but additionally, we fit the vibrational spectra of the simple amides (average rms error over four compounds, 34 cm^?1), and examined more carefully electrostatic interactions, including charge-charge and charge-dipole interactions. The parameters were obtained and tested by examining four simple amides, five electrostatic model complexes, two dipeptides, six crystalline cyclic peptides, and the protein Crambin. The average root-mean-square deviation from the X-ray structures for the six cyclic peptide crystals was only 0.10 Å for the nonhydrogen atomic positions, and 0.011 Å, 1.0°, and 4.9° for bond lengths, bond angles, and torsional angles, respectively. The parameter set was then further tested by minimizing the high resolution crystal structure of the hydrophobic protein Crambin. The resultant root-mean-square deviations for the non-hydrogen atomic data, in the presence of the crystal lattice, are 0.22 Å, 0.023 Å, 2.0°, and 6.4° for coordinates, bond lengths, bond angles, and torsional angles, respectively.     

Modeling of molecular structures of (464)macrotricyclic chelates in ternary systems M(II) ion–mercaptomethanethioamide–formaldehyde

The geometric parameters of the molecular structures of (464)macrotricyclic M(II) complexes with a tetradentate chelating ligand with the (NSSN)-coordination of donor sites formed by the template reactions in the M(II)–mercaptomethanethioamide H₂N–C(=S)SH–formaldehyde CH₂O systems have been calculated by the OPBE/TZVP density functional theory (DFT) method. The bond lengths, bond angles, and some nonbonded angles in these complexes are reported. The standard enthalpies and Gibbs energies of formation of these compounds have been calculated. A conclusion has been made that the template synthesis in these systems can be realized when the corresponding reactions are carried out under traditional conditions (in solution of in the solid phase).     

Structural features of <Emphasis Type="Italic">N</Emphasis>-acylcytisines

N-Acyl cytisine derivatives were synthesized by acylation with acetic anhydride; benzoyl and o-bromo- and p-nitrobenzoyl chlorides; and crotonyl and cinnamoyl chlorides. The structures of the synthesized compounds were studied using IR, PMR, and x-ray structure analysis (XSA). PMR spectra of the N-acylcytisines in solution typically had two rotational isomers around the N12–CO bond. Conformational analysis was performed using XSA for the position of the acyl group relative to the cytisine core. Bond lengths and angles of the acyl groups involved in the conjugation were analyzed.     

Linear heterocyclic aromatic fluorescence compounds having various donor-acceptor spacers prepared by the combination of carbon-carbon bond and carbon-nitrogen bond cross-coupling reactions

A family of novel linear 1,10-phenanthroline-based (A-D-A-D-A) and oligothiophene-based (A-D-D-D-(D)-A) heterocyclic aromatic fluorescence compounds having N-containing imidazole and pyridine tails with effective π-conjugated systems, prepared by the combination of carbon-carbon (C-C) bond and carbon-nitrogen (C-N) bond cross-coupling reactions, is described. They have molecular lengths of more than 2.30 nm in the cases of 4, 6, 9, and 26, various D-A spacers, and certain N-coordination sites (phen, imidazole, and pyridine). X-ray single-crystal structures of 13 compounds reveal a variety of trans and cis configurations with different dihedral angles between adjacent aromatic heterocycles. Synthetic, computational, and spectral studies have been made to reveal the differences between cross-coupling approaches on the C-C bond and C-N bond formation as well as band gaps and energy levels and optical and electrochemical properties for related compounds. The influences of introducing a β-methyl group to the thiophene ring on reaction activity, solubility, and conformation of related compounds have also been discussed.     

Force field parametrization and molecular dynamics simulation of flexible POSS-linked (NHC; phosphine) Ru catalytic complexes

In recent years, N-heterocyclic carbene (NHC) or phospine groups have been put forward as candidate catalysts ligands for olefin metathesis reactions to be performed using multistep methods. Some of these proposed ligands contain polyhedral oligomeric silsesquioxane (POSS) structures linked to NHC rings by means of alkyl chains. Some important properties for the prediction of catalytic activity, such as the theoretically defined buried volume, are related to the conformational characteristics of these complex ligands that can be studied through molecular dynamics simulations. However, the chemical structure of resulting catalytic complexes usually contains atoms or groups that are not included in the common forcefields used in simulations. In this work we focus on complexes formed by a catalytic metal center (Ru) with both phospine and POSS-linked NHC groups. The central part of the complexes contain atoms and groups that have bonds, bond angles, and torsional angles whose parameters have not been previously evaluated and included in existing force fields. We have performed basic ab initio quantum mechanical calculations based on the density functional theory to obtain energies for this central section. The force field parameters for bonds, bond angles, and torsional angles are then calculated from an analysis of energies calculated for the equilibrium and different locally deformed structures. Nonbonded interactions are also conveniently evaluated. From subsequent molecular dynamics simulations, we have obtained results that illustrate the conformational characteristics most closely connected with the catalytic activity.     

The conformational properties of glycosidic linkages

The developments in stereochemistry which have made possible our present appreciation of the preferred orientation of the aglycon for a glycopyranoside are briefly reviewed. Recent studies in this laboratory are presented wherein, for model compounds, measurements were made of the coupling constant between the ¹³C-aglyconic carbons and anomeric hydrogens as an estimate of the torsion angles, of ¹³C-chemical shifts as a measure of relative steric compressions at the anomeric centers, and of contributions to the molecular rotations by units of conformational asymmetry defined by atoms about the glycosidic bond. These measurements are compared to the results of hard-sphere calculations. It is concluded that the exo-anomeric effect offers an important resistance to rotation about the anomeric carbon to glycosidic bond (φ angles) and that the preferred conformation for a glycopyranoside arise mainly from rotation about the aglyconic carbon to glycosidic oxygen bond (ψ angles).     

GenStar: A method for de novo drug design

Summary A novel method, which we call GenStar, has been developed to suggest chemically reasonable structures which fill the active sites of enzymes. The proposed molecules provide good steric contact with the enzyme and exist in low-energy conformations. These structures are composed entirely of sp³ carbons which are grown sequentially, but which can also branch or form rings. User-selected enzyme seed atoms may be used to determine the area in which structure generation begins. Alternatively, GenStar may begin with a predocked inhibitor core from which atoms are grown. For each new atom generated by the program, several hundred candidate positions representing a range of reasonable bond lengths, bond angles, and torsion angles are considered. Each of these candidates is scored, based on a simple enzyme contact model. The selected position is chosen at random from among the highest scoring cases. Duplicate structures may be removed using a variety of criteria. The compounds may be energy minimized and displayed using standard modeling programs. Also, it is possible to analyze the collection of all structures created by GenStar and locate binding motifs for common fragments such as benzene and naphthylene. Tests of the method using HIV protease, FK506 binding protein (FKBP-12) and human carbonic anhydrase (HCA-II) demonstrated that structures similar to known potent inhibitors may be generated with GenStar.     

Allylic boranes are chemist’s best friends: Reactivity, applications, new opportunities

Fruitful methods for the preparation of various (poly)unsaturated, (poly)cyclic and cage organic compounds with the use of allylic type organoboranes have been developed. Allylborane reactions proceeding with the rearrangement of allylic moiety or via a direct rupture of the B-C bond (with retention) little known to the boron community are considered. Synthesis of boron containing clathrochelates and some transformations of 1-boraadamantane, a unique cage compound, are also described.     

Semiempirical methods applied to long-wave satellites in X-ray emission spectra

Conclusions The following conclusions are drawn. Calculations from the CI model improve the interpretation of the observed x-ray spectra by comparison with the one-electron approximation. The two compounds show strong correlation effects for the internal MO, which agrees with the picture established in the literature of restricted applicability for the one-electron HF approximation.This method of analyzing the long-wave satellite structure on the basis of 2 hp configurations alone gives qualitative agreement with the available evidence for CO and SO₂ and evidently incorporates most of the correlation interactions.When one extends the MO basis in the CI calculations, one can describe much of the correlation effect for the outer MO. Consequently, one can use this model for qualitative or semiquantitative evaluation of long-wave satellite structures and multielectron limits arising from interaction between closely spaced 2hp configurations in the final state in the x-ray transitions, which appear in the x-ray spectra for coordination compounds. It is particularly important to determine the multielectron limit for a coordination compound because measurements are used in drawing conclusions on the bond types, reactivities, and ligand interactions [39, 40], where one considers also the form of the long-wave part of the spectrum.Institute of Inorganic Chemistry, Siberian Branch, USSR Academy of Sciences. Translated from Zhurnal Strukturnoi Khimii, Vol. 30, No. 2, pp. 80–91, March–April, 1989.     

极性分子键角与键偶极矩的关系

研究了基态极性分子的键角和键偶极矩之间的关系。我们采用原子偶极矩校正的Hirshfeld （ADCH）电荷来计算键偶极矩,利用电子的局域函数和键临界点处的局域函数值来分析键的电子结构。通过对IVA族（IVA = C,Si,Ge）、VA族（VA = N,P,As ）、VIA族（VIA = O,S,Se）和VIIA族（VIIA = F,Cl,Br）元素形成的系列共价型基态分子,以及环状基态分子的键角和键偶极矩数据进行分析,发现在键的电子结构类似的情况下,由于键偶极矩的排斥作用,这些分子的键角随键偶极矩的增加而增大。这一发现有助于加深我们对分子几何结构的认识。