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PubMed2006

Molecular structure and bonding of copper cluster monocarbonyls CunCO (n = 1-9).

In this work we analyze CO binding on small neutral copper clusters, Cun (n = 1-9). Molecular structures and reactivity descriptors of copper clusters are computed and discussed. The results show that the condensed Fukui functions and the frontier molecular orbital theory are useful tools to predict the selectivity of CO adsorption on these small clusters. To get further insight into the CO binding to copper clusters, an energy decomposition analysis of the CO binding energy is performed. The Cs symmetry of the formed CunCO clusters (n = 1-8) allows the separation between the orbital interaction terms corresponding to donation and back-donation. It is found that, energetically, the donation is twice as important as back-donation.

Journal Article↗
PubMedDate not supplied

Computer-assisted studies of molecular structure and carcinogenic activity.

Both quantitative and qualitative studies of the structure-activity relationships (SAR) of carcinogenic compounds are discussed. Using the ADAPT software system, examples are given of (1) predicting the gas and liquid chromatographic retention behavior of polycyclic aromatic compounds, (2) predicting the carcinogenicity of N-nitrosamines, and (3) predicting the mutagenic behavior of pesticides and other compounds in short-term test systems. It is concluded that the complexity and lack of understanding of the carcinogenic response should not prevent scientists from searching for useful empirical relationships between molecular structure and carcinogenicity. Computer generated molecular descriptors and statistical and pattern recognition techniques can be useful tools in this research.

Animals↗
PubMed2004

Molecular structure and organization of crustacean hyperglycemic hormone genes of Penaeus monodon.

The Crustacean hyperglycemic hormone (CHH) has been shown to exist as multiple molecular forms in several crustacean species. In Penaeus monodon, a gene encoding CHH (so-called Pem-CHH1) was recently described. In this study, the molecular structures of two other CHH genes (Pem-CHH2 and Pem-CHH3) are reported. Both the Pem-CHH2 and Pem-CHH3 genes contain three exons that are separated by two introns that are similar to the structure of other genes in the same family. An analysis of the upstream nucleotide sequences of each Pem-CHH gene has identified the putative promoter element (TATA box) and putative binding sites for several transcription factors. The binding sites for CREB, Pit-1, and AP-1 were found upstream of all three Pem-CHH genes. A Southern blot analysis showed that at least one copy of each Pem-CHH gene was located within the same 10 kb genomic DNA fragment. These results suggest that the CHH genes are arranged in a cluster in the genome of P. monodon, and that their expression may be modulated by similar mechanisms.

3' Untranslated Regions↗
PubMed1986

Influence of molecular structure on half-life and hydrolysis of dipeptides in plasma: importance of glycine as N-terminal amino acid residue.

To investigate the effect of molecular structure on plasma disappearance and metabolism of dipeptides, rats were injected intravenously with individual dipeptides, and at various intervals after injection, dipeptide and amino acid concentrations were measured in plasma, tissues, and urine. In addition, plasma hydrolase activity against individual dipeptides was investigated. The half-lives of Ala-Leu, Ala-Tyr, and Ala-Gln were shorter than those of dipeptides with glycine substituting for alanine. Furthermore, the increases in plasma concentrations of leucine, tyrosine, and glutamine and rates of dipeptide hydrolysis by plasma enzymes were far greater with alanyl than glycyl dipeptides. In fact, Ala-Leu behaved like a mixture of corresponding free amino acids in raising the plasma concentration of leucine while Gly-Leu did not. There was no significant difference in either plasma half-life or hydrolysis when Leu-Gly and Leu-Ala were used as substrates, but both had rapid rates of hydrolysis in plasma. In comparison to Gly-Leu, Phe-Leu and Arg-Leu had shorter half-lives and greater rates of hydrolysis in plasma. On the other hand, Asp-Leu had a slower rate of plasma hydrolysis than Gly-Leu, but its excretion in the urine was much greater than that of Gly-Leu. In contrast to Gly-Leu and Ala-Leu, Gly-Pro was detected intracellularly in liver, muscle, and particularly, kidney. In fact, the intracellular concentration of Gly-Pro in kidney was either equal to or greater than Gly-Pro concentration in plasma. Increases in intracellular amino acid concentration after injection of individual dipeptides were considerably greater in the kidney than in either liver or muscle.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acids↗
PubMed2004

DNA nucleosides and their radical anions: molecular structures and electron affinities.

The deoxyribonucleosides have been studied to determine the properties of combinations of 2-deoxyribose with each of the isolated DNA bases for both neutral and anionic species. We have used a carefully calibrated theoretical method [Chem. Rev. 2002, 102, 231], employing the B3LYP hybrid Hartree-Fock/DFT functional with the DZP++ basis set. Predictions are made of the geometric parameters, adiabatic electron affinities, charge distributions based on natural population analysis, and decomposition enthalpy for the neutral and anionic forms of the four 2'-deoxyribonucleosides in DNA: 2'-deoxyriboadenosine (dA), 2'-deoxyribocytidine (dC), 2'-deoxyriboguanosine (dG), and 2'-deoxyribothymidine (dT). Geometric changes in the anions show that the glycosidic bond exhibits little change with excess charge for the guanosine but significant shortening for the adenosine and for the pyrimidines. The zero-point corrected adiabatic electron affinities in eV for each of the 2'-deoxyribonucleosides are as follows: 0.06, dA; 0.09, dG; 0.33, dC; and 0.44, dT. These values are uniformly greater than those of the corresponding isolated bases (-0.28, A; -0.07, G; 0.03, C; 0.20, T) and the isolated 2-deoxyribose (-0.38) at the same level of theory. The vertical detachment energies of dT and dC are substantial, 0.72 and 0.94 eV, and these anions should be observable. A high VDE, 0.91 eV, is also found for dA but its anion is unlikely to be stable due to the small AEA of 0.06 eV. The high VDE reflects the fact that the molecular structures of the anions and the corresponding neutral species are quite different. Valence character is displayed for the SOMOs of dA, dC, and dT, while some component of diffuse character is visible in the SOMO of dG. Further analysis of electronic changes upon electron attachment include an examination of the NPA charges, which show that in the neutral 2'-deoxyribonucleosides the sum of NPA charges for every base is the same, -0.28 with the sum of 2-deoxyribose charges being positive, +0.28. In the anions, the trend in charge division varies based on the nature of the excess electron in the anions. Thermodynamically, the overall enthalpy change for the reaction of water with the neutral nucleosides to give bases and ribose is approximately zero. The analogous decomposition is exothermic by 8 to 11 kcal mol-1 for the anions, indicating possible challenges for anionic gas-phase nucleoside exploration in the presence of water.

Anions↗
PubMed1979

The molecular structure of lecithin dihydrate.

Lecithin is a major structural component of biological membranes. Because of their amphipathic nature, lecithin and related phospholipids tend to aggregate as bilayer structures in which the hydrophilic head groups are orientated towards the surface and the hydrophobic hydrocarbon chains towards the interior. A detailed knowledge of the three-dimensional structure of lecithins will aid in the understanding of their role in membrane structure and function, but is still lacking. To this end we have now crystallised and solved the molecular structure of 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC), a lecithin species in the naturally occurring configuration. This compound crystallises from a water-containing solution, with two water molecules (5% w/w) of hydration.

Crystallography↗
PubMedDate not supplied

Data mining for seeking an accurate quantitative relationship between molecular structure and GC retention indices of alkenes by projection pursuit.

Primary data mining on alkenes for seeking an accurate quantitative relationship between the molecular structure and retention indices of gas chromatography is developed in this paper. Based on the results obtained from projection pursuit, all alkenes investigated show an interesting classification. Thus, a new variable named class distance variable of alkenes, which essentially describes information about the branch, position of the double bonds, the number of double bonds, and so on for alkenes, is proposed. With the help of the new variable, both fitting and prediction accuracy of the regression model can be dramatically improved. The results obtained in this work show that the technique of projection pursuit developed in statistics is a quite promising tool for seeking an accurate quantitative structure-retention relationship (QSRR).

Journal Article↗
PubMed2003

Predicting the genotoxicity of polycyclic aromatic compounds from molecular structure with different classifiers.

Classification models were developed to provide accurate prediction of genotoxicity of 277 polycyclic aromatic compounds (PACs) directly from their molecular structures. Numerical descriptors encoding the topological, geometric, electronic, and polar surface area properties of the compounds were calculated to represent the structural information. Each compound's genotoxicity was represented with IMAX (maximal SOS induction factor) values measured by the SOS Chromotest in the presence and absence of S9 rat liver homogenate. The compounds' class identity was determined by a cutoff IMAX value of 1.25-compounds with IMAX > 1.25 in either test were classified as genotoxic, and the ones with IMAX < or = 1.25 were nongenotoxic. Several binary classification models were generated to predict genotoxicity: k-nearest neighbor (k-NN), linear discriminant analysis, and probabilistic neural network. The study showed k-NN to provide the highest predictive ability among the three classifiers with a training set classification rate of 93.5%. A consensus model was also developed that incorporated the three classifiers and correctly predicted 81.2% of the 277 compounds. It also provided a higher prediction rate on the genotoxic class than any other single model.

Animals↗
PubMed1997

Comparison of a left-handed Z-DNA molecular structure determined by X-rays with that simulated by a molecular dynamics.

The 1.0 A resolution X-ray crystal structures of the left-handed Z-DNA(Z-I and Z-II conformations) were compared with that of the simulated molecular dynamics(MD) structure both in vacuo and in solution. Whilst the X-ray structure showed a tendency for the d(CG)3 molecule to take on a Z-II conformation in high salt solution or in strongly ionized conditions, the MD simulation with Na ion for 30 ps revealed that the left-handed d(CG)3 structure with the Z-I conformation was transformed into the Z-II conformation in the torsion angles of the C3, G4 and C5 phosphate groups, and furthermore, when K+ ion was used as the counterion instead of Na+ ion, the torsion angles in almost the entire d(CG)3 molecule were preserved. On the other hand, the MD calculation resulted in some very important changes on the sugar puckerings; the simulation with Na+ ion indicated that all the sugar puckerings of cytosine residues were changed from C2'-endo to C3'-endo, while those for guanosine residues tended to keep unchanged (C3'-endo) except for a terminal residue (G6).

Crystallization↗
PubMed1997

Molecular Structure of Trifluorophosphine Tetraborane(8), B(4)H(8)PF(3), As Determined in the Gas Phase by Electron Diffraction and ab Initio Computations.

The molecular structure of trifluorophosphine tetraborane(8), B(4)H(8)PF(3), has been studied in the gas phase by electron diffraction. The experimental data can be fitted using a model which represents the gas as consisting solely of the endo conformer with C(s)() symmetry, the PF(3) group staggered with respect to the B(1)-H(1) bond. Important experimental structural parameters (r(alpha) degrees ) are r[B(1)-B(2)] (hinge-wing) = 184.7(9) pm, r[B(1)-B(3)] (hinge-hinge) = 172.2(12) pm, r[B(2)-B(3)] = 179.9(10) pm,r[B(1)-P] = 179.8(9) pm, and r(P-F) (mean) = 152.8(1) pm; B(3)B(1)P = 131.6(11) degrees, and the dihedral ("butterfly") angle between the planes B(1)B(2)B(3) and B(1)B(4)B(3) is 133.9(23) degrees. These values agree well with the ab initio (MP2/TZP level) optimized molecular geometry for the endo conformer; at the MP2/TZP//MP2/TZP + ZPE(HF/6-31G) level, the exo conformer is predicted to represent ca. 2% of the compound vapor, consistent with the experimental (11)B NMR solution spectrum. The experimental and theoretical geometries are supported by comparison of the calculated (IGLO) (11)B NMR chemical shifts with the experimental NMR data.

Journal Article↗
PubMed1997

Changes in the molecular structure of hair in insulin-dependent diabetes.

Low-angle synchrotron X-ray diffraction has revealed clear and consistent changes in the molecular structure of alpha-keratin of hair in insulin-dependent diabetes (IDDM) both for human IDDM subjects and for baboons with streptozocin induced diabetes. These changes in both meridional and equatorial intensity distributions are fully explained by a newly developed hexagonally packed model for keratin which locates the modification produced in hair in IDDM in the labile structure of the matrix at established intermediate filament linkage sites. The nature of the extracellular bonding suggests that the change is endogenous, occurring via the blood during the aggregation of the IFs in the follicle. The reproducibility of these changes indicate that hair may represent an easily accessible tissue for the study of how hyperglycaemia can modify extracellular matrix materials which lead to diabetic complications.

Adult↗
PubMed2006

EPR theoretical study of local molecular structure and thermal expansion coefficient for octahedral Mn2+ centers in zinc fluosilicate.

A theoretical method for studying the inter-relation between electronic and molecular structure has been proposed by diagonalizing the complete energy matrices for a d(5) configuration ion in a trigonal ligand field and considering the second-order and fourth-order EPR parameters D and (a - F) simultaneously. As for ZnSiF(6).6H(2)O:Mn(2+) and ZnSiF(6).6D(2)O:Mn(2+) complex molecules, the local lattice distortion and local thermal expansion coefficient for the octahedral Mn(2+) centers in zinc fluosilicate have been investigated, respectively. The calculations indicate that the local lattice structure around an octahedral Mn(2+) center has an expansion distortion, whether the Mn(2+) ion is doped in ZnSiF(6).6H(2)O or ZnSiF(6).6D(2)O. Moreover, the total tendency of the local lattice expansion distortion will be more and more obvious with the temperature rising, apart from some slight variations at T = 60 K for the ZnSiF(6).6H(2)O. By simulating the two low-symmetry EPR parameters D and (a - F) simultaneously, the local lattice structure parameters R and theta have been determined to vary from 2.204 Angstroms to 2.256 Angstroms and from 53.417 degrees to 52.710 degrees, respectively, in the temperature range 19-297 K for ZnSiF(6).6H(2)O:Mn(2+) and to vary from 2.215 Angstroms to 2.255 Angstroms and from 53.346 degrees to 52.714 degrees, respectively, in the temperature range 50-300 K for ZnSiF(6).6D(2)O:Mn(2+). Subsequently the dependence of local thermal expansion coefficients on the temperature is studied and the corresponding theoretical values of the local thermal expansion coefficients are reported firstly. Some characteristics of local thermal expansion coefficients of Mn(2+) in ZnSiF(6).6H(2)O:Mn(2+) and ZnSiF(6).6D(2)O:Mn(2+) systems are also analyzed.

Journal Article↗