Constitutional Vs Conformational Isomers
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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 -
Bader's Theory of Atoms in Molecules
J. Chem. Sci. Vol. 128, No. 10, October 2016, pp. 1527–1536. c Indian Academy of Sciences. Special Issue on CHEMICAL BONDING DOI 10.1007/s12039-016-1172-3 PERSPECTIVE ARTICLE Bader’s Theory of Atoms in Molecules (AIM) and its Applications to Chemical Bonding P SHYAM VINOD KUMAR, V RAGHAVENDRA and V SUBRAMANIAN∗ Chemical Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai, Tamil Nadu 600 020, India e-mail: [email protected]; [email protected] MS received 22 July 2016; revised 17 August 2016; accepted 19 August 2016 Abstract. In this perspective article, the basic theory and applications of the “Quantum Theory of Atoms in Molecules” have been presented with examples from different categories of weak and hydrogen bonded molecular systems. Keywords. QTAIM; non-covalent interaction; chemical bonding; H-bonding; electron density 1. Introduction account of the bonding within a molecule or crystal. Specially, the derivative of electron density on BCP It is now possible to define the structure of molecules is zero. Bader’s group has made several seminal con- quantum mechanically with the help of Bader’s Quan- tributions to the development of the QTAIM theory tum Theory of Atoms in Molecules (QTAIM).1,2 This and its applications to unravel chemical bonding.10 13 theory has been widely applied to unravel atom-atom Popelier and coworkers have employed the QTAIM interactions in covalent and non-covalent interactions to address several issues in chemistry.14 16 Particu- in molecules,3 molecular clusters,4 small molecular larly, they have demonstrated the possibility of devel- crystals,5 proteins,6 DNA base pairing and stacking.7 oping structure-activity-relationship to predict various Basic motive of QTAIM is to exploit charge density or physico-chemical properties.17 They have used the the- electron density of molecules ρ(r; X) as a vehicle to ory of Quantum Chemical Topology (QCT), to provide study the nature of bonding in molecular systems. -
FORCE FIELDS for PROTEIN SIMULATIONS by JAY W. PONDER
FORCE FIELDS FOR PROTEIN SIMULATIONS By JAY W. PONDER* AND DAVIDA. CASEt *Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 51. Louis, Missouri 63110, and tDepartment of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037 I. Introduction. ...... .... ... .. ... .... .. .. ........ .. .... .... ........ ........ ..... .... 27 II. Protein Force Fields, 1980 to the Present.............................................. 30 A. The Am.ber Force Fields.............................................................. 30 B. The CHARMM Force Fields ..., ......... 35 C. The OPLS Force Fields............................................................... 38 D. Other Protein Force Fields ....... 39 E. Comparisons Am.ong Protein Force Fields ,... 41 III. Beyond Fixed Atomic Point-Charge Electrostatics.................................... 45 A. Limitations of Fixed Atomic Point-Charges ........ 46 B. Flexible Models for Static Charge Distributions.................................. 48 C. Including Environmental Effects via Polarization................................ 50 D. Consistent Treatment of Electrostatics............................................. 52 E. Current Status of Polarizable Force Fields........................................ 57 IV. Modeling the Solvent Environment .... 62 A. Explicit Water Models ....... 62 B. Continuum Solvent Models.......................................................... 64 C. Molecular Dynamics Simulations with the Generalized Born Model........ -
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. -
Functional Behavior of Molecular Baskets and Structure-Activity Studies on Trapping Organophosphorus Nerve Agents in Water
Functional Behavior of Molecular Baskets and Structure-Activity Studies on Trapping Organophosphorus Nerve Agents in Water DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Yian Ruan Graduate Program in Chemistry The Ohio State University 2014 Dissertation Committee: Jovica D. Badjic, Advisor Christopher M. Hadad Jon R. Parquette Copyright by Yian Ruan 2014 Abstract Molecular recognition is exploited by nature to carry out delicately regulated reactions and form precisely organized structures in living organisms. Enzymes promote reactions by preorganizing substrates and stabilizing transition states in an active site via covalent and non-covalent interactions. Receptor proteins and antibodies can respond selectively to stimuli and trigger subsequent activities. These protein-substrate interactions have been great inspirations for chemists in the design of synthetic receptors as hosts and the study of their molecular recognition properties. Investigation of recognition behaviors can help decipher sub-cellular processes. Moreover, some artificial host-guest complexes have found applications in catalysis, sensing, imaging and drug delivery systems. The Badjic group has developed a family of host molecules called molecular baskets to study the effect of gating on molecular recognition. These baskets possess a cavity formed by a benzene base and phthalimide side walls. Pyridine-based gates close the basket via hydrogen bonds or metal chelation. Tuning the electronic and steric characteristics of gates affects the rate of guests entering and departing the basket. ii With all the knowledge about molecular gating, questions arise as to whether these gates can be applied to other platforms and how the mechanism of gating will be affected. -
1 an Introduction to the Quantum Theory of Atoms in Molecules
1 1 An Introduction to the Quantum Theory of Atoms in Molecules Che´rif F. Matta and Russell J. Boyd 1.1 Introduction The observation that some properties attributed to atoms and functional groups are transferable from one molecule to another has played a key role in the devel- opment of chemistry. This observation provides a basis for group additivity schemes and is exemplified by the constancy of group contributions to thermody- namic and spectroscopic properties. But what is the electronic basis of this empir- ical transferability? The quantum theory of atoms in molecules (QTAIM) [1], de- veloped by Professor Richard F. W. Bader and his coworkers, relies on quantum observables such as the electron density rðrÞ and energy densities to answer such a question. Other important (related) questions addressed by QTAIM include: What is an atom in a molecule or a crystal? How can an atom or a group of atoms be transferable sometimes in very different external potentials? Can one define bonding in molecules unambiguously especially in borderline cases? This chapter contains a summary of some of the main concepts of QTAIM. A more comprehensive and mathematically elegant treatment can be found in Bader’s book [1]. (Often in this chapter, the word ‘‘molecule’’ includes extended systems such as polymers, weakly bonded molecular complexes, and molecular and ionic crystals, in addition to its more traditional meaning of a single, finite, isolated chemically bonded group of atoms. It will be clear from the context when this term is used in its traditional or in its larger sense.) 1.2 The Topology of the Electron Density The topology of the electron density is dominated by the attractive forces of the nuclei imparting it with its principal topological feature – a substantial local max- The Quantum Theory of Atoms in Molecules. -
Electronic Reprint Critical Examination of the Radial Functions in the Hansen
electronic reprint Acta Crystallographica Section A Foundations of Crystallography ISSN 0108-7673 Critical examination of the radial functions in the Hansen–Coppens multipole model through topological analysis of primary and refined theoretical densities Anatoliy Volkov and Philip Coppens Copyright © International Union of Crystallography Author(s) of this paper may load this reprint on their own web site provided that this cover page is retained. Republication of this article or its storage in electronic databases or the like is not permitted without prior permission in writing from the IUCr. Acta Cryst. (2001). A57, 395–405 Volkov and Coppens ¯ Hansen–Coppens multipole model research papers Acta Crystallographica Section A Foundations of Critical examination of the radial functions in Crystallography the Hansen±Coppens multipole model through ISSN 0108-7673 topological analysis of primary and refined theoretical densities Received 22 December 2000 Accepted 6 February 2001 Anatoliy Volkov and Philip Coppens* Department of Chemistry, State University of New York at Buffalo, Buffalo, NY 14260-3000, USA. Correspondence e-mail: [email protected] A double-zeta (DZ) multipolar model has been applied to theoretical structure factors of four organic molecular crystals as a test of the ability of the multipole model to faithfully retrieve a theoretical charge density. The DZ model leads to signi®cant improvement in the agreement with the theoretical charge density along the covalent bonds and its topological parameters, and eliminates some of the bias introduced by the limited ¯exibility of the radial functions when a theoretical density is projected into the conventional multipole formalism. The DZ model may be too detailed for analysis of experimental data sets of the # 2001 International Union of Crystallography accuracy and resolution typically achieved at present, but provides guidance for Printed in Great Britain ± all rights reserved the type of algorithms to be adapted in future studies. -
Some Notes On: What Is an Atom in a Molecule
Topological and AIM analyses beyond the Born-Oppenheimer paradigm: New opportunities Mohammad Goli and Shant Shahbazian* Faculty of Chemistry, Shahid Beheshti University, G. C. , Evin, Tehran, Iran, 19839, P.O. Box 19395-4716. Tel/Fax: 98-21-22431661 E-mail: (Shant Shahbazian) [email protected] * Corresponding author 1 Abstract The multi-component quantum theory of atoms in molecules (MC-QTAIM) analysis is done on methane, ethylene, acetylene and benzene as selected basic hydrocarbons. This is the first report on applying the MC-QTAIM analysis on polyatomic species. In order to perform the MC-QTAIM analysis, at first step the nuclear-electronic orbital method at Hartree-Fock level (NEO-HF) is used as a non-Born-Oppenheimer (nBO) ab initio computational procedure assuming both electrons and protons as quantum waves while carbon nuclei as point charges in these systems. The ab initio calculations proceed substituting all the protons of each species first with deuterons and then tritons. At the next step, the derived nBO wavefunctions are used for the "atoms in molecules" (AIM) analysis. The results of topological analysis and integration of atomic properties demonstrate that the MC-QTAIM is capable of deciphering the underlying AIM structure of all the considered species. Also, the results of the analysis for each isotopic composition are distinct and the fingerprint of the mass difference of hydrogen isotopes is clearly seen in both topological and AIM analyses. This isotopic distinction is quite unique in the MC-QTAIM and not recovered by the orthodox QTAIM that treats nuclei as clamped particles. The results of the analysis also demonstrate that each quantum nucleus that forms an atomic basin resides within its own basin. -
1.3 Structures of Covalent Compounds 13
01_BRCLoudon_pgs5-1.qxd 12/8/08 11:48 AM Page 13 1.3 STRUCTURES OF COVALENT COMPOUNDS 13 1.9 Draw an appropriate bond dipole for the carbon–magnesium bond of dimethylmagnesium. Ex- plain your reasoning. H3C Mg CH3 dimethylmagnesium 1.3 STRUCTURES OF COVALENT COMPOUNDS We know the structure of a molecule containing covalent bonds when we know its atomic con- nectivity and its molecular geometry. Atomic connectivity is the specification of how atoms in a molecule are connected. For example, we specify the atomic connectivity within the water molecule when we say that two hydrogens are bonded to an oxygen. Molecular geometry is the specification of how far apart the atoms are and how they are situated in space. Chemists learned about atomic connectivity before they learned about molecular geom- etry. The concept of covalent compounds as three-dimensional objects emerged in the latter part of the nineteenth century on the basis of indirect chemical and physical evidence. Until the early part of the twentieth century, however, no one knew whether these concepts had any physical reality, because scientists had no techniques for viewing molecules at the atomic level. By the second decade of the twentieth century, investigators could ask two questions: (1) Do organic molecules have specific geometries and, if so, what are they? (2) How can molecular geometry be predicted? A. Methods for Determining Molecular Geometry Among the greatest developments of chemical physics in the early twentieth century were the discoveries of ways to deduce the structures of molecules. Such techniques include various types of spectroscopy and mass spectrometry, which we’ll consider in Chapters 12–15. -
DFT and QTAIM Study of the Tetra-Tert ... -.:. Michael Pittelkow
Journal of Molecular Structure 1026 (2012) 127–132 Contents lists available at SciVerse ScienceDirect Journal of Molecular Structure journal homepage: www.elsevier.com/locate/molstruc DFT and QTAIM study of the tetra-tert-butyltetraoxa[8]circulene regioisomers structure ⇑ Gleb V. Baryshnikov a, Boris F. Minaev a, , Valentina A. Minaeva a,b, Alina T. Baryshnikova a, Michael Pittelkow c a Bohdan Khmelnytsky National University, 18031 Cherkasy, Ukraine b Theoretical Chemistry, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden c Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark highlights " Tetra-tert-butyltetraoxa[8]circulene regioisomers were studied by DFT method. " Electronic density distribution was calculated by the QTAIM method. " The presence of stabilizing non-valence bonds is detected by X-ray experiment. " The HÁÁÁH contacts are dynamically unstable due to high ellipticity. " The energy of the HÁÁÁH and CHÁÁÁO contacts was estimated by the Espinosa equation. article info abstract Article history: The recently synthesized tetra-tert-butyltetraoxa[8]circulene regioisomers characterized by unusual Received 6 March 2012 solution-state aggregation behavior are calculated at the density functional theory (DFT) level with the Received in revised form 24 May 2012 quantum theory of atoms in molecules (QTAIMs) approach to the electron density distribution analysis. Accepted 24 May 2012 The presence of stabilizing intramolecular hydrogen bonds and hydrogen–hydrogen interactions in the Available online 31 May 2012 studied molecules is predicted and the energies of these interactions are estimated with QTAIM. Occur- rence of the CHÁÁÁO bonds is detected by the single-crystal X-ray analysis for two regioisomers, obtained Keywords: in high purity. -
Unit-2 Conformational Isomerism
UNIT-2 CONFORMATIONAL ISOMERISM In chemistry, conformational isomerism is a form of stereoisomerism in which the isomers can be interconverted exclusively by rotations about formally single bonds. Such isomers are generally referred to as conformational isomers or conformers and specifically as rotamers when the rotation leading to different conformations is restricted (hindered) rotation, in the sense that there exists a rotational energy barrier that needs to be overcome to convert one conformer to another. Conformational isomers are thus distinct from the other classes of stereoisomers for which interconversion necessarily involves breaking and reforming of chemical bonds. The rotational barrier, or barrier to rotation, is the activation energy required to interconvert rotamers. Conformers of butane, shown in Newman projection. The two gauche as well as the anti form are staggered conformations Types of conformational isomerism Butane has three rotamers: two gauche conformers, which are enantiomeric and an anti conformer, where the four carbon centres are coplanar. The three eclipsed conformations with dihedral angles of 0°,120° and 240° are not considered to be rotamers, but are instead transition states. Some important examples of conformational isomerism include: 1. Linear alkane conformations with staggered, eclipsed and gauche conformers, and 2. Ring conformation o Cyclohexane conformations with chair and boat conformers. o Carbohydrate conformation 3. Atropisomerism- due to restricted rotation about a bond, a molecule can become chiral 4. Folding of molecules, where some shapes are stable and functional, but others are not. Conformations of Ethane While there are an infinite number of conformations about any sigma bond, in ethane two particular conformers are noteworthy and have special names. -
Atoms in Molecules
Acc. Chem. Res. 1985,18, 9-15 9 Atoms in Molecules R. F. W. Bader Department of Chemistry, McMaster University, Hamilton, Ontario, Canada L8S 4M1 Received May 25, 1984 (Revised Manuscript Received September 28, 1984) Approximate quantum mechanical state functions of atoms linked by a network of bonds is the operational have recently been obtained for the norbornyl cation.1 principle underlying our classification and present un- These calculations have yielded the energy of its derstanding of chemical behavior. Therefore, it would equilibrium geometry and the relative energies of appear that to find chemistry within the framework of neighboring geometries. It is the purpose of this ac- quantum mechanics one must find a way of determining count to illustrate that more chemical information than the values of observables for pieces, that is, subsystems, simply energies and their associated geometries can be of a total system. But how is one to choose the pieces? obtained directly from a state function. A state func- Is there only one or are there many ways of dividing a tion contains the necessary information to both define molecule into atoms and its properties into atomic the atoms in a molecule and determine their average contributions? If there is an answer to this problem properties.2 It also enables one to assign a structure, then the necessary information must be contained in that is, determine the network of bonds linking the the state function, for 'k tells us everthing we can know atoms in a molecule and determine whether or not the about a system. structure is stable.3 The state function further de- Thus the question “Are there atoms in molecules?” termines where electronic charge is locally concentrated is equivalent to asking two equally necessary questions and depleted.