Biologically relevant molecules

As has been discussed in the introduction, the possibility of a relation between parity violating energy differences and the biochemical homochirality observed on earth has been noted by Yamagata [11] a decade after the discovery of parity violation in nuclear physics. Various different kinetic mechanisms have been proposed which could possibly amplify the tiny energy difference between enantiomeric structures to result in an almost exclusive chiral bias on a time scale relevant for the biochemical evolution. This aspect as well as other hypotheses regarding the origin of the biochemical homochirality have been discussed and reviewed multiple times (see for instance [33,37-39,190-193] and literature cited therein) so that we can concentrate here on the computational aspects of molecular parity violating effects in biochemical systems. 

L-alanine was the first system studied in this respect. Mason and Tranter [109-111] computed parity violating potentials in the zwitterionic form of L-alanine. The structure employed was the crystal structure determined by neutron diffraction [194]. The dependence of the parity violating potentials on conformational changes, which involved rotations around the C-C 

In addition, parity violating potentials in formylglycinamid were calculated for two combinations of the dihedral angles around the central C-C and C-N single bonds, which were considered as representative for an cx-helix or /3-sheet structure of a polypeptide [110, 111]. For both of these structures a negative sign of V y was obtained within the UCHF approach. 

It was stated [111] that the sign of the energy difference between the enantiomers of the a-amino acids and of the polypeptides in the regular a-helix and /3-sheet conformation indicated, that the members of the L-series were preferentially stabilised by the parity violating weak interaction. 

By virtue of these results, it was repeatedly claimed that L-amino acids were systematically stabilised with respect to their D-counterparts due to parity violating weak interactions and this alleged stabilisation was frequently interpreted as evidence for a possible link between parity violating interactions and the observed biochemical homochirality in terrestrial organisms. 

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Central to the quality of any computational smdy is the mathematical model used to relate the structure of a system to its energy. General details of the empirical force fields used in the study of biologically relevant molecules are covered in Chapter 2, and only particular information relevant to nucleic acids is discussed in this chapter. 

Second-Order Rate Constants for the Repair of Carotenoid Radical Cations by Four Biologically Relevant Molecules in Triton Detergent Micelles... 

Multicomponent reactions (MCRs) have been known to produce highly complex and diverse structures [76]. There is a considerable interest in the application of new multicomponent reactions to access biologically relevant molecules [77,78] and natural products [79]. A recent report has disclosed multicomponent Passerini and Ugi reactions to produce, rapid and efficiently, a library of redox-active selenium and tellurium compounds [80]. The compounds showed promising cytotoxicity against several cancer cell lines. 

Synthesis of clusters inside the cavities of biologically relevant molecules as well as biomolecules in this method, gold ions are sequestered into the cavities of biomolecules and are subsequently reduced into gold clusters. 

Formation of Quantum Clusters Inside the Cavities of Biologically Relevant Molecules as well as Biomolecules... 

To characterize interactions between biologically relevant molecules, e.g., protein-protein and protein-nucleic acid interactions, as well as immunoreactions... 

Q and 3Q correlations can be utilized in combination with highest efficiency. In some cases more than one spectrum of each is worthwhile to acquire because cross peak intensity is an explicit function of all coupling constants involved [6, 27, 28]. Coherences of higher order than 3Q exhibit significantly reduced sensitivity. Also, few spin systems in biologically relevant molecules allow sufficient communication between multiple spins to allow observation of higher order spin systems. 

The reaction of [Pt(dien)Cl]Cl with S-adenosyl-L-homocysteine (SAH, a biologically relevant molecule, as it is the coproduct of the methyl transfer reaction by S-adenosyl-L-methionine see Fig. 15) results in a mixture of complexes (193), i.e., the mononuclear complex (1) [Pt(dien)(SAH-S)]2+, with platination of SAH at the sulfur atom, the mononuclear complex (2) [Pt(dien)(SAH-ADJ+, which has a Pt(dien)2+ unit coordinated to the amino group of the homocysteine unit, and the dinuclear complex (3) [ Pt(dien) 2(SAH-S,AD]3+, which has a Pt(dien)2+ unit coordinated to the sulfur atom as well as a Pt(dien)2+... 

Raman spectroscopy has been successfully used to detect nanomolar concentrations of biologically relevant molecules, to distinguish between structurally similar peptides (e.g. aEp3 and a5pi integrins [22]) and also to detect peptide S-nitrosylation and phosphorylation [23, 24]. Raman spectroscopy has been used to determine the functionalisation of carbon nanotubes and other particles with bioactive peptides (e.g. RGD), whereby their biofunctionalisation has enabled their accumulation at specific sites (e.g. tumours) within small animal models [25]. Furthermore, the in vivo distribution and... 

Soai K (2002) Asymmetric autocatalysis and the origin of chiral homogeneity of biologically relevant molecules. In Pdlyi G, Zucchi C, Caglioti L (eds) Fundamentals of life. Elsevier, Paris, p 427... 

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