Conformational Analysis
Conformational analysis involves studying the different spatial arrangements of atoms in a molecule due to rotation around single bonds. It explores the energy differences and stabilities of these conformations, providing insights into the structure and behavior of molecules. This analysis is crucial for understanding the reactivity, biological activity, and physical properties of organic compounds.
6 Key excerpts on "Conformational Analysis"
eBook - ePubPeptides
Synthesis, Structures, and Applications
- Bernd Gutte(Author)
- 1995(Publication Date)
- Academic Press(Publisher)
...This approximation can be calibrated to reproduce vibrational spectra, relative energetics of conformational minima, and rates of conformational transitions. Despite the limitations which curtail exact quantitative applications, molecular mechanics can provide three-dimensional insight as the geometric relations between molecules are adequately represented. Electrical field potentials can be calculated and compared to give a qualitative basis for rationalizing differences in activity. Molecular modeling and its graphical representation allow the chemist to explore the three-dimensional aspects of molecular recognition and to generate hypotheses which lead to design and synthesis of new ligands. The more accurate the representation of the potential surface of the molecular system under investigation, the more likely that the modeling studies will provide qualitatively correct solutions. Once a proper set of parameters for the system under study has been selected, the force field provides the fundamental basis for simulating the system either through Newtonian mechanics or molecular dynamics, or through a stochastic generation of the relevant partition function, by Monte Carlo simulations. B. Conformational Analysis Whereas interaction with a receptor will certainly perturb the conformational energy surface of a flexible peptide, high affinity would suggest that the peptide binds in a conformation which is not exceptionally different from one of its low-energy conformers (i.e., conformers whose energy is not dramatically higher than that of the global minimum-energy conformer). By determining the set of low-energy conformers, one attempts to generate a description of the equilibrium states of a peptide and to avoid the limitations inherent in static representations of the conformational possibilities of a peptide...
eBook - ePub- Michael North(Author)
- 2017(Publication Date)
- CRC Press(Publisher)
...It can be used in conjunction with experimental data to predict chemical reactivity, to determine the conformations adopted by cyclic compounds, including those which contain medium and large rings, and to design molecules of a specified shape to fit into a biological receptor to elicit or block a biological response. In this section, it has been possible to give only a very brief overview of the methodology; more detail will be found in the recommended further reading. 8.12 Further reading General Stereochemistry of Organic Compounds E.L. Eliel and S.H. Wilen. Wiley: London, 1994, chapters 10 and 11. Conformations of five-membered rings Topics in Stereochemistry Vol. 10, B. Fuchs (E.L. Eliel and N.L. Allinger eds). Wiley: Chichester, 1978, chapter 1. The anomeric effect The Anomeric Effect and Related Stereoelectronic Effects at Oxygen A.J. Kirby. Springer-Verlag: Berlin, 1983. Stereoelectronic effects Stereoelectronic Effects in Organic Chemistry P. Deslongchamps. Pergamon: Oxford, 1983. Stereoelectronic Effects Oxford Chemistry Primer Number 36, A.J. Kirby. Oxford University Press: Oxford, 1996. Circular dichroism and optical rotary dispersion Optical Rotary Dispersion C. Djerassi. McGraw-Hill: London, 1960. Optical Rotary Dispersion and Circular Dichroism in Organic Chemistry P. Crabbe. Holden-Day: London, 1965. Optical Circular Dichroism L. Velluz, M. Legrand and M. Grosjean. Verlag Chemie, 1965. Conformations of biopolymers Chemistry of Biomolecules: An Introduction R.J. Simmonds. Royal Society of Chemistry: Cambridge, 1992. Natural Products their Chemistry and Biological Significance J. Mann, R.S. Davidson, J.B. Hobbs, D.V. Banthorpe and J.B. Harborne. Longman: Harlow, 1994. NMR techniques in Conformational Analysis Biomolecular NMR Spectroscopy J.N.S. Evans. Oxford University Press: Oxford, 1995. Introduction to Organic Spectroscopy Oxford Chemistry Primer Number 43, L.M. Harwood and T.D.W. Claridge...
eBook - ePub- Mukesh Doble, Anil Kumar Kruthiventi, Vilas Ganjanan Gaikar, Mukesh Doble, Anil Kumar Kruthiventi, Vilas Ganjanan Gaikar(Authors)
- 2004(Publication Date)
- CRC Press(Publisher)
...For example, if one considers an assembly of four atoms A, B, C, and D. One can envisage different types of connectivity, such as A-B-C-D, A-B-D-C, B-A-D-C, and so on. For any one of these molecules, which are constitutional isomers of A-B-C-D, even if we assume constant bond angles ABC and BCD, one can generate an infinite number of structures changing the torsion angle ABC/BCD. These structures are the different conformers of the molecule A-B-C-D. In spite of this infinite 3D structures possible for molecules, thankfully, since these structures differ in energies, the molecule exists in only a few (sometimes only in one) rapidly interchanging conformers. Thus, it is possible to predict the 3D structure of any molecule by studying the energy of the conformers. The lowest energy conformer is the state in which any molecule will exist in ground state. Thus, for cyclic structures, such as cyclopentane and cyclohexane (which we normally encounter in biologic systems), the probable low-energy conformers are the envelope form for the cyclopentane and the two chair forms for the cyclohexane (as shown in Fig. 2.11). One has to be cautious when applying these above principles because based on the substitutions on theses ring systems the lowest energy conformer may be different. However, these principles being the first principles are of great value in understanding the 3D structure of most of the biomolecules, thereby, their reactivity. FIGURE 2.11 Stable conformations of cyclopentane and cyclohexane. 2.4.3 Summary: Learning Outcome The representation of molecules as the structural formula. Given a molecular formula, there can be more than one compound having the same constituent atoms...
eBook - ePub- J Fisher, J.R.P. Arnold, Julie Fisher, John Arnold(Authors)
- 2020(Publication Date)
- Taylor & Francis(Publisher)
...The eclipsed conformation in which the methyl groups are in line with each other is labeled syn ; this is the highest energy conformation. The range of energies encompassed in conformational variations is readily depicted in an energy profile (Figure 4). Figure 4 The energy profile for conformational flexing in n-butane. Conformational isomerism is also possible in cyclic systems. For example, cyclohexane (C 6 H 12), can adopt a range of conformations via bond rotations which occur to relieve the strain energy (or torsional strain) that would be present if the ring was forced to be planar. The energy profile, with a representation of the distinct conformational isomers of cyclohexane is shown in Figure 5(a), together with the Newman projections of the (i) chair and (ii) boat conformations of cyclohexane (Figure 5(b)). Figure 5 (a) The energy profile for conformational flexing in cyclohexane, and (b) the Newman projections for the (i) chair and (ii) boat conformations. The possibility of conformational isomerism is very import antinbiology and canhave profound effects on the shape and functionality of biological macromolecules. For example, the cyclic sugar systems that are part of DNA and RNA molecules (Sections K2, M2, and M4) are flexible but preferentially adopt chair-like conformations referred to as C 2, -endo (or South) and C 3, -endo (or North), respectively (Figure 6). As a result, polymers of DNA are generally long and thin, whereas those of RNA are shorter and wider (Section M2). Figure 6 The conformational preferences of sugar rings found in (a) DNA and (b) RNA. Fischer projections The Fischer projection is another way to display, in two dimensions, the three-dimensional shape of a molecule. For example, the Fischer projection for butane is shown in Figure 7(a). Figure 7 (a) The Fischer projection for n-butane and (b) the three-dimensional shape it represents. The horizontal and vertical lines are reflecting the eclipsed conformation by convention...
eBook - ePub- Graham Patrick(Author)
- 2004(Publication Date)
- Taylor & Francis(Publisher)
...Each carbon in the chair has two C–H bonds, one of which is equatorial and one of which is axial. A chair structure can invert through a high energy boat intermediate such that the equatorial bonds become axial and the axial bonds become equatorial. If a substituent is present, the most stable chair conformation is where the substituent is equatorial. In the axial position, the substituent experiences two gauche interactions with C–C bonds in the ring. Definition Conformational isomers are essentially different shapes of the same molecule resulting from rotation round C–C single bonds. Since rotation round a single bond normally occurs easily at room temperature, conformational isomers are not different compounds and are freely interconvertable. Unlike constitutional and configurational isomers, conformational isomers cannot be separated. Alkanes Conformational isomers arise from the rotation of C–C single bonds. There are many different shapes which a molecule like ethane could adopt by rotation around the C–C bond. However, it is useful to concentrate on the most distinctive ones (Figure 1). The two conformations I and II are called ‘staggered’ and ‘eclipsed’ respectively. In conformation I, the C–H bonds on carbon 1 are staggered with respect to the Figure 1. (a) ‘Staggered’ conformation (I) of ethane ; (b) ‘eclipsed’ conformation (II) of ethane. Figure 2. Newman projections of the (a) staggered and (b) eclipsed conformations of ethane. C–H bonds on carbon 2. In conformation II, they are eclipsed. Newman projections (Figure 2) represent the view along the C1–C2 bond and emphasize the difference. Carbon 1 is represented by the small black circle and carbon 2 is represented by the larger sphere...
eBook - ePub- Leslie H. Sperling(Author)
- 2015(Publication Date)
- Wiley-Interscience(Publisher)
...CHAPTER 2 CHAIN STRUCTURE AND CONFIGURATION In the teaching of physical polymer science, a natural progression of material begins with chain structure, proceeds through morphology, and leads on to physical and mechanical behavior. To a significant measure, one step determines the properties of the next (1). Polymer chains have three basic properties: 1. The molecular weight and molecular weight distribution of the molecules. These properties are discussed in Chapter 3. 2. The conformation of the chains in space. The term conformation refers to the different arrangements of atoms and substituents of the polymer chain brought about by rotations about single bonds. Examples of different polymer conformations include the fully extended planar zigzag, helical, folded chain, and random coils. Some conformations of a random coil might be (2.1) The methods of determining polymer chain conformation are discussed in Chapters 3 and 5. 3. The configuration of the chain. The term “configuration” refers to the organization of the atoms along the chain. Some authors prefer the term “microstructure” rather than configuration. Configurational isomerism involves the different arrangements of the atoms and substituents in a chain, which can be interconverted only by the breakage and reformation of primary chemical bonds. The configuration of polymer chains constitutes the principal subject of this chapter. 2.1 EXAMPLES OF CONFIGURATIONS AND CONFORMATIONS 2.1.1 Head-to-Head and Head-to-Tail Configurations Before proceeding with the development of theory and instruments, a simple but important example of chain configuration is given. This involves the difference between head-to-head and head-to-tail placement of the monomeric units, or mers, during polymerization...
