Molecular structure, comparison

A coalition of animal protection organizations, led by the British Union for the Abolition of Vivisection (BUAV), proposed a completely non-animal testing strategy. They claimed that such a strategy, involving consideration of molecular structure, comparison with related compounds, tests on cell cultures and tests on human volunteers (for example for skin irritancy of substances not thought to be... 

Cone, M.M., Venkataraghavan, R. and McLafferty, F.W. (1977). Molecular Structure Comparison Program for the Identification of Maximal Common Substructures. JAm.Chem.Soc., 99, 7668-7671. 

Cone MM, Venkataraghavan R, McLafferty FW. Molecular structure comparison program for the identification of maximal common substructures. J Am Chem Soc 1977 99 7668-7671. 

A major use of IR data is structure determination, which for nucleobases includes tautomeric forms and cluster structures to model base pair interactions and microhydration. This capability also makes it possible to follow other properties as a function of structure. For the nucleobases, it turns out that self-protection against UV photodamage by internal conversion depends dramatically on molecular structure. Comparison with solution experiments probably further elucidates these findings and stimulates further research. 

Hohn L and C Sander 1993. Protein Structure Comparison by Alignment of Distance Matrices. Joun Molecular Biology 233 123-138. 

Fig. 1-6). The structure obtained for thiazoie is surprisingly close to an average of the structures of thiophene (169) and 1,3,4-thiadiazole (170) (Fig. 1-7). From a comparison of the molecular structures of thiazoie, thiophene, thiadiazole. and pyridine (171), it appears that around C(4) the bond angles of thiazoie C(4)-H with both adjacent C(4)-N and C(4)-C(5) bonds show a difference of 5.4° that, compared to a difference in C(2)-H of pyridine of 4.2°, is interpreted by L. Nygaard (159) as resulting from an attraction of H(4) by the electron lone pair of nitrogen. 

Fullerenes are described in detail in Chapter 2 and therefore only a brief outline of their structure is presented here to provide a comparison with the other forms of carbon. The C o molecule, Buckminsterfullerene, was discovered in the mass spectrum of laser-ablated graphite in 1985 [37] and crystals of C o were fust isolated from soot formed from graphite arc electrodes in 1990 [38]. Although these events are relatively recent, the C o molecule has become one of the most widely-recognised molecular structures in science and in 1996 the codiscoverers Curl, Kroto and Smalley were awarded the Nobel prize for chemistry. Part of the appeal of this molecule lies in its beautiful icosahedral symmetry - a truncated icosahedron, or a molecular soccer ball, Fig. 4A. 

With respect to the carrier mechanism, the phenomenology of the carrier transport of ions is discussed in terms of the criteria and kinetic scheme for the carrier mechanism the molecular structure of the Valinomycin-potassium ion complex is considered in terms of the polar core wherein the ion resides and comparison is made to the Enniatin B complexation of ions it is seen again that anion vs cation selectivity is the result of chemical structure and conformation lipid proximity and polar component of the polar core are discussed relative to monovalent vs multivalent cation selectivity and the dramatic monovalent cation selectivity of Valinomycin is demonstrated to be the result of the conformational energetics of forming polar cores of sizes suitable for different sized monovalent cations. 

Our discussion concentrates on experimental information providing some insight into the difficulties and limitations of these studies. In places, results from quantum chemical calculations will be invoked for comparison however, a critical analysis of the application of these methods to sulfones and sulfoxides is beyond the scope of this section. As in previous reviews in this series3,6,7, we shall be concerned primarily with the geometrical aspects of molecular structures. 

Fig. 2 Molecular structures of the molecules S7O (left) and, for comparison, of S7 (symmetry Cs) in the crystal SS bond lengths in pm (after [1, 65])...

Figure 5.66 Molecular structures of Idoxifene and its deutrated internal standard ds-Idoxifene. Reprinted from J. Chromatogr., B, 757, Comparison between liqnid chromatography-time-of-flightmass spectrometry and selected-reaction monitoring liqnid chromatography-mass spectrometry for qnantitative determination of Idoxifene in hnman plasma , Zhang, H. and Henion, I., 151-159, Copyright (2001), with permission from Elsevier Science.

The influence of the decay scheme on the retention (through differences in the percent conversion of y-transitions) was demonstrated by comparison of the -decay products of Pb and Pb in Pb(CgH5)3Cl. The retention of Bi in Bi(CgH5)3Cl2 was 17—19% and of Bi about 50%. According to Nefedov, this isotope effect is directly proportional to the conversion coefficients of the two isotopes. Corresponding to the complement of the conversion coefficient, 1—a, the molecular structure should be preserved to the extent of 80% for the two isotopes. The probability of chemical reaction for change or preservation of molecular structure is the same for the two cases. 

P. Willett and V. Winterman, A comparison of some measures for the determination of inter-molecular structural similarity. Measures of inter-molecular structural similarity. Quant. Struct.- Act. Relat., 5 (1986) 18-25. 

The molecular structure of the f-butyl derivative [BpBut]ZnBul has been determined by an x-ray diffraction study, which confirms a distorted trigonal planar coordination environment for zinc, as shown by the two views in Figs. 26 and 27 (80). In comparison to tetrahedral coordination, three-coordinate zinc alkyl complexes are rare (84). 

UV/VIS spectrophotometry can be used to determine many physico-chemical characteristics of compounds and thus can provide information as to the identity of a particular compound. Although UV/VIS spectra do not enable absolute identification of an unknown, they are frequently used to confirm the identity of a substance through comparison of the measured spectrum with a reference spectrum. However, UV spectrophotometry is not highly specific, and can obviously only be applied to polymer additives which are absorbers of UV radiation, i.e. contain chromophoric groups. Both UV and IR monitor functional entities rather than the entire molecular structure. A functional group s proximity to other electropositive or electronegative structures in a molecule affects the absorbance spectrum, allowing one to infer some details of molecular structure. 

Pietrzyk, P., Piskorz, W., Sojka, Z. et al. (2003) Molecular structure, spin density distribution, and hyperfine coupling constants of the i7l CuNO n adduct in the ZSM-5 zeolite DFT calculations and comparison with EPR data, J. Phys. Chem. B., 107, 6105. 

This article is an attempt at evaluating new important features of tin(II) chemistry the central point is the interrelationship between molecular structure and reactivity of molecular tin(II) compounds. To define these compounds more closely, only those are discussed which are stable, monomeric in solvents and which may be classified as carbene analogs21. Thus, not a complete survey of tin(II) chemistry is given but stress is laid on the structures and reactions of selected compounds. A general introduction to the subject precedes the main chapters. For comparison, also solid-state tin(II) chemistry is included to demonstrate the great resemblance with molecular tin(II) chemistry. Tin(II) compounds, which are either generated as intermediates or only under definite conditions such as temperature or pressure, are not described in detail. 

These features should be useful in attempts to estimate the stability or reactivity of a compound or reaction system which does not appear in this Handbook. The effects on stability or reactivity of changes in the molecular structure to which the destabilising or reactive group(s) is attached are in some cases discussed in the group entry. Otherwise such information may be gained from comparison of the information available from the individual compound entries listed collectively (now in alphabetical order, with serial number) in the group entry. 

Wesson, D.M., Porter, C. and Collins, F.H. (1992) Sequence and secondary structure comparisons of ITS rDNA in mosquitoes (Diptera Culicidae). Molecular Phylogenetics and Evolution 1, 253—269. 

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