Beng 130 Lecture 3 & 4

Beng 130 Lecture 3 & 4 - Molecular Interactions Are...

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Molecular Forces Molecular Structures and Interactions Molecular Structures and Interactions - Introduction Introduction Electrostatic Interactions London -van der Waals Interactions van der Waals Interactions Hydrogen Bonding Interactions Reading: Chapter 9 and Lecture Notes Chapter 9 and Lecture Notes Molecular Physical Chemistry - Lecture 3 Molecular Interactions Are Important in Many Processes in Life Structure Energetics (Properties) Mechanism Dynamics Molecular and Cellular Architecture: Self assembly into higher order structures Life processes: Molecular recognition, replication, transcription, translation and cellular functions D helix of a polypeptide Double helix of DNA Ribosome The peptide bond and stereoisomers of amino acids Strong interactions; Fixed arrangement of atoms in a molecule . Weak interactions between atoms (intra- and inter-molecular) ; Flexible spatial arrangement of atoms in the molecules by rotating around covalent bonds. Molecular Interactions Covalent bonds & configurations Non-covalent bonds & conformations Covalent Chemical Bonds The phosphodiester bonds link the nucleotides together in the linear polymer of the DNA molecules 3-1
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Covalent Bonds The potential energy of a covalent bond r 0 A + B A B ' H 0 A-B A + B The enthalpy of formation of the covalent bond Covalent Bond Stretching and Bending - Classic Mechanics CC r C C C T Covalent Bonds – Bond Stretching 2 0 ) ( 2 1 r r k U r 0 ! r Covalent Bonds – Bond Angle Bending 2 0 ) ( 2 1 T 0 ! B k U C C C T
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Covalent Bonds – Rotation Around Bonds ) cos( 360 n n V U q . ! J I function, spring harmonic simple a as d not treate is V function. periodic the of forms the but takes phase the is and function, the of period the is n minima. the of position the defines that angle Covalent Bonds – Rotation Around Bonds Covalent Bonds and Noncovalent Interactions – Orders of Magnitudes Quantum Mechanics: Wavefunctions and Electron Distributions Wavefunctions (1s orbitals) Electron Density Distributions 90% of electron in the sphere of 1s orbital of H Electron distribution of 1s orbital of H
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Coulomb’s Law of Electrostatic Forces/Interactions r q q r U H SH 0 2 1 4 ) ( ! 2 0 2 1 4 r q q dr U F ! w w 0 ! QE F ! 2 0 1 2 4 r q q F E ! ! r q 1 q 2 Coulomb’s Law: Electric Field from point charges and a dipole Interaction energy between two charges: Force of interaction: Electric field: V 0 0 0 2 charge total ) ( 2 ! ! ! E A A x E Coulomb’s Law of Electrostatic Forces/Interactions Electric field from a charged planar surface Electrostatic Potential ³ ³ ³ ³ ³ 0 0 0 ! £ 0 ! ! 0 2 1 2 1 2 1 2 1 1 2 z z x y y y x x x l l dz E dx E dx E d q dw l E \ l E F d q d dw £ 0 ! £ 0 ! ¸ ¹ · ¨ © § w w 0 ¸ ¹ · ¨ © § w w 0 ¸ ¹ · ¨ © § w w 0 ! . . ! x x x E E E E z y x r q dr r q d r r 0 2 0 4 4 ! 0 ! £ 0 ! ³ ³ f f l E Electrostatic potential of a point charge at position r: The work for moving a charge l distance along the electric field E: The difference in the electrostatic potential energy is defined as the work of moving a unit charge along the E field:
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This homework help was uploaded on 04/07/2008 for the course BENG 130, 103B, taught by Professor Gough during the Spring '08 term at UCSD.

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Beng 130 Lecture 3 & 4 - Molecular Interactions Are...

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