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PubMed2005

[Quantitative relationship between molecular structure of polychlorinated biphenyls (PCBs) and enthalpy change (deltaH), entropy change (deltaS') in chromatographic process].

The relationship between the rule of chromatographic retention value and molecular structure is an important part in the research of chromatographic thermodynamics. The topological index structural parameter JG and the topological index adjoining parameter LJ are put forward. Parameter J(G) describes the correlation of quantity and position of chlorine atoms in polychlorinated biphenyl (PCB) molecules. Parameter L(J) describes the ortho-position correlation of chlorine atoms in PCB molecules. The relational expression between the PCB molecular structures and their enthalpy change (deltaH), entropy change (deltaS') in chromatographic process was discovered. The values of enthalpy change and entropy change for about 140 kinds of polychlorinated biphenyls in chromatographic process on three stationary phases, DB-1, DB-5 and DB-1701, were determined. In comparison with deltaH and deltaS' of the experimental data those calculated from the relational expression had the average relative deviations for deltaH and deltaS' are 0.56% -0.97% and 0.55% - 1.06%, respectively.

Chromatography↗

PubMed2006

Ab initio and DFT studies of the molecular structures and vibrational spectra of succinonitrile.

The Molecular structure, conformational stability and vibrational frequencies of succinonitrile NCCH2CH2CN have been investigated with ab initio and density functional theory (DFT) methods implementing the standard 6-311++G* basis set. The potential energy surfaces (PES) have been explored at DFT-B3LYP, HF and MP2 levels of theory. In agreements with previous experimental results, the molecule was predicted to exist in equilibrium mixture of trans and gauche conforms with the trans form being slightly lower in energy. The vibrational frequencies and the corresponding vibrational assignments of succinonitrile in both C2h and C2 symmetry were examined theoretically and the calculated Infrared and Raman spectra of the molecule were plotted. Observed frequencies for normal modes were compared with those calculated from normal mode coordinate analysis carried out on the basis of ab initio and DFT force fields using the standard 6-311++G* basis set of the theoretical optimized geometry. Theoretical IR intensities and Raman activities are reported.

Models, Chemical↗

PubMedDate not supplied

Structure Elucidator: a versatile expert system for molecular structure elucidation from 1D and 2D NMR data and molecular fragments.

StrucEluc is an expert system that allows the computer-assisted elucidation of chemical structures based on the inputs of a series of spectral data including 1D and 2D NMR and mass spectra. The system has been enabled to allow a chemist to utilize fragments stored in a fragment database as well as user-defined fragments submitted by the chemist in the structure elucidation process. The association of fragments in this way has been shown to dramatically speed up the process of structure generation from 2D NMR data and has helped to minimize or eliminate the need for user intervention thereby further enabling the vision of automated elucidation. The use of fragments has frequently transformed very difficult 2D NMR elucidation challenges into easily solvable tasks. A strategy to utilize molecular fragments has been developed and optimized based on specific challenging examples. This strategy will be described here using real world examples. Experience gained by solving more than 150 structure elucidation problems from a variety of literature sources is also reviewed in this work.

Journal Article↗

PubMed2004

Molecular structure of 1,1,2,2-tetra-tert-butyldisilane: unusual structural motifs in sterically crowded disilanes.

The molecular structure of 1,1,2,2-tetra-tert-butyldisilane has been determined by gas-phase electron diffraction supported by ab initio calculations, in the solution phase by Raman spectroscopy, and in the solid phase by Raman spectroscopy and X-ray crystallography. The gas-phase structure (C2 symmetry) was found to be almost anticlinal, a most unusual and unexpected result. In the favoured conformation, contact between tert-butyl groups at each end of the molecule is avoided by a large deviation of the angles around the silicon atoms from the parent tetrahedral angle of 109.5 degrees. In fact, the Si-Si-C angles returned from the gas electron diffraction refinement are 117.0(5) and 110.7(6) degrees, indicating the large degree of flexibility about the silicon centres. The ab initio methods and gas electron diffraction results indicate that there is only one conformer of But2HSiSiHBut2 in the gaseous mixture. Variable temperature Raman studies indicate the possibility of a further higher energy conformer existing in the liquid phase. However, this seems quite improbable from other observations made for the Raman spectra at all temperatures. The X-ray structure is close to that observed in the gas phase, with phiHSiSiH = 94.2(18) degrees. There is a large amount of disorder about one of the silicon postions and one of the tert-butyl groups within the crystal structure, which makes detailed direct comparison with the gaseous structure difficult.

Journal Article↗

PubMed1996

The molecular structure of apolipoprotein A-II modulates the capacity of HDL to promote cell cholesterol efflux.

The influence of apolipoprotein A-II (apoA-II) molecular structure on the capacity of high density lipoproteins (HDL) to promote cellular cholesterol efflux was investigated in cultured mouse peritoneal macrophages (MPM). Conversion by reduction and carboxamidomethylation of the naturally occurring dimeric apoA-II to its monomeric form in both native or reconstituted HDL did not change apolipoprotein secondary structure and lipoprotein size/composition. All particles containing monomeric apoA-II, i.e., native HDL3 or reconstituted HDL with or without apoA-I, showed a higher ability to promote cholesterol efflux originating from plasma membrane and intracellular stores, compared to particles containing dimeric apoA-II. These findings indicate that apolipoprotein molecular structure is a major determinant of HDL capacity to promote cholesterol efflux from cells.

Animals↗

PubMed2005

Molecular dynamics of transient oil flows in nanopores. II. Density profiles and molecular structure for decane in carbon nanotubes.

We report molecular dynamics simulations of nanotubes imbibing decane at an oil/vapor interface at 300 K. We find that the smallest (7,7) nanotubes imbibe extremely rapidly (< or =800 ms), with the imbibition speed slowing as the tube's radius increases. The density profiles of the imbibing fluid in the pores are analyzed as a function of time. We find that the imbibing liquid is well described by the advection-diffusion equation and present expressions for the density profiles (in x and t) of the imbibing fluid as a function of the adsorption energy and surface friction of the pore. In addition we have analyzed the molecular structure of the imbibed fluid in nanotubes and describe how molecular conformations change with nanotube radius and position in the pore. We are therefore able to provide a complete description of the imbibition of a wetting fluid, decane, for a wide range of nanopores.

Journal Article↗

PubMed2003

Predicting the genotoxicity of thiophene derivatives from molecular structure.

We report several binary classification models that directly link the genetic toxicity of a series of 140 thiophene derivatives with information derived from the compounds' molecular structure. Genetic toxicity was measured using an SOS Chromotest. IMAX (maximal SOS induction factor) values were recorded for each of the 140 compounds both in the presence and in the absence of S9 rat liver homogenate. Compounds were classified as genotoxic if IMAX >or= 1.5 in either test or nongenotoxic if IMAX < 1.5 for both tests. The molecular structures were represented by numerical descriptors that encoded the topological, geometric, electronic, and polar surface area properties of the thiophene derivatives. The classification models used were linear discriminant analysis (LDA), k-nearest neighbor classification (k-NN), and the probabilistic neural network (PNN). These were used in conjunction with either a genetic algorithm or a generalized simulated annealing to find optimal subsets of descriptors for each classifier. The quality of the resulting models was determined by the number of misclassified compounds, with preference given to models that produced fewer false negative classifications. Model sizes ranged from seven descriptors for LDA to three descriptors for k-NN and PNN. Very good classification results were obtained with all three classifiers. Classification rates for the LDA, k-NN, and PNN models were 80, 85, and 85%, respectively, for the prediction set compounds. Additionally, a consensus model was generated that incorporated all three of the basic model types. This consensus model correctly predicted the genotoxicity of 95% of the prediction set compounds.

DNA Damage↗

PubMed2002

Electron transfer through bridging molecular structures.

Pairs of reducible pentakis(thiophenyl)benzene subunits are linked by different molecular structures as model compounds for reducible molecular-wire-type synthons showing varying electron-transfer ability as a function of the bridging structures, consisting of either para-divinylbenzene, bis-hydrazone, or diacetylene. Their electron-transfer ability from one reducible subunit to the other was investigated by electrochemical and spectroelectrochemical methods. In the case of the bis-hydrazone bridge and the diacetylene bridge, the solid-state structures support the experimental findings. While the para-divinylbenzene bridge completely isolates the reducible subunits (class I system) the diacetylene bridge electronically connects the two reducible structures (class III system), demonstrating its potential application as a "molecular wire." The bis-hydrazone linked dimer displays electronic communication only to a small extend, which was only observed in the spectroelectrochemical investigation. The diacetylene connection as active electron-transfer linker together with poly(thiophenyl)benzene as reducible subunits was used to design more complex molecular architectures. Linear rodlike structures did allow adjustment of the length of these type of molecular wires and investigation of the extent of electron mobility. Cyclic structures addressed the possibility of moving electrons on a bent molecular wire.

Benzene↗

PubMed2005

Influence of surfactant molecular structure on two-dimensional surfactant-DNA complexes: Langmuir balance study.

In this paper, we used two simplified methods to understand the influence of surfactant molecular structure on the properties of surfactant-DNA complexes. First, we selected Langmuir balance technique, a two-dimensional (2D) method, which allows complex formation under equilibrium-like conditions, avoiding some of the inherent problems involved in solution. Secondly, two series of simple quaternary ammonium surfactants were used. The cationic surfactant-DNA complex monolayers were formed at the air-water interface through the electrostatic interaction between the ammonium groups of the surfactants and the phosphate groups of DNA at the air-water interface. Combining the results of pi-A isotherms, pi-t isotherms, and atomic force microscopy (AFM) measurements, it was found that the surfactant molecular structures affect the surface properties and morphologies of 2D surfactant-DNA complexes. We expect that the study of the properties of 2D surfactant-DNA complexes will help us to understand the physicochemical properties of surfactant-DNA complexes, which are important for gene delivery.

Aluminum Silicates↗

PubMed2006

Electronic and molecular structure of photoexcited [Ru(II)(bpy)3]2+ probed by picosecond X-ray absorption spectroscopy.

L(2,3) X-ray absorption spectra of aqueous [Ru(II)(bpy)3]2+ have been recorded in its ground and excited states, 50 ps after short pulse laser excitation. Significant changes in both the XANES (X-ray Near-Edge Absorption Structure) and the EXAFS (Extended X-ray Absorption Fine Structure) regions of the excited state complex are detected. The XANES line shapes have been quantitatively simulated using a crystal field multiplet code in trigonal symmetry. In addition, spectral changes in the EXAFS region of both ground and excited states are analyzed in order to extract structural parameters of their corresponding molecular structures. We obtain a Ru-N bond contraction by approximately 0.03 angstroms in the excited-state complex, as compared to the ground-state compound. This contraction results from electrostatic and polarization contributions, limited by steric constraints on the bpy ligands.

Journal Article↗

PubMed1989

Antitumor drug nogalamycin binds DNA in both grooves simultaneously: molecular structure of nogalamycin-DNA complex.

The three-dimensional molecular structures of the complexes between an interesting antitumor drug, nogalamycin, and two DNA hexamers, d[CGT(pS)ACG] and d[m5CGT(pS)Am5CG], were determined at high resolution by X-ray diffraction analyses. Two nogalamycins bind to the DNA double helix in a 2:1 ratio with the aglycon chromophore intercalated between the CpG steps at both ends of the helix. The nogalose and aminoglucose sugars lie in the minor and major grooves, respectively, of the distorted B-DNA double helix. The binding of nogalamycin to DNA requires that the base pairs in DNA open up transiently to allow the bulky sugars to go through. Specific hydrogen bonds are found in the complex between the drug and guanine bases. We suggest that nogalamycin may prefer GC sequences embedded in a stretch of AT sequences.

DNA↗

PubMed2006

Comparative analyses of a family of potential self-replicators: the subtle interplay between molecular structure and the efficacy of self-replication.

It is envisioned that protocols based on self-replication will emerge as a formidable synthetic apparatus for the production of nanoscale assemblies through molecular structures that are capable of automultiplication with high reaction rates and selectivities. To achieve this goal, a complete understanding of the relationship between molecular structure and replication efficiency is necessary. Rigorous experimental and theoretical analyses of a series of self-complementary scaffolds that are intimately related in a constitutional sense, manufactured through the Diels-Alder reaction of complementary subunits, were undertaken. Experimental and computational methods were employed to map the key determinants that dictate the emergence of self-replicative function, as well as the efficiency, rate and selectivity of the self-replicative processes.

Crystallography, X-Ray↗

PubMedDate not supplied

Predicting physical-chemical properties of compounds from molecular structures by recursive neural networks.

In this paper, we report on the potential of a recently developed neural network for structures applied to the prediction of physical chemical properties of compounds. The proposed recursive neural network (RecNN) model is able to directly take as input a structured representation of the molecule and to model a direct and adaptive relationship between the molecular structure and target property. Therefore, it combines in a learning system the flexibility and general advantages of a neural network model with the representational power of a structured domain. As a result, a completely new approach to quantitative structure-activity relationship/quantitative structure-property relationship (QSPR/QSAR) analysis is obtained. An original representation of the molecular structures has been developed accounting for both the occurrence of specific atoms/groups and the topological relationships among them. Gibbs free energy of solvation in water, Delta(solv)G degrees , has been chosen as a benchmark for the model. The different approaches proposed in the literature for the prediction of this property have been reconsidered from a general perspective. The advantages of RecNN as a suitable tool for the automatization of fundamental parts of the QSPR/QSAR analysis have been highlighted. The RecNN model has been applied to the analysis of the Delta(solv)G degrees in water of 138 monofunctional acyclic organic compounds and tested on an external data set of 33 compounds. As a result of the statistical analysis, we obtained, for the predictive accuracy estimated on the test set, correlation coefficient R = 0.9985, standard deviation S = 0.68 kJ mol(-1), and mean absolute error MAE = 0.46 kJ mol(-1). The inherent ability of RecNN to abstract chemical knowledge through the adaptive learning process has been investigated by principal components analysis of the internal representations computed by the network. It has been found that the model recognizes the chemical compounds on the basis of a nontrivial combination of their chemical structure and target property.

Journal Article↗

PubMed2004

Divalent germanium compound with a radical-anionic ligand: molecular structures of (dpp-BIAN)- GeCl and its hydrochloration products [(dpp-BIAN)(H)2]+ [GeCl3]- and [[(dpp-BIAN)(H)2*+]2(Cl-)]+ [GeCl3]- (dpp-BIAN=1,2-Bis[(2,6-diisopropylphenyl)imino]acenaphthene).

The germanium(II) compound (dpp-BIAN)GeCl (1), which contains the radical anion of dpp-BIAN can be prepared either by reacting free dpp-BIAN ligand with 2 equiv of GeCl2(1,4-dioxane) in Et2O or by metathetical reaction of the sodium salt of dpp-BIAN with germanium dichloride in Et2O or benzene. The reaction of benzene solutions of 1 with 2 or 3 equiv of HCl led to protonation of the dpp-BIAN ligand affording [(dpp-BIAN)(H)2]*+[GeCl3]- (2) and [[(dpp-BIAN)(H)2*+]2(Cl-)]+ [GeCl3]- (3), which incorporate the radical cation of the protonated ligand. Compounds 1-3 have been characterized by elemental analysis, IR, UV-vis, and electron spin resonance (ESR) spectroscopy. Molecular structures of 1-3 were determined by single-crystal X-ray diffraction. In molecule 1, the Ge atom is positioned at the apex of the slightly distorted trigonal pyramid. The Ge-N bond lengths in 1 are 2.0058(19) and 2.004(2) A. The molecular structure of 2 consists of contact ions [(dpp-BIAN)(H)2]+ and [GeCl3]-. In the molecular structure of 3, two radical cations of [(dpp-BIAN)(H)2]+ are "coordinated" by the chlorine anion. The ESR signal of 1 indicates the presence of a dpp-BIAN radical anion and shows a hyperfine structure due to the coupling of an unpaired electron to 14N, 73Ge, 35Cl, 37Cl, and 1H nuclei (AN=0.48 (2 N), AGe=0.96, ACl=0.78 (35Cl), ACl=0.65 (37Cl), AH=0.11 (4 H) mT, g=2.0014). Both 2 and 3 reveal ESR signals of radical cation [(dpp-BIAN)(H)2]*+ (septet, AN=0.53, AH=0.48 mT, g=2.0031).

Journal Article↗

PubMed2004

Does alpha-fluorination affect the structural trans-influence and kinetic trans-effect of an alkyl ligand? Molecular structures of Pd(TMEDA)(CH(3))(R(F)) and a kinetic study of the trans to cis isomerization of Pt(TMEDA)(CH(3))(2)I(R(F)) [R(F) = CF(2)CF(3), CFHCF(3), CH(2)CF(3)].

Reaction of Pd(TMEDA)(CH(3))(2) [TMEDA = tetramethylethylenediamine] with fluoroalkyl iodides R(F)I affords a series of square planar Pd(II) complexes Pd(TMEDA)(CH(3))(R(F)) [R(F) = CF(2)CF(3) (9), CFHCF(3) (10), CH(2)CF(3) (11)], presumably by oxidative addition followed by reductive elimination of CH(3)I. The solid-state structures of each compound have been determined by single crystal X-ray diffraction studies, allowing the effect of increasing alpha-fluorination on the structural trans-influence of alkyl ligands to be examined. In these compounds there is no significant difference observed in the trans-influence of the three fluorinated alkyl ligands toward the trans-N atom, although a significant cis-influence on the neighboring methyl ligand is apparent. Oxidative addition of the same series of fluoroalkyl ligands to the corresponding Pt(TMEDA)(CH(3))(2) affords octahedral Pt(IV) complexes trans-Pt(TMEDA)(CH(3))(2)(R(F))I [R(F) = CF(2)CF(3) (12), CFHCF(3) (13), CH(2)CF(3) (14)] as the kinetic products. In each case, subsequent isomerization to the corresponding all cis-isomers is observed; in the case of 13, the stereocenter at the alpha-carbon results in two diastereomeric cis-isomers, which are formed at different rates. The molecular structures of 13 and its more stable all cis-isomer 16b have been crystallographically determined. Kinetic studies of the trans-cis isomerization reactions show the mechanism to involve a polar transition state, presumably involving iodide dissociation, followed by rearrangement of the cation, and iodide recombination. High dielectric solvents increase the rate, but solvent coordinating ability has no effect. Dissolved salts (LiI, LiOTf) show normal accelerative salt effects, with no inhibition in the case of added iodide, consistent with the formation of an intimate ion pair intermediate. The kinetic parameters show that the trans-effects of fluoroalkyl ligands in these compounds follow the order expected from the relative sigma-donor properties of the ligands, with CF(2)CF(3) < CFHCF(3) < CH(2)CF(3).

Journal Article↗

PubMed1982

Structure-activity relationships in the ansamycins. Molecular structure and activity of 3-carbomethoxy rifamycin S.

The X-ray and NMR structural study of 3-carbomethoxy rifamycin S5 was undertaken in order to determine whether its low antimicrobial activity was related to a conformation of the molecule which was unfavorable for interaction with bacterial DNA-dependent RNA polymerase. However, the molecule assumes a conformation similar to that of the active rifamycins. Indeed the compound was found to be active on the isolated enzyme, so that its low activity on whole bacteria has to be attributed to factors affecting its penetration through the bacterial cell wall.

Anti-Bacterial Agents↗

PubMed2006

Molecular structure and benzene ring deformation of three ethynylbenzenes from gas-phase electron diffraction and quantum chemical calculations.

The molecular structures of ethynylbenzene and s-triethynylbenzene have been accurately determined by gas-phase electron diffraction and ab initio/DFT MO calculations and are compared to that of p-diethynylbenzene from a previous study [Domenicano, A.; Arcadi, A.; Ramondo, F.; Campanelli, A. R.; Portalone, G.; Schultz, G.; Hargittai, I. J. Phys. Chem. 1996, 100, 14625]. Although the equilibrium structures of the three molecules have C2v, D3h, and D2h symmetry, respectively, the corresponding average structures in the gaseous phase are best described by nonplanar models of Cs, C3v, and C2v symmetry, respectively. The lowering of symmetry is due to the large-amplitude motions of the substituents out of the plane of the benzene ring. The use of nonplanar models in the electron diffraction analysis yields ring angles consistent with those from MO calculations. The molecular structure of ethynylbenzene reported from microwave spectroscopy studies is shown to be inaccurate in the ipso region of the benzene ring. The variations of the ring C-C bonds and C-C-C angles in p-diethynylbenzene and s-triethynylbenzene are well interpreted as arising from the superposition of independent effects from each substituent. In particular, experiments and calculations consistently show that the mean length of the ring C-C bonds increases by about 0.002 A per ethynyl group. MO calculations at different levels of theory indicate that though the length of the C[triple bond]C bond of the ethynyl group is unaffected by the pattern of substitution, the C(ipso)-C(ethynyl) bonds in p-diethynylbenzene are 0.001-0.002 A shorter than the corresponding bonds in ethynylbenzene and s-triethynylbenzene. This small effect is attributed to conjugation of the two substituents through the benzene ring. Comparison of experimental and MO results shows that the differences between the lengths of the C(ipso)-C(ethynyl) and C(ipso)-C(ortho) bonds in the three molecules, 0.023-0.027 A, are correctly computed at the MP2 and B3LYP levels of theory but are overestimated by a factor of 2 when calculated at the HF level.

Journal Article↗

PubMed1997

Synthesis of Volatile Cyclic Silylamines and the Molecular Structures of Two 1-Aza-2,5-disilacyclopentane Derivatives.

An optimized synthetic procedure for alpha,omega-bis(bromosilyl)alkanes, BrH(2)Si(CH(2))(n)()SiH(2)Br (with n = 2 and 3), is proposed. 1,2-Bis(bromosilyl)ethane reacts with ammonia to give 1,4-bis(1-aza-2,5-disilacyclopentane-1-yl)-1,4-disilabutane, traces of 1,6-diaza-2,5,7,10,11,14-hexasilabicyclo[4.4.4]tetradecane and nonvolatile products. The primary reaction products undergo slow redistribution reactions whereby (1-aza-2,5-disilacyclopentane-1-yl)-1,4-disilabutane is formed as the major product. Reactions of alpha,omega-bis(bromosilyl)alkanes, BrH(2)Si(CH(2))(n)()SiH(2)Br (with n = 2 and 3), with isopropylamine afford the heterocycles 1-isopropyl-1-aza-2,5-disilacyclopentane and 1-isopropyl-1-aza-2,6-disilacyclohexane, whereas the analogous reaction with bis(bromosilyl)methane gives 1,5-diisopropyl-1,5-diaza-2,4,6,8-tetrasilacyclooctane rather than a four-membered ring compound. All compounds have been characterized by elemental analysis, mass spectrometry, and IR and NMR spectroscopy [(1)H, (13)C, (15)N and (29)Si including the measurement of (1)J((29)Si(15)N) coupling constants]. The molecular structure of 1-isopropyl-1-aza-2,5-disilacyclopentane, determined by analysis of gas-phase electron-diffraction data augmented by restraints derived from ab initio calculations, is compared with the molecular structure of the isoelectronic 1-(dimethylamino)-1-aza-2,5-disilacyclopentane. The latter also was determined by gas-phase electron-diffraction (supported by ab initio calculations) and by low-temperature crystallography. The presence of a beta-donor Si.N interaction in the latter compound, leading to a narrow Si-N-N angle, is apparent from a significant distortion of the molecular structure as compared with the isoelectronic reference compound.

Journal Article↗