10: Aggregates and Macromolecules
- Page ID
- 519143
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)- 10.1: Mass Spectrometry
- Mass spectrometry is used widely in chemistry and biochemistry to identify molecules. This page starts by describing the three basic functional blocks of a mass spectrometer (ion source, mass filter and detector). Then focuses on particular versions of the building blocks most applicable to large molecules and macromolecules.
- 10.2: X-Ray Crystallography
- X-Ray crystallography provides precise information on the geometry of molecules and molecular aggregates. It requires solid crystalline samples that must be nearly flaw free to get the most precise information. This section provides an overview of X-ray diffraction, crystal lattices, Miller indices and Bragg's law, followed by a description of the complexities involved in interpreting the scattering generated by crystals of macromolecules.
- 10.3: Cryo-Electron Microscopy
- Beginning about 2013 it became possible to use cryoEM (cryo-transmission electron microscopy) to determine the in solution structure of macromolecules and aggregates at atomic resolution. This section provides an overview of the technique and a brief history of the key developments that made it possible.
- 10.4: Intermolecular Forces
- Intermolecular forces are the attractions and repulsions between chemical species that occur without changing the chemical identity of the species or breaking bonds. This section provides a summary of these types of interactions, mathematical models for their strength and directionality, plus a description of how they combine to give the overall distance dependence observed for van der Waals attractions.
- 10.5: Structure of Gases, Liquids and Glasses
- This section describes the radial distribution function which is used to characterize the small amount of order seen in gases, liquids and glasses.
- 10.6: Macromolecules
- The relative positions of atoms in macromolecules (polymers) are restricted by the bonding in the molecules. Because bond angles are somewhat flexible and there is nearly free rotation about any single bonds, macromolecules can take on many conformations. This section starts with a simple physical model for how these long chains can behave. As examples of real molecules we will look briefly at biologically important macromolecules and biological molecular aggregates.
- 10.7: Simulations
- Computer simulations are often used to understand and predict the behavior and structure of molecules. With modern computers it is practical to perform simulations involving macromolecules. This section provides brief descriptions of molecular dynamics simulations (MD) for predicting behavior and machine learning (ML/AI) for the prediction of macromolecular structures.