Computational chemistry is a branch of chemistry that uses computer simulation to assist in solving chemical problems. It uses methods of theoretical chemistry, incorporated into computer programs, to calculate the structures and properties of molecules, groups of molecules, and solids. It is essential because, apart from relatively recent results concerning the hydrogen molecular ion, the quantum many-body problem cannot be solved analytically, much less in closed form. While computational results normally complement the information obtained by chemical experiments, it can in some cases predict hitherto unobserved chemical phenomena. It is widely used in the design of new drugs and materials.
Quantum chemistry, also called molecular quantum mechanics, is a branch of physical chemistry focused on the application of quantum mechanics to chemical systems, particularly towards the quantum-mechanical calculation of electronic contributions to physical and chemical properties of molecules, materials, and solutions at the atomic level. These calculations include systematically applied approximations intended to make calculations computationally feasible while still capturing as much information about important contributions to the computed wave functions as well as to observable properties such as structures, spectra, and thermodynamic properties. Quantum chemistry is also concerned with the computation of quantum effects on molecular dynamics and chemical kinetics.
Theoretical chemistry is the branch of chemistry which develops theoretical generalizations that are part of the theoretical arsenal of modern chemistry: for example, the concepts of chemical bonding, chemical reaction, valence, the surface of potential energy, molecular orbitals, orbital interactions, and molecule activation.
In quantum chemistry and molecular physics, the Born–Oppenheimer (BO) approximation is the best-known mathematical approximation in molecular dynamics. Specifically, it is the assumption that the wave functions of atomic nuclei and electrons in a molecule can be treated separately, based on the fact that the nuclei are much heavier than the electrons. Due to the larger relative mass of a nucleus compared to an electron, the coordinates of the nuclei in a system are approximated as fixed, while the coordinates of the electrons are dynamic. The approach is named after Max Born and J. Robert Oppenheimer who proposed it in 1927, in the early period of quantum mechanics.
In physics, electronic structure is the state of motion of electrons in an electrostatic field created by stationary nuclei. The term encompasses both the wave functions of the electrons and the energies associated with them. Electronic structure is obtained by solving quantum mechanical equations for the aforementioned clamped-nuclei problem.
In classical and quantum mechanics, geometric phase is a phase difference acquired over the course of a cycle, when a system is subjected to cyclic adiabatic processes, which results from the geometrical properties of the parameter space of the Hamiltonian. The phenomenon was independently discovered by S. Pancharatnam (1956), in classical optics and by H. C. Longuet-Higgins (1958) in molecular physics; it was generalized by Sir Michael Berry in (1984). It is also known as the Pancharatnam–Berry phase, Pancharatnam phase, or Berry phase. It can be seen in the conical intersection of potential energy surfaces and in the Aharonov–Bohm effect. Geometric phase around the conical intersection involving the ground electronic state of the C6H3F3+ molecular ion is discussed on pages 385–386 of the textbook by Bunker and Jensen. In the case of the Aharonov–Bohm effect, the adiabatic parameter is the magnetic field enclosed by two interference paths, and it is cyclic in the sense that these two paths form a loop. In the case of the conical intersection, the adiabatic parameters are the molecular coordinates. Apart from quantum mechanics, it arises in a variety of other wave systems, such as classical optics. As a rule of thumb, it can occur whenever there are at least two parameters characterizing a wave in the vicinity of some sort of singularity or hole in the topology; two parameters are required because either the set of nonsingular states will not be simply connected, or there will be nonzero holonomy.
In chemistry, molecular orbital theory is a method for describing the electronic structure of molecules using quantum mechanics. It was proposed early in the 20th century.
The adiabatic theorem is a concept in quantum mechanics. Its original form, due to Max Born and Vladimir Fock (1928), was stated as follows:
Vibronic coupling in a molecule involves the interaction between electronic and nuclear vibrational motion. The term "vibronic" originates from the combination of the terms "vibrational" and "electronic", denoting the idea that in a molecule, vibrational and electronic interactions are interrelated and influence each other. The magnitude of vibronic coupling reflects the degree of such interrelation.
In quantum physics and quantum chemistry, an avoided crossing is the phenomenon where two eigenvalues of a Hermitian matrix representing a quantum observable and depending on N continuous real parameters cannot become equal in value ("cross") except on a manifold of N-2 dimensions. The phenomenon is also known as the von Neumann–Wigner theorem. In the case of a diatomic molecule, this means that the eigenvalues cannot cross at all. In the case of a triatomic molecule, this means that the eigenvalues can coincide only at a single point.
One of the guiding principles in modern chemical dynamics and spectroscopy is that the motion of the nuclei in a molecule is slow compared to that of its electrons. This is justified by the large disparity between the mass of an electron, and the typical mass of a nucleus and leads to the Born–Oppenheimer approximation and the idea that the structure and dynamics of a chemical species are largely determined by nuclear motion on potential energy surfaces. The potential energy surfaces are obtained within the adiabatic or Born–Oppenheimer approximation. This corresponds to a representation of the molecular wave function where the variables corresponding to the molecular geometry and the electronic degrees of freedom are separated. The non separable terms are due to the nuclear kinetic energy terms in the molecular Hamiltonian and are said to couple the potential energy surfaces. In the neighbourhood of an avoided crossing or conical intersection, these terms cannot be neglected. One therefore usually performs one unitary transformation from the adiabatic representation to the so-called diabatic representation in which the nuclear kinetic energy operator is diagonal. In this representation, the coupling is due to the electronic energy and is a scalar quantity that is significantly easier to estimate numerically.
In quantum chemistry, a conical intersection of two or more potential energy surfaces is the set of molecular geometry points where the potential energy surfaces are degenerate (intersect) and the non-adiabatic couplings between these states are non-vanishing. In the vicinity of conical intersections, the Born–Oppenheimer approximation breaks down and the coupling between electronic and nuclear motion becomes important, allowing non-adiabatic processes to take place. The location and characterization of conical intersections are therefore essential to the understanding of a wide range of important phenomena governed by non-adiabatic events, such as photoisomerization, photosynthesis, vision and the photostability of DNA. The conical intersection involving the ground electronic state potential energy surface of the C6H3F3+ molecular ion is discussed in connection with the Jahn–Teller effect in Section 13.4.2 on pages 380-388 of the textbook by Bunker and Jensen.
The Born–Huang approximation is an approximation closely related to the Born–Oppenheimer approximation. It takes into account diagonal nonadiabatic effects in the electronic Hamiltonian better than the Born–Oppenheimer approximation. Despite the addition of correction terms, the electronic states remain uncoupled under the Born–Huang approximation, making it an adiabatic approximation.
Car–Parrinello molecular dynamics or CPMD refers to either a method used in molecular dynamics or the computational chemistry software package used to implement this method.
In atomic, molecular, and optical physics and quantum chemistry, the molecular Hamiltonian is the Hamiltonian operator representing the energy of the electrons and nuclei in a molecule. This operator and the associated Schrödinger equation play a central role in computational chemistry and physics for computing properties of molecules and aggregates of molecules, such as thermal conductivity, specific heat, electrical conductivity, optical, and magnetic properties, and reactivity.
William Hughes Miller is a professor at the University of California, Berkeley and a leading researcher in the field of theoretical chemistry.
CP2K is a freely available (GPL) quantum chemistry and solid state physics program package, written in Fortran 2008, to perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. It provides a general framework for different methods: density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW) via LDA, GGA, MP2, or RPA levels of theory, classical pair and many-body potentials, semi-empirical and tight-binding Hamiltonians, as well as Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid schemes relying on the Gaussian Expansion of the Electrostatic Potential (GEEP). The Gaussian and Augmented Plane Waves method (GAPW) as an extension of the GPW method allows for all-electron calculations. CP2K can do simulations of molecular dynamics, metadynamics, Monte Carlo, Ehrenfest dynamics, vibrational analysis, core level spectroscopy, energy minimization, and transition state optimization using NEB or dimer method.
Sourav Pal is an Indian theoretical chemist, a professor of chemistry at IIT Bombay, and the director of the Indian Institute of Science Education and Research, Kolkata. He was a director of the CSIR-National Chemical Laboratory in Pune and an adjunct professor at the Indian Institute of Science Education and Research, Pune.
Surface hopping is a mixed quantum-classical technique that incorporates quantum mechanical effects into molecular dynamics simulations. Traditional molecular dynamics assume the Born-Oppenheimer approximation, where the lighter electrons adjust instantaneously to the motion of the nuclei. Though the Born-Oppenheimer approximation is applicable to a wide range of problems, there are several applications, such as photoexcited dynamics, electron transfer, and surface chemistry where this approximation falls apart. Surface hopping partially incorporates the non-adiabatic effects by including excited adiabatic surfaces in the calculations, and allowing for 'hops' between these surfaces, subject to certain criteria.
Evgeny E. Nikitin is a Russian theoretical chemist and emeritus professor at the Technion in Haifa, Israel.
