Subject: Molecular Architecture

From: "Frank Marchese" <[email-masked]>
Date: Thu, 24 Apr 2003 08:57:52 -0400

Hi All,

Architects and structural chemists have similar design goals. Below are
a few architecture concepts that can be mapped to molecules.

1. Architecture defines space. 
So do molecules. For example, cage compounds, zeolites, many 
proteins define spaces for other molecules to inhabit. 
(keywords: host-guest compounds, cages, cryptands, protein active site) 

2. Form follows function. 
For example, the "shapes" of proteins have evoled to perform a specific
function.

3. Architectural orders. 
There is a systematic way in which atoms are combined to create spatial
structure. Models such as VSEPR are easy heuristic models to look at this. Correlations may be made with Palladian motifs. Mitchell's book "The Logic of Architecture" talks about "a Palladian grammar" that is used to understand how Palladio designed his buildings. The periodic table and rules of chemical combination are a more complex 3D grammar.

As another example... Proteins are built from a set of architectural "motifs" (e.g. "greek key"). A good place to look is "Introduction to Protein Structure" by Carl Branden and John Tooze.

Finally, molecules crystallize in regular patterns, very much like "wall paper" patterns. Books on symmetry and crystallography are good places to look for info.

4. Inorganic vs organic architecture. 
Inorganic substances have highly regular structures (e.g. salt (NaCl)). But 
most organic molecules are less-so. There is a whole class of molecules
called "dendritic molecules" that have branching patterns much like 
trees or bushes.

5. Positive vs Negative space. 
The Seagram building in NYC is my favorite example of this. Mies van der Rohe's 
monolithic structure defines a complmentary rectangular volume.  Many atomic
arrangements create these types of  spatial relationships. For example, the packing
arrangement of Cl- ions in the NaCl lattice defines spaces for the smaller Na+ ions
to occupy.

Enough for now.

Regards
Frank

Dr. Francis T. Marchese
Professor
Dept. of Computer Science
Pace University
163 William Street, 2nd Floor
NY, NY 10038

and

Director
Center for Advanced Media
http://csis.pace.edu/~cam

and 

Director
Pace Digital Gallery
http://www.pace.edu/DigitalGallery

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