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PubMed2004

The molecular structure of the tris(2-mercapto-1-tolylimidazolyl)hydroborato zinc(2-mercapto-1-tolylimidazole) complex, [[Tm(p-Tol)]Zn(mim(p-Tol))][ClO4]: intermolecular N-H...OClO3versus intramolecular N-H...S hydrogen bonding interactions of the mercaptoimidazole ligand.

The molecular structure of the tris(2-mercapto-1-tolylimidazolyl)hydroborato complex [[Tm(p-Tol)]Zn(mim(p-Tol))][ClO(4)].3MeCN has been determined by X-ray diffraction, thereby demonstrating that the mim(p-Tol) ligand exhibits a N-H...O hydrogen bond with the [ClO(4)](-) counterion, [[Tm(p-Tol)]Zn(mim(p-Tol))...(OClO(3))], rather than hydrogen bond with a sulfur of the [Tm(p-Tol)] ligand. DFT calculations on a series of related complexes, namely [[Tm(Me)]Zn(mim(Me))](+), [[Tm(Me)]Zn(mim(Me))]...(OClO(3))], [[Tm(Me)]Zn(mim(Me))]...[O(H)Me]](+), and [[Tm(Me)]Zn(mim(Me))]...(NCMe)](+) demonstrate that an intramolecular N-H...S hydrogen bond within [[Tm(Me)]Zn(mim(Me))](+) is also less favored than the corresponding hydrogen bonding interactions with MeCN, MeOH, and [ClO(4)](-). The inability of the sulfur atoms of [Tm(R)] ligand to act as an effective hydrogen bond acceptor is in marked contrast to the ability of sulfur atoms in thiolate ligands to participate in the formation of N-H...S hydrogen bonds, an observation that reflects the "thione"versus"thiolate" nature of the [Tm(R)] ligand.

Crystallography, X-Ray↗

PubMed1998

Gas-Phase Reaction of Tetraborane(10) and Ethyne: Molecular Structure of nido-1,2-C(2)B(3)H(7) in the Gas Phase.

The molecular structure of nido-1,2-C(2)B(3)H(7), 1, the principal volatile carborane generated in the quenched gas-phase reaction of B(4)H(10) and ethyne at 70 degrees C, has been determined by a combined analysis of gas-phase electron-diffraction data and rotation constants restrained by ab initio computations at the CCSD(T)/TZP' level. The structure is consistent with a geometry having C(s)() symmetry, similar to that of pentaborane(9). The apical position is occupied by a carbon atom, displaced toward B(4) from a position directly above the B(5).B(3) vector, and hydrogen atoms asymmetrically bridge the B-B bonds. The basal atoms are almost coplanar, C(2) lying ca. 2 degrees below the B(3)-B(4)-B(5) plane. Important experimental structural parameters (r(alpha) degrees /pm, angle(alpha)/ degrees ) are r[C(1)-C(2)] = 162.6(6); r[C(1)-B(3)] = 161.4(3); r[C(2)-B(3)] = 154.3(2); r[C(1)-B(4)] = 157.4(5); r[B(3)-B(4)] = 185.7(3); <B(3)-B(4)-B(5) = 80.9(1). In addition to this and the other previously reported carboranes, 2,3-C(2)B(4)H(8), 2-Me-2,3,4-C(3)B(3)H(6), and 4-Me-2-CB(5)H(8), several new derivatives have been identified among the volatile products. These include the dicarbahexaboranes 2,4-Me(2)-2,3-C(2)B(4)H(6) and 5-Et-2,3-C(2)B(4)H(7) (the major volatile products obtained when the reaction is allowed to go to completion, previously reported as tricarbahexaboranes) and the derivatives 2,5-Me(2)-2,3-C(2)B(4)H(6), 4-Et-2,3-C(2)B(4)H(7), 1-Me-2,3,4-C(3)B(3)H(6), 2-Me-2-CB(5)H(8), 3-Me-2-CB(5)H(8), and 2,3,4,5-C(4)B(2)H(6). The complex mechanism of the reaction is discussed in light of these new results.

Journal Article↗

PubMed2003

Molecular structure of alcohol-water mixtures.

We use x-ray emission spectroscopy to elucidate the molecular structure of liquid methanol, water, and methanol-water solutions. We find that molecules in the pure liquid methanol predominantly persist as hydrogen-bonded chains and rings with six and/or eight molecules of equal abundance. For water-methanol solutions we find evidence of incomplete mixing at the microscopic level. Our results provide a new explanation for a smaller entropy increase in the solution due to water molecules bridging methanol chains to form rings.

Journal Article↗

PubMedDate not supplied

Effects of the molecular structure of two amphiphilic antidepressant drugs on the formation of complexes with human serum albumin.

Interactions of two amphiphilic antidepressant drugs, imipramine and desipramine hydrochlorides, with the blood protein human serum albumin (HSA) were investigated to gain an understanding of the effects of drug molecular structure on the complex formation of drug-protein molecules. To elucidate the mechanisms of such effects, the protein-antidepressant interactions in aqueous buffered solutions of pH 3.0 and 5.5 (isoelectric point of HSA = 4.9) were investigated using conductivity, zeta potential, and dynamic light scattering. An increase of the critical micelle concentration of both antidepressants was detected as a consequence of extensive binding to the protein. From zeta-potential measurements, the Gibbs energies of adsorption of the drugs onto the protein were derived using the proposed models of Kayes and Ottewill and Watanabe. Measurements of the hydrodynamic radii of HSA-antidepressant complexes as a function of the drug concentration have shown a gradual increase of size of a saturation rather than a denaturation process of the protein. A larger drug adsorption at pH 5.5 than at pH 3.0 was also observed, as a consequence of a more important specific binding at the former pH.

Adsorption↗

PubMed1985

Crystal and molecular structure of the inhibitor eglin from leeches in complex with subtilisin Carlsberg.

The crystal structure of the molecular complex of eglin, a serine proteinase inhibitor from leeches, with subtilisin Carlsberg has been determined at 2.0 A resolution by the molecular replacement method. The complex has been refined by restrained-parameter least-squares. The present crystallographic R factor (Formula: see text) is 0.183. Eglin is a member of the potato inhibitor 1 family, a group of serine proteinase inhibitors lacking disulfide bonds. Eglin shows strong structural homology to CI-2, a related inhibitor from barley seeds. The structure of subtilisin Carlsberg in this complex is very similar to the known structure from barley seeds. The structure of subtilisin Carlsberg in this complex is very similar to the known structure of subtilisin novo, despite changes of 84 out of 274 amino acids.

Amino Acid Sequence↗

PubMed1991

Influence of aglycone modifications on the binding of anthracycline drugs to DNA: the molecular structure of idarubicin and 4-O-demethyl-11-deoxydoxorubicin complexed to d(CGATCG).

X-ray diffraction analyses of the complexes between two anthracycline antitumor compounds, idarubicin (IDR) and 4-O-demethyl-11-deoxydoxorubicin (ddDOX), with the DNA hexamer d(CGATCG) provided the detailed three-dimensional molecular structures at 1.7 A and 1.8 A resolution, respectively. Their structures have been refined with the constrained refinement procedure to final R-factors of 0.188 (1724 reflections for IDR) and 0.179 (1247 reflections for ddDOX). The overall structures of both complexes are similar to those of the previously studied DAU- and DOX-DNA complexes. In both complexes, two IDR (and ddDOX) molecules bind to the DNA hexamer double helix with the elongated aglycone chromophore intercalated between the CpG steps at both ends of the helix. The aglycone chromophore spans the GC Watson-Crick base pairs with its amino sugar lying in the minor groove where little structural difference is seen, compared with the daunorubicin-d(CGATCG) and doxorubicin-d(CGATCG) complexes. In contrast, the missing C4 methoxy of IDR and the missing methyl group at the O4 position of ddDOX result in a different binding surface in the major groove. The O4 hydroxyl group is capable of receiving and/or donating a hydrogen bond to proteins that bind to the drug-DNA complex. The missing O11 hydroxyl group in ring B creates an empty space in the intercalation cavity between the two GC base pairs, which appears to affect the stacking interactions between the aglycone and the DNA base pairs. Those structural changes in the major groove of the drug-DNA complexes due to the modifications of the aglycone chromophore may be responsible in part for the difference in their biological activities.

Crystallography↗

PubMed2003

Prediction of human pharmacokinetics from animal data and molecular structural parameters using multivariate regression analysis: volume of distribution at steady state.

The aim of this study was to develop a regression equation for predicting volume of distribution at steady state (Vd(ss)) in humans to enable application to various types of drugs using animal experimental data for rats and dogs and some molecular structural parameters. The Vd(ss) data for rats, dogs and humans of 64 drugs were obtained from literature. The compounds have various structures, pharmacological activities and pharmacokinetic characteristics. In addition, the molecular weight, calculated partition coefficient (clogP), and the number of hydrogen bond acceptors were used as possible descriptors related to the Vd(ss) in humans. Multivariate regression analyses, multiple linear regression analysis and the partial least squares (PLS) method were used to predict Vd(ss) in humans. Interaction terms were also introduced into the regression analysis to evaluate the non-linear relationship. For the data set used in the present study, PLS with quadratic term descriptors gave the best predictive performance. The PLS model using Vd(ss) data for only two animal species and using easily calculated structural parameters could generally predict Vd(ss) in humans better than an allometric method. In addition, the PLS model with only animal data gave almost the same predictive performance as the PLS model with quadratic term descriptors. This model may be easier to use and be practical in a realistic situation, and could predict Vd(ss) in humans better than the allometric method.

Animals↗

PubMed1986

Alterations in molecular structure of renal mitochondria associated with cyclosporine A treatment.

We examined whether ultrastructural changes in renal mitochondria associated with Cyclosporine A treatment might reflect underlying alterations in mitochondrial molecular structure. A nonrejected renal transplant removed from a patient treated with Cyclosporine A showed a decreased level of beta subunit antigen of mitochondrial F1-ATPase compared to controls. This decrease was more marked in the medulla than in the cortex (56% vs. 70% of pooled controls). Spontaneously hypertensive rats treated with a high dose of Cyclosporine A showed a similar decrease of beta-subunit antigen in the renal medulla and decreased levels of two subunit antigens of cytochrome c oxidase, but had increased medullary levels of the alpha subunit antigen of the F1-ATPase. Such changes were not detected in a normotensive strain of rats. Our data indicate that Cyclosporine A administration is associated with structural alterations in renal mitochondria at the molecular level, predominantly in the medulla, and that additional renal damage due to ischemia or hypertension may predispose to this cyclosporine effect.

Adenosine Triphosphatases↗

PubMed1984

The effects of pressure on the molecular structure and physiological functions of cell membranes.

The effects of high pressure on the phase state and molecular structure of pure lipid bilayers are discussed. The relations of delta H, delta S and delta V in phase transitions are straightforward and are discernible in heterogeneous bilayers in natural membranes. The effects of pressure on the dynamic properties of bilayer constituents are less clearly understood, but order parameters obtained at pressure by different techniques show agreement. The extent and significance of hydration is poorly understood. Four physiological functions are discussed: passive permeability, active transport, membrane excitability and synaptic transmission. It is shown that a full interpretation of the kinetic effects of pressure on these processes requires much more detailed molecular information than is available at present.

Action Potentials↗

PubMed2006

CHIH-DFT determination of the molecular structure and IR and UV spectra of solanidine.

Solanidine is the steroidal aglycon of some potato glycoalkaloids and a very important precursor for the synthesis of hormones and some pharmacologically active compounds. In this work, we make use of a new chemistry model within Density Functional Theory, called CHIH-DFT, to calculate the molecular structure of solanidine, as well to predict its infrared and ultraviolet spectra. The calculated values are compared with the experimental data available for this molecule as a means of validation of our proposed chemistry model.

Diosgenin↗

PubMed2006

CHIH-DFT determination of the molecular structure and infrared and ultraviolet spectra of gamma-solanine.

Glycoalkaloids are toxic secondary plant metabolites found in potatoes, tomatoes, and eggplants and they are considered potential precursors of steroids for applications in bionanotechnology. In this work, we make use of a new model chemistry within density functional theory, which is called CHIH-DFT, to calculate the molecular structure of gamma-solanine, as well to predict its infrared (IR) and ultraviolet (UV-vis) spectra, and some other electronic parameters.

Biotechnology↗

PubMed2001

Predicting plasticization efficiency from three-dimensional molecular structure of a polymer plasticizer.

PURPOSE: In polymeric coatings, plasticizers are used to improve the film-forming characteristic of the polymers. In this study, a computerized method (VolSurf with GRID) was used as a novel tool for the prediction plasticization efficiency (beta) of test compounds, and for determining the critical molecular properties needed for polymer plasticization. METHODS: The film-former, starch acetate DS 2.8 (SA), was plasticized with each of 24 tested compounds. A decrease in glass transition temperature of the plasticized free films (determined by differential scanning calorimeter (DSC)) was used as an indicator for beta. Partial least squares discriminant analysis was used to correlate the experimental data with the theoretical molecular properties of the plasticizers. RESULTS: A good correlation (r2 = 0.77, q2 = 0.58) between the molecular modeling results and the experimental data demonstrated that beta can be predicted from the three-dimensional molecular structure of a compound. Favorable structural properties identified for the potent SA plasticizer were strong hydrogen bonding capacity and a definitive hydrophobic region on the molecule. CONCLUSIONS: The VolSurf method is a valuable tool for predicting the plasticization efficiency of a compound. The correlation between experimental and calculated glass transition temperature values verifies that physicochemical properties are primary factors influencing plasticization efficiency of a compound.

Models, Chemical↗

PubMed1991

Crystal and molecular structure of the dehydropeptide Ac-delta Phe-Val-delta Phe-NH-Me.

The dehydropeptide Ac-delta Phe-L-Val-delta Phe-NH-Me, containing two dehydrophenylalanine (delta Phe) residues, crystallizes from methanol/water in space group P212121, with a = 12.622 (1), b = 12.979 (1), and c = 15.733 (1) A. In the solid state, the molecular structure is characterized by the presence of two intramolecular hydrogen bonds which form two consecutive beta-bends. The (phi, psi) torsion angles of the three residues are very similar and close to the standard values of type III beta-bends, so the molecular conformation corresponds to an incipient right-handed 3(10)-helix, only slightly distorted. In the crystal, the molecules are linked by head-to-tail hydrogen bonds, thus forming continuous helical columns packed in antiparallel mode. There are no lateral hydrogen bonds; the only interactions are hydrophobic contacts between the apolar side chains of neighboring helical columns.

Amino Acid Sequence↗

PubMedDate not supplied

[Study of the molecular structure and mechanisms of pond snail neuron cholinoreceptor function by means of in vivo chemical modification].

The molecular structure of acetylcholine receptors (AChR) of Lymnaea stagnalis neurons has been studied using specific agents to definite chemical groups. The disulphide bond important for AChR function was discovered, the reduction of which by dithiotreitol (DTT) inactivates AChR. The drugs exciting AChR protect the disulphide bond against modification with DTT likely due to the conformational changes of an active site and its environment. Desensitized AChR can also be modified by DDT (if it is not occupied by agonist). It is suggested that the system transmitting the conformational change from the AChR active site to its ionophore is responsible for desensitization.

Acetylcholine↗

PubMed1997

Molecular structure and gas chromatographic retention behavior of the components of Ylang-Ylang oil.

Using quantitative structure-retention relationships (QSRR) methodologies the Kovats gas chromatographic retention indices for both apolar (DB-1) and polar (DB-Wax) columns for 48 compounds from Ylang-Ylang essential oil were empirically predicted from calculated and experimental data on molecular structure. Topological, geometric, and electronic descriptors were obtained for model generation. Relationships between descriptors and the retention data reported were established by linear multiple regression, giving equations that can be used to predict the Kovats indices for compounds present in essential oils, both in DB-1 and DB-Wax columns. Factor analysis was performed to interpret the meaning of the descriptors included in the models. The prediction model for the DB-1 column includes descriptors such as Randic's first-order connectivity index (1X), the molecular surface (MSA), the sum of the atomic charge on all the hydrogens (QH), Randic's third-order connectivity index (3X) and the molecular electronegativity (chi). The prediction model for the DB-Wax column includes the first three descriptors mentioned for the DB-1 column (1X, MSA and QH) and the most negative charge (MNC), the global softness (S), and the difference between Randic's and Kier and Hall's third-order connectivity indexes (3X-3XV).

Chromatography, Gas↗

PubMed1985

The search for functional correspondences in molecular structure between two dissimilar molecules.

Where structural similarities between molecular ligands are suspected in competitive binding, these similarities may be represented by a set of correspondences between analogous ligand points in the two molecules. This paper describes an algorithm which searches through all possible sets of this form, to find the one which gives the best geometric fit between matched points. Two parameters are supplied to the algorithm, giving the number of correspondences required and the tolerance permitted in the fit. A tree-search technique is used, and methods are described which prune the tree and thus limit the search. The marine neurotoxins, saxitoxin and tetrodotoxin, are used to test a computer implementation of the procedure.

Binding, Competitive↗

PubMed1991

Molecular structure of extraordinarily stable RNA: model building and X-ray analysis.

A tridecaribonucleotide, rUGAGCUUCGGCUC which adopts the extraordinarily thermally stable hairpin structure, was chemically synthesized. The crystallographic study of this RNA molecule was done. Crystals grew as plates belonging to space group C2 with a = 38.49A b = 32.30A c = 38.76A and beta = 117.56. and one molecule per asymmetric unit. Intensity data were collected at a resolution 2.1A. Structure determination using molecular replacement method has been underway. The favorable three-dimensional model of hairpin was built by molecular dynamics and molecular mechanics calculations.

Base Sequence↗

PubMed1986

The molecular structure of cyclonucleotide hexamer, CoGoCoGoCoGo having a high-anti conformation.

Cyclonucleotide hexamer, CoGoCoGoCoGo, was synthesized and crystallized as orthorhombic with space group C222(1), and unit cell dimensions: a = 48.30, b = 41.53, and c = 31.76A. The X-ray diffraction data up to 1.8A resolution were collected, and the crystal structure analysis by molecular replacement technique is now in progress using two energetically adequate left-handed helical models, which are obtained by conformational energy calculation.

Models, Molecular↗