Biochemistry 675, Lecture 8 Electrostatic Interactions

Size: px
Start display at page:

Download "Biochemistry 675, Lecture 8 Electrostatic Interactions"

Transcription

1 Biochemistry 675, Lecture 8 Electrostatic Interactions Previous Classes Hydrophobic Effect Hydrogen Bonds Today: Electrostatic Interactions Reading: Handout:P.R. Bergethon & E.R. Simons, Biophysical Chemistry, Springer-Verlag Portions of Ch. 11 & 12

2 Charged residues are found on the surface of proteins

3 The surfaces of biological molecules can be highly charged The EMBO Journal (2006) 25, , doi: /sj.emboj Molecular basis of RNA recognition by the human alternative splicing factor Fox-1 Sigrid D Auweter, Rudi Fasan, Luc Reymond, Jason G Underwood, Douglas L Black, Stefan Pitsch and Frédéric H-T Allain Overview of the solution structure of the RBD of Fox-1 in complex with UGCAUGU

4 The surfaces of biological molecules can be highly charged camp-dependent protein Kinase (1YDR) bound to peptidic H7 protein kinase inhibitor

5

6 Electrostatic interactions are long range and fall off in strength gradually with distance E 1/r n

7 Electrostatic interactions are strong Coulomb s law Interaction energy between an Na + and Cl - separated by 3Å is-110 kcal/mol (in vacuum) Interaction energies of 2 opposite charges in a protein 10 Å apart:-16 kcal/mol (if dielectric is 2) But!Competing interactions with water: desolvation of a unit charge costs about 60 kcal/mol

8 Interaction of Charges with water; The Born Model

9

10 Born Model: A model for understanding Ion-water interactions-a thermodynamic cycle w discharge + w transfer + w charging + (-ΔG i-s )=0 There are no interactions in the transfer of the uncharged sphere into water so w transfer =0 and ΔG i-s = w discharge + w charging

11 ΔG i-s = w discharge + w charging w discharge : Can be determined from the work of charging a sphere in a vacuum; work of transferring infinitesimal bits of charge to the sphere until it has the correct charge w ch arg ing = (z i e o )2 8πε o r i Therefore: w disch arg e = (z i e o )2 8πε o r i For the work of charging the sphere in solvent we have to consider solvent. The dielectric constant must influence charging in solvent. remember: F q 1 q 2 4πε o εr 2 Work of charging the sphere in the solvent: w ch arg ing = (z i e o )2 8πε o εr i

12 ΔG i s = w disch arg e + w ch arg ing ( ΔG i s = z e i o) 2 ( + z e i o) 2 8πε o r i 8πε o εr i ( ΔG i s = z e i o) 2 (1 1 8πε o r i ε ) MolarBasis ΔG i s = N A Enthalpy ( z i e o ) 2 (1 1 8πε o r i ε ) ΔG i s = ΔH i s TΔS i s ΔH i s = N A z i e o ( ) 2 8πε o r i (1 1 ε T ε 2 ε T )

13 Compare the theoretical prediction to the experimentally measured enthalpies of solvation (Fig )

14 Add the structural features of water: 1. Water is a dipole 2. Three types of water can be considered Bulk water An immobilized layer An intermediate layer

15 Thermodynamic cycle For the modified Born Model

16 Good agreement between the calculated and Measured enthalpies of ion-solvent interactions

17 Consider the significance of ion-solvent interactions for everyday procedures used in the lab Example: Salting out

18 What about the other ions?

19 Ion:ion interactions What is the free energy of ion:ion interactions ΔG i-i? Consider an ion in a solution with many other ions: ΔG i i = n i µ i i n i is the number of ions that the reference ion interacts with and µ i-i is the chemical potential for each ion that interacts with the reference. The chemical potential of a single ionic species will be related to the work of charging up a mole of ions of interest while in the proximity of other ions. w ch arg ing = (z i e o )2 8πε o εr i In terms of chemical potential: Δµ i i = N A w ch arg ing Δµ i i = N A z i e o 2 ψ ψ is the electrostatic potential of the ion

20 In order to determine the chemical potential change for the interaction between the total ionic assembly and the ion of interest we must know the electrostatic field at each individual ion that is a result of the other ions in solution. This requires information about the spatial distribution of the ions in the solution relative to the reference ion.

21

22 Erich Armand Arthur Joseph Hückel (in Engl. often spelled Huckel or Hueckel) b. August 9, 1896, Berlin, Germany d. 1980, Marburg, Germany A German physicist and physical chemist. He is known for two major contributions: (a) The Debye-Hückel theory of electrolytic solutions, (b) The Hückel method of approximate molecular orbital (MO) calculations on p-electron systems.

23 Petrus (Peter) Josephus Wilhelmus Debye was born March 24, 1884, at Maastricht, the Netherlands. Debye won Nobel Prize in Chemistry, 1936, "for his contributions to our knowledge of molecular structure through his investigations on dipole moments and on the diffraction of X-rays and electrons in gases". Debye died on November 2, 1966, and was buried on Pleasant Grove Cemetery, Cayuga Heights, Tompkins County, New York, U.S.A.

24 Debye-Hückel Model 1923 Treatment: A reference ion residing in a dielectric continuum. Dielectric constant is 80 Reference ion is charged-therefore, in its immediate vicinity there will be neutralization by the continuum of charge that surrounds it. At equilibrium the charge on the central ion will be exactly counterbalanced by the counter charge atmosphere: Principle of Electroneutrality: z i e o X i = 0

25

Bchem 675 Lecture 9 Electrostatics-Lecture 2 Debye-Hückel: Continued Counter ion condensation

Bchem 675 Lecture 9 Electrostatics-Lecture 2 Debye-Hückel: Continued Counter ion condensation Bchem 675 Lecture 9 Electrostatics-Lecture 2 Debye-Hückel: Continued Counter ion condensation Ion:ion interactions What is the free energy of ion:ion interactions ΔG i-i? Consider an ion in a solution

More information

Free energy, electrostatics, and the hydrophobic effect

Free 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 information

The change in free energy on transferring an ion from a medium of low dielectric constantε1 to one of high dielectric constant ε2:

The 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 information

Peter Debye and Electrochemistry

Peter Debye and Electrochemistry Peter Debye and Electrochemistry A K Shukla and T Prem Kumar A K Shukla is Professor and Chairman, Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore. His research interests

More information

Molecule Matters van der Waals Molecules

Molecule Matters van der Waals Molecules Molecule Matters van der Waals Molecules 3. Rg HF Complexes are Debye Molecules! E Arunan In this article, Debye s contributions to understanding van der Waals attractive forces, specifically, dipole induced

More information

Biochemistry,530:,, Introduc5on,to,Structural,Biology, Autumn,Quarter,2015,

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 information

Molecular Modeling -- Lecture 15 Surfaces and electrostatics

Molecular 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 information

BIOC : Homework 1 Due 10/10

BIOC : 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 information

Other Cells. Hormones. Viruses. Toxins. Cell. Bacteria

Other 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 information

Electrolytes. Chapter Basics = = 131 2[ ]. (c) From both of the above = = 120 8[

Electrolytes. Chapter Basics = = 131 2[ ]. (c) From both of the above = = 120 8[ Chapter 1 Electrolytes 1.1 Basics Here we consider species that dissociate into positively and negatively charged species in solution. 1. Consider: 1 H (g) + 1 Cl (g) + ()+ () = { } = (+ )+ ( ) = 167[

More information

Solutions and Non-Covalent Binding Forces

Solutions 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 information

Phys 102 Lecture 2 Coulomb s Law & Electric Dipoles

Phys 102 Lecture 2 Coulomb s Law & Electric Dipoles Phys 102 Lecture 2 Coulomb s Law & Electric Dipoles 1 Today we will... Get practice using Coulomb s law & vector addition Learn about electric dipoles Apply these concepts! Molecular interactions Polar

More information

schematic diagram; EGF binding, dimerization, phosphorylation, Grb2 binding, etc.

schematic diagram; EGF binding, dimerization, phosphorylation, Grb2 binding, etc. Lecture 1: Noncovalent Biomolecular Interactions Bioengineering and Modeling of biological processes -e.g. tissue engineering, cancer, autoimmune disease Example: RTK signaling, e.g. EGFR Growth responses

More information

16 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. 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 information

Protein Folding experiments and theory

Protein Folding experiments and theory Protein Folding experiments and theory 1, 2,and 3 Protein Structure Fig. 3-16 from Lehninger Biochemistry, 4 th ed. The 3D structure is not encoded at the single aa level Hydrogen Bonding Shared H atom

More information

Chem 321 Lecture 11 - Chemical Activities 10/3/13

Chem 321 Lecture 11 - Chemical Activities 10/3/13 Student Learning Objectives Chem 321 Lecture 11 - Chemical Activities 10/3/13 One of the assumptions that has been made in equilibrium calculations thus far has been to equate K to a ratio of concentrations.

More information

Biophysics II. Hydrophobic Bio-molecules. Key points to be covered. Molecular Interactions in Bio-molecular Structures - van der Waals Interaction

Biophysics 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 information

Aqueous solutions. Solubility of different compounds in water

Aqueous solutions. Solubility of different compounds in water Aqueous solutions Solubility of different compounds in water The dissolution of molecules into water (in any solvent actually) causes a volume change of the solution; the size of this volume change is

More information

A Gentle Introduction to (or Review of ) Fundamentals of Chemistry and Organic Chemistry

A 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 information

Lecture 2 and 3: Review of forces (ctd.) and elementary statistical mechanics. Contributions to protein stability

Lecture 2 and 3: Review of forces (ctd.) and elementary statistical mechanics. Contributions to protein stability Lecture 2 and 3: Review of forces (ctd.) and elementary statistical mechanics. Contributions to protein stability Part I. Review of forces Covalent bonds Non-covalent Interactions: Van der Waals Interactions

More information

Chap 10 Part 4Ta.notebook December 08, 2017

Chap 10 Part 4Ta.notebook December 08, 2017 Chapter 10 Section 1 Intermolecular Forces the forces between molecules or between ions and molecules in the liquid or solid state Stronger Intermolecular forces cause higher melting points and boiling

More information

Chapter 1. Topic: Overview of basic principles

Chapter 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 information

Principles of Enzyme Catalysis Arthur L. Haas, Ph.D. Department of Biochemistry and Molecular Biology

Principles of Enzyme Catalysis Arthur L. Haas, Ph.D. Department of Biochemistry and Molecular Biology Principles of Enzyme Catalysis Arthur L. Haas, Ph.D. Department of Biochemistry and Molecular Biology Review: Garrett and Grisham, Enzyme Specificity and Regulation (Chapt. 13) and Mechanisms of Enzyme

More information

An introduction to Molecular Dynamics. EMBO, June 2016

An introduction to Molecular Dynamics. EMBO, June 2016 An introduction to Molecular Dynamics EMBO, June 2016 What is MD? everything that living things do can be understood in terms of the jiggling and wiggling of atoms. The Feynman Lectures in Physics vol.

More information

CHAPTER 21: Reaction Dynamics

CHAPTER 21: Reaction Dynamics CHAPTER 21: Reaction Dynamics I. Microscopic Theories of the Rate Constant. A. The Reaction Profile (Potential Energy diagram): Highly schematic and generalized. A---B-C B. Collision Theory of Bimolecular

More information

INTERMOLECULAR AND SURFACE FORCES

INTERMOLECULAR AND SURFACE FORCES INTERMOLECULAR AND SURFACE FORCES SECOND EDITION JACOB N. ISRAELACHVILI Department of Chemical & Nuclear Engineering and Materials Department University of California, Santa Barbara California, USA ACADEMIC

More information

Why Proteins Fold. How Proteins Fold? e - ΔG/kT. Protein Folding, Nonbonding Forces, and Free Energy

Why 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 information

BIBC 100. Structural Biochemistry

BIBC 100. Structural Biochemistry BIBC 100 Structural Biochemistry http://classes.biology.ucsd.edu/bibc100.wi14 Papers- Dialogue with Scientists Questions: Why? How? What? So What? Dialogue Structure to explain function Knowledge Food

More information

Contents. 2. Fluids. 1. Introduction

Contents. 2. Fluids. 1. Introduction Contents 1. Introduction 2. Fluids 3. Physics of Microfluidic Systems 4. Microfabrication Technologies 5. Flow Control 6. Micropumps 7. Sensors 8. Ink-Jet Technology 9. Liquid Handling 10.Microarrays 11.Microreactors

More information

Lec.1 Chemistry Of Water

Lec.1 Chemistry Of Water Lec.1 Chemistry Of Water Biochemistry & Medicine Biochemistry can be defined as the science concerned with the chemical basis of life. Biochemistry can be described as the science concerned with the chemical

More information

Module 8: "Stability of Colloids" Lecture 38: "" The Lecture Contains: Calculation for CCC (n c )

Module 8: Stability of Colloids Lecture 38:  The Lecture Contains: Calculation for CCC (n c ) The Lecture Contains: Calculation for CCC (n c ) Relation between surface charge and electrostatic potential Extensions to DLVO theory file:///e /courses/colloid_interface_science/lecture38/38_1.htm[6/16/2012

More information

Chapter 11 section 6 and Chapter 8 Sections 1-4 from Atkins

Chapter 11 section 6 and Chapter 8 Sections 1-4 from Atkins Lecture Announce: Chapter 11 section 6 and Chapter 8 Sections 1-4 from Atkins Outline: osmotic pressure electrolyte solutions phase diagrams of mixtures Gibbs phase rule liquid-vapor distillation azeotropes

More information

BIOC 530 Fall, 2011 BIOC 530

BIOC 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 information

All-atom Molecular Mechanics. Trent E. Balius AMS 535 / CHE /27/2010

All-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 information

Topic0990 Electrical Units In attempting to understand the properties of chemical substances, chemists divide chemistry into two parts.

Topic0990 Electrical Units In attempting to understand the properties of chemical substances, chemists divide chemistry into two parts. Topic99 Electrical Units In attempting to understand the properties of chemical substances, chemists divide chemistry into two parts. In one part, chemists are interested in understanding intramolecular

More information

CHEM 110: CHAPTER 8 Basic Concepts of Chem Bonding. Lewis Structures of Atoms: The Lewis Dot Diagram

CHEM 110: CHAPTER 8 Basic Concepts of Chem Bonding. Lewis Structures of Atoms: The Lewis Dot Diagram 1 CHEM 110: CHAPTER 8 Basic Concepts of Chem Bonding Lewis Structures of Atoms: The Lewis Dot Diagram Lewis Dot Diagrams (developed by chemist Gilbert Lewis) are used to indicate the number of valence

More information

Molecular Forces in Biological Systems - Electrostatic Interactions; - Shielding of charged objects in solution

Molecular Forces in Biological Systems - Electrostatic Interactions; - Shielding of charged objects in solution Molecular Forces in Biological Systems - Electrostatic Interactions; - Shielding of charged objects in solution Electrostatic self-energy, effects of size and dielectric constant q q r r ε ε 1 ε 2? δq

More information

3. Solutions W = N!/(N A!N B!) (3.1) Using Stirling s approximation ln(n!) = NlnN N: ΔS mix = k (N A lnn + N B lnn N A lnn A N B lnn B ) (3.

3. Solutions W = N!/(N A!N B!) (3.1) Using Stirling s approximation ln(n!) = NlnN N: ΔS mix = k (N A lnn + N B lnn N A lnn A N B lnn B ) (3. 3. Solutions Many biological processes occur between molecules in aqueous solution. In addition, many protein and nucleic acid molecules adopt three-dimensional structure ( fold ) in aqueous solution.

More information

Multimedia : Boundary Lubrication Podcast, Briscoe, et al. Nature , ( )

Multimedia : Boundary Lubrication Podcast, Briscoe, et al. Nature , ( ) 3.05 Nanomechanics of Materials and Biomaterials Thursday 04/05/07 Prof. C. Ortiz, MITDMSE I LECTURE 14: TE ELECTRICAL DOUBLE LAYER (EDL) Outline : REVIEW LECTURE #11 : INTRODUCTION TO TE ELECTRICAL DOUBLE

More information

Molecular Simulation III

Molecular Simulation III Molecular Simulation III Quantum Chemistry Classical Mechanics E = Ψ H Ψ ΨΨ U = E bond +E angle +E torsion +E non-bond Molecular Dynamics Jeffry D. Madura Department of Chemistry & Biochemistry Center

More information

Atoms & Their Interactions

Atoms & 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 information

2 Structure. 2.1 Coulomb interactions

2 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 information

Chapter Notes Subject: Chemistry Class: XI Chapter: Thermodynamics Top concepts

Chapter Notes Subject: Chemistry Class: XI Chapter: Thermodynamics Top concepts Chapter Notes Subject: Chemistry Class: XI Chapter: Thermodynamics Top concepts 1. The branch of science which deals with study of different forms of energy and their interconversion is called thermodynamics.

More information

Thinking Like a Chemist UNIT 5 DAY 1

Thinking Like a Chemist UNIT 5 DAY 1 Thinking Like a Chemist UNIT 5 DAY 1 What are we going to learn today? Note some important details on the syllabus Become familiar with the course website Meet the teaching team Review the Mechanics of

More information

Ligand-receptor interactions

Ligand-receptor interactions University of Silesia, Katowice, Poland 11 22 March 2013 Ligand-receptor interactions Dr. Pavel Polishchuk A.V. Bogatsky Physico-Chemical Institute of National Academy of Sciences of Ukraine Odessa, Ukraine

More information

Chapter 13. Properties of Solutions. Lecture Presentation. John D. Bookstaver St. Charles Community College Cottleville, MO

Chapter 13. Properties of Solutions. Lecture Presentation. John D. Bookstaver St. Charles Community College Cottleville, MO Lecture Presentation Chapter 13 Properties of John D. Bookstaver St. Charles Community College Cottleville, MO are homogeneous mixtures of two or more pure substances. In a solution, the solute is dispersed

More information

1044 Lecture #14 of 18

1044 Lecture #14 of 18 Lecture #14 of 18 1044 1045 Q: What s in this set of lectures? A: B&F Chapter 13 main concepts: Section 1.2.3: Diffuse double layer structure Sections 13.1 & 13.2: Gibbs adsorption isotherm; Electrocapillary

More information

q 2 Da This looks very similar to Coulomb doesn t it? The only difference to Coulomb is the factor of 1/2.

q 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 information

Enduring Understandings & Essential Knowledge for AP Chemistry

Enduring 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 information

Water. 2.1 Weak Interactions in Aqueous Sy stems Ionization of Water, Weak Acids, and Weak Bases 58

Water. 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 information

Lecture: P1_Wk1_L1 IntraMolecular Interactions. Ron Reifenberger Birck Nanotechnology Center Purdue University 2012

Lecture: P1_Wk1_L1 IntraMolecular Interactions. Ron Reifenberger Birck Nanotechnology Center Purdue University 2012 Lecture: IntraMolecular Interactions Distinguish between IntraMolecular (within a molecule) and InterMolecular (between molecules) Ron Reifenberger Birck Nanotechnology Center Purdue University 2012 1

More information

Rama Abbady. Zina Smadi. Diala Abu-Hassan

Rama Abbady. Zina Smadi. Diala Abu-Hassan 1 Rama Abbady Zina Smadi Diala Abu-Hassan (00:00) (10:00) Types of Molecules in the Cell 1. Water Molecules: a large portion of the cell mass is water (70% of total cell mass). 2. Organic molecules (carbon

More information

Biochemistry 530: Introduction to Structural Biology. Autumn Quarter 2014 BIOC 530

Biochemistry 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 information

StudyHub: AP Chemistry

StudyHub: AP Chemistry StudyHub+ 1 StudyHub: AP Chemistry Solution Composition and Energies, Boiling Point, Freezing Point, and Vapor Pressure StudyHub+ 2 Solution Composition: Mole Fraction: Formula: Mole Fraction of Component

More information

Protein Folding & Stability. Lecture 11: Margaret A. Daugherty. Fall How do we go from an unfolded polypeptide chain to a

Protein Folding & Stability. Lecture 11: Margaret A. Daugherty. Fall How do we go from an unfolded polypeptide chain to a Lecture 11: Protein Folding & Stability Margaret A. Daugherty Fall 2004 How do we go from an unfolded polypeptide chain to a compact folded protein? (Folding of thioredoxin, F. Richards) Structure - Function

More information

Chpt 8 Chemical Bonding Forces holding atoms together = Chemical Bonds

Chpt 8 Chemical Bonding Forces holding atoms together = Chemical Bonds Chpt 8 Chemical Bonding Forces holding atoms together = Chemical Bonds Kinds of chemical bonds: 1. Ionic 2. Covalent 3. Metallic Useful guideline: Octet rule Atoms tend to gain, lose, or share e - to achieve

More information

BCMP 201 Protein biochemistry

BCMP 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 information

40 46, 51, ,

40 46, 51, , cha02680_fm.indd Page xxvi 12/27/12 4:05 PM GG-009 /Volumes/107/GO01228/CHANG_11E/ANCILLARY/CHANG/007_665610_1_P1 BIG IDEA 1: The chemical elements are fundamental building materials of matter, and all

More information

Copyright 2018 Dan Dill 1

Copyright 2018 Dan Dill 1 TP Do we get the same amount of energy back from making bonds between an ion and water molecules, as it took to break the ionic bonds holding an ion in the solid? + 1. The energy is the same 2. More energy

More information

CHEM 545 Theory and Practice of Molecular Electronic Structure. Anna I. Krylov. DON T PANIC.

CHEM 545 Theory and Practice of Molecular Electronic Structure. Anna I. Krylov.   DON T PANIC. CHEM 545 Theory and Practice of Molecular Electronic Structure Anna I. Krylov http://iopenshell.usc.edu/chem545/ DON T PANIC USC Fall 2014 Things to do: 1. Install IQmol (by this Thursday). http://iqmol.org/.

More information

Chemical thermodynamics the area of chemistry that deals with energy relationships

Chemical thermodynamics the area of chemistry that deals with energy relationships Chemistry: The Central Science Chapter 19: Chemical Thermodynamics Chemical thermodynamics the area of chemistry that deals with energy relationships 19.1: Spontaneous Processes First law of thermodynamics

More information

21 Electric Fields Karl Haab,

21 Electric Fields Karl Haab, 21 Electric Fields Karl Haab, 2008 1 Objectives Calculate el. force between charges electric field and field strength electric potential, p.d. application: the electron gun 2 Some fundamental facts Objects

More information

Chapter 9. Chemical Bonding I: The Lewis Model. HIV-Protease. Lecture Presentation

Chapter 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 information

Thermodynamic Studies of Some Symmetrical Electrolyte s Solution in Aqueous-Organic Solvent Mixtures

Thermodynamic Studies of Some Symmetrical Electrolyte s Solution in Aqueous-Organic Solvent Mixtures ISSN 122-8594 JUJS 218 Jahangirnagar University Journal of Science Vol. 41, No.1, pp.87-98 Thermodynamic Studies of Some Symmetrical Electrolyte s Solution in Aqueous-Organic Solvent Mixtures Md. Minarul

More information

Lecture 5: Electrostatic Interactions & Screening

Lecture 5: Electrostatic Interactions & Screening Lecture 5: Electrostatic Interactions & Screening Lecturer: Prof. Brigita Urbanc (brigita@drexel.edu) PHYS 461 & 561, Fall 2009-2010 1 A charged particle (q=+1) in water, at the interface between water

More information

Chapter 6 Part 1 Structure of the atom

Chapter 6 Part 1 Structure of the atom Chapter 6 Part 1 Structure of the atom What IS the structure of an atom? What are the properties of atoms? REMEMBER: structure affects function! Important questions: Where are the electrons? What is the

More information

Week 14/Th: Lecture Units 34 & 35

Week 14/Th: Lecture Units 34 & 35 Week 14/Th: Lecture Units 34 & 35 Unit 33: Colligative Properties Unit 34: Introduction to Equilibria -- Rate of reaction -- Reaction pathway -- Forward / Reverse Rxns. Unit 35: Equilibrium Constants --

More information

Ch 9 Liquids & Solids (IMF) Masterson & Hurley

Ch 9 Liquids & Solids (IMF) Masterson & Hurley Ch 9 Liquids & Solids (IMF) Masterson & Hurley Intra- and Intermolecular AP Questions: 2005 Q. 7, 2005 (Form B) Q. 8, 2006 Q. 6, 2007 Q. 2 (d) and (c), Periodic Trends AP Questions: 2001 Q. 8, 2002 Q.

More information

2.Ionization Energies

2.Ionization Energies 2.Ionization Energies Ionization energy, IE, is the energy required to remove one electron from an atom or ion; an endothermic process that is, A A + + 1 e - H = +ve The energy, in kj mol -1, required

More information

Physics (

Physics ( Question 2.12: A charge of 8 mc is located at the origin. Calculate the work done in taking a small charge of 2 10 9 C from a point P (0, 0, 3 cm) to a point Q (0, 4 cm, 0), via a point R (0, 6 cm, 9 cm).

More information

Proton Acidity. (b) For the following reaction, draw the arrowhead properly to indicate the position of the equilibrium: HA + K + B -

Proton Acidity. (b) For the following reaction, draw the arrowhead properly to indicate the position of the equilibrium: HA + K + B - Proton Acidity A01 Given that acid A has a pk a of 15 and acid B has a pk a of 10, then: (a) Which of the two acids is stronger? (b) For the following reaction, draw the arrowhead properly to indicate

More information

Unit 7: Basic Concepts of Chemical Bonding. Chemical Bonds. Lewis Symbols. The Octet Rule. Transition Metal Ions. Ionic Bonding 11/17/15

Unit 7: Basic Concepts of Chemical Bonding. Chemical Bonds. Lewis Symbols. The Octet Rule. Transition Metal Ions. Ionic Bonding 11/17/15 Unit 7: Basic Concepts of Chemical Bonding Topics Covered Chemical bonds Ionic bonds Covalent bonds Bond polarity and electronegativity Lewis structures Exceptions to the octet rule Strength of covalent

More information

Lecture 2-3: Review of forces (ctd.) and elementary statistical mechanics. Contributions to protein stability

Lecture 2-3: Review of forces (ctd.) and elementary statistical mechanics. Contributions to protein stability Lecture 2-3: Review of forces (ctd.) and elementary statistical mechanics. Contributions to protein stability Part I. Review of forces Covalent bonds Non-covalent Interactions Van der Waals Interactions

More information

Fundamentals of Distribution Separations (III)

Fundamentals of Distribution Separations (III) Fundamentals of Distribution Separations (III) (01/16/15) K = exp -Δμ 0 ext i - Δμ i RT distribution coefficient C i = exp -Δμ 0 RT - - Δμ i = ΔH i TΔS i 0 0 0 solubility q A---B A + B 0 0 0 ΔH i = ΔH

More information

V. Electrostatics. MIT Student

V. Electrostatics. MIT Student V. Electrostatics Lecture 26: Compact Part of the Double Layer MIT Student 1 Double-layer Capacitance 1.1 Stern Layer As was discussed in the previous lecture, the Gouy-Chapman model predicts unphysically

More information

More Chemical Bonding

More Chemical Bonding More Chemical Bonding Reading: Ch 10: section 1-8 Ch 9: section 4, 6, 10 Homework: Chapter 10:.31, 33, 35*, 39*, 43, 47, 49* Chapter 9: 43, 45, 55*, 57, 75*, 77, 79 * = important homework question Molecular

More information

CHEMISTRY XL-14A CHEMICAL BONDS

CHEMISTRY 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 information

Chem 112 Dr. Kevin Moore

Chem 112 Dr. Kevin Moore Chem 112 Dr. Kevin Moore Gas Liquid Solid Polar Covalent Bond Partial Separation of Charge Electronegativity: H 2.1 Cl 3.0 H Cl δ + δ - Dipole Moment measure of the net polarity in a molecule Q Q magnitude

More information

Peptide folding in non-aqueous environments investigated with molecular dynamics simulations Soto Becerra, Patricia

Peptide folding in non-aqueous environments investigated with molecular dynamics simulations Soto Becerra, Patricia University of Groningen Peptide folding in non-aqueous environments investigated with molecular dynamics simulations Soto Becerra, Patricia IMPORTANT NOTE: You are advised to consult the publisher's version

More information

Properties of Aqueous Solutions

Properties of Aqueous Solutions Properties of Aqueous Solutions Definitions A solution is a homogeneous mixture of two or more substances. The substance present in smaller amount is called the solute. The substance present in larger

More information

1. Poisson-Boltzmann 1.1. Poisson equation. We consider the Laplacian. which is given in spherical coordinates by (2)

1. Poisson-Boltzmann 1.1. Poisson equation. We consider the Laplacian. which is given in spherical coordinates by (2) 1. Poisson-Boltzmann 1.1. Poisson equation. We consider the Laplacian operator (1) 2 = 2 x + 2 2 y + 2 2 z 2 which is given in spherical coordinates by (2) 2 = 1 ( r 2 ) + 1 r 2 r r r 2 sin θ θ and in

More information

Chapter 8. Basic Concepts of Chemical Bonding. Lecture Presentation. John D. Bookstaver St. Charles Community College Cottleville, MO

Chapter 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 information

Lecture 6. NONELECTROLYTE SOLUTONS

Lecture 6. NONELECTROLYTE SOLUTONS Lecture 6. NONELECTROLYTE SOLUTONS NONELECTROLYTE SOLUTIONS SOLUTIONS single phase homogeneous mixture of two or more components NONELECTROLYTES do not contain ionic species. CONCENTRATION UNITS percent

More information

Chapter 13 Properties of Solutions

Chapter 13 Properties of Solutions Chemistry, The Central Science, 10th edition Theodore L. Brown; H. Eugene LeMay, Jr.; and Bruce E. Bursten Chapter 13 Properties of John D. Bookstaver St. Charles Community College St. Peters, MO 2006,

More information

First Law of Thermodynamics

First Law of Thermodynamics First Law of Thermodynamics Remember: ΔE univ = 0 Total energy of the universe is constant. Energy can be transferred: ΔE = q + w q = heat w = work (F*D) = ΔPV 1 st Law, review For constant volume process:

More information

Thermodynamics: Free Energy and Entropy. Suggested Reading: Chapter 19

Thermodynamics: Free Energy and Entropy. Suggested Reading: Chapter 19 Thermodynamics: Free Energy and Entropy Suggested Reading: Chapter 19 System and Surroundings System: An object or collection of objects being studied. Surroundings: Everything outside of the system. the

More information

6, Physical Chemistry -II (Statistical Thermodynamics, Chemical Dynamics, Electrochemistry and Macromolecules)

6, Physical Chemistry -II (Statistical Thermodynamics, Chemical Dynamics, Electrochemistry and Macromolecules) Subject Paper No and Title Module No and Title Module Tag 6, Physical -II (Statistical Thermodynamics, Chemical Dynamics, Electrochemistry and Macromolecules) 25, Activity and Mean Activity coefficient

More information

Chemistry 1B Fall 2012

Chemistry 1B Fall 2012 Chemistry 1B Fall 2012 Lecture 9 (chapter 13; pp 593-612) [596-614] 7th 2 bonding in molecules Chapter 13 (pp 593-612) Overview of bonding and ionic bonding (lect 9) Chapter 13 (pp 612-650)- Classical

More information

12A Entropy. Entropy change ( S) N Goalby chemrevise.org 1. System and Surroundings

12A Entropy. Entropy change ( S) N Goalby chemrevise.org 1. System and Surroundings 12A Entropy Entropy change ( S) A SPONTANEOUS PROCESS (e.g. diffusion) will proceed on its own without any external influence. A problem with H A reaction that is exothermic will result in products that

More information

Chapters 11 and 12: Intermolecular Forces of Liquids and Solids

Chapters 11 and 12: Intermolecular Forces of Liquids and Solids 1 Chapters 11 and 12: Intermolecular Forces of Liquids and Solids 11.1 A Molecular Comparison of Liquids and Solids The state of matter (Gas, liquid or solid) at a particular temperature and pressure depends

More information

GHW#3. Chapter 3. Louisiana Tech University, Chemistry 481. POGIL(Process Oriented Guided Inquiry Learning) Exercise on Chapter 3.

GHW#3. Chapter 3. Louisiana Tech University, Chemistry 481. POGIL(Process Oriented Guided Inquiry Learning) Exercise on Chapter 3. GHW#3. Chapter 3. Louisiana Tech University, Chemistry 481. POGIL(Process Oriented Guided Inquiry Learning) Exercise on Chapter 3. Energetics of Ionic Bonding. Why? What are the properties of ionic compounds?

More information

Downloaded from

Downloaded from I.I.T.Foundation - XI Chemistry MCQ #4 Time: 45 min Student's Name: Roll No.: Full Marks: 90 Chemical Bonding I. MCQ - Choose Appropriate Alternative 1. The energy required to break a chemical bond to

More information

Electrochemical Properties of Materials for Electrical Energy Storage Applications

Electrochemical Properties of Materials for Electrical Energy Storage Applications Electrochemical Properties of Materials for Electrical Energy Storage Applications Lecture Note 3 October 11, 2013 Kwang Kim Yonsei Univ., KOREA kbkim@yonsei.ac.kr 39 Y 88.91 8 O 16.00 7 N 14.01 34 Se

More information

Inorganic Pharmaceutical Chemistry

Inorganic Pharmaceutical Chemistry Inorganic Pharmaceutical Chemistry Lecture No. 4 Date :25/10 /2012 Dr. Mohammed Hamed --------------------------------------------------------------------------------------------------------------------------------------

More information

Phase Equilibria and Molecular Solutions Jan G. Korvink and Evgenii Rudnyi IMTEK Albert Ludwig University Freiburg, Germany

Phase Equilibria and Molecular Solutions Jan G. Korvink and Evgenii Rudnyi IMTEK Albert Ludwig University Freiburg, Germany Phase Equilibria and Molecular Solutions Jan G. Korvink and Evgenii Rudnyi IMTEK Albert Ludwig University Freiburg, Germany Preliminaries Learning Goals Phase Equilibria Phase diagrams and classical thermodynamics

More information

Lecture 9. Chemistry 1B Fall 2013 Lecture 9. Chemistry 1B. Fall (chapter 13; pp )

Lecture 9. Chemistry 1B Fall 2013 Lecture 9. Chemistry 1B. Fall (chapter 13; pp ) bonding in molecules Chemistry 1B Fall 2013 Lecture 9 (chapter 13; pp 596-614) Chapter 13 (pp 596-614) Overview of bonding and ionic bonding (lect 9) Chapter 13 (pp 621-650)- Classical picture of (pp 602-606)

More information

Chapter 12 Section 1

Chapter 12 Section 1 hapter 12 Section 1 Kinetic Molecular Description of Liquids and Solids Noncovalent Forces Intermolecular interactions Electrostatic Forces Dispersion Forces -bonding DNA, RNA Mary J. Bojan hem 110 1 What

More information

Lecture Notes 1: Physical Equilibria Vapor Pressure

Lecture Notes 1: Physical Equilibria Vapor Pressure Lecture Notes 1: Physical Equilibria Vapor Pressure Our first exploration of equilibria will examine physical equilibria (no chemical changes) in which the only changes occurring are matter changes phases.

More information

Chapter 3. Crystal Binding

Chapter 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 information

Biomolecules are dynamic no single structure is a perfect model

Biomolecules are dynamic no single structure is a perfect model Molecular Dynamics Simulations of Biomolecules References: A. R. Leach Molecular Modeling Principles and Applications Prentice Hall, 2001. M. P. Allen and D. J. Tildesley "Computer Simulation of Liquids",

More information