Unit-2 Conformational Isomerism
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The Conformations of Cycloalkanes
The Conformations of Cycloalkanes Ring-containing structures are a common occurrence in organic chemistry. We must, therefore spend some time studying the special characteristics of the parent cycloalkanes. Cyclical connectivity imposes constraints on the range of motion that the atoms in rings can undergo. Cyclic molecules are thus more rigid than linear or branched alkanes because cyclic structures have fewer internal degrees of freedom (that is, the motion of one atom greatly influences the motion of the others when they are connected in a ring). In this lesson we will examine structures of the common ring structures found in organic chemistry. The first four cycloalkanes are shown below. cyclopropane cyclobutane cyclopentane cyclohexane The amount of energy stored in a strained ring is estimated by comparing the experimental heat of formation to the calculated heat of formation. The calculated heat of formation is based on the notion that, in the absence of strain, each –CH2– group contributes equally to the heat of formation, in line with the behavior found for the acyclic alkanes (i.e., open chains). Thus, the calculated heat of formation varies linearly with the number of carbon atoms in the ring. Except for the 6-membered ring, the experimental values are found to have a more positive heat of formation than the calculated value owning to ring strain. The plots of calculated and experimental enthalpies of formation and their difference (i.e., ring strain) are seen in the Figure. The 3-membered ring has about 27 kcal/mol of strain. It can be seen that the 6-membered ring possesses almost no ring strain. -
Compact Hyperbolic Tetrahedra with Non-Obtuse Dihedral Angles
Compact hyperbolic tetrahedra with non-obtuse dihedral angles Roland K. W. Roeder ∗ January 7, 2006 Abstract Given a combinatorial description C of a polyhedron having E edges, the space of dihedral angles of all compact hyperbolic polyhe- dra that realize C is generally not a convex subset of RE [9]. If C has five or more faces, Andreev’s Theorem states that the correspond- ing space of dihedral angles AC obtained by restricting to non-obtuse angles is a convex polytope. In this paper we explain why Andreev did not consider tetrahedra, the only polyhedra having fewer than five faces, by demonstrating that the space of dihedral angles of com- pact hyperbolic tetrahedra, after restricting to non-obtuse angles, is non-convex. Our proof provides a simple example of the “method of continuity”, the technique used in classification theorems on polyhe- dra by Alexandrow [4], Andreev [5], and Rivin-Hodgson [19]. 2000 Mathematics Subject Classification. 52B10, 52A55, 51M09. Key Words. Hyperbolic geometry, polyhedra, tetrahedra. Given a combinatorial description C of a polyhedron having E edges, the space of dihedral angles of all compact hyperbolic polyhedra that realize C is generally not a convex subset of RE. This is proved in a nice paper by D´ıaz [9]. However, Andreev’s Theorem [5, 13, 14, 20] shows that by restricting to compact hyperbolic polyhedra with non-obtuse dihedral angles, E the space of dihedral angles is a convex polytope, which we label AC R . It is interesting to note that the statement of Andreev’s Theorem requires⊂ ∗rroeder@fields.utoronto.ca 1 that C have five or more faces, ruling out the tetrahedron which is the only polyhedron having fewer than five faces. -
Using Information Theory to Discover Side Chain Rotamer Classes
Pacific Symposium on Biocomputing 4:278-289 (1999) U S I N G I N F O R M A T I O N T H E O R Y T O D I S C O V E R S I D E C H A I N R O T A M E R C L A S S E S : A N A L Y S I S O F T H E E F F E C T S O F L O C A L B A C K B O N E S T R U C T U R E J A C Q U E L Y N S . F E T R O W G E O R G E B E R G Department of Molecular Biology Department of Computer Science The Scripps Research Institute University at Albany, SUNY La Jolla, CA 92037, USA Albany, NY 12222, USA An understanding of the regularities in the side chain conformations of proteins and how these are related to local backbone structures is important for protein modeling and design. Previous work using regular secondary structures and regular divisions of the backbone dihedral angle data has shown that these rotamers are sensitive to the protein’s local backbone conformation. In this preliminary study, we demonstrate a method for combining a more general backbone structure model with an objective clustering algorithm to investigate the effects of backbone structures on side chain rotamer classes and distributions. For the local structure classification, we use the Structural Building Blocks (SBB) categories, which represent all types of secondary structure, including regular structures, capping structures, and loops. -
Comparing Models for Measuring Ring Strain of Common Cycloalkanes
The Corinthian Volume 6 Article 4 2004 Comparing Models for Measuring Ring Strain of Common Cycloalkanes Brad A. Hobbs Georgia College Follow this and additional works at: https://kb.gcsu.edu/thecorinthian Part of the Chemistry Commons Recommended Citation Hobbs, Brad A. (2004) "Comparing Models for Measuring Ring Strain of Common Cycloalkanes," The Corinthian: Vol. 6 , Article 4. Available at: https://kb.gcsu.edu/thecorinthian/vol6/iss1/4 This Article is brought to you for free and open access by the Undergraduate Research at Knowledge Box. It has been accepted for inclusion in The Corinthian by an authorized editor of Knowledge Box. Campring Models for Measuring Ring Strain of Common Cycloalkanes Comparing Models for Measuring R..ing Strain of Common Cycloalkanes Brad A. Hobbs Dr. Kenneth C. McGill Chemistry Major Faculty Sponsor Introduction The number of carbon atoms bonded in the ring of a cycloalkane has a large effect on its energy. A molecule's energy has a vast impact on its stability. Determining the most stable form of a molecule is a usefol technique in the world of chemistry. One of the major factors that influ ence the energy (stability) of cycloalkanes is the molecule's ring strain. Ring strain is normally viewed as being directly proportional to the insta bility of a molecule. It is defined as a type of potential energy within the cyclic molecule, and is determined by the level of "strain" between the bonds of cycloalkanes. For example, propane has tl1e highest ring strain of all cycloalkanes. Each of propane's carbon atoms is sp3-hybridized. -
Isomerism in Organic Compounds
DEPARTMENT OF ORGANIC CHEMISTRY PHARMACEUTICAL FACULTY SEMMELWEIS UNIVERSITY László Szabó − Gábor Krajsovszky ISOMERISM IN ORGANIC COMPOUNDS Budapest 2017 © László Szabó © Gábor Krajsovszky ISBN 978-963-12-9206-0 Publisher: Dr. Gábor Krajsovszky 2 Acknowledgements The Author is thankful to dr. Ruth Deme assistant lecturer for drawing the structural formulas, as well as to Mrs. Zsuzsanna Petró-Karátson for the typewriting of the text part. The Author is thankful to dr. Péter Tétényi for the translation of the manuscript to English language. Dr. Gábor Krajsovszky 3 ISOMERISM IN ORGANIC COMPOUNDS Isomers are the compounds with the same qualitative and quantitative composition of elements, therefore their relative molecular weights and general formulas are identical, but their structures – including in the 3D arrangement – are different. The compounds propyl chloride and propane are not isomers, since their qualitative composition of elements are different. The compounds propane and propene are not isomers, although they are built from the same elements, but with different quanti- tative composition of elements. The compounds propene and cyclohexane are not isomers, although they are built from the same elements, with the same ratio of ele- ments, their relative molecular weights are different. However, the compounds butane and isobutane are isomers, since they have the same general formula, but their 3D arrangement is different. Only one compound or many compounds may have the same general formulas. For example, methane (a linear saturated -
Today's Class Will Focus on the Conformations and Energies of Cycloalkanes
Name ______________________________________ Today's class will focus on the conformations and energies of cycloalkanes. Section 6.4 of the text provides an introduction. 1 Make a model of cyclopentane. Use the 2-piece "lockable" bond connectors — these rotate more easily than the smaller ones. You may need to twist them to "lock" so that they don't pop apart. The text shows two conformations of this ring — the envelope and the half-chair. Why is cyclopentane non-planar? The two conformations are below. In the envelope, 4 Cs are in a plane; in the half-chair 3 Cs are in a plane. Th first conformer is easy. To get your model to look like the second one, start with a planar ring, keep the "front" 3 Cs in the plane, and twist the "back" C–C bond so that one C goes above that plane and the other goes below. Add Hs to each of these structures — no wedges and dashes here — these are "perspective" drawings (like the drawings of chair cyclohexane rings on p 197). Just use your model and sketch the Hs where they appear to be. fast If we were to replace one H in each of these conformers with a methyl group, what do you think would be the most favorable position for it? Circle the one H on each structure above that you would replace with a CH3. In general, what happens to the ring C–C–C angles when a ring goes from planar to non-planar? Lecture outline Structures of cycloalkanes — C–C–C angles if planar: 60° 90° 108° 120° actual struct: planar |— slightly |— substantially non-planar —| non-planar —> A compound is strained if it is destabilized by: abnormal bond angles — van der Waals repulsions — eclipsing along σ-bonds — A molecule's strain energy (SE) is the difference between the enthalpy of formation of the compound of interest and that of a hypothetical strain-free compound that has the same atoms connected in exactly the same way. -
Predicting Backbone Cα Angles and Dihedrals from Protein Sequences by Stacked Sparse Auto-Encoder Deep Neural Network
Predicting backbone C# angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network Author Lyons, James, Dehzangi, Abdollah, Heffernan, Rhys, Sharma, Alok, Paliwal, Kuldip, Sattar, Abdul, Zhou, Yaoqi, Yang, Yuedong Published 2014 Journal Title Journal of Computational Chemistry DOI https://doi.org/10.1002/jcc.23718 Copyright Statement © 2014 Wiley Periodicals, Inc.. This is the accepted version of the following article: Predicting backbone Ca angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network Journal of Computational Chemistry, Vol. 35(28), 2014, pp. 2040-2046, which has been published in final form at dx.doi.org/10.1002/jcc.23718. Downloaded from http://hdl.handle.net/10072/64247 Griffith Research Online https://research-repository.griffith.edu.au Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network James Lyonsa, Abdollah Dehzangia,b, Rhys Heffernana, Alok Sharmaa,c, Kuldip Paliwala , Abdul Sattara,b, Yaoqi Zhoud*, Yuedong Yang d* aInstitute for Integrated and Intelligent Systems, Griffith University, Brisbane, Australia bNational ICT Australia (NICTA), Brisbane, Australia cSchool of Engineering and Physics, University of the South Pacific, Private Mail Bag, Laucala Campus, Suva, Fiji dInstitute for Glycomics and School of Information and Communication Technique, Griffith University, Parklands Dr. Southport, QLD 4222, Australia *Corresponding authors ([email protected], [email protected]) ABSTRACT Because a nearly constant distance between two neighbouring Cα atoms, local backbone structure of proteins can be represented accurately by the angle between Cαi-1−Cαi−Cαi+1 (θ) and a dihedral angle rotated about the Cαi−Cαi+1 bond (τ). -
Toroidal Diffusions and Protein Structure Evolution
Toroidal diffusions and protein structure evolution Eduardo García-Portugués1;7, Michael Golden2, Michael Sørensen3, Kanti V. Mardia2;4, Thomas Hamelryck5;6, and Jotun Hein2 Abstract This chapter shows how toroidal diffusions are convenient methodological tools for modelling protein evolution in a probabilistic framework. The chapter addresses the construction of ergodic diffusions with stationary distributions equal to well-known directional distributions, which can be regarded as toroidal analogues of the Ornstein–Uhlenbeck process. The important challenges that arise in the estimation of the diffusion parameters require the consideration of tractable approximate likelihoods and, among the several approaches introduced, the one yielding a spe- cific approximation to the transition density of the wrapped normal process is shown to give the best empirical performance on average. This provides the methodological building block for Evolutionary Torus Dynamic Bayesian Network (ETDBN), a hidden Markov model for protein evolution that emits a wrapped normal process and two continuous-time Markov chains per hid- den state. The chapter describes the main features of ETDBN, which allows for both “smooth” conformational changes and “catastrophic” conformational jumps, and several empirical bench- marks. The insights into the relationship between sequence and structure evolution that ETDBN provides are illustrated in a case study. Keywords: Directional statistics; Evolution; Probabilistic model; Protein structure; Stochastic differential equation; Wrapped -
Cycloalkanes, Cycloalkenes, and Cycloalkynes
CYCLOALKANES, CYCLOALKENES, AND CYCLOALKYNES any important hydrocarbons, known as cycloalkanes, contain rings of carbon atoms linked together by single bonds. The simple cycloalkanes of formula (CH,), make up a particularly important homologous series in which the chemical properties change in a much more dramatic way with increasing n than do those of the acyclic hydrocarbons CH,(CH,),,-,H. The cyclo- alkanes with small rings (n = 3-6) are of special interest in exhibiting chemical properties intermediate between those of alkanes and alkenes. In this chapter we will show how this behavior can be explained in terms of angle strain and steric hindrance, concepts that have been introduced previously and will be used with increasing frequency as we proceed further. We also discuss the conformations of cycloalkanes, especially cyclo- hexane, in detail because of their importance to the chemistry of many kinds of naturally occurring organic compounds. Some attention also will be paid to polycyclic compounds, substances with more than one ring, and to cyclo- alkenes and cycloalkynes. 12-1 NOMENCLATURE AND PHYSICAL PROPERTIES OF CYCLOALKANES The IUPAC system for naming cycloalkanes and cycloalkenes was presented in some detail in Sections 3-2 and 3-3, and you may wish to review that ma- terial before proceeding further. Additional procedures are required for naming 446 12 Cycloalkanes, Cycloalkenes, and Cycloalkynes Table 12-1 Physical Properties of Alkanes and Cycloalkanes Density, Compounds Bp, "C Mp, "C diO,g ml-' propane cyclopropane butane cyclobutane pentane cyclopentane hexane cyclohexane heptane cycloheptane octane cyclooctane nonane cyclononane "At -40". bUnder pressure. polycyclic compounds, which have rings with common carbons, and these will be discussed later in this chapter. -
H2O2 and NH 2 OH
Int. J. Mol. Sci. 2006 , 7, 289-319 International Journal of Molecular Sciences ISSN 1422-0067 © 2006 by MDPI www.mdpi.org/ijms/ A Quest for the Origin of Barrier to the Internal Rotation of Hydrogen Peroxide (H 2O2) and Fluorine Peroxide (F 2O2) Dulal C. Ghosh Department of Chemistry, University of Kalyani, Kalyani-741235, India Email: [email protected], Fax: +91-33 25828282 Received: 2 July 2006 / Accepted: 24 July 2006 / Published: 25 August 2006 Abstract: In order to understand the structure-property relationship, SPR, an energy- partitioning quest for the origin of the barrier to the internal rotation of two iso-structural molecules, hydrogen peroxide, H 2O2, and fluorine peroxide, F 2O2 is performed. The hydrogen peroxide is an important bio-oxidative compound generated in the body cells to fight infections and is an essential ingredient of our immune system. The fluorine peroxide is its analogue. We have tried to discern the interactions and energetic effects that entail the nonplanar skew conformation as the equilibrium shape of the molecules. The physical process of the dynamics of internal rotation initiates the isomerization reaction and generates infinite number of conformations. The decomposed energy components faithfully display the physical process of skewing and eclipsing as a function of torsional angles and hence are good descriptors of the process of isomerization reaction of hydrogen peroxide (H 2O2) and dioxygen difluoride (F 2O2) associated with the dynamics of internal rotation. It is observed that the one-center, two-center bonded and nonbonded interaction terms are sharply divided in two groups. One group of interactions hinders the skewing and favours planar cis/trans forms while the other group favours skewing and prefers the gauche conformation of the molecule. -