The use of computational chemistry is to address the
problem of chemical. It is inevitable in the use of computers is how to use the
software. Hidden problems of this activity is about how well the answers
obtained. Several approaches to computational chemistry begin to know is to ask
some of these questions:
How accurate the results obtained will be obtained?
How long perhitunganya be completed?
What approach should be made? '
Is the approach used in the calculations are
significant to the considered problem?
Source:
http://www.scribd.com/doc/73340630/Manfaat-Kimia-Komputasi-Dalam-Penelitian,
Dr. Dwi Harno Pranowo, M.Si (Computational Approaches in Learning Chemistry). To answer this, it should be traced to the
development of computational chemistry so that it will get a picture of how the
utilization of computational chemistry.
Computational Chemistry in Drug Design
Computational chemistry, is the use of
computers in reviewing aspects of the chemistry. Description of chemical
properties in a computer experiment. Molecular model used is the result of a
theoretical chemist, but calculations have used "means" a particular
algorithm with computer programming language. The process of designing new
drugs and distribute them to the public is a long process for many years (5-7
years) and high costs (50-100 million USD) .This is a challenge for researchers
to generate strategies and efforts effective and economical for new drug
discovery , One strategy that has been developed to design new drug molecules
are computational chemistry.
Beginning of Computational Chemistry
The development of computational chemistry very
rapidly began in the 1950s. Some concepts of chemistry, especially on the
molecular scale can be studied using molecular model (Leach, 1996). One advantage
of this is the use of a computer with the programming language so that the
properties of complex molecules can be calculated, and the results
perhitunganya provide significant correlation to the experimental data.
DEVELOPMENT
OF COMPUTATION CHEMISTRY
The development of computer experiments to
substantially alter the traditional relationship between theory and experiment.
Simulation requires an accurate method to model the system under study.
Simulations can often be done with conditions very similar to the experiments
so that the results of computational chemistry calculations can be compared
directly with experiment, if this is the case, then the simulation is a very
useful tool, not only to understand and interpret experimental data in
microscopic level, but may also examine the part that can not be reached
experimentally, as a reaction to the conditions of very high pressure gas or a
reaction involving dangerous.
Chemical research by means of a computer in the
1950s began with an assessment of the chemical structure of the compound with
physiological activity. One chemist who made a large contribution in this field
is John Pople who successfully convert theories in physics and mathematics to
chemistry through computer programs. Computational chemistry methods allow
chemists determined the structure and properties of a chemical system quickly.
Field greatly helped by developing computational chemistry is a field of
crystallography.
Two researchers in the field of computational
chemistry have won Nobel science in 1998 that Walter Kohn with Density
Functional Theory (Density Functional Theory, DFT) and John A. Pople who had
been instrumental in developing computational methods in quantum chemistry,
they have members opportunities chemists studying the molecular properties and
interactions between molecules. John Pople has been developing quantum
chemistry as a method that can be used by almost all fields of chemistry and
chemical bring into a new era that experiment and theory can work together in
exploring the properties of molecular systems. One of the products of chemical
computing program produced by Pople is GAUSSIAN.
In recent years this can be seen in the increase in
the number of people who work in theoretical chemistry, most researchers are
working part-time theorist yes that those already working in the field of
chemistry in addition to the chemical theory. The increase in the number of
researchers in the field of theoretical chemistry is supported by the
development of computers and software capabilities are increasingly easy to
use, it caused a lot of people who do a job in the field of computational
chemistry, even without having enough knowledge about how chemical calculations
were carried out by computer, as a result , many people do not know even the
very basic explanation of how the calculations once executed so that the
resulting work can be the result which actually means or just a
"rubbish".
Needs
Facilities
Support facilities determines the quality of work.
Minimal need for chemical komputaasi actually affordable. A computer with
standard specifications and primarily uses minimal operating system Windows 9X.
A minimum of a Pentium processor with 16 MB RAM and an empty capacity of
approximately 700 MB hard disk - 1500 MB for software installation (depending
on the need) The ability of computer graphics higher the better. Only color
printers needed to print and make laporan.Kebutuhan important is the
application (software). Applications that are used for visualization of molecular
structures can be both commercial and freeware (free) or shareware (free for
the time being or for free for a limited version of the software).
Role
of Computational Chemistry in the field of Molecular Drug Design
Method of in vitro and in vivo commonly used in the
drug discovery process. Computers offers a method of in silico, -a method that
uses computer capability in the design drug- as the complement of in vitro and
in vivo.
Computing power increases exponentially is an
opportunity to develop simulations and calculations in designing new drugs.
Computational chemistry software that can be used is
as HyperChem (www.hypercub.com) provide adequate facilities to "see"
the shape of molecules', enjoy vibration bonding between atoms that is recorded
as infrared spectra, and the dynamics of changes in the molecular structure due
to the influence of the reaction system.
Drug design is an iterative process begins with a
determination of compounds that show important biological properties and ends
with optimization measures, both of profile activity and synthesis of chemical
compounds.
Without complete knowledge of the biochemical
processes responsible for biological activity, drug design hypothesis is
generally based on testing of structural similarity and distinction between
active and inactive molecules.
The existence of a computer equipped with
computational chemistry applications, enabling computational medicinal chemists
describe drug compounds in three dimensions (3D) and do a comparison on the
basis of similarity and energy with other compounds already known to have high
activity (pharmacophore query).
Various derivatives and analogues can be
"synthesized" in silico or are often given a hypothetical compound
term
Molecular
Modeling
Some applications in computational chemistry are
molecular modeling. Some use include: molecular graphics: describe a molecule,
giving a description of its characteristics; molecular visualizations:
visiualisasi form; computational chemistry: computational chemistry;
computational quantum chemistry: quantum chemistry theory; theoretical
chemistry: theoretical chemistry aspect.
Data
on Molecular Modeling
Molecular Modeling is usually initiated
through three main methods:
1. Building using standard geometries - particularly
primary bond lengths and angles,
2. Build the molecule using the known fragments
logically geometriesnya aspect - this is usually corrected by some method of
"optimization"; and
3. Using molecular builds physical data obtained
from experiments - usually X-ray crystallography, neutron diffraction, the
structure deduced from the data of nuclear magnetic resonance (NMR).
Methods
In Computational Chemistry
The term computational chemistry is always used if a
mathematical method is intended to be run automatically by komputer.Perlu noted
that the word "exact" and "perfect" does not appear in the
definition of computational chemistry. Very few aspects of chemistry that can
be solved exactly. Almost every aspect of chemistry described in qualitative or
kuantitatif.Terdapat three categories in computational chemistry methods:
Method ab initio Quantum Mechanics, Quantum Mechanics and Molecular Mechanics
semiempirical.
Ab
initio method Quantum Mechanics
There are several sets base choice in this program.
The set of standard base used, among others, STO-3G, 3-21G, 6-31G * and 6-31G
**.
Extra base functions (s, p, d, sp, spd) can be added
to individual atoms or group of atoms.
Users can also define their own base set or modify
existing base set using HyperChem's documented basis set file format.
Quantum
Mechanics semiempirical
• Hyperchem offers ten methods semiempirical
molecular orbital, with the option of organic compounds and compounds of the
major groups, for the compounds of the transition and for the simulation of
spectra.
• Methods provided are Extended Huckel (by
Hoffmann), CNDO and INDO (by Pople et al), MINDO3, MNDO, MNDO / d and AM1 (by
Dewar et al) PM3 (by Stewart), ZINDO / 1 and ZINDO / S (by Zerner et al).
Molecular
Mechanics
HyperChem is an application that can be used
easily in generating 3D molecular structure, with a choice of four methods of
molecular mechanics, geometry optimization techniques to obtain a stable
molecular structure and molecular dynamics techniques to get search and
investigate conformational changes in the structure.
Four force field method (force field) allows us to
explore the stability and dynamics of molecular systems for compounds that have
an iron atom mass besar.Untuk general-purpose use MM +, while for biomolecules
can be used one of the three methods of force fields: AMBER, BIO + and OPLS
MM +
According
to the majority of non-biological species.
• Based on the MM2 (1977) compiled by the NL
Allinger.
• Using the parameters set in 1991.
• There will be a default parameter in the case of
MM2 parameter is not available
AMBER
• AMBER force field force field composed by Kollman
• Suitable for use on polypeptides and nucleic acids
with all hydrogen atoms were included in the calculation
OPLS
• Designed for the calculation of nucleic acids and
peptides
• OPLS prepared by Jorgensen
• Parameter not bonded optimized interaction of
calculations with solvent included.
BIO +
• CHARMM force field composed by Karplus
• Devoted to the calculation of macromolecules
• Compiled Primarily designed to explore
macromolecules
• Includes CHARMM parameters for the calculation of
amino acids.
Reference:
1. Cramer, C.
J., 2004, Essentials of Computational Chemistry, Theories and Models, John
Wiley & Sons Ltd
2. Frisch M.
J., Trucks G. W., Schlegel H. B., Scuseria G. E., Robb M. A. et al., 1995,
Gaussian98 (Revision A.1), Gaussian, Inc., Pittsburgh PA
3. Leach, A.
R., 2001, Molecular Modelling, Principles and Applications, Pearson Education
Ltd., Essex
4. Rogers, D.
W., 2003, Computational Chemistry Using the PC, John Wiley & Sons, Inc.
5. Young, D.
C., 2001, Computational Chemistry, A Practical Guide for Applying Techniques to
Real Worlds Problems, Wiley-Interscience, New York
6. Website : .http://www.molecules.org/.
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