Chemistry in Computers:

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Nov 18, 2013 (3 years and 8 months ago)

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Chemistry in Computers:

From Educational Tools

to Computational Chemistry

Rituraj Kalita

Sr. Lecturer in Chemistry, Cotton College, Guwahati

(web
-
site: www.geocities.com/riturajkalita)


Essay & Presentation Finalized in: June, 2006

(web
-
page: www.geocities.com/riturajkalita/ccworkshop.htm)

Chemistry in Computers


Why?


Chemistry is a science of mobile three
-
dimensional
entities (species) such as molecules, radicals, ions &
macromolecules etc., and of their mutual interactions.
Two
-
dimensional and static figures on paper or on the
blackboard can’t properly explain or represent these!


So, chemistry
-
education is greatly facilitated with
in
-
computer
visual models

and visual software
-
packages,
say in stereochemistry & organic
-
reaction mechanisms.


The branch of
computational chemistry

(also called
theoretical chemistry
) utilizes quantum mechanics etc. to
theoretically calculate thermodynamic, spectroscopic &
kinetic properties of chemical species, existing or even
hypothetical. This job requires immense computations!

Visual Models & Packages:

Those Pre
-
built for You


There remains several multimedia software packages for
aiding in one’s chemistry learning, either available in the
market or even freely obtainable on the internet.


These packages include visual models of molecules that
can be rotated / translated by the user, and moving visual
models of reactions such as of S
N
1 & S
N
2 reaction
-
types.


The internationally reputed chemistry textbooks for the
degree & postgraduate levels also, nowadays, provide a
CD containing such visual models relevant to the book,


Such a multimedia package has also been developed at
the Chemistry Department of Pandu College, Guwahati!

Pre
-
built Visual Models:
A Rotating Model of Iodo
-
Methane

(may now observe the slight rotation)

Visual Models & Packages:

Models to be Built by You


Packages discussed above do not offer a facility for creating
your own visual models, or for modifying the existing ones.



In contrast, drawing packages such as
ISIS/Draw

and
modelling packages such as
ArgusLab

allows you to
create your own molecular
-
structure drawings/ models.


Any such drawing or modelling package is based on the
idea that a molecule or radical can be represented by
specifying the
nuclear
-
framework

only, i.e., only by the
specification of the identities and positions of each of the
constituent nuclei. The electrons constantly keep moving
to form the
electron
-
cloud
, and so are un
-
specifiable. So,
there, you need to draw out only the nuclear
-
framework.

The Drawing Package ISIS/Draw:

Drawing Structures for Word
-
Processors


Ever needed to draw chemical structures using Microsoft
Word or PageMaker? Or using Paint? It’s too difficult.


ISIS/Draw

is meant for that purpose: to draw chemical
structures for putting them into a word
-
processor
document such as an news
-
essay, or into a presentation
(e.g., power
-
point) file to present in front of a gathering.


ISIS/Draw

is developed by MDL Information Systems
Inc. (USA), and is available to anybody as a
freeware
.


To get
ISIS/Draw

from the internet, search for
ISIS/Draw

in a search engine (e.g., www.google.com),
locate the home
-
page (it is now
www.mdli.com
) of
MDL, and download
ISIS/Draw
(and its help
-
system)

The Modelling Package ArgusLab:

3
-
D Visual Models of Molecular Systems


ISIS/Draw

does not give you a full
-
fledged 3
-
D model of
the structure you’ve drawn. The picture formed can’t be
rotated to understand its 3
-
dimensional intricacies!


So we may use
ArgusLab
, a leading Chemical Modelling
Software, to draw in it proper visual models.


ArgusLab

is developed by Planaria Software,
(
www.planaria
-
software.com
), and is available for
free
.


ArgusLab

allows us to draw structures as if on paper,
substitute, move, and delete atoms, and fix distances in
space. We can here grow structures with complete
control of stereochemistry. Even drug
-
macromolecule
docking could be performed in
ArgusLab

now .

The Basis Behind the Visual View:

Hidden Nuclear
-
Framework Mathematics


In case of any visual
molecular model

worth this term,
the view isn’t preserved in the form a image (picture) file
as it would have made 3
-
D rotations rather impossible!


The visual model is actually preserved as a
text

file (with
extensions
.xyz
,
.c3d
or
.mop
etc.) that contains list of the
identities

(H, C, N, O etc.) &
position
-
coordinates

of all
the constituent nuclei, and also the molecular
net charge
.


The model
-
viewer software
-
package such as

ArgusLab,
ORTEP
or

Protein Explorer
can read such data from
such
molecular
-
model

text file, and then generates the
visual view instantaneously to be viewed by the user.

The Basis Behind the Visual View:

An Actual Nuclear
-
Framework Expression


In the following
molecular model

file of the
.xyz

type,
the identities of the nuclei and their Cartesian (x,y,z)
position
-
coordinates are kept listed (1 line for 1 nucleus)


The
unit

of distance for the position
-
coordinates is
Angstrom

(10

10

m) as a universally accepted convention

The Basis Behind the Visual View:

Two Types of Framework Specifications


The above specification isn’t, however, the
only

possible
way of specification for the molecular
nuclear
-
framework
.


Such
Cartesian

specifications are used in case of
.xyz

(XYZ type) and
.c3d

(Chem
-
3D type) files. However in
the
.mop

(Mopac type) files etc., specification is in another
way, called the
z
-
matrix relative
-
coordinates

specification.


In this way, a nuclear position is specified relative to a
bond
-
distance
, a
bond
-
angle

and a
dihedral
-
angle

with
respect to
some other

(pre
-
specified) nuclei. This way is,
obviously, closer to any chemist’s heart.


The angles are kept, by universal convention, in degrees.

The Basis Behind the Visual View:

Z
-
Matrix Type Coordinates
-
Specification

The Mathematical Basis of the Visual:

Computational Chemistry Flies Herefrom


For any computational chemistry
computation
-
package

to
theoretically calculate

the properties of any molecule or
any other chemical species, the molecule or chemical
species must be specified to it in a
definitive

manner.


The afore
-
mentioned
mathematical

aspect of the
(molecular) model serves exactly this purpose. Thus the
computational software knows
what

species to calculate.


A computational software
-
package (such as
PC
-
GAMESS
,
a
freeware
) is a very powerful tool at the hand of chemists.
Using it along with a PC for several hours, they can
calculate

properties of (not
-
so
-
big) chemical species even
without

doing any experiment! Even the pre
-
assumed
molecular structure may be made better via
optimization
.

Does Computational Chemistry Work?
A Study of a Silly Chemical Reaction


As we can see here,
computational chemistry

can really
predict whether two molecules will react or not!


Prediction is faster and better for small ones.


To do that, we need to make a model of the molecule
-
combination (
supermolecule
) with the molecules far
apart, then ask the package for a
structure
-
optimization
.


For larger molecules, meaningful computation requires
more accurate level of computations: this means much
more computer
-
time (hours for ~50 atom supermolecule)


To find that NH
3

& BF
3

will react with
D
E~65 kJ mol

1
,
forming N
-
B coordinate bond ~2 A
o

long etc., takes only
less than a minute using PC
-
Gamess in a Pentium
-
II PC

Computational Chemistry Working:


Some Works that PC
-
GAMESS Does Are


Calculation of molecular energies at diff. levels of accuracy


Calculation of molecular electronic wavefunctions


Calculation of dipole and multi
-
pole moments


Optimization of the pre
-
assumed molecular structure


Calculation of vibrational normal modes, vibrational
frequencies and IR
-
spectra intensities


Prediction of reactivity and reaction
-
path (with mechanism)


Calculation of electron density as a function of space

Demonstration of ArgusLab v4.0

(Demonstration to be Performed by the Instructor)



Learning:



about
Builder Toolkit
,
Add Atoms Mode

&
Auto Bonds

in
ArgusLab



about drawing (non
-
H) main
-
chain with proper bond distance & bond angle



Building (i.e., drawing) a molecular
-
structure model of
butanol



Showing (adding) & hiding hydrogen atoms in the above model



Substituting an H
-
atom to change model to that of
2
-
methyl butanol



Rotating, z
-
Rotating, Translating & Zooming the model



Saving the molecular
-
structure model as an
.xyz

file in disk



Auto
-
correcting the built (i.e., drawn) structural geometry of model



Closing, then opening the pre
-
saved molecular
-
structure model file



Viewing the above structural model with & without atom
-
labels



Deleting an hydrogen atom to build model of a radical species



Building model of
2
-
nitro toluene

from
Benzene

in
Builder Toolkit

Demonstration of PC
-
GAMESS v6.4

(Demonstration to be Performed by the Instructor)


Installing
PC
-
GAMESS helper package

developed by this author


Copying nuclear coordinates from a
.xyz

file created by
ArgusLab


Replacing nuclear coordinates part in the
Work2Do.inp

input file


Introducing suitable 2nd column in that nuclear coordinates part


Checking this
PC
-
GAMESS

input file for format, multiplicity etc.


Running
PC
-
GAMESS

with this modified & checked input file


Searching the output file for the final energy (find
Total Energy=
)


Searching output to observe optimization (find
Coordinates of all
)


Copying the nuclear coordinates from the last
-
optimized geometry


Replacing nuclear coordinates to modify
.xyz

file by pasting these


Removing the
odd

2nd column and saving the corrected
.xyz

file


Opening this
.xyz

file with
ArgusLab

to view optimized structure