Understanding Computational Chemistry in Research

Computational chemistry is a branch of chemistry that uses the results of theoretical chemistry on translated into a computer program to calculate the properties of molecules and their changes as well as perform simulations on large systems (macromolecules such as proteins or molecules many systems such as gas, liquid, solid, and liquid crystal) , and implement the program on a real chemical systems. Examples of properties of molecules are counted among other structures (ie the location of its constituent atoms), energy and energy difference, charge, dipole moment, reactivity, vibration frequency and magnitude of other spectroscopy. Simulation of macromolecules (such as proteins and nucleic acids) and large systems could include a review of the molecular conformation and amendments (ie. The process of protein denaturation), phase change, as well as forecasting macroscopic properties (such as specific heat) based on the behavior of atomic and molecular level. Computational chemistry term is sometimes used also to areas of overlap-tindah between computer science and chemistry.

The term theoretical chemistry may be defined as a mathematical description of chemistry, whereas computational chemistry is usually used when a mathematical method developed well enough to be used in a computer program. It should be noted that the word "right" or "perfect" does not appear here, as very few aspects of chemistry that can be calculated accurately. Almost all aspects of chemistry can be described in qualitative or quantitative computational scheme approximations.

Molecules consist of nuclei and electrons, so that the necessary methods of quantum mechanics. Computational chemists often attempt to solve the non-relativistic Schrödinger equation, with the addition of relativistic corrections, although some progress has been made to solve the fully relativistic Schrödinger equation. In principle, Schrödinger equation may be resolved, either in the form of time-dependent or non-dependent-time, adapted to the problem studied, but in practice it is not possible except for very small systems. Therefore, a large number of approximation methods developed to achieve the best compromise between accuracy and computational cost calculation.

In theoretical chemistry, chemists and physicists together develop algorithms and computer programs to allow forecasting the properties of atoms and molecules, and / or reaction trajectories for chemical reactions, as well as the simulation of macroscopic systems. Computational chemists mostly "just" using the computer program and existing methodologies and apply them to specific chemical problems. Among most of the time is used for this, computational chemists can also be involved in the development of new algorithms, as well as the selection of the appropriate chemical theory, in order to obtain the most computationally efficient and accurate.

There are several approaches that can be done:

• The computational studies can be performed to find a starting point for the synthesis in the laboratory.
• The computational studies can be used to explore the reaction mechanism and explain the observations on the reactions in the laboratory.
• The computational studies can be used to understand the nature and changes in macroscopic systems through simulations based on the laws of interaction that exist in the system.

There are several key areas in these topics, among others:

• Presentation of atomic and molecular computing
• The approach in the storage and retrieval of chemical species (chemical data Basis)
• The approach in determining the patterns and relationships between chemical structure and its properties (QSPR, QSAR).
• Structure elucidation theoretically based on the simulation of styles
• Computational approaches to assist the efficient synthesis of compound
• Computational approaches to design molecules that interact in ways that specifically, especially in drug design.
• Simulation of the phase transition process
• Simulation of the properties of materials such as polymers, metals, and crystals (including liquid crystal).
• Programs used in computational chemistry are based on quantum-chemical methods that solve the Schrödinger equation for molecules, as well as the approach of classical physics (molecular mechanics) for the simulation of large systems. Quantum-chemical method that does not include the parameters of empirical and semi-empirical equation called ab-initio methods. The types of ab-initio methods which are popular are: Hartree-Fock, Møller-Plesset interference theory, configuration interaction, coupled cluster, the reduced density matrices, and density functional theory.

The term in Computational Chemistry:

Density functional theory (DFT, Density functional theory) is one of several popular approaches to the calculation of the electron structure of many-particle quantum mechanics to molecular systems and meeting materials. The density function theory (DFT) is a theory of quantum mechanics used in chemical fisikadan to observe the ground state of the system of many particles.

Hartree-Fock method is a repetition of the self-consistent procedure for calculating the "best possible" solution sole determinant terhadappersamaan not time-dependent Schrödinger of many electron systems in the fixed core Coulomb potential

Roothaan equation is often used in the numerical calculations to approximate the value obtained from the calculation using the Hartree-Fock equation. This equation is composed of the base set are not orthogonal to each other, such as in the Gaussian functions or Slater. This equation applies only to a closed system in which all of the electrons in the orbital has a pair.

Molecule is defined as a group of atoms (at least two) are linked to each other with a very strong (covalent) in a specific arrangement and electrically neutral, and is quite stable. [1] [2] According to this definition, different molecules polyatomic ions. In organic chemistry and biochemistry, the term molecule is used less rigid, so that the charged organic molecules and biomolecules also be deemed to include molecules.

Atom is a basic unit of matter, which consists of nuclei and negatively charged awanelektron that surrounds it. Atomic nucleus consists of positively charged protons and electrically neutral neutrons (except in the core atomHidrogen-1, which has no neutrons). The electrons in an atom bound to the atomic nucleus by the electromagnetic force.

Parallel computing is a computing technique simultaneously by utilizing multiple independent computers simultaneously. It is generally required when the required capacity is very large, either because they have to process large amounts of data (in the financial industry, bioinformatics, etc.) or because of the demands of the computing process that much.

Hückel is a simple method and estimates for semi-empirical quantum mechanics calculations. The method used in the expanded Huckel HyperChem only useful for the calculation of a single piece, not for geometry optimization or molecular dynamics calculations. Extended Huckel calculations produce a qualitative description or semi-quantitative molecular orbital and electronic properties (eg, cost and distribution of clean atomic spin).

· CNDO is the simplest of methods SCF for a semi-empirical quantum mechanics calculations. It is useful to calculate the electronic ground state properties of open systems and closed-shell, optimization of geometry, and the total energy. HyperChem using CNDO / 2.

· INDO an SCF method for semi-empirical quantum mechanics calculations. It improves on the CNDO by accounting must be the center of repulsion between electrons on the same atom. Useful to calculate the ground-state electronic properties of open systems and closed-shell, optimization of geometry, and the total energy.

· Mindo / 3 is the SCF method for semi-empirical quantum mechanics calculations. INDO extension, Mindo / 3 using parameters suitable for the experiment, not an accurate calculation. Useful for large organic molecules, cations, and compound polynitro. Calculating electronic properties, geometry optimization and total energy.

· MNDO SCF is a method for semi-empirical quantum mechanics calculations. Useful for a variety of organic molecules containing elements of long lines 1 and 2 of the periodic table, but not a transition metal. Eliminate some errors in MNDO / 3. Calculate the electronic properties, the geometry is optimized, total energy, and the heat of formation

· AMI is a semi-empirical SCF method for chemical calculations. Improvement of MNDO method. Useful for molecules that contain elements of long lines 1 and 2 of the periodic table, but not a transition metal. Together with PM3, AM1 semi-empirical method is generally the most accurate included in HyperChem. Calculate the electronic properties, the geometry is optimized, total energy, and the heat of formation.

· PM3 is a semi-empirical SCF method for chemical calculations. PM3 is reparametrization of AM1 method. PM3 and AM1 generally the most accurate method in HyperChem. PM3 has parameters for many of the main group elements and some transition metals.

· ZINDO / 1 is a modified version of the Base INDO / 1 and can be used ZINDO / 1 to calculate the energy states in transition metal-containing molecules.

ZINDO / S is a INDO method parameters to reproduce the visible UV spectroscopy of transition when used by itself-excited configuration interaction (CI) methods.Use ZINDO / 1 than ZINDO / S for geometry optimization and comparison of total energy.

Semi-empirical quantum chemical calculations is the kind of mechanics that use parameters derived from experiments to simplify the calculation process.

Molecular modeling is a method for designing and analyzing the structure and properties of the specific molecule by using techniques of computational chemistry and graphical visualization technique that aims to provide three-dimensional geometric structures in accordance with the conditions specified parameters. (Leach, 2001).

 Molecular docking is a technique used to study the interaction of a complex molecule. Molecular docking to predict the orientation of a molecule to another molecule when it binds to form a stable complex. (Funkhouser, 2007).

 Molecular Operating Environment (MOE) developed Chemical Computing Group (www.chemcomp.com). MOE addition to offering complete facilities are also user-friendly so suitable for use in learning. Only computational chemistry applications are user-friendly so that is usually expensive cost efficiency reasons no longer relevant.

OV (Orbital Viewer) is a free software to describe atomic and molecular orbitals, create animations and to see cross section (in the structure) orbital. 3D images can also be made (which can be viewed with 3D glasses as He used to see 3D soap opera). (Module structure and reactivity of Inorganic Chemistry, Dr. Ismunandar)

Ab initio derived from the Latin that was given to mark calculation derived directly from theoretical principles, without entering the experimental data. Ab initio quantum mechanics refers to the calculation through some mathematical approaches, such as the use of the simplified equation (Born Oppenheimer approximation) or approaches to the settlement of differential equations. (INTRODUCTION TO CHEMICAL COMPUTATION, Dr. Harno Dwi Pranowo, M.Si)

Quantum chemistry is an application of quantum mechanics to chemistry. Quantum chemistry allows us to understand and predict the structure, properties and reaction mechanisms of various materials. BS (Balls & Sticks) is a free software to describe the chemical structure, especially crystal, in 3D and can produce a bitmap image that can be copied to clipboard and pasted (paste) in a word processing document (Word for example).

Computational Chemistry benefits for Learning, Such us:

1. Can calculate molecular properties of complex calculations and results correlated significantly with the experiment.

2. Can -as well as calculators to help kalkulator- numerically completion of mathematical equations that describe the nature of the system, for example in the completion of a stoichiometric calculations, including the automation of measuring devices that can convert electronic signals into numerical data.

3. Can a visualization and animation tools;

4. Help us to explore the nature of the compound and in general the program has been equipped with visualization and animation, such as the program HyperChem, Gaussian, Turbomol, RasMol etc.

5. Calculate the properties of molecules and their changes as well as carry out simulation of large systems (macromolecules such as proteins or molecules many systems such as gas, liquid, solid, and liquid crystals), and implementing the program in real chemical systems.

6. Simulation of the macromolecules (such as proteins and nucleic acids) and large systems could include a review of the molecular conformation and amendments (ie. The process denatrasi protein), phase change, as well as forecasting macroscopic properties (such as specific heat) based on behavior at the atomic level.

Benefits of Computational Chemistry to Research, such us:

1. To find a starting point for synthesis in the laboratory

2. To explore the reaction mechanism and explain the completion of the reaction in the laboratory

3. To understand the nature and changes in macroscopic systems through simulations based on the laws of interaction that exist in the system

4. For the determination of orbital interactions boundary (frontier) between the donor and acceptor molecules such as those described in the Diels-Alder cyclization reaction

5. To obtain partial atomic charge using Mulliken population analysis to predict the molecules that are easily attacked by the reagent.

6. To generate electrostatic potential maps to illustrate the trajectory in the application process of docking between drugs and receptors.

7. To calculate the density of unpaired spin to identify the reactive side of the molecule or to compare with the data ESR

8. For quantum chemical calculations can predict the intensity and the wavelength of the electronic transitions and can also predict the location of non-active state sepktroskopi

9. For quantum chemical calculations to estimate the intensity and wave number of the vibration absorption lines and also can describe the motion of a normal mode by using vector and animation.