Beng 130 Lecture 5

Beng 130 Lecture 5 - Molecular Driving Forces Solvation and...

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Molecular Driving Forces: Solvation and Hydrophobic Effect Water, hydrogen bonds Water, hydrogen bonds Hydrophilic Hydrophilic solvation solvation Hydrophobic effect ( Hydrophobic effect ( solvation ) Molecular structures in media (solvents) Molecular structures in media (solvents) Molecular forces in biomolecules Molecular forces in biomolecules Reading: Chapter 9 and Lecture Notes Reading: Chapter 9 and Lecture Notes Molecular Physical Chemistry - Lecture 5 Molecular Interactions Are Important in All Processes in Life Molecular and Cellular Architecture: Self assembly into higher-order structures FIGURE 1–11 Structural hierarchy in the molecular organization of cells. In this plant cell, the nucleus is an organelle containing several types of supramolecular complexes, including chromosomes. Chromosomes consist of macromolecules of DNA and many different proteins. Each type of macromolecule is made up of simple subunits— DNA of nucleotides (deoxyribonucleotides), for example. Molecular Interactions Are Important in All Processes in Life Life processes: Molecular recognition, DNA Replication, Gene Transcription, Protein Translation, Cellular circuitry and 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
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Let us look at water solvation! Hydrophilic Solvation Hydrophobic Solvation Solvation Hydration FIGURE 2–1 Structure of the water molecule. The dipolar nature of the H2O molecule is shown by (a) ball-and-stick and (b) space-filling models. The dashed lines in (a) represent the nonbonding orbitals. There is a nearly tetrahedral arrangement of the outer-shell electron pairs around the oxygen atom; the two hydrogen atoms have localized partial positive charges () and the oxygen atom has a partial negative charge (2). (c) Two H2O molecules joined by a hydrogen bond (designated here, and throughout this book, by three blue lines) between the oxygen atom of the upper molecule and a hydrogen atom of the lower one. Hydrogen bonds are longer and weaker than covalent OOH bonds. FIGURE 2–5 Directionality of the hydrogen bond. The attraction between the partial electric charges (see Fig. 2–1) is greatest when the three atoms involved (in this case O, H, and O) lie in a straight line. When the hydrogen-bonded moieties are structurally constrained (as when they are parts of a single protein molecule, for example), this ideal geometry may not be possible and the resulting hydrogen bond is weaker.
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Beng 130 Lecture 5 - Molecular Driving Forces Solvation and...

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