A molecular-dynamics study of the rhodopsin chromophore using ultrasoft pseudopotentials
|
|
- Noah Dixon
- 7 years ago
- Views:
Transcription
1 Progress of Theoretical Physics Supplement No. 138, A molecular-dynamics study of the rhodopsin chromophore using ultrasoft pseudopotentials Minoru Sugihara, 1 ) Peter Entel, 1 Hendrik Meyer, 2 Volker Buss, 3 Frank Terstegen, 4 and Jürgen Hafner 5 1 Theoretical Physics, University of Duisburg, Duisburg, Germany 2 Max-Planck Institute for Polymer Science, Mainz, Germany 3 Theoretical Chemistry, University of Duisburg, Duisburg, Germany 4 Theoretical Chemistry, University of Zürich, 8057 Zürich, Switzerland 5 Materials Physics Institute, University of Vienna, 1090 Vienna, Austria (Received October 11, 1999) We investigate the effect of different environments on the chromophore of the protein rhodopsin by using the Vienna ab initio simulation package which is based on Density Functional Theory with a plane wave basis set and the implementation of Vanderbilt s ultrasoft pseudopotentials. We have calculated the energy dependence of 11-cis-retinal on the - double bond twist angle in the ground state and our results show that the isomerization in the ground state of the retinal chromophore is more difficult in the presence of the counter ion than without it. 1. Introduction Rhodopsin is a membrane protein, which is responsible for black and white vision in the vertebrate eye. 1) It consists mainly of seven so-called transmembrane helices which form a pocket. It was established that the visual pigment rhodopsin contains as chromophore 11-cis-retinal protonated Schiff base 2) and the visual process is initiated by the photochemical isomerization of 11-cis to all-trans. The isomerization eventually leads to the chemical signal of a nerve impulse sent to the brain which enables us to see. Of all double bonds in the molecule which can theoretically undergo cis-trans isomerization, only the - double bond is affected by the action of light: When rhodopsin absorbs light of 500 nm the chromophore makes a Franck-Condon transition into the first excited singlet state where it isomerizes to the all-trans isomer bathorhodopsin, a process which is complete within 200 fs. On the other hand, the dark-isomerization of the chromophore occurs in the ground state. The isomerization of this thermally activated event requires activation energies in the range of 0.99 ev/molecule (23 kcal/mol) to 1.17 ev/molecule (27 kcal/mol), which is significantly less than the energy of 1.95 ev/molecule (45 kcal/mol) required for the photoisomerization. 3), 4) In this work we have addressed the question whether the dark-isomerization of 11-cis-retinal Schiff base is easier in the protonated or in the deprotonated form. We have calculated the energy dependence of the molecule on the - double bond twist angle in the ground state, and we have also investigated the effect of the environment on the - bond of ) address: minoru@thp.uni-duisburg.de typeset using PTPTEX.sty <ver.1.0>
2 108 M. Sugihara, P. Entel, H. Meyer, V. Buss, F. Terstegen, and J. Hafner the chromophore. We have used thevienna ab initio simulation package (VASP) which is a program designed for molecular-dynamics (MD) simulations based on Density Functional Theory. It uses a plane wave basis set and Vanderbilt s ultrasoft pseudopotentials. All calculations are performed for a periodic supercell and the details are described in the publication of its authors. 5) 2. Simulation of 11-cis-retinal Figure 1 shows the structure of the 11-cis-retinal protonated Schiff base. The chromophore of rhodopsin is connected via amino acid Lys-296 to the protein. The nitrogen atom is protonated, and thus the chromophore has a net positive charge. In the simulation we assume for simplicity a uniform background charge of -e per unit cell to achieve charge neutrality. Figure 2 shows the structure of the 11-cis-retinal protonated Schiff base with a counter ion HCOO and one water molecule. The counter ion models part of the amino acid Glu-113. This is the simplest structure where the proton can move from the nitrogen via the water molecule to a negatively charged counter ion HCOO. The whole structure is electrically neutral. Both the protonated Schiff base and the base with HCOO and H 2 O have been optimized by the restricted Hartree-Fock method (Gaussian 98). 6), 7) + N Fig cis-retinal protonated Schiff base. N + Fig cis-retinal protonated Schiff base with counter ion HCOO and H 2O. Figure 3 shows the total energy change of these structures as the retinal molecule is twisted about the - bond. The calculation has been done in a Å 3 simulation box and one k-point (Γ -point only). The cut-off energy was 260 ev. Because of the many atoms which constitute the chromophore, the system
3 A molecular-dynamics study of the rhodopsin chromophore 109 Energy (ev/molecule) twist angle Fig. 3. With VASP calculated relative energies of 11-cis-retinal protonated Schiff base without (dotted lines) and with (solid lines) couter ion HCOO and a water molecule as a function of the - cis-double bond twist angle. Squares correspond to the protonated species, circles to the deprotonated species, where the proton is attached to the water molecule Energy (kcal/mol) has many meta-stable structures. In order to obtain the optimized conformation of the molecule, MD simulations with a time step of 0.5 fs have been done for all arrangements (with and without counter ion and also for the case when the twist angle has been fixed) and for a efficiently long time ( 600 fs) at temperature of 2 K. Considering the isolated molecule first, the calculations show that the protonated Schiff base twists around the - bond more easily than the de-protonated Schiff base. This is a consequence of the protonation of the nitrogen atom and the fact that the double bond character of the - bond is decreased compared to the deprotonated form. When the counter ion and the water molecule are added to the chromophore, the character of the - bond is changed. Figure 3 shows that there is no energy difference between the protonated and the de-protonated Schiff bases. The counter ion seems to give back charge to the chromophore. The calculated results by Gaussian 98 also show the same effect of the counter ion and a water molecule. 8) 3. Discussion: HOMO and LUMO analysis Figures 4 and 5 show the electron charge density distribution of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of the 11-cis-retinal protonated Schiff base. The charge in the HOMO is mainly localized on the double bonds, except for the - bond, a consequence of the protonation of the nitrogen atom. On the other hand, the charge in the LUMO resides mainly on the single bonds. Figures 6 and 7 show the corresponding charge distribution for the 11-cis-retinal protonated Schiff base with counter ion HCOO and H 2 O. When the counter ion and
4 110 M. Sugihara, P. Entel, H. Meyer, V. Buss, F. Terstegen, and J. Hafner Fig. 4. HOMO electron charge density distribution of 11-cis-retinal protonated Schiff base. Fig. 5. LUMO electron charge density distribution of 11-cis-retinal protonated Schiff base. Fig. 6. HOMO electron charge density distribution of 11-cis-retinal protonated Schiff base with counter ion HCOO and H 2O.
5 A molecular-dynamics study of the rhodopsin chromophore 111 Fig. 7. LUMO electron charge density distribution of 11-cis-retinal protonated Schiff base with counter ion HCOO and H 2O. Fig. 8. HOMO electron charge density distribution of 11-cis-retinal de-protonated Schiff base. Fig. 9. HOMO electron charge density distribution of 11-cis-retinal de-protonated Schiff base with counter ion HCOO and H 2O. the water molecule are added to the chromophore, significant changes are observed. In particular the - bond in the HOMO acquires significant charge density becoming more like a double-bond. On the other hand, the LUMO charge densities don t change significantly and remain concentrated mainly on the single bonds. This means that the counter ion gives back negative charge to the chromophore and that
6 112 M. Sugihara, P. Entel, H. Meyer, V. Buss, F. Terstegen, and J. Hafner the isomerization of the chromophore in the ground state becomes more difficult. H. de Groot and co-workers have simulated the 11-cis to all-trans isomerization with a Car-Parrinello ab initio MD. 9) In their simulation, the counter ion is a chloride ion (Cl ) instead of the more realistic counter ion HCOO and H 2 O. As consequence, the - bond of their HOMO electron charge distribution is still single-bond like and very similar to the HOMO electron charge distribution of isolated 11-cisretinal. 10) We conclude that the ground state isomerization of protonated Schiff base is more difficult in the presence of a counter ion: As a consequence the environment of the chromophore has to be taken into account when studying the isomerization process. Fig. 8 and 9 show the corresponding charge distribution for the 11-cis-retinal deprotonated Schiff base without and with couter ion HCOO and H 2 O. The change in the HOMO of - of the de-protonated Schiff base is double-bond like. There is no significant effect of the counter ion and the water molecule in the de-protonated case. In this work the ground state properties of 11-cis-retinal have been studied by ab initio MD. We have investigated the effect of the environment on the - bond of 11-cis-retinal Schiff base. Our results show the significance of the counter ion on the - bond, rendering the isomerization of the retinal chromophore in the ground state more difficult. The calculated HOMO and LUMO electron charge density distributions support our conclusion. Acknowledgements This work has been supported by the Graduate College Structure and Dynamics of Heterogeneous Systems and by the Sonderforschungsbereich 445 on Nanoparticles from the Gas Phase: Nucleation, Characterization and Properties. References 1) R. R. Birge, Biochem. Biophys. Acta 293 (1990), ) G. Wald, Science 162 (1968), ) R. R. Birge, Biochem. Biophys. Acta 1016 (1990), ) R. B. Barlow, R. R. Birge, E. Kapian, and J. R, Tallent, Nature 366 (1993), 64. 5) G. Kresse and J. Furthmüller, Phys. Rew. B 54 (1996), ) F. Terstegen and V. Buss, J. Mol. Struct. (Theochem) 369 (1996), 53. 7) F. Terstegen and V. Buss, unpublished. 8) F. Terstegen, private communication. 9) F. Buda, H. J. M. de Groot, and A. Bifone, Phys. Rev. Lett. 77 (1996), ) A. Bifone, H. J. M. degroot, andf. Buda, J. Phys. Chem. B101 (1997), 2954.
13.4 UV/VIS Spectroscopy
13.4 UV/VIS Spectroscopy The spectroscopy which utilizes the ultraviolet (UV) and visible (VIS) range of electromagnetic radiation, is frequently referred to as Electronic Spectroscopy. The term implies
More informationUltraviolet Spectroscopy
Ultraviolet Spectroscopy The wavelength of UV and visible light are substantially shorter than the wavelength of infrared radiation. The UV spectrum ranges from 100 to 400 nm. A UV-Vis spectrophotometer
More informationUNIT 2 PRACTICE EXAM (Part 1: General Chemistry)
UIT 2 PRACTICE EXAM (Part 1: General Chemistry) 1. Which would be the best definition of an ionic bond? a. The attraction between the partial positive region of one molecule and the partial negative region
More informationPhotoinduced volume change in chalcogenide glasses
Photoinduced volume change in chalcogenide glasses (Ph.D. thesis points) Rozália Lukács Budapest University of Technology and Economics Department of Theoretical Physics Supervisor: Dr. Sándor Kugler 2010
More informationUV-Vis Vis spectroscopy. Electronic absorption spectroscopy
UV-Vis Vis spectroscopy Electronic absorption spectroscopy Absortpion spectroscopy Provide information about presence and absence of unsaturated functional groups Useful adjunct to IR Determination of
More informationMolecular Models Experiment #1
Molecular Models Experiment #1 Objective: To become familiar with the 3-dimensional structure of organic molecules, especially the tetrahedral structure of alkyl carbon atoms and the planar structure of
More informationCHEM 322 Organic Chemistry II - Professor Kathleen V. Kilway
CHEM 322 Organic Chemistry II - Professor Kathleen V. Kilway "Organic Chemistry" by Maitland Jones, 4th edition Chapter 12 Homework: 1, 2, 4, 5, 6, 7, 15, 16, 17, 19, 21, 24, 26, 28, 29, 30, 38, 39, 44,
More informationPROTEINS THE PEPTIDE BOND. The peptide bond, shown above enclosed in the blue curves, generates the basic structural unit for proteins.
Ca 2+ The contents of this module were developed under grant award # P116B-001338 from the Fund for the Improvement of Postsecondary Education (FIPSE), United States Department of Education. However, those
More informationName period AP chemistry Unit 2 worksheet Practice problems
Name period AP chemistry Unit 2 worksheet Practice problems 1. What are the SI units for a. Wavelength of light b. frequency of light c. speed of light Meter hertz (s -1 ) m s -1 (m/s) 2. T/F (correct
More informationHydrogen Bonds The electrostatic nature of hydrogen bonds
Hydrogen Bonds Hydrogen bonds have played an incredibly important role in the history of structural biology. Both the structure of DNA and of protein a-helices and b-sheets were predicted based largely
More informationMolecular Models in Biology
Molecular Models in Biology Objectives: After this lab a student will be able to: 1) Understand the properties of atoms that give rise to bonds. 2) Understand how and why atoms form ions. 3) Model covalent,
More informationGetting the most from this book...4 About this book...5
Contents Getting the most from this book...4 About this book....5 Content Guidance Topic 1 Atomic structure and the periodic table...8 Topic 2 Bonding and structure...14 Topic 2A Bonding....14 Topic 2B
More informationAP CHEMISTRY 2009 SCORING GUIDELINES
AP CHEMISTRY 2009 SCORING GUIDELINES Question 6 (8 points) Answer the following questions related to sulfur and one of its compounds. (a) Consider the two chemical species S and S 2. (i) Write the electron
More informationChapter 6 An Overview of Organic Reactions
John E. McMurry www.cengage.com/chemistry/mcmurry Chapter 6 An Overview of Organic Reactions Why this chapter? To understand organic and/or biochemistry, it is necessary to know: -What occurs -Why and
More informationCHEMISTRY STANDARDS BASED RUBRIC ATOMIC STRUCTURE AND BONDING
CHEMISTRY STANDARDS BASED RUBRIC ATOMIC STRUCTURE AND BONDING Essential Standard: STUDENTS WILL UNDERSTAND THAT THE PROPERTIES OF MATTER AND THEIR INTERACTIONS ARE A CONSEQUENCE OF THE STRUCTURE OF MATTER,
More informationCombinatorial Biochemistry and Phage Display
Combinatorial Biochemistry and Phage Display Prof. Valery A. Petrenko Director - Valery Petrenko Instructors Galina Kouzmitcheva and I-Hsuan Chen Auburn 2006, Spring semester COMBINATORIAL BIOCHEMISTRY
More informationHow To Understand The Human Body
Introduction to Biology and Chemistry Outline I. Introduction to biology A. Definition of biology - Biology is the study of life. B. Characteristics of Life 1. Form and size are characteristic. e.g. A
More informationChemistry 151 Final Exam
Chemistry 151 Final Exam Name: SSN: Exam Rules & Guidelines Show your work. No credit will be given for an answer unless your work is shown. Indicate your answer with a box or a circle. All paperwork must
More informationDetermination of Equilibrium Constants using NMR Spectroscopy
CHEM 331L Physical Chemistry Laboratory Revision 2.1 Determination of Equilibrium Constants using NMR Spectroscopy In this laboratory exercise we will measure the equilibrium constant for the cis-trans
More informationList the 3 main types of subatomic particles and indicate the mass and electrical charge of each.
Basic Chemistry Why do we study chemistry in a biology course? All living organisms are composed of chemicals. To understand life, we must understand the structure, function, and properties of the chemicals
More informationSupplementary Figures S1 - S11
1 Membrane Sculpting by F-BAR Domains Studied by Molecular Dynamics Simulations Hang Yu 1,2, Klaus Schulten 1,2,3, 1 Beckman Institute, University of Illinois, Urbana, Illinois, USA 2 Center of Biophysics
More information13C NMR Spectroscopy
13 C NMR Spectroscopy Introduction Nuclear magnetic resonance spectroscopy (NMR) is the most powerful tool available for structural determination. A nucleus with an odd number of protons, an odd number
More informationTRANSITION METALS AND COORDINATION CHEMISTRY
CHAPTER TWENTY-ONE TRANSITION METALS AND COORDINATION CHEMISTRY For Review 1. Chromium ([Ar]:4s 0 3d 5 ) and copper [Ar]:4s 1 3d 10 ) have electron configurations which are different from that predicted
More information5.111 Principles of Chemical Science
MIT OpenCourseWare http://ocw.mit.edu 5.111 Principles of Chemical Science Fall 2008 For information about citing these materials or our Terms of Use, visit: http://ocw.mit.edu/terms. 5.111 Principles
More informationDetermination of Equilibrium Constants using NMR Spectrscopy
CHEM 331L Physical Chemistry Laboratory Revision 1.0 Determination of Equilibrium Constants using NMR Spectrscopy In this laboratory exercise we will measure a chemical equilibrium constant using key proton
More informationLecture Overview. Hydrogen Bonds. Special Properties of Water Molecules. Universal Solvent. ph Scale Illustrated. special properties of water
Lecture Overview special properties of water > water as a solvent > ph molecules of the cell > properties of carbon > carbohydrates > lipids > proteins > nucleic acids Hydrogen Bonds polarity of water
More informationUV-Visible Spectroscopy
UV-Visible Spectroscopy UV-Visible Spectroscopy What is UV-Visible Spectroscopy? Molecular spectroscopy that involves study of the interaction of Ultra violet (UV)-Visible radiation with molecules What
More informationBiomolecular Modelling
Biomolecular Modelling Carmen Domene Physical & Theoretical Chemistry Laboratory University of Oxford, UK THANKS Dr Joachim Hein Dr Iain Bethune Dr Eilidh Grant & Qi Huangfu 2 EPSRC Grant, Simulations
More informationModelling Compounds. 242 MHR Unit 2 Atoms, Elements, and Compounds
6.3 Figure 6.26 To build the Michael Lee-Chin Crystal at the Royal Ontario Museum, models were used at different stages to convey different types of information. Modelling Compounds The Michael Lee-Chin
More informationSurvival Organic Chemistry Part I: Molecular Models
Survival Organic Chemistry Part I: Molecular Models The goal in this laboratory experience is to get you so you can easily and quickly move between empirical formulas, molecular formulas, condensed formulas,
More informationNMR and other Instrumental Techniques in Chemistry and the proposed National Curriculum.
NMR and other Instrumental Techniques in Chemistry and the proposed National Curriculum. Dr. John Jackowski Chair of Science, Head of Chemistry Scotch College Melbourne john.jackowski@scotch.vic.edu.au
More informationChemistry Workbook 2: Problems For Exam 2
Chem 1A Dr. White Updated /5/1 1 Chemistry Workbook 2: Problems For Exam 2 Section 2-1: Covalent Bonding 1. On a potential energy diagram, the most stable state has the highest/lowest potential energy.
More informationChemical Calculations: The Mole Concept and Chemical Formulas. AW Atomic weight (mass of the atom of an element) was determined by relative weights.
1 Introduction to Chemistry Atomic Weights (Definitions) Chemical Calculations: The Mole Concept and Chemical Formulas AW Atomic weight (mass of the atom of an element) was determined by relative weights.
More informationMolecular Dynamics Simulations
Molecular Dynamics Simulations Yaoquan Tu Division of Theoretical Chemistry and Biology, Royal Institute of Technology (KTH) 2011-06 1 Outline I. Introduction II. Molecular Mechanics Force Field III. Molecular
More informationLewis Dot Structures of Atoms and Ions
Why? The chemical properties of an element are based on the number of electrons in the outer shell of its atoms. We use Lewis dot structures to map these valence electrons in order to identify stable electron
More informationAP CHEMISTRY 2007 SCORING GUIDELINES (Form B)
AP CHEMISTRY 2007 SCORING GUIDELINES (Form B) First Ionization Energy Question 6 Second Ionization Energy Third Ionization Energy (kj mol 1 ) (kj mol 1 ) (kj mol 1 ) Element 1 1,251 2,300 3,820 Element
More informationCHAPTER 5: MOLECULAR ORBITALS
Chapter 5 Molecular Orbitals 5 CHAPTER 5: MOLECULAR ORBITALS 5. There are three possible bonding interactions: p z d z p y d yz p x d xz 5. a. Li has a bond order of. (two electrons in a bonding orbital;
More informationH 2O gas: molecules are very far apart
Non-Covalent Molecular Forces 2/27/06 3/1/06 How does this reaction occur: H 2 O (liquid) H 2 O (gas)? Add energy H 2O gas: molecules are very far apart H 2O liquid: bonding between molecules Use heat
More informationVisualizing Molecular Orbitals: A MacSpartan Pro Experience
Introduction Name(s) Visualizing Molecular Orbitals: A MacSpartan Pro Experience In class we have discussed Lewis structures, resonance, VSEPR, hybridization and molecular orbitals. These concepts are
More informationPeptide bonds: resonance structure. Properties of proteins: Peptide bonds and side chains. Dihedral angles. Peptide bond. Protein physics, Lecture 5
Protein physics, Lecture 5 Peptide bonds: resonance structure Properties of proteins: Peptide bonds and side chains Proteins are linear polymers However, the peptide binds and side chains restrict conformational
More informationChapter 2: The Chemical Context of Life
Chapter 2: The Chemical Context of Life Name Period This chapter covers the basics that you may have learned in your chemistry class. Whether your teacher goes over this chapter, or assigns it for you
More informationChapter 1 Structure and Bonding. Modified by Dr. Daniela Radu
John E. McMurry www.cengage.com/chemistry/mcmurry Chapter 1 Structure and Bonding Modified by Dr. Daniela Radu What is Organic Chemistry? Living things are made of organic chemicals Proteins that make
More informationChapter 9. Chemical reactivity of molecules depends on the nature of the bonds between the atoms as well on its 3D structure
Chapter 9 Molecular Geometry & Bonding Theories I) Molecular Geometry (Shapes) Chemical reactivity of molecules depends on the nature of the bonds between the atoms as well on its 3D structure Molecular
More informationIonic and Covalent Bonds
Ionic and Covalent Bonds Ionic Bonds Transfer of Electrons When metals bond with nonmetals, electrons are from the metal to the nonmetal The becomes a cation and the becomes an anion. The between the cation
More informationObjectives. PAM1014 Introduction to Radiation Physics. Constituents of Atoms. Atoms. Atoms. Atoms. Basic Atomic Theory
PAM1014 Introduction to Radiation Physics Basic Atomic Theory Objectives Introduce and Molecules The periodic Table Electronic Energy Levels Atomic excitation & de-excitation Ionisation Molecules Constituents
More informationName: Class: Date: 3) The bond angles marked a, b, and c in the molecule below are about,, and, respectively.
Name: Class: Date: Unit 9 Practice Multiple Choice Identify the choice that best completes the statement or answers the question. 1) The basis of the VSEPR model of molecular bonding is. A) regions of
More informationPolymers: Introduction
Chapter Outline: Polymer Structures Hydrocarbon and Polymer Molecules Chemistry of Polymer Molecules Molecular Weight and Shape Molecular Structure and Configurations Copolymers Polymer Crystals Optional
More informationCovalent Bonding & Molecular Orbital Theory
Covalent Bonding & Molecular Orbital Theory Chemistry 754 Solid State Chemistry Dr. Patrick Woodward Lecture #16 References - MO Theory Molecular orbital theory is covered in many places including most
More informationSeparation of Amino Acids by Paper Chromatography
Separation of Amino Acids by Paper Chromatography Chromatography is a common technique for separating chemical substances. The prefix chroma, which suggests color, comes from the fact that some of the
More informationSection Activity #1: Fill out the following table for biology s most common elements assuming that each atom is neutrally charged.
LS1a Fall 2014 Section Week #1 I. Valence Electrons and Bonding The number of valence (outer shell) electrons in an atom determines how many bonds it can form. Knowing the number of valence electrons present
More informationElements in the periodic table are indicated by SYMBOLS. To the left of the symbol we find the atomic mass (A) at the upper corner, and the atomic num
. ATOMIC STRUCTURE FUNDAMENTALS LEARNING OBJECTIVES To review the basics concepts of atomic structure that have direct relevance to the fundamental concepts of organic chemistry. This material is essential
More informationChemistry. CHEMISTRY SYLLABUS, ASSESSMENT and UNIT PLANNERS GENERAL AIMS. Students should be able to
i CHEMISTRY SYLLABUS, ASSESSMENT and UNIT PLANNERS GENERAL AIMS Students should be able to - apply and use knowledge and methods that are typical to chemistry - develop experimental and investigative skills,
More informationProtein Dynamics Intro
Protein Dynamics Intro From rigid structures to motions on energy landscapes Do you all remember Anfinsen? What concept now associated with his name made Anfinsen famous? Right, it is the concept that
More informationOrder of Filling Subshells
Bonding: General Concepts Ionic Bonds Sections 13.2-13.6 Covalent Bonds Section 13.7 Covalent Bond Energy & Chemical Reactions Section 13.8-13.9 Lewis Structures Sections 13.10-13.12 VSEPR Theory Section
More information3 CHEMICAL FOUNDATIONS: ELEMENTS, ATOMS AND IONS
3 CHEMICAL FOUNDATIONS: ELEMENTS, ATOMS AND IONS All matter is built up from chemical combinations of elements. As of 2003, there are 114 known elements, of which 88 are naturally occurring; the remaining
More informationMolecular Geometry and VSEPR We gratefully acknowledge Portland Community College for the use of this experiment.
Molecular and VSEPR We gratefully acknowledge Portland ommunity ollege for the use of this experiment. Objectives To construct molecular models for covalently bonded atoms in molecules and polyatomic ions
More informationIonization of amino acids
Amino Acids 20 common amino acids there are others found naturally but much less frequently Common structure for amino acid COOH, -NH 2, H and R functional groups all attached to the a carbon Ionization
More informationCHAPTER 6 AN INTRODUCTION TO METABOLISM. Section B: Enzymes
CHAPTER 6 AN INTRODUCTION TO METABOLISM Section B: Enzymes 1. Enzymes speed up metabolic reactions by lowering energy barriers 2. Enzymes are substrate specific 3. The active site in an enzyme s catalytic
More informationTest Bank - Chapter 4 Multiple Choice
Test Bank - Chapter 4 The questions in the test bank cover the concepts from the lessons in Chapter 4. Select questions from any of the categories that match the content you covered with students. The
More informationSample Exercise 12.1 Calculating Packing Efficiency
Sample Exercise 12.1 Calculating Packing Efficiency It is not possible to pack spheres together without leaving some void spaces between the spheres. Packing efficiency is the fraction of space in a crystal
More informationChapter 2 The Chemical Context of Life
Chapter 2 The Chemical Context of Life Multiple-Choice Questions 1) About 25 of the 92 natural elements are known to be essential to life. Which four of these 25 elements make up approximately 96% of living
More informationChemistry Diagnostic Questions
Chemistry Diagnostic Questions Answer these 40 multiple choice questions and then check your answers, located at the end of this document. If you correctly answered less than 25 questions, you need to
More informationThe Synthesis of trans-dichlorobis(ethylenediamine)cobalt(iii) Chloride
CHEM 122L General Chemistry Laboratory Revision 2.0 The Synthesis of trans-dichlorobis(ethylenediamine)cobalt(iii) Chloride To learn about Coordination Compounds and Complex Ions. To learn about Isomerism.
More informationOrganic Functional Groups Chapter 7. Alcohols, Ethers and More
Organic Functional Groups Chapter 7 Alcohols, Ethers and More 1 What do you do when you are in Pain? What do you do when you are in a lot of pain? 2 Functional Groups A functional group is an atom, groups
More informationWhat does pka tell you?
ph and pka What does pka tell you? pka tells you if a given molecule is going to either give a proton to water at a certain ph, or remove a proton A pka of 2 for substance X means that at a ph of 2, X
More informationIB Chemistry. DP Chemistry Review
DP Chemistry Review Topic 1: Quantitative chemistry 1.1 The mole concept and Avogadro s constant Assessment statement Apply the mole concept to substances. Determine the number of particles and the amount
More informationName Class Date. What is ionic bonding? What happens to atoms that gain or lose electrons? What kinds of solids are formed from ionic bonds?
CHAPTER 1 2 Ionic Bonds SECTION Chemical Bonding BEFORE YOU READ After you read this section, you should be able to answer these questions: What is ionic bonding? What happens to atoms that gain or lose
More informationLaboratory 11: Molecular Compounds and Lewis Structures
Introduction Laboratory 11: Molecular Compounds and Lewis Structures Molecular compounds are formed by sharing electrons between non-metal atoms. A useful theory for understanding the formation of molecular
More informationAcids and Bases: Molecular Structure and Acidity
Acids and Bases: Molecular Structure and Acidity Review the Acids and Bases Vocabulary List as needed. Tutorial Contents A. Introduction B. Resonance C. Atomic Radius D. Electronegativity E. Inductive
More informationATOMS AND BONDS. Bonds
ATOMS AND BONDS Atoms of elements are the simplest units of organization in the natural world. Atoms consist of protons (positive charge), neutrons (neutral charge) and electrons (negative charge). The
More informationProton Nuclear Magnetic Resonance Spectroscopy
Proton Nuclear Magnetic Resonance Spectroscopy Introduction: The NMR Spectrum serves as a great resource in determining the structure of an organic compound by revealing the hydrogen and carbon skeleton.
More informationChemistry Assessment Unit AS 1
Centre Number 71 Candidate Number ADVANCED SUBSIDIARY (AS) General Certificate of Education January 2011 Chemistry Assessment Unit AS 1 assessing Basic Concepts in Physical and Inorganic Chemistry [AC111]
More informationThe Empirical Formula of a Compound
The Empirical Formula of a Compound Lab #5 Introduction A look at the mass relationships in chemistry reveals little order or sense. The ratio of the masses of the elements in a compound, while constant,
More informationSection 3: Crystal Binding
Physics 97 Interatomic forces Section 3: rystal Binding Solids are stable structures, and therefore there exist interactions holding atoms in a crystal together. For example a crystal of sodium chloride
More informationEXPERIMENT 9 Dot Structures and Geometries of Molecules
EXPERIMENT 9 Dot Structures and Geometries of Molecules INTRODUCTION Lewis dot structures are our first tier in drawing molecules and representing bonds between the atoms. The method was first published
More informationWhich substance contains positive ions immersed in a sea of mobile electrons? A) O2(s) B) Cu(s) C) CuO(s) D) SiO2(s)
BONDING MIDTERM REVIEW 7546-1 - Page 1 1) Which substance contains positive ions immersed in a sea of mobile electrons? A) O2(s) B) Cu(s) C) CuO(s) D) SiO2(s) 2) The bond between hydrogen and oxygen in
More informationA REVIEW OF GENERAL CHEMISTRY: ELECTRONS, BONDS AND MOLECULAR PROPERTIES
A REVIEW OF GENERAL CEMISTRY: ELECTRONS, BONDS AND MOLECULAR PROPERTIES A STUDENT SOULD BE ABLE TO: 1. Draw Lewis (electron dot and line) structural formulas for simple compounds and ions from molecular
More informationMULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question.
Chapter 2 The Neural Impulse Name Period Date MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question. 1) The cell body is enclosed by the. A) cell membrane
More information1 The water molecule and hydrogen bonds in water
The Physics and Chemistry of Water 1 The water molecule and hydrogen bonds in water Stoichiometric composition H 2 O the average lifetime of a molecule is 1 ms due to proton exchange (catalysed by acids
More informationCHAPTER 6 Chemical Bonding
CHAPTER 6 Chemical Bonding SECTION 1 Introduction to Chemical Bonding OBJECTIVES 1. Define Chemical bond. 2. Explain why most atoms form chemical bonds. 3. Describe ionic and covalent bonding.. 4. Explain
More informationChemistry B11 Chapter 4 Chemical reactions
Chemistry B11 Chapter 4 Chemical reactions Chemical reactions are classified into five groups: A + B AB Synthesis reactions (Combination) H + O H O AB A + B Decomposition reactions (Analysis) NaCl Na +Cl
More informationAb initio study of gas-phase sulphuric acid hydrates containing 1 to 3 water molecules
Ab initio study of gas-phase sulphuric acid hydrates containing 1 to 3 water molecules Hanna Arstila Department of Physics, P.O. Box 9, 00014 University of Helsinki, Finland Kari Laasonen Department of
More informationInfrared Spectroscopy: Theory
u Chapter 15 Infrared Spectroscopy: Theory An important tool of the organic chemist is Infrared Spectroscopy, or IR. IR spectra are acquired on a special instrument, called an IR spectrometer. IR is used
More informationCopyright 1999 2010 by Mark Brandt, Ph.D. 12
Introduction to Absorbance Spectroscopy A single beam spectrophotometer is comprised of a light source, a monochromator, a sample holder, and a detector. An ideal instrument has a light source that emits
More informationChapter 2. The Chemistry of Life Worksheets
Chapter 2 The Chemistry of Life Worksheets (Opening image courtesy of David Iberri, http://en.wikipedia.org/wiki/file:camkii.png, and under the Creative Commons license CC-BY-SA 3.0.) Lesson 2.1: Matter
More informationVSEPR Model. The Valence-Shell Electron Pair Repulsion Model. Predicting Molecular Geometry
VSEPR Model The structure around a given atom is determined principally by minimizing electron pair repulsions. The Valence-Shell Electron Pair Repulsion Model The valence-shell electron pair repulsion
More informationName: Hour: Elements & Macromolecules in Organisms
Name: Hour: Elements & Macromolecules in Organisms Most common elements in living things are carbon, hydrogen, nitrogen, and oxygen. These four elements constitute about 95% of your body weight. All compounds
More informationChapter 5 Student Reading
Chapter 5 Student Reading THE POLARITY OF THE WATER MOLECULE Wonderful water Water is an amazing substance. We drink it, cook and wash with it, swim and play in it, and use it for lots of other purposes.
More informationSolution problem 13: Absorption of Light by Molecules
Solution problem 13: Absorption of Light by Molecules 13.1 A = εcd = 1.5 10 5 mol -1 L cm -1 4 10-6 mol L -1 10-4 cm = 6 10-5 Since A = log(p 0 /P), the ratio P/P 0 is 0.999862. This is the percentage
More informationA mutual electrical attraction between the nuclei and valence electrons of different atoms that binds the atoms together is called a(n)
Chemistry I ATOMIC BONDING PRACTICE QUIZ Mr. Scott Select the best answer. 1) A mutual electrical attraction between the nuclei and valence electrons of different atoms that binds the atoms together is
More information6.5 Periodic Variations in Element Properties
324 Chapter 6 Electronic Structure and Periodic Properties of Elements 6.5 Periodic Variations in Element Properties By the end of this section, you will be able to: Describe and explain the observed trends
More informationTransmembrane proteins span the bilayer. α-helix transmembrane domain. Multiple transmembrane helices in one polypeptide
Transmembrane proteins span the bilayer α-helix transmembrane domain Hydrophobic R groups of a.a. interact with fatty acid chains Multiple transmembrane helices in one polypeptide Polar a.a. Hydrophilic
More informationOrganic Spectroscopy. UV - Ultraviolet-Visible Spectroscopy. !! 200-800 nm. Methods for structure determination of organic compounds:
Organic Spectroscopy Methods for structure determination of organic compounds: X-ray rystallography rystall structures Mass spectroscopy Molecular formula -----------------------------------------------------------------------------
More informationBonding & Molecular Shape Ron Robertson
Bonding & Molecular Shape Ron Robertson r2 n:\files\courses\1110-20\2010 possible slides for web\00bondingtrans.doc The Nature of Bonding Types 1. Ionic 2. Covalent 3. Metallic 4. Coordinate covalent Driving
More informationCHEMISTRY 113 EXAM 4(A)
Summer 2003 1. The molecular geometry of PF 4 + ion is: A. bent B. trigonal planar C. tetrahedral D. octahedral CHEMISTRY 113 EXAM 4(A) 2. The Cl-C-Cl bond angle in CCl 2 O molecule (C is the central atom)
More informationPiotr Piecuch. Department of Chemistry, Michigan State University, East Lansing, Michigan 48824
NEW COUPLED-CLUSTER METHODS FOR MOLECULAR POTENTIAL ENERGY SURFACES: II. EXCITED-STATE APPROACHES Piotr Piecuch Department of Chemistry, Michigan State University, East Lansing, Michigan 48824 P. Piecuch
More information19.1 Bonding and Molecules
Most of the matter around you and inside of you is in the form of compounds. For example, your body is about 80 percent water. You learned in the last unit that water, H 2 O, is made up of hydrogen and
More informationChapter 8: An Introduction to Metabolism
Chapter 8: An Introduction to Metabolism Name Period Concept 8.1 An organism s metabolism transforms matter and energy, subject to the laws of thermodynamics 1. Define metabolism. The totality of an organism
More informationPeptide Bonds: Structure
Peptide Bonds: Structure Peptide primary structure The amino acid sequence, from - to C-terminus, determines the primary structure of a peptide or protein. The amino acids are linked through amide or peptide
More informationBASIC CONCEPTS OF HAIR PHYSIOLOGY AND COSMETIC HAIR DYES
Staple here TECHNICAL MANUAL BASIC CONCEPTS OF HAIR PHYSIOLOGY AND COSMETIC HAIR DYES COVER PAGE MACRO-STRUCTURE OF THE HAIR The hair is formed by the shaft and the piliferous bulb. The visible part of
More information