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Computational Chemistry

Computational chemistry is a natural outgrowth of theoretical chemistry, the traditional role of which involves the creation and discrimination of a penetrating conceptual infrastructure for the chemical sciences, particularly at the atomic and molecular levels.

Theoretical chemistry has also devised to use quantitative algorithms to organize huge number of lab related data, and also to predict the due course and extent of chemical phenomena for possibilities considered as difficult or even impossible to observe directly. Hence, today it is very unlikely to classify many lines of research as just "theoretical" or "computational".

The present article tends toward the term theoretical or computational and any kind of distinction between the two areas is found to be rather misleading because the subject demands both quantitative characterization and conceptual understanding.

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Computational Chemistry Definition

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This is a branch of chemistry which is based on the principles of computer science. In this, the theoretical chemistry’s products are used which are converted into computational program for calculating the molecular properties and changes such as structure of molecules, energy, dipole moment, electronic charge, wave frequency and spectroscopy measurements etc. And also for performing simulation to macromolecules system such as proteins, or system of large number of molecules like gases, liquid and liquid crystal. It is also used in making new drugs and materials.

Computational Chemistry Methods

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As expectations on the outcomes of applications of current computational chemistry methods are rising, the researchers use such techniques to study larger systems and to anticipate more accurate results.

This is impetus for the development of more efficient methods based on the first-principle multi-level simultaneous appropriate for complex species. The methods are listed below.
  • Ab initio methods

    The programs used in computational chemistry are based on many different quantum-chemical methods that solve the molecular Schrodinger equation associated with the molecular Hamiltonian.

  • Density functional methods

    Density functional theory (DFT) methods are often considered to be ab initio methods used in finding the molecular electronic structure, even though many of the most common functional use parameters derived from empirical data, or from more complex calculations.

  • Semi-empirical and empirical methods

    Semi-empirical quantum chemistry methods are based on the Hartree–Fock formalism, but make many approximations and obtain some parameters from empirical data.

  • Molecular mechanics

    In many cases, large molecular systems can be modeled successfully while avoiding quantum mechanical calculations entirely.
    The molecular mechanic simulations, for example, use a single classical expression for the energy of a compound, for instance the harmonic oscillator.

  • Methods for solids

    Computational chemical methods can be applied to solid state physics problems. The electronic structure of a crystal is in general described by a band structure, which defines the energies of electron orbitals for each point in the Brillouin zone.

  • Chemical dynamics

    Once the electronic and nuclear variables are separated (within the Born–Oppenheimer representation), in the time-dependent approach, the wave packet corresponding to the nuclear degrees of freedom is propagated via the time evolution operator (physics) associated to the time-dependent Schrodinger equation (for the full molecular Hamiltonian).

  • Molecular dynamics

    Molecular dynamics (MD) use either quantum mechanics, Newton's laws of motion or a mixed model to examine the time-dependent behavior of systems, including vibrations or Brownian motion and reactions. The MD combined with density functional theory leads to hybrid models.

Essentials of Computational Chemistry

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Methods used in computational chemistry:
  • Each isomer of a molecule has potential energy surface which is the minimum energy. This minimum energy is produced by total energy of molecule. The total energy is the function of the coordinates of all the nuclei.
  • The lowest local minimum energy is called global minimum energy, most stable isomer.
  • The stationary point is considered as a geometry of the derivative of the energy in respect to all nuclei displacements and is found to be zero.
  • If any particular coordinate change decreases the total energy in both directions then the stationary point becomes a transition structure and the resultant coordinate becomes the reaction coordinate.
  • The process of calculating stationary points is called geometry optimization.
  • The total energy is measured by approximate solutions of the time-dependent Schrodinger equation, by use of the Born-Oppenheimer approximation.
  • The total energy is measured as the sum of the repulsion energy of the nuclei and the electronic energy at fixed nuclei positions.
  • In case of large systems, the relative total energies are compared using molecular mechanics.
There are various ways for determining the total energy to know about molecular structures. These are the essentials of computational chemistry. The description are given below:
  1. Ab initio methods
  2. Density functional methods
  3. Semi-empirical and empirical methods
  4. Molecular mechanics
  5. Methods for solids
  6. Chemical dynamics
  7. Molecular dynamics

Ab initio methods

The programs of computational chemistry are based on many various quantum-chemical methods that solve the Molecular Schrodinger equation and Molecular Hamiltonian. So, the Ab initio methods are the methods which are used without empirical or semi-empirical standards in the equations and theoretical principles are used for their derivations. They are evaluated as approximate Quantum Mechanical Calculations.

The simplest calculation is done with the Hartree-Fock (HF) scheme. This is considered as the extended version of molecular orbital theory in which only the average effect of repulsion electrons or electronic correlation is used for calculation. The limiting value of energy and wave function with increasing basic set size is called the Hartree-Fock limit. These steps are approached to the exact solution of the non-relativistic Schrodinger equation due to their limits. The spin orbit and relativistic terms are also included in these methods for heavy atoms.

Ab initio Methods

Electronic structure methods in terms of energy:
Ab initio methods need to be defined from a particular level of theory and from a basis set.
The Hartree-Fock wave functions are used in bond breaking processes, have single configuration.
The total molecular energy can be taken as function of the molecular geometry.
A series of post Hartree-Fock methods are better known as quantum chemistry composite, used in computational thermo chemistry to calculate the quantities of thermo chemistry.

Density functional methods (DST)

Density functional theory is used for determining the molecular electronic structure. The total energy is calculated in terms of the one-electron density total not as the wave function in density functional methods. Approximate Hamiltonian and an approximation considered for the total electron density and is used for calculations. The accuracy of these methods is very good at small computational cost. In DST, the density functional exchange active with the Hartree-Fock exchange term is combined in some methods, and is better known as hybrid functional methods.

Semi-empirical and empirical methods

They are based on the Hartree-Fock formalism. These are very useful methodolgy in computational chemistry while dealing with large molecule as the full Hartree-Fock method without the approximations is too costly. The empirical parameters with inclusion of correlation effects are also used in some methods. The two-electron part of the Hamiltonian is not included in the empirical methods of semi-empirical methods. Erich H$\ddot{u}$ckel's proposed H$\ddot{u}$ckel method and the extended H$\ddot{u}$ckel method proposed by Roald Hoffman are given for $\Pi$-electron systems and for all of valence electron systems respectively.

Molecular mechanics

Molecular mechanics simulations for example single classical expression for the energy of a compound and harmonic oscillator in which all constants of the equations should be obtained from the experimental data. The force field, the set of parameters and functions, is very important in molecular mechanics calculations. These methods can be used especially for proteins and biological molecules.

Methods for solids

The problems of solid state physics can be resolved with the use of Computational chemical methods. Like orbital energies which is used in band structure calculations, can be calculated by ab initio and semi-empirical calculations.

Chemical dynamics

The most popular methods for calculating the wave packet related to the molecular geometry are: the split operator technique, the chebyshev polynomial, the hartree method (MCTDH) (Multi configurated time dependent) and the semi classical method.

Molecular dynamics

The quantum mechanics, Newton's laws of motion or vibrations or Brownian motion and reactions are used in MD. These methods are combined with density functional theory.

Computational Quantum Chemistry

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The computational quantum chemistry is based on quantum mechanics. The theory of computational quantum chemistry is based on the fact that nuclei of a molecule have various configurations in a particular electronic state. Each configuration has a particular potential energy of the system. So, potential energy surface is a map of the potential energy against nuclear configuration by which the molecular structure, energetic and dynamics are evaluated.

The potential energy surfaces of a molecule can be constructed by the formalism of quantum mechanics. The formalism of quantum mechanics can be used to get the information about the structure and properties of the molecules. No real substance is involved in the process of determining molecular structure and properties.

Molecular Hierarchy

The semantic conception of theory is used to examine the philosophical significance of computational quantum chemistry. There are some important analysis to understand the semantic conception of theory and computational quantum chemistry which are given below:
  1. Intended scope of the theory : It's the class of all mechanical phenomena of interacting bodies.
  2. Physical system : Physical system is the system which describes the behavior of abstract system. So, the description of the physical systems in the theory, gives a counter factual characterization of the actual phenomena.
  3. Theory-induced physical system : For the correctness of the theory, the class of theory-induced physical system and the class of causally possible physical system should be identical.
  4. Predicting phenomena : As only the class of theory-induced physical system is directly evaluated in theories but they can also be used to predict phenomena. By applying semantic analysis of computational quantum chemistry, the quantum mechanics gives the reliable result.

Computational Chemistry List (CCL)

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It is an independent electronic forum for chemistry researchers and educators from around the world; it was established on January 11, 1991. More than 3000 members in more than 50 countries are reading CCL messages regularly and discuss the matter of computational chemistry. This chemistry list is widely used by many chemistry communities and also organized by many resources on computational chemistry.

Computational Chemistry Applications

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The UNICORE software provides general framework for running user application. This includes input preparation, job submission and control and finally post processing of the results. Advanced visualization and access to the databases and other distributed sources of information should also be considered here. The wide functionality and especially flexibility obtained with plugin concept makes UNICORE good candidate for general framework for access to the various not only computational resources.

As computational chemistry has become easier to use, professional computational chemists have shifted their attention to more difficult modeling problems. No matter how easy computational chemistry becomes, there will always be problems so difficult that only an expert in the field can tackle them. The well developed mathematical methods which can directly implemented on computer are used in computational chemistry.

A Computational chemist can easily apply existing computer programs and methodologies to specific chemical questions.

Computational chemistry is used in various fields. Some of the applications are given below:

  1. They are used to find a starting point for a laboratory synthesis, for understanding experimental data like spectroscopic graphs and peaks, etc.
  2. These studies are used to know the structure of completely unknown molecule whose studies are not possible only by experimental means and to find the new chemical objects.
  3. The molecular structure can be evaluated by the use of the simulation of forces, quantum chemical methods.
  4. The computational chemistry methods are used to find stationary points on the energy surface.
  5. The chemical data bases are used to Store and search the data for chemical entities.
  6. This is used to identify the reactions between chemical structures and properties
  7. Computational methods help for synthesis of compounds.
  8. Computational approaches are used to design molecules especially in drug design and catalysis.

Computational organic chemistry-Computational organic chemistry is the branch of theoretical chemistry in which the mathematical models are developed and used to calculate the molecular structure of organic molecule. Algorithms are also used to get the right path of organic reaction in this chemistry. This is useful tool in organic chemistry laboratory because of development and easy use of computer software.

The different methods of computational chemistry have many applications in various fields. For example- to store and search chemical data, to identify and find correlations between chemical structures and properties, theoretical measurement of molecular structures and electronic properties, design of molecules that interact with other molecules.

Two kinds of studies are done in Computational organic chemistry.
  • Computational studies for laboratory experiments and
  • Computational studies for exploring reaction mechanisms and observations of experiments.

The computational organic chemistry methods are especially used for chemical related problems which are based on the approaches used to describe atoms and electrons in the molecules under investigation. The classical physics like molecular mechanics and molecular dynamics is used to describe the properties of large molecules.

But the investigation of chemical problems which depend on the electronic properties of a molecule like reactivity (which involve bond formation and cleavage) is not possible with classical physics methods. The quanta chemical methods (like Hartree-Fock and post Hartree-Fock methods) are used for that. The investigation of the reactivity of molecules contain many electrons and can be tractable only using semi empirical methods or from methods based on the density functional theory.
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