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PubMed1994

Molecular structures and conformational studies of triarylcyclopropyl and related nonsteroidal antiestrogens.

Molecular structures and conformational characteristics of a series of 1,1-dichloro-2,2,3-triarylcyclopropanes (DTACs), which were reported previously to be distinctly antiestrogenic and inhibitors of the estrogen-receptor-positive MCF-7 human breast cancer cells in culture, are reported. In addition, structural and conformational features of the DTACs were compared to the first-known nonsteroidal antiestrogen, MER25, and the clinically useful antiestrogen Tamoxifen. The molecular structures of four DTAC compounds were determined by X-ray diffraction. Crystallographic structures show that the DTAC molecules have nearly the same relative conformation for the three aryl rings which is designated as a "nonpropeller" conformation in contrast to the observed "propeller" conformation for the three rings in all known triarylethylenes. Systematic conformational searches were performed to find the conformational preferences of DTACs, MER25, and Tamoxifen using idealized model compounds built from their respective crystal structure. Energy-minimization and conformational-search studies demonstrated that all DTAC molecules have a common, single global minimum energy conformer for their central core containing the dichlorotriarylcyclopropyl system, which is similar to that found in their crystal structures. Conformational search of MER25 showed that the molecule can assume a number of low-energy conformers of which two, one anti (A1) and one gauche (G1A), have about the same energy. The anti conformation is similar to the one observed in its crystal structure and resembles the estrogenic E-isomer of Tamoxifen, while the lowest energy gauche conformer of MER25 resembles more closely the antiestrogenic Z-isomer of Tamoxifen. NMR spectroscopic analysis of MER25 showed that the molecule exists predominantly in the anti conformation in solution. A comparative review of the structural features and bioactivities of Tamoxifen, DTACs, and MER25 provides a possible explanation for their low estrogen receptor binding affinity which is common to these compounds together with their antiestrogenic activity.

Crystallization↗
PubMed1994

The molecular structure of human erythropoietin.

The molecular structure of EPO has been discussed, and the gradual emergence of information about EPO has been reviewed. The importance of certain regions of the molecule and of glycosylation to EPO's structure and function are clear. Although its nucleotide and amino acid sequences are known, its tertiary structure remains elusive. Antipeptide antibody and mutagenesis studies have increased our ability to study structure/function and certain spatial relationships. Undoubtedly, additional information will continue to become available in this exciting area, providing a better understanding of the mechanisms behind EPO's central role in erythropoiesis.

Amino Acid Sequence↗
PubMed1994

Crystal and molecular structures of pyridazinone cardiovascular agents.

The crystal and molecular structures of 11 6-substituted pyridazinone derivatives: 6-phenyl-3(2H)-pyridazinone-acetic acid (1/1) (1), 6-(4-aminophenyl)- 3(2H)-pyridazinone (2), 6-(4-aminophenyl)- 5-methyl-3(2H)-pyridazinone (3), 6-(4-acetamidophenyl)- 3(2H)-pyridazinone (4), 6-(4-acetamido-2- methoxyphenyl)-3(2H)-pyridazinone (5), 6-(2-aminophenyl)-3(2H)- pyridazinone (6), 6-phenyl-3(2H)- pyrazinone (7), 6-(4-aminophenyl)-4,5-dihydro- 3(2H)-pyridazinone (8), (R)-(-)-6[4-(3-bromopropionamido)phenyl]- 4,5-dihydro-5-methyl-3(2H)-pyridazinone (9), (R)-(-)-6-(4-ammoniophenyl)-4,5- dihydro-5-methyl-3(2H)-pyridazinone (-)-tartrate-dichloromethane-methanol (1/1/1) (10), 4,5-dihydro-6-methyl-3(2H)-pyridazinone (11) have been determined as part of a study to determine the relationship between their cardiovascular properties and molecular structure and dimensions. For the two optically resolved chiral derivatives (9) and (10) the absolute configuration has been determined.

Cardiovascular Agents↗
PubMed2005

Molecular structure calculations without clamping the nuclei.

A number of recent papers have considered ways in which molecular structure may be calculated when both the electrons and the nuclei are treated from the outset as quantum particles. This is in contrast to the conventional approach in which the nuclei initially have their positions fixed and so merely provide a potential for electronic motion. The usual approach is generally assumed to be justified by the 1927 work of Born and Oppenheimer. In this paper we discuss what precisely might be anticipated in the way of molecular structure from a mathematical consideration of the spectral properties of the full Coulomb Hamiltonian, to what extent the very idea of molecular structure might be dependent upon treating the nuclei simply as providing a potential and the extent to which the work of Born and Oppenheimer can be used to support this position.

Algorithms↗
PubMed2003

Effect of polymer tacticity on the molecular structure of polyelectrolyte/surfactant stoichiometric complexes in solutions and gels.

The molecular structure of polystyrene sulphonate/CTAB stoichiometric complexes has been examined by means of small-angle neutron scattering in solutions and in the gel state for two different tacticities of the polystyrene moiety, namely atactic polystyrene and isotactic polystyrene. It is found that tacticity has no influence on the molecular structure in solution, while it plays a role in the gel state. The neutron scattering curves are interpreted with different helical models. The thermal properties of the gels are discussed in the light of the neutron scattering outcomes.

1-Butanol↗
PubMed2006

Molecular aggregation of rhodamine dyes in dispersions of layered silicates: influence of dye molecular structure and silicate properties.

The molecular aggregation of six rhodamine dyes (rhodamine 560, B, 3B, 19, 6G, 123) in layered silicate (saponite and fluorohectorite) dispersions was investigated by using visible (vis) spectroscopy. The dye molecular aggregation was influenced by the properties of both the silicates and the dyes themselves. The layer charge of the silicates enhanced the molecular aggregation of the hydrophilic, cationic dyes. The presence of a carboxyl acid group in the dye molecules inhibited adsorption of the dyes on the surface of fluorohectorite, a silicate with a high charge density. A lower or no adsorption could be observed by vis spectroscopy. Strong association of the dyes to the silicate surface led to remarkable changes in the dye spectra, mainly due to the molecular aggregation. Dye assemblies initially formed after mixing the dye solutions with silicate dispersions were unstable. Decomposition of the dye molecular assemblies, and the formation of new species or molecular aggregate rearrangements, were studied on the bases of time-difference spectra. The reaction pathways were specific, not only for the dyes, depending upon their molecular structure and properties, but also on the silicate substrates.

Journal Article↗
PubMed1986

Molecular structure and absolute configuration of suberogorgin.

In the present paper it is reported that the molecular structure and absolute configuration of poisonous suberogorgin are determined by using X-ray diffraction method. The crystal of suberogorgin belongs to orthogonal system with space group D4(2)-P2(1)2(1)2(1). The crystallographic parameters are: a = 16.135A, b = 13.189A, c = 12.901A, Z = 8. The initial model of the crystal structure was solved by the direct method. The refinement of the structure parameters was carried out by using the least square method and led to a final R-factor of 0.056. In accordance with the molecular structure of suberogorgin mentioned above, the solvent effect of NMR has been further discussed and the relationship between the molecular structure of suberogorgin and its toxicity has also been preliminarily investigated.

Animals↗
PubMed2005

Strong effects of molecular structure on electron transport in carbon/molecule/copper electronic junctions.

Carbon/molecule/copper molecular electronic junctions were fabricated by metal deposition of copper onto films of various thicknesses of fluorene (FL), biphenyl (BP), and nitrobiphenyl (NBP) covalently bonded to flat, graphitic carbon. A "crossed-wire" junction configuration provided high device yield and good junction reproducibility. Current/voltage characteristics were investigated for 69 junctions with various molecular structures and thicknesses and at several temperatures. The current/voltage curves for all cases studied were nearly symmetric, scan rate independent, repeatable at least thousands of cycles and exhibited negligible hysteresis. Junction conductance was strongly dependent on the dihedral angle between phenyl rings and on the nature of the molecule/copper "contact". Junctions made with NBP showed a decrease in conductivity of a factor of 1300 when the molecular layer thickness increased from 1.6 to 4.5 nm. The slope of ln(i) vs layer thickness for both BP and NBP was weakly dependent on applied voltage and ranged from 0.16 to 0.24 A(-1). These attenuation factors are similar to those observed for similar molecular layers on modified electrodes used to study electrochemical kinetics. All junctions studied showed weak temperature dependence in the range of approximately 325 to 214 K, implying activation barriers in the range of 0.06 to 0.15 eV. The carbon/molecule/copper junction structure provides a robust, reproducible platform for investigations of the dependence of electron transport in molecular junctions on both molecular structure and temperature. Furthermore, the results indicate that junction conductance is a strong function of molecular structure, rather than some artifact resulting from junction fabrication.

Journal Article↗
PubMed1995

The molecular structure of human antibodies specific for the human immunodeficiency virus.

The molecular structure of human antibodies that are specific for human immunodeficiency virus-1 (HIV-1) are of increasing interest as AIDS research progresses toward passive immunotherapeutics in the maintenance and prevention of infection. In recent years a number of human, HIV-specific hybridomas and EBV-transformed B cell lines, as well as a combinatorial library, have been developed and characterized at the molecular level. These sources have provided valuable information on the immunoglobulin heavy- and light-chain variable-region gene usage and the extent and appearance of somatic mutation in a disease where the immune system is under constant stimulation over a long period of time. In this article we review the current data available on the molecular structure of these antibodies.

Amino Acid Sequence↗
PubMed2006

A line-shape function in terms of changes in both molecular structure and force constants: a Gaussian approximation.

We propose a new expression of a line-shape function (LSF) including the effects of changes in both force constants and the molecular structure within the harmonic-oscillator approximation. This expression enables us to calculate the LSF using only the data on molecular structures, force constants, and electronic energies in the initial and final electronic states without solving the eigenvalue equation for the normal vibration of a molecule. To derive the LSF expression, we consider one-photon emission from a polyatomic molecule thermalized in an electronic excited state, and derive the intensity distribution function for one-photon emission using not Lax and Kubo and Toyozawa's [J. Chem. Phys. 20, 1752 (1952); Prog. Theor. Phys. 13, 160 (1955)] generating function method but rather the density-matrix method. As a simple application, a Gaussian approximate LSF is applied to SO(2). As a result, it is found that the effect of change in force constants between the initial and final electronic states cannot be ignored, nor can the effect of change in the molecular structure between these two states. The LSF expression obtained is applicable to studies of not only radiative transition but also of electron-transfer and energy-transfer processes where both changes in molecular structure and force constants between the initial and final electronic states cannot be disregarded.

Journal Article↗
PubMedDate not supplied

A new graph descriptor for molecules containing cycles. Application as screening criterion for searching molecular structures within large databases of organic compounds.

The search of molecular structures inside a large database of chemical compounds is a critical step for many computer programs used in several domains of chemistry. During the last years, the size of many chemical databases has dramatically increased, hence in the meantime, search engines needed to be more and more powerful. The speed and the efficiency of screening processes of the chemical compounds are thus essential. Looking forward for algorithms dedicated to structure and substructure search, we have developed a new graph descriptor for structures containing cycles in order to find efficient indexation and classification criteria of molecular structures. This graph descriptor can be used as a screening criteria for structure and substructure search in large databases of organic compounds.

Journal Article↗
PubMed1987

Defining the active site of cytochrome P-450: the crystal and molecular structure of an inhibitor, SKF-525A.

The crystal and molecular structure of the cytochrome P-450 inhibitor, SKF-525A [2-(diethylamino)ethyl 2,2-diphenylpentenoate; proadifen hydrochloride] is described. Proadifen hydrochloride crystallized from an ethyl acetate and acetic acid mixture in the space group P2(1)/c with one molecule in the asymmetric unit. Cell constants are a = 18.716(4), b = 8.906(1), c = 14.201(3), beta = 109.41(1) degrees. The structure was solved using direct methods and was refined to an R value of 0.047; weighted R of 0.061 using 3757 reflections. From the crystal and molecular structure, it is seen that SKF-525A has two principal modes of complementary interactions with the enzyme available: polar and non-polar. Polar interactions that principally involve the chloride anion, the quaternary nitrogen atom and the carbonyl oxygen atom. In particular, there are two strong hydrogen bonds, one between Cl ... H-N, 3.090(1) A, the other between O2 ... H-C111 (one of the ethyl hydrogen atoms) at 3.411(2) A. The other is through non-polar interactions involving the phenyl and alkyl groups. Comparisons between proadifen hydrochloride and other inhibitors whose atomic coordinates are available reveal common features which correlate with their function. These include groups to provide necessary intermolecular contacts and bulk, such as a phenyl group and a hydrogen bond acceptor, as well as a tetrahedral atom, which allows for substrate flexibility.

Crystallization↗
PubMed2001

Molecular structure of fulvic acids by electrospray with quadrupole time-of-flight mass spectrometry.

Characterisation of the molecular structure of aquatic fulvic acids (FA) has been performed using a quadrupole time-of-flight (Q-TOF) mass spectrometer equipped with an electrospray ionisation interface. Molecular masses centred around 450 Da and sinusoidal spectral distributions have been obtained for all fulvic acids. Tandem mass spectrometry (MS/MS) experiments showed losses of 18 Da (H(2)O) and 44 Da (CO(2)), and possible molecular structures were determined for the first time to our knowledge. A methodology is reported for evaluating the average elemental composition of FA from high-resolution mass spectra by processing post-acquisition data calculations using molecular size distributions and atomic compositions of ions. The results are found to be consistent with elemental analysis data.

Benzopyrans↗
PubMed1979

On the molecular structure of some prostaglandin receptors.

Hypotheses are presented of the detailed molecular structure of two prostaglandin receptors both concerned in tumor-promotion processes. These structures have been derived by the comparison of the molecular structure of agents active at the site with (i) a simple theoretical protein structure and (ii) the known x-ray structure of phospholipase A2. The first model receptor is stimulatory to the tumor-promotion process and may be located on the control system for ornithine decarboxylase. The binding of PG here is cooperative with the binding of Ca++. Naturally-occurring agonists at this receptor may include members of the cathartic class of drugs such as colocynth, chrysarobin, etc. Naturally-occurring antagonists at this site may include a number of anti-tumor compounds such as datiscoside. The second model receptor (PGE1) is inhibitory to the tumor-promotion process and is located at a specific allosteric site on the x-ray-determined structure of phospholipase A2. This site overlaps for one for lysolecithin (excitatory), for which tumor-promoting phorbol esters such as TPA are agonists and some anti-tumor drugs such as maytansine may be antagonists.

Antineoplastic Agents↗