Back to molecular interac/ons Quantum theory and molecular structure
|
|
- Philomena Gray
- 5 years ago
- Views:
Transcription
1 Back to molecular interac/ons Quantum theory and molecular structure Atoms are arranged in 3D to cons1tute a molecule. Atoms in one molecule are connected by strong covalent bonds that are not easily broken by thermal fluctua1ons (>40kcal/mol vs thermal 0.6 kcal/mol) Bond length and bond angles are well defined by the covalent geometry Single bonds are rotatable Drug molecule can get transformed by cell enzymes and ionized before it becomes bioac1ve
2 Boltzmann s factor and probability If we have two states, A and B, say two rotamers of a drug, the probability to find a higher energy state is If you have two energies differing by 0.6 kcal/mole the higher energy state will be found e (2.71) 1mes less frequently. 1.4 kcal/mol 10 1mes less ΔG = 1.4*pKd = -Log(Kd, 10) ln K = Δ rg o RT G [A] [B] = A G B e RT p e ΔE RT
3 Two classes of drugs: covalent and non-covalent Covalently bound to the target (the minority). Examples: aspirin, alkyla1ng agents, rivas1gmine,.. They use covalent mechanism and may be considered irreversible or reversible depending on kine1cs. Cys, Ser/Thr, Tyr, Asp/Glu, N+,.. Non-covalently bound to the target. The majority To understand chemical reac1vity and forma1on of covalent bonds we need to study the molecular orbitals and electronic transi1ons.
4 Non-covalent Interac1ons Drug gets converted into its ac1ve form Atoms get par1al of full charges (pka + electrosta1c field ) Drug atoms interact with atoms of the following main molecules: Other atoms of the same molecule Water molecules Lipids Receptor atoms
5 Main contribu1ons to molecular energe1cs G = H-TS Quantum effects covalent bonds (bonding orbitals) atom repulsion (Pauli exclusion principle) Electrosta/c interac/ons Interac1ons between full charges, dipoles, induced dipoles, hydrogen bonds, agrac1ve part of the Lennard-Jones poten1al Entropic effects a part of the hydrophobic effect Conforma1onal entropy changes upon binding.. Concentra1on-dependent entropies of mixing Other energy terms are either subtypes of the main class, or combina1ons of the main types (e.g. hydrophobic interac1ons)
6 Electrosta1c Interac1ons Coulomb s poten1al energy, in SI units q q U = 1 2 el 4πε ε r 0 Energy in Joules, distance in meters, charges in C (1 Coulomb = Ampere x second) Like charges repel one another Opposite charges agract one another The force of repulsion/agrac1on get weaker as the charges are farther apart. 1 Coulomb, Charles Augus1n
7 A more prac1cal formula Charges in electron units (-1,1,-0.5), distance in Ångstroms, energy in kcal/ mol, C = 332 ε is dielectric constant of the medium ε=1 for vacuum +1 and -1 charges at 3 A get 100 kcal/ mol!!! (10nM drug ~ 10kcal/mol) U = C q 1 q 2 εr
8 Polariza1on, solva1on and ε Electrosta1c interac1ons are reduced by ε because of the polariza1on of the media. U = C q q 1 ε r 2 ε=80 in water at 300K. Electronic polariza1on, dipole relaxa1on. Water is a strong dipole In the hydrocarbon layer of membranes ε~2 to 4 in proteins ε~ 4 to 10
9 Dielectric constants at 25C Water 78.5 Methanol 33.0 Ethanol 24.3 Ammonia 16.9 Benzene 2.3 Cyclohexane 2.0 Methane 100K 1.8
10 A Charge in a fog Dipoles reorient, electron density flows to compensate the charge Le Chatelier principle screened Na + Na + ε
11 Three consequences of high ε Charged atoms are almost completely screened in water (U w =U vacuum /80=U fat /40) Direct charge-charge interac1on is weak in water (Na+)(Cl-): d=2.5a, E= -1.7km Charged (and polar) atoms are extremely happy in water (low energy) and do not want to go to media with smaller ε. screened Na + ε Ignoring fellow charges ε Na+ Cl- Sorry, I feel nothing Happy Na + ε = 80 charge is screened Unhappy Na + ε = 4
12 Solva1on Energy of Charges Born formula for the solva1on energy of a charge with radius r q, C=332 The solva1on energy of the ion: water U solv q when moved from apolar solvent to water (U is nega1ve) ε = C 2 q r 2 ε 1 w 1 ε Na + ε w Apolar medium e.g. membrane ε If ε = 2 and r =2A, U = -332./8. ~ -40 kcal/mol
13 Mnemonic device What is the Coulomb energy of interac1on of ion with itself? To compare between two media with ε w and ε : U 1-2 = U 1 -U 2 If one compares with the ion in vacuum, ε = 1 U U w m U solv = = Cq 2r C q 2 q 2r q R ε 1 ε w q (2 2 r q 1 ε ε 2 Cq 1 = 1 2rq ε w )
14 Even simpler for water-fat transfers Transfer from water to a medium with ε=4 (membrane, or protein interior): r q - is the Born radius of an ion, and Z is its charge in electron units: U transfer = 40 Z r q 2 [ kcal / mol]
15 Solva1on energies of important ions Δ G solv (Na + ) = ~100 kcal/mol (water/vapor) Δ G solv (K + ) = ~ 80 kcal/mol Standard state solva1on free energy data from: Noyes RM. Thermodynamics of ion hydra1on as a measure of effec1ve dielectric proper1es of water. J Am Chem Soc 84 (4) , Inside membrane Δ G memb (Na+) is only a frac1on of 100 kcal/mol. Biological membranes are pracacally impermeable to anything charged Even polar compounds can not go through (rule of 5)
16 How mosquito calms you down? Histamine: Arousal, inflamma1on biogenic amines and drugs Serotonin Happiness, appe1te Dopamine Parkinsons, Schizophrenia cocaine, methamphetamine are amplifiers Adrenaline Fight or flight
17 Energy and Force U = C q 1 q 2 εr Don t mix up Energy and Force Energy is primary, Force is literally a derivaave of the Energy du = Fd x F = U F = C q 1 q 2 εr 2 Force is a nega1ve gradient of the Energy func1on (a slope) Force causes instability and accelera1on
18 Charges in Drug Molecules Ibuprofen, pka=4.91 Which atoms in ibuprofen are charged? At neutral ph ibuprofen s oxygens in solu1on are charged In stomach the carboxyl gets uncharged The neutral form gets absorbed Then it gets charged again and binds to its target COX2 In both charged and uncharged forms the electron density is redistributed with respect to the posi1vely charged nuclei. The balance projected on the nuclei can be described as par1al charges.
19 Formal and Par1al atom charges Physical reality: a molecule can have a different number of protons and electrons. The integer difference gives the formal charge of the molecule. The orbitals may be distributed and both atomic formal charges and par1al charges are simplifica1ons Formal Charge (FC): If an atom has more or less electrons in a molecule than in a free, neutral state, FC +1, -1, +2,..-1/2 Frac1ons result from a redistribu1on of an integer number between several atoms. Lewis structures (electron dot diagrams) FC=N valence els N lone_pair_els - ½ N shared els ) Par1al charges: the formal charge gets redistributed so each atom gets an effec1ve frac1onal charge. -1/2-1/2
20 The Bond Spliyng Method Draw a Lewis structure, e.g. Split bonds into two electrons Count electrons and compare with the valence number (C:4, N:5, O:6,..) Be aware of the resonance structures, e.g. -1/2-2/3
21 An implicit solvent electrosta1c model Water is replaced by a polarizable con1nuum with ε = 80 Proteins, membrane,.. are geometric shapes with low dielectric medium ε=2-10 ε=80 ε=4 ε=4 Atomic charges are immersed in low dielectric medium at a par1cular loca1ons inside or on the surface of the shapes
22 Poisson-Boltzmann Equa1on Input: shapes with different dielectric constant and charges at certain loca1ons Output: the electrosta1c poten1al Φ at any point in space Energy of one charge is E i = q i Φ ε=80 ε=4 ε=4
23 Numerical Solu1on of the Poisson Equa1on Goal: calculate polariza1on charges at each element of the molecular surface
Biochemistry,530:,, Introduc5on,to,Structural,Biology, Autumn,Quarter,2015,
Biochemistry,530:,, Introduc5on,to,Structural,Biology, Autumn,Quarter,2015, Course,Informa5on, BIOC%530% GraduateAlevel,discussion,of,the,structure,,func5on,,and,chemistry,of,proteins,and, nucleic,acids,,control,of,enzyma5c,reac5ons.,please,see,the,course,syllabus,and,
More informationSolutions and Non-Covalent Binding Forces
Chapter 3 Solutions and Non-Covalent Binding Forces 3.1 Solvent and solution properties Molecules stick together using the following forces: dipole-dipole, dipole-induced dipole, hydrogen bond, van der
More informationCh. 2 Chemical Context of Life BIOL 222
Ch. 2 Chemical Context of Life BIOL 222 Ma1er Organisms are composed of ma1er Ma8er anything that takes up space and has mass Ma8er is made up of elements Lowest end of the structural organiza@on of life
More informationElectronega+vity Review
Electronega+vity Review Remember from the first course that electronega+vity is an es+mate of how atoms pull electrons towards themselves in a molecule. The higher the electron affinity, the more the element
More informationA Gentle Introduction to (or Review of ) Fundamentals of Chemistry and Organic Chemistry
Wright State University CORE Scholar Computer Science and Engineering Faculty Publications Computer Science and Engineering 2003 A Gentle Introduction to (or Review of ) Fundamentals of Chemistry and Organic
More informationCHEMISTRY XL-14A CHEMICAL BONDS
CHEMISTRY XL-14A CHEMICAL BONDS July 16, 2011 Robert Iafe Office Hours 2 July 18-July 22 Monday: 2:00pm in Room MS-B 3114 Tuesday-Thursday: 3:00pm in Room MS-B 3114 Chapter 2 Overview 3 Ionic Bonds Covalent
More informationAtomic Structure and Chemical Bonds. Chapter 16
Atomic Structure and Chemical Bonds Chapter 16 Sec7on 1 Why do Atoms Combine? Let s remember the basics: Ma@er is made up of Atoms The center of an atom contains a small nucleus that has a posi7ve charge.
More informationCovalent Bonds. single bond, or single covalent bond. sharing of one pair of valence electrons. double bond, or double covalent bond
Covalent Bonds Molecule two or more atoms held together by covalent bonds single bond, or single covalent bond sharing of one pair of valence electrons double bond, or double covalent bond sharing of two
More informationCh. 2 Chemical Context of Life BIOL 222
Ch. 2 Chemical Context of Life BIOL 222 Ma1er Organisms are composed of ma1er Ma8er is anything that takes up space and has mass Ma8er is made up of elements Lowest end of the structural organiza@on of
More informationFree energy, electrostatics, and the hydrophobic effect
Protein Physics 2016 Lecture 3, January 26 Free energy, electrostatics, and the hydrophobic effect Magnus Andersson magnus.andersson@scilifelab.se Theoretical & Computational Biophysics Recap Protein structure
More informationName: Hr: 8 Basic Concepts of Chemical Bonding
8.1-8.2 8.3-8.5 8.5-8.7 8.8 Name: Hr: 8 Basic Concepts of Chemical Bonding 8.1 Chemical Bonds, Lewis Symbols, and the Octet Rule State the type of bond (ionic, covalent, or metallic) formed between any
More informationWhy Proteins Fold. How Proteins Fold? e - ΔG/kT. Protein Folding, Nonbonding Forces, and Free Energy
Why Proteins Fold Proteins are the action superheroes of the body. As enzymes, they make reactions go a million times faster. As versatile transport vehicles, they carry oxygen and antibodies to fight
More informationChapter 11 Chemical Bonds: The Formation of Compounds from Atoms Advanced Chemistry Periodic Trends in Atomic Properties Learning Objective
Chapter 11 Chemical Bonds: The Formation of Compounds from Atoms Advanced Chemistry 11.1 Periodic Trends in Atomic Properties Discuss the atomic trends Metals are located on the left side of the periodic
More informationBiophysics II. Hydrophobic Bio-molecules. Key points to be covered. Molecular Interactions in Bio-molecular Structures - van der Waals Interaction
Biophysics II Key points to be covered By A/Prof. Xiang Yang Liu Biophysics & Micro/nanostructures Lab Department of Physics, NUS 1. van der Waals Interaction 2. Hydrogen bond 3. Hydrophilic vs hydrophobic
More informationThe role of atomic radius in ion channel selectivity :
5.111 Lecture Summary #10 Readings for today: Sections 2.14-2.16 (2.15-2.17 in 3rd ed), Section 2.5 (2.6 in 3rd ed) and Section 2.6 (2.7 in 3rd ed). Read for Lecture #11: Section 2.7 (2.8 in 3rd ed) Resonance,
More informationChapter 8 Concepts of Chemical. Bonding
Chapter 8 Concepts of 8.1 Bonds Three basic types of bonds: Ionic Electrostatic attraction between ions Covalent Sharing of electrons Metallic Metal atoms bonded to several other atoms. Electrons are free
More informationBIOC : Homework 1 Due 10/10
Contact information: Name: Student # BIOC530 2012: Homework 1 Due 10/10 Department Email address The following problems are based on David Baker s lectures of forces and protein folding. When numerical
More informationThe change in free energy on transferring an ion from a medium of low dielectric constantε1 to one of high dielectric constant ε2:
The Born Energy of an Ion The free energy density of an electric field E arising from a charge is ½(ε 0 ε E 2 ) per unit volume Integrating the energy density of an ion over all of space = Born energy:
More informationChapter 9. Chemical Bonding I: The Lewis Model. HIV-Protease. Lecture Presentation
Lecture Presentation Chapter 9 Chemical Bonding I: The Lewis Model HIV-Protease HIV-protease is a protein synthesized by the human immunodeficiency virus (HIV). This particular protein is crucial to the
More informationName Date. Chapter 2 - Chemistry Guide Microbiology (MCB 2010C) Part 1
Name Date Chapter 2 - Chemistry Guide Microbiology (MCB 2010C) Part 1 The study of biology in the 21 st century is actually the study of biochemistry. In order to be successful in this course, it is important
More informationPhysiology Unit 1 CHEMISTRY REVIEW
Physiology Unit 1 CHEMISTRY REVIEW Defini7ons Types of energy Kine7c vs. poten7al Forms of energy Chemical Ex: ATP Ma0er and Energy Electrical Ex: Ac7on poten7al of an neuron Mechanical Ex: Ac7on of muscles
More informationCovalent Compounds: Bonding Theories and Molecular Structure
CHM 123 Chapter 8 Covalent Compounds: Bonding Theories and Molecular Structure 8.1 Molecular shapes and VSEPR theory VSEPR theory proposes that the geometric arrangement of terminal atoms, or groups of
More informationOther Cells. Hormones. Viruses. Toxins. Cell. Bacteria
Other Cells Hormones Viruses Toxins Cell Bacteria ΔH < 0 reaction is exothermic, tells us nothing about the spontaneity of the reaction Δ H > 0 reaction is endothermic, tells us nothing about the spontaneity
More informationq 2 Da This looks very similar to Coulomb doesn t it? The only difference to Coulomb is the factor of 1/2.
Born Lets now think about a somewhat different, but related problem that is associated with the name Born. Using a name (usually the name of the guy who first discovered or solved the problem) to describe
More informationBiochemistry 530: Introduction to Structural Biology. Autumn Quarter 2014 BIOC 530
Biochemistry 530: Introduction to Structural Biology Autumn Quarter 2014 Course Information Course Description Graduate-level discussion of the structure, function, and chemistry of proteins and nucleic
More informationChimica Farmaceutica
Chimica Farmaceutica Drug Targets Why should chemicals, some of which have remarkably simple structures, have such an important effect «in such a complicated and large structure as a human being? The answer
More informationAtoms & Their Interactions
Lecture 2 Atoms & Their Interactions Si: the heart of electronic materials Intel, 300mm Si wafer, 200 μm thick and 48-core CPU ( cloud computing on a chip ) Twin Creeks Technologies, San Jose, Si wafer,
More informationChapter 13: Phenomena
Chapter 13: Phenomena Phenomena: Scientists measured the bond angles of some common molecules. In the pictures below each line represents a bond that contains 2 electrons. If multiple lines are drawn together
More informationCovalent Bonding 10/29/2013
Bond Energies or Bond Dissociation Energies Tables 8.4 and 8.5 on page 72 gives a list of the energy required to dissociate or break bonds. This value is used to determine whether covalent bonds will form
More informationSection 8.1 The Covalent Bond
Section 8.1 The Covalent Bond Apply the octet rule to atoms that form covalent bonds. Describe the formation of single, double, and triple covalent bonds. Contrast sigma and pi bonds. Relate the strength
More informationChapter 8. Basic Concepts of Chemical Bonding. Lecture Presentation. John D. Bookstaver St. Charles Community College Cottleville, MO
Lecture Presentation Chapter 8 of Chemical John D. Bookstaver St. Charles Community College Cottleville, MO Chemical Bonds Three basic types of bonds Ionic Electrostatic attraction between ions. Covalent
More informationChapter 13: Phenomena
Chapter 13: Phenomena Phenomena: Scientists measured the bond angles of some common molecules. In the pictures below each line represents a bond that contains 2 electrons. If multiple lines are drawn together
More informationMULTIPLE CHOICE 2 points each
Name: Date: Score: / 110 Chapter 1/ TEST 1 OPEN BOOK KEY Organic Chemistry MULTIPLE CHOICE 2 points each 1. An atom of which element would have an electron configuration of 1s 2 2s 2 2p 6 3s 2 3p 1? a.
More informationLife Science 1a Review Notes: Basic Topics in Chemistry
Life Science 1a Review Notes: Basic Topics in Chemistry Atomic Structure and the Periodic Table The history of the discovery of the atom will be left for you to read in the textbook. What are atoms? What
More informationChapter 12. Chemical Bonding
Chapter 12 Chemical Bonding Chapter 12 Introduction to Chemical Bonding Chemical Bonding Valence electrons are the electrons in the outer shell (highest energy level) of an atom. A chemical bond is a mutual
More informationChapter 11: Chemical Bonding I: Basic Concepts
General Chemistry Principles and Modern Applications Petrucci Harwood Herring 8 th Edition Chapter 11: Chemical Bonding I: Basic Concepts Philip Dutton University of Windsor, Canada N9B 3P4 Prentice-Hall
More informationSystems, Matter, & Energy Chapter 2. Friday, August 14 th, 2015
Systems, Matter, & Energy Chapter 2 Friday, August 14 th, 2015 Chapter Overview Questions What are major components and behaviors of complex systems? What are the basic forms of matter, and what makes
More informationChapter 6 Chemical Bonding
Chapter 6 Chemical Bonding Section 6-1 Introduction to Chemical Bonding Chemical Bonds Valence electrons are attracted to other atoms, and that determines the kind of chemical bonding that occurs between
More informationMolecular Modeling -- Lecture 15 Surfaces and electrostatics
Molecular Modeling -- Lecture 15 Surfaces and electrostatics Molecular surfaces The Hydrophobic Effect Electrostatics Poisson-Boltzmann Equation Electrostatic maps Electrostatic surfaces in MOE 15.1 The
More information16 years ago TODAY (9/11) at 8:46, the first tower was hit at 9:03, the second tower was hit. Lecture 2 (9/11/17)
16 years ago TODAY (9/11) at 8:46, the first tower was hit at 9:03, the second tower was hit By Anthony Quintano - https://www.flickr.com/photos/quintanomedia/15071865580, CC BY 2.0, https://commons.wikimedia.org/w/index.php?curid=38538291
More informationChemistry 6/15/2015. Outline. Why study chemistry? Chemistry is the basis for studying much of biology.
Chemistry Biology 105 Lecture 2 Reading: Chapter 2 (pages 20-29) Outline Why study chemistry??? Elements Atoms Periodic Table Electrons Bonding Bonds Covalent bonds Polarity Ionic bonds Hydrogen bonding
More information( ) Reac%on Rates and Temperature N A. = exp ΔE /k N B. Boltzmann law: At higher temperatures, more molecules have enough energy to react.
eac%on ates and Temperature Boltzmann law: B A ( ) = exp ΔE /k B T! B E A At higher temperatures, more molecules have enough energy to react. Thus, reac;on rates increase with temperature: Arrhenius Equa%on
More information2. Polar Covalent Bonds: Acids and Bases
2. Polar Covalent Bonds: Acids and Bases Based on McMurry s Organic Chemistry, 6 th edition, Chapter 2 2003 Ronald Kluger Department of Chemistry University of Toronto 2.1 Polar Covalent Bonds: Electronegativity!
More informationLewis Theory of Shapes and Polarities of Molecules
Lewis Theory of Shapes and Polarities of Molecules Sulfanilamide Lewis Structures and the Real 3D-Shape of Molecules Molecular Shape or Geometry The way in which atoms of a molecule are arranged in space
More informationChemical Bonding AP Chemistry Ms. Grobsky
Chemical Bonding AP Chemistry Ms. Grobsky What Determines the Type of Bonding in Any Substance? Why do Atoms Bond? The key to answering the first question are found in the electronic structure of the atoms
More informationBonding Chapter 7. Bond an attractive force that holds two atoms together. Atoms bond to obtain a more stable electronic configuration.
Bonding Chapter 7 Bond an attractive force that holds two atoms together. Atoms bond to obtain a more stable electronic configuration. Ionic bonds attraction between oppositely charged atoms/molecules
More informationChapter 8: Bonding. Section 8.1: Lewis Dot Symbols
Chapter 8: Bonding Section 8.1: Lewis Dot Symbols The Lewis electron dot symbol is named after Gilbert Lewis. In the Lewis dot symbol, the element symbol represents the nucleus and the inner electrons.
More informationAll-atom Molecular Mechanics. Trent E. Balius AMS 535 / CHE /27/2010
All-atom Molecular Mechanics Trent E. Balius AMS 535 / CHE 535 09/27/2010 Outline Molecular models Molecular mechanics Force Fields Potential energy function functional form parameters and parameterization
More informationOrganic Chemistry I Dr Alex Roche Organic chemistry is the chemistry of Carbon and its compounds. Organic molecules constitute the essence of life (fats, sugars, proteins, DNA), and also permeate our everyday
More informationChemistry 304B, Spring 99 Lecture 2 1
Chemistry 04B, Spring 99 Lecture 2 1 Consider Acidity and Basicity Recall carboxylic acids and amines (base). Jones: p 27-8; 149, 291, 822-826, 1086-1090, 958-96, 878-882 General terms: Lewis acid: capable
More informationEx. 1) F F bond in F = 0 < % covalent, no transfer of electrons
#60 Notes Unit 8: Bonding Ch. Bonding I. Bond Character Bonds are usually combinations of ionic and covalent character. The electronegativity difference is used to determine a bond s character. Electronegativity
More informationChapter 3. Crystal Binding
Chapter 3. Crystal Binding Energy of a crystal and crystal binding Cohesive energy of Molecular crystals Ionic crystals Metallic crystals Elasticity What causes matter to exist in three different forms?
More informationChapter 1. Topic: Overview of basic principles
Chapter 1 Topic: Overview of basic principles Four major themes of biochemistry I. What are living organism made from? II. How do organism acquire and use energy? III. How does an organism maintain its
More informationCh 2 Polar Covalent Bonds
h 2 Polar ovalent Bonds Two primary bond types: ovalent (shared e -1 s) and Ionic (transferred e -1 s) Ionic bonds can have covalent character, such as with Na:l. An e -1 pair on l -1 can fill the 3s orbital
More informationShapes of Molecules VSEPR
Shapes of Molecules In this section we will use Lewis structures as an introduction to the shapes of molecules. The key concepts are: Electron pairs repel each other. Electron pairs assume orientations
More informationChapter 8 The Concept of the Chemical Bond
Chapter 8 The Concept of the Chemical Bond Three basic types of bonds: Ionic - Electrostatic attraction between ions (NaCl) Metallic - Metal atoms bonded to each other Covalent - Sharing of electrons Ionic
More informationAnglo-Chinese School (Independent) International Baccalaureate Diploma Programme Scheme Of Work Year 5 Chemistry HL
Topic 1 Quantitative Chemistry Topic 11 Measurement and Data Processing Topic 9 Redox equation 1.1 The mole concept and Avogadro s constant a) Determine the number of particles and the amount of substance
More informationChapter 8 Basic Concepts of Chemical Bonding
Sec$on 8.1 Types of Chemical Bonds Chapter 8 Basic Concepts of Chemical Bonding Chapter 8 Ques$ons to Consider What is meant by the term chemical bond? Why do atoms bond with each other to form compounds?
More informationThe energy associated with electrostatic interactions is governed by Coulomb s law:
Chapter 8 Concepts of Chemical Bonding Chemical Bonds Three basic types of bonds: Ionic Electrostatic attraction between ions Covalent Sharing of electrons Metallic Metal atoms bonded to several other
More informationPH 3 + H + à PH 4 PH 4. H 3 O + is pyramidal, bond angle 107 ; steric 4, 1LP Lone pair from O donated to H +
Metallic bonding AS Bonding & Periodicity Test: Answers Ionic Bonding Ti is a giant metallic lacce. There is strong electrosta2c afrac2on between posi2ve metal ions and sea of delocalised electrons. Layers
More informationChapter Eight. p328. Bonding: General Concepts
Chapter Eight p328 Bonding: General Concepts 1 Contents 8-1 Types of Chemical Bonds p330 Coulomb s law The energy of interaction between a pair of ions can be calculated using Coulomb s law: E 19 Q1Q 2
More informationChapter 6 Chemistry Review
Chapter 6 Chemistry Review Multiple Choice Identify the choice that best completes the statement or answers the question. Put the LETTER of the correct answer in the blank. 1. The electrons involved in
More informationORGANIC CHEMISTRY. Meaning of Organic?
ORGANIC CHEMISTRY Meaning of Organic? Initially scientists believed there was a special force in living organisms -this was assumed the unique component of organic material In 1828 Wöhler synthesized urea
More informationBCMP 201 Protein biochemistry
BCMP 201 Protein biochemistry BCMP 201 Protein biochemistry with emphasis on the interrelated roles of protein structure, catalytic activity, and macromolecular interactions in biological processes. The
More informationChemical Bonding Chapter 9
Chemical Bonding Chapter 9 Covalent Bonds and Ionic Bonds: Octet Rule Explain each of the following observations in terms of the "octet rule": Na atoms and Cl atoms will combine to form NaCl. Why does
More informationLecture outline: Section 9. theory 2. Valence bond theory 3. Molecular orbital theory. S. Ensign, Chem. 1210
Lecture outline: Section 9 Molecular l geometry and bonding theories 1. Valence shell electron pair repulsion theory 2. Valence bond theory 3. Molecular orbital theory 1 Ionic bonding Covalent bonding
More informationBIOC 530 Fall, 2011 BIOC 530
Fall, 2011 Course Information Course Description Graduate-level discussion of the structure, function, and chemistry of proteins and nucleic acids, control of enzymatic reactions. Please see the course
More informationChemical Bonding I: Basic Concepts
Chapter 8 Chemical Bonding I: Basic Concepts Dr. A. Al-Saadi 1 Chapter 8 Preview Ionic Bonding vs. covalent bonding. Electronegativity and dipole moment. Bond polarity. Lewis structure: ow to draw a Lewis
More informationDefinition of Matter. Subatomic particles 8/20/2012
Interplay of Biology and Chemistry Here is a link to the video these beetles are fairly common locally an amazing adaptation, and a good example of chemistry and physics in biology. Also look for creationist-evolutionist
More informationBig Idea #5: The laws of thermodynamics describe the essential role of energy and explain and predict the direction of changes in matter.
KUDs for Unit 6: Chemical Bonding Textbook Reading: Chapters 8 & 9 Big Idea #2: Chemical and physical properties of materials can be explained by the structure and the arrangement of atoms, ion, or molecules
More informationChemistry 121: Topic 4 - Chemical Bonding Topic 4: Chemical Bonding
Topic 4: Chemical Bonding 4.0 Ionic and covalent bonds; Properties of covalent and ionic compounds 4.1 Lewis structures, the octet rule. 4.2 Molecular geometry: the VSEPR approach. Molecular polarity.
More informationChapter 8. Bonding: General Concepts
Chapter 8 Bonding: General Concepts Chapter 8 Table of Contents 8.1 Types of Chemical Bonds 8.2 Electronegativity 8.3 Bond Polarity and Dipole Moments 8.4 Ions: Electron Configurations and Sizes 8.5 Energy
More informationChemistry 1411 Practice Exam 2, Chapters 5-8 Brown
Chemistry 1411 Practice Exam 2, Chapters 5-8 Brown Some constants and equations: E = q + w q = C p T Heat = m T Cs h = 6.626 X 10 34 J. s c = 2.998 X 10 8 m/s R H = 2.18 X 10 18 J E = (2.18 X 10 18 J)(1/n
More informationAtomic and molecular interaction forces in biology
Atomic and molecular interaction forces in biology 1 Outline Types of interactions relevant to biology Van der Waals interactions H-bond interactions Some properties of water Hydrophobic effect 2 Types
More informationChemical Bonding Petrucci, Harwood and Herring: Chapters 10 and 11
Chemical Bonding Petrucci, Harwood and Herring: Chapters 10 and 11 Aims: To look at bonding and possible shapes of molecules We will mainly do this through Lewis structures To look at ionic and covalent
More information3/30/2015. Third energy level. Second energy level. Energy absorbed. First energy level. Atomic nucleus. Energy released (as light)
Chapter 2 An Introduction Chemistry Lecture 2: Energy Levels and Chemical Bonding Electrons are always moving Outside the nucleus in atomic orbitals Maybe usually Average distance from nucleus (size of
More informationC H E M 1 CHEM 101-GENERAL CHEMISTRY CHAPTER 7 CHEMICAL BONDING & MOLECULAR STRUCTURE INSTR : FİLİZ ALSHANABLEH
C H E M 1 CHEM 101-GENERAL CHEMISTRY CHAPTER 7 CHEMICAL BONDING & MOLECULAR STRUCTURE 0 1 INSTR : FİLİZ ALSHANABLEH CHAPTER 7 CHEMICAL BONDING & MOLECULAR STRUCTURE The Ionic Bond Formation of Ions The
More informationCh. 9- Molecular Geometry and Bonding Theories
Ch. 9- Molecular Geometry and Bonding Theories 9.0 Introduction A. Lewis structures do not show one of the most important aspects of molecules- their overall shapes B. The shape and size of molecules-
More informationbond energy- energy required to break a chemical bond -We can measure bond energy to determine strength of interaction
bond energy- energy required to break a chemical bond -We can measure bond energy to determine strength of interaction ionic compound- a metal reacts with a nonmetal Ionic bonds form when an atom that
More informationsharing or transferring electrons between atoms covalent ionic polar covalent Quantitative description: Quantum mechanics
Chapter. 3 Chemical Bonding: The Classical Description Two or more atoms approach -> their electrons interact and form new arrangements of electrons with lower total potential energy than isolated atoms
More informationChapter 9 Ionic and Covalent Bonding
Chem 1045 Prof George W.J. Kenney, Jr General Chemistry by Ebbing and Gammon, 8th Edition Last Update: 06-April-2009 Chapter 9 Ionic and Covalent Bonding These Notes are to SUPPLIMENT the Text, They do
More informationBiotech 2: Atoms and Molecules OS Text Reading pp Electron cloud Atoms & Nucleus 2e Subatomic Particles Helium Electron cloud
9/4/017 Biotech : Atoms and Molecules OS Text Reading pp. 34-4 Atoms & Subatomic Particles Nucleus Helium e cloud cloud e Protons Neutrons Mass number = 4 s Nucleus Carbon atomic number = # of protons
More informationChemistry: The Central Science. Chapter 8: Basic Concepts of Chemical Bonding
Chemistry: The Central Science Chapter 8: Basic Concepts of Chemical Bonding The properties of substances are determined in large part by the chemical bonds that hold their atoms together 8.1: Chemical
More informationChemical Bonding II. Molecular Geometry Valence Bond Theory Phys./Chem. Properties Quantum Mechanics Sigma & Pi bonds Hybridization MO theory
Chemical Bonding II Molecular Geometry Valence Bond Theory Phys./Chem. Properties Quantum Mechanics Sigma & Pi bonds ybridization MO theory 1 Molecular Geometry 3-D arrangement of atoms 2 VSEPR Valence-shell
More informationOrganic Chemistry. Review Information for Unit 1. Atomic Structure MO Theory Chemical Bonds
Organic Chemistry Review Information for Unit 1 Atomic Structure MO Theory Chemical Bonds Atomic Structure Atoms are the smallest representative particle of an element. Three subatomic particles: protons
More informationBonding, structure and trends (periodicity)
Bonding, structure and trends (periodicity) Bonding and structure revision Objec
More informationMolecular Dynamics. Molecules in motion
Molecular Dynamics Molecules in motion 1 Molecules in mo1on Molecules are not sta1c, but move all the 1me Source: h9p://en.wikipedia.org/wiki/kine1c_theory 2 Gasses, liquids and solids Gasses, liquids
More informationValence Shell Electron Pair repulsion
Molecular Geometry Valence Shell Electron Pair repulsion The valence shell electron pair repulsion model (VSEPR model) assumes that electron pairs repel one another. (VSEPR) model gives helps determine
More informationLecture 19: Building Atoms and Molecules
Lecture 19: Building Atoms and Molecules +e r n = 3 n = 2 n = 1 +e +e r y even Lecture 19, p 1 Today Nuclear Magnetic Resonance Using RF photons to drive transitions between nuclear spin orientations in
More informationWater. 2.1 Weak Interactions in Aqueous Sy stems Ionization of Water, Weak Acids, and Weak Bases 58
Home http://www.macmillanhighered.com/launchpad/lehninger6e... 1 of 1 1/6/2016 3:07 PM 2 Printed Page 47 Water 2.1 Weak Interactions in Aqueous Sy stems 47 2.2 Ionization of Water, Weak Acids, and Weak
More informationChem 11 Unit 4 POLARITY, MOLECULE SHAPE, and BEHAVIOUR
Chem 11 Unit 4 POLARITY, MOLECULE SHAPE, and BEHAVIOUR Polarity is unequal distribution of a charge on a molecule caused by: 1) some degree of ionic character in the bonding (i.e. unequal electron sharing)
More informationMirror Charges, Hydrogen Bonds, And the Water-Dielectric Interface
Mirror Charges, ydrogen Bonds, And the Water-Dielectric Interface Kevin Cahill cahill@unm.edu http://dna.phys.unm.edu/ 1 Field Energy The energy E of an electric field E( x, t) is the space integral of
More information14. Use reactions 1 and 2 to determine the value of H (in kj) for reaction 3.
11. A 2.85 g sample of a food substance was burned in a calorimeter that had a heat capacity of 9.84 kj/ C. The temperature of the calorimeter increased from 22.51 C to 35.66 C. Calculate the amount of
More informationChapter 7: Chemical Bonding and Molecular Structure
Chapter 7: Chemical Bonding and Molecular Structure Ionic Bond Covalent Bond Electronegativity and Bond Polarity Lewis Structures Orbital Overlap Hybrid Orbitals The Shapes of Molecules (VSEPR Model) Molecular
More informationAP Chemistry Chapter 7: Bonding
AP Chemistry Chapter 7: Bonding Types of Bonding I. holds everything together! I All bonding occurs because of! Electronegativity difference and bond character A. A difference in electronegativity between
More information1. Know which elements correspond to metals, non-metals, and semi-conductors
Chemistry 106 Lectures 2 & 3: Chemical Foundations II: Atomic Structure and the Periodic Table; Properties of Important Elements; Ionic vs. Covalent Bonding; Lewis Structures; Drawing Molecules 9/26/18,
More information2 Structure. 2.1 Coulomb interactions
2 Structure 2.1 Coulomb interactions While the information needed for reproduction of living systems is chiefly maintained in the sequence of macromolecules, any practical use of this information must
More informationChapter 8: Concepts of Chemical Bonding
Chapter 8: Concepts of Chemical Bonding Learning Outcomes: Write Lewis symbols for atoms and ions. Define lattice energy and be able to arrange compounds in order of increasing lattice energy based on
More informationEnduring Understandings & Essential Knowledge for AP Chemistry
Enduring Understandings & Essential Knowledge for AP Chemistry Big Idea 1: The chemical elements are fundamental building materials of matter, and all matter can be understood in terms of arrangements
More informationChapter 8 Concepts of Chemical. Bonding
Chemistry, The Central Science, 10th edition Theodore L. Brown; H. Eugene LeMay, Jr.; and Bruce E. Bursten Chapter 8 Concepts of John D. Bookstaver St. Charles Community College St. Peters, MO 2006, Prentice
More information