Chemical Bonding in Crystals: New Directions
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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........ -
Bonding in Solids, Structural and Chemical Properties - R
MATERIALS SCIENCE AND ENGINEERING – Vol. I – Bonding in Solids, Structural and Chemical Properties - R. W. Grimes BONDING IN SOLIDS, STRUCTURAL AND CHEMICAL PROPERTIES R. W. Grimes Imperial College, London, UK Keywords: Atomic structure, band structure, bonding, bulk modulus, conductivity, covalent, defects, electrons, energy level, hydrogen bonding, hybridization, insulators, ionic, metal, molecule, orbital, quantum, Schrödinger equation, semi-conductors, wave function. Contents 1. Introduction 2. Atomic Orbitals: their Origin and their Shapes 2.1. The Four Quantum Numbers 2.2. The Schrödinger Equation 2.3. Atoms with more than One Electron 3. Forming Bonds between like Atoms: Bonding and Anti-bonding Molecular Orbitals, Sigma and Pi-bonds 3.1. The Born-Oppenheimer Approximation 3.2. The Molecular Orbital Approximation 3.3. Linear Combination of Atomic Orbitals + 3.4. The Binding Curve for H2 3.5. Predicting the Stability of Other Simple Molecules 3.6. The Fluorine Diatomic Molecule: Another Homonuclear Molecule 4. Forming Bonds between Unlike Atoms: Polar Covalent and Ionic Bonds, Two Extremes of the Same Process 4.1. HF, a Polar Covalent Molecule 4.2. NaF, an Ionic Molecule 5. A Simple Model for an Ionic Solid: A Balance between Coulombic Attraction and Short-range Repulsion 5.1. Effective Potentials for Ionic Molecules 5.2. Extending the Model to Bulk NaF 5.3. CalculatingUNESCO the Bulk Modulus – EOLSS 6. From Hybridization to Conjugation to Band Structures: Why Diamond and Graphite have such Different Properties 6.1. Carbon 6.2. HybridizationSAMPLE and Molecular Orbitals CHAPTERS 7. More about Bands: Metals, Insulators and Semiconductors 7.1. Forming Bands in Metals 7.2. -
BONDING in SOLIDS Engineering Physics
Vignan BONDING IN SOLIDS Engineering Physics 1.1 Types of Bonding:- Different charge distributions in the atoms give rise to different types of bonding. They classified into five classes 1. Ionic bonding 2. Covalent bonding 3. Metallic bonding 4. Hydrogen bonding 5. Vander-Waals bonding Based on the bond strength atomic bonding can be grouped into “primary” and “secondary” bonding. Primary bonding:- Primary bonding have energies in the range of 1-10 eV. Ionic, covalent and metallic bonds are examples of primary bonding among these ionic and covalent bondings are generally stronger than the metallic bonding. Secondary bonding:- Secondary bonding have energies in the range of 0.01- 0.5 eV/ bond Hydrogen bonding and Vander Waals bonding are examples of secondary bonding. Generally, Vander Waals bonding is the weakest of all. 1 Vignan BONDING IN SOLIDS Engineering Physics 1.2 Ionic bonding (or) Hetro-Polar bond:- 1. Ionic bond is also called as “Hetro-Polar bond”. 2. Crystals in which ionic bond is present are known as “ionic crystals”. Ionic crystals are mostly insulating in character. Ex:-Nacl, NaBr, KBr, Mgo etc... 3. An Ionic bonding can only be formed between two different atoms, one electropositive and other electronegative. 4. Electropositive elements readily give up electrons and are usually group Ι (or) ΙΙ Elements e.g. Na, k, Ba. 5. Whereas electronegative elements readily take up electrons and are usually Group VΙ (or) VΙΙ elements e.g. Cl, Br and O. An example of the ionic bonding is NaCl. When neutral atom of a Na and Cl are brought close together it is easy for the valence electron of the sodium atom to be transferred to the chlorine atom so that both of them acquire a stable inert gas electronic configuration. -
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. -
Representation of the States of Matter
Chapter 10 Liquids & Solids Return to Slide 3 Representation of the states of Sublimation matter. Dry ice (solid CO2). Photo courtesy of American Color. PV = nRT ? ? Changes of State Intermolecular Forces • A change of state or phase transition is a Forces between (rather than within) molecules. change of a substance from one state to another. º dipole-dipole attraction: molecules with dipoles orient themselves so that “+” and gas “−” ends of the dipoles are close to each boiling condensation other. sublimation liquid condensation or º hydrogen bonds: dipole-dipole attraction in (see Figure 11.3) deposition which hydrogen is bound to a highly melting freezing electronegative atom. (F, O, N) solid 1 Hydrogen Bonding • Hydrogen bonding is a force that exists between a hydrogen atom covalently bonded to a very electronegative atom, X, and a lone pair of electrons on a very electronegative atom, Y. • To exhibit hydrogen bonding, one of the following three structures must be present. : : : H NOHFH • Only N, O, and F are electronegative enough to leave the hydrogen nucleus exposed. Dipole-Dipole Forces • Polar molecules can attract one another Figure 11.23: through dipole-dipole forces. Fluoromethane • The dipole-dipole force is an attractive and methanol. intermolecular force resulting from the tendency of polar molecules to align themselves positive end to negative end. δ+ H Cl δ− δ+ H Cl δ− Figure 11.21 shows the alignment of polar molecules. Hydrogen Bonding Figure 10.2: • A hydrogen atom bonded to an electronegative (a) The electrostatic interaction of two atom appears to be special. polar molecules. • The electrons in the O-H bond are drawn to the O (b) The interaction atom, leaving the dense positive charge of the of many dipoles in a hydrogen nucleus exposed. -
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. -
Introduction • Bonding in Solids • Ionic Bond • Covalent Bond • Metallic Bond • Intermolecular Forces
Topic 1: Introduction. Families of materials and applications Universidad Carlos III de Madrid MATERIALSCIENCIA E INGENIERÍA SCIENCE AND DE ENGINEERING MATERIALES www.uc3m.es TOPIC 1.2. BONDING IN SOLIDS. RELATION BETWEEN BONDING, STRUCTURE AND PROPERTIES OF MATERIALS • Introduction • Bonding in solids • Ionic bond • Covalent bond • Metallic bond • Intermolecular forces Dpt. Materials Sci. and Eng. and Chem. Eng. UC3M Sophia A. Tsipas / Dania Olmos 1 Topic 1: Introduction. Families of materials and applications INTRODUCTION Nature of bonding <> properties <> type of materials <> Processing and applications Applications Processing Structure Properties Dpt. Materials Sci. and Eng. and Chem. Eng. UC3M Sophia A. Tsipas / Dania Olmos 2 Topic 1: Introduction. Families of materials and applications IONIC BOND It forms between a metal and a non metal. There is electron transfer from the less electronegative atom to the more electronegative . Bonding forces ⇒ F electrostatic attraction between opposite charged ions. • Pure ionic bond: ideal. • ⇒ Always exists covalent participation Dpt. Materials Sci. and Eng. and Chem. Eng. UC3M Sophia A. Tsipas / Dania Olmos 3 Topic 1: Introduction. Families of materials and applications IONIC BOND Ionic compounds are crystalline solids It is a non directional bond formed by strong electrostatic interactions LATTICE ENERGY: Energy released when a mole of ionic solid is formed from its ions in the gas state. Born-Haber cycle for LiF. Step ΔH(kJ/mol) Na+ Sublimation of Li 155.2 Cl- Dissociation of F2 (g) 150.6 Ionization of Li(g) 520 - Gain of e of F(g) -328 Formation of LiF from Li(s) and -594.1 ½F2(g) Dpt. Materials Sci. -
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.