Computational Chemistry

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The use of computer simulation to model and predict the behavior of chemical systems.

Molecular Mechanics: Computational method used in studying the physical properties of molecules and how they interact.

Quantum Mechanics: Study of atoms and molecules on the quantum level.

Density Functional Theory: Method for calculating the electronic structure of atoms, molecules, and materials.

Molecular Dynamics: Simulation of the motion and behavior of molecules over time.

Monte Carlo Methods: Statistical method for simulating probability distributions.

Ab Initio Calculations: Calculations based on fundamental principles and constants, without empirical data.

Molecular Docking: Process of predicting the binding of a small molecule to a target protein or nucleic acid.

Statistical Mechanics: Branch of physics that studies the behavior of large numbers of particles, including molecules.

Force Fields: Mathematical function used to describe the potential energy of a system.

Chemical Kinetics: Study of the rates of chemical reactions.

What is computational chemistry and how does it assist in solving chemical problems?

"Computational chemistry is a branch of chemistry that uses computer simulation to assist in solving chemical problems."

What methods are used in computational chemistry to calculate the structures and properties of molecules, groups of molecules, and solids?

"It uses methods of theoretical chemistry, incorporated into computer programs, to calculate the structures and properties of molecules, groups of molecules, and solids."

What are some examples of properties that can be calculated through computational chemistry?

"Examples of such properties are structure (i.e., the expected positions of the constituent atoms), absolute and relative (interaction) energies, electronic charge density distributions, dipoles and higher multipole moments, vibrational frequencies, reactivity, or other spectroscopic quantities."

How do computational chemistry results complement information obtained through chemical experiments?

"While computational results normally complement the information obtained by chemical experiments, it can in some cases predict hitherto unobserved chemical phenomena."

How is computational chemistry used in the design of new drugs and materials?

"It is widely used in the design of new drugs and materials."

What factors affect the computational resources required for a study in computational chemistry?

"The computer time and other resources (such as memory and disk space) increase quickly with the size of the system being studied."

What do ab initio methods in computational chemistry rely on?

"Ab initio methods are based entirely on quantum mechanics and basic physical constants."

What are some differences between ab initio and semi-empirical approaches in computational chemistry?

"Both ab initio and semi-empirical approaches involve approximations. These range from simplified forms of the first-principles equations that are easier or faster to solve, to approximations limiting the size of the system, to fundamental approximations to the underlying equations that are required to achieve any solution to them at all."

What is the Born-Oppenheimer approximation, and how is it used in ab initio calculations?

"For example, most ab initio calculations make the Born–Oppenheimer approximation, which greatly simplifies the underlying Schrödinger equation by assuming that the nuclei remain in place during the calculation."

What is the goal of computational chemistry?

"The goal of computational chemistry is to minimize this residual error while keeping the calculations tractable."

In what cases are classical approximations used instead of electronic calculations in computational chemistry?

"In some cases, the details of electronic structure are less important than the long-time phase space behavior of molecules. This is the case in conformational studies of proteins and protein-ligand binding thermodynamics."

What methods are used in cheminformatics, a field related to computational chemistry?

"Furthermore, cheminformatics uses even more empirical (and computationally cheaper) methods like machine learning based on physicochemical properties."

What is a typical problem in cheminformatics?

"One typical problem in cheminformatics is to predict the binding affinity of drug molecules to a given target."

What are some other problems that cheminformatics can tackle?

"Other problems include predicting binding specificity, off-target effects, toxicity, and pharmacokinetic properties."

Can the quantum many-body problem be solved analytically?

"Apart from relatively recent results concerning the hydrogen molecular ion, the quantum many-body problem cannot be solved analytically, much less in closed form."

How quickly does the computational resources required increase with the size of the system being studied?

"The computer time and other resources (such as memory and disk space) increase quickly with the size of the system being studied."

What approximation is commonly used in ab initio calculations?

"Most ab initio calculations make the Born–Oppenheimer approximation."

What types of properties can be calculated using computational chemistry methods?

"Examples of such properties are structure, absolute and relative (interaction) energies, electronic charge density distributions, dipoles and higher multipole moments, vibrational frequencies, reactivity, or other spectroscopic quantities."

What is the main difference between ab initio and semi-empirical methods in computational chemistry?

"Both ab initio and semi-empirical approaches involve approximations, but ab initio methods are based entirely on quantum mechanics and basic physical constants."

What is the purpose of using classical approximations in conformational studies of proteins and protein-ligand binding thermodynamics?

"The purpose is to enable longer simulations of molecular dynamics, as these classical approximations are computationally less intensive than electronic calculations."