What is Computational chemistry: Definition and 26 Discussions

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 efficient computer programs, to calculate the structures and properties of molecules and solids. It is necessary because, apart from relatively recent results concerning the hydrogen molecular ion (dihydrogen cation, see references therein for more details), 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.
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, and cross sections for collision with other particles.
The methods used cover both static and dynamic situations. In all cases, the computer time and other resources (such as memory and disk space) increase rapidly with the size of the system being studied. That system can be one molecule, a group of molecules, or a solid. Computational chemistry methods range from very approximate to highly accurate; the latter are usually feasible for small systems only. Ab initio methods are based entirely on quantum mechanics and basic physical constants. Other methods are called empirical or semi-empirical because they use additional empirical parameters.
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 (for example, periodic boundary conditions), to fundamental approximations to the underlying equations that are required to achieve any solution to them at all. 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. In principle, ab initio methods eventually converge to the exact solution of the underlying equations as the number of approximations is reduced. In practice, however, it is impossible to eliminate all approximations, and residual error inevitably remains. The goal of computational chemistry is to minimize this residual error while keeping the calculations tractable.
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. Classical approximations to the potential energy surface are used, typically with molecular mechanics force fields, as they are computationally less intensive than electronic calculations, to enable longer simulations of molecular dynamics. Furthermore, cheminformatics uses even more empirical (and computationally cheaper) methods like machine learning based on physicochemical properties. One typical problem in cheminformatics is to predict the binding affinity of drug molecules to a given target. Other problems include predicting binding specificity, off-target effects, toxicity, and pharmacokinetic properties.

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  1. R

    Phonon Density of States (PDOS) at Gamma Point

    Hello everyone! I'm trying to replicate phonon density of states (PHDOS) diagrams for some solids using Quantum Espresso. The usual way I do it is the following one: scf calculation at minima (pw.x) Calculation of dynamical matrix in reciprocal space with nq=1 or 2 (ph.x) Calculation of...
  2. E

    Finding Help with Computational Chemistry on PF

    How did you find PF?: via Google Hello everyone, I hope you are doing well? Recently, I’ve been trying to calculate the optimization and Uv spectra of organometallic compounds using the Gaussian software .it’s my first time for the computational chemistry and I am inexperienced . When I...
  3. C

    A How are the thermal expansion of a solid and the stress tensor related?

    My idea is this: tensor stress is directly related to the internal pressure of a solid. That is to the force that the neighboring atoms exert each other in relation to a unit of surface. When I heat a solid we can have the phenomenon of thermal expansion: this is connected to the fact that a...
  4. Jorzef

    How can I solve for the x force component in this force expression?

    Hello everyone, I'm stuck doing this problem, I've tackled the partial derivative but i can't figure out the derive for x component part, i solved the partial derivative part, i came to this result: What do can i do from here on, thank you!
  5. J

    Exploring DF vs. RI Approximations

    Hi everybody! I am trying to find the difference between density fitting (DF) and resolution of the Identity (RI) approximations. I have read the following in the article [J. Chem. Phys. 118, 8149 (2003)]: "Density fitting mathematically resembles a resolution of the identity RI in the...
  6. L

    A What is best way to start learning DMRG for Fermions?

    I want to learn the density matrix renormalization group (DMRG) method in traditional formalism (not MPS). While there are many good introductory level articles available for bosonic (and spin) systems, I have not encountered any introductory level article which deals with fermionic systems i.e...
  7. twist.1995

    A Symmetry Considerations in Hartree-Fock-Roothaan Method

    Hello, dear Quantum Chemists or Physicists. I have been extensively researching the restricted closed-shell Hartree-Fock method, and wrote a code that is working for diatomic molecules, like H2 or He2++. I, however, have a few unresolved questions that do not allow me to proceed further in...
  8. Hamza Elkotfi

    A What resources are available for using DFT to study 1D materials in physics?

    hello dear physicists I will work in my thesis on 1D materials using DFT as a numerical method to find the properietes of these 1D materials I would be very happy if someone can help me with references (books, links, articles, vedios ...) that could help me to advance in my work Thank you
  9. H

    How to Calculate Ideal Gas State Properties Using Molecular Dynamics?

    Dear all, I want to calculate thermodynamical properties of my molecule which I am calculating its thermodynamical properties of non-ideal part using Molecular dynamics. I need ideal gas state total energy, Cp, and Cv in several different temperatures. I am using opt+freq at B3lyp/6-311++G(d,p)...
  10. sams

    Inquiring about Computer HW Specifications for Time-Intensive Calculations

    Dear Everyone, We are a research group doing research in computational sciences. We are considering ordering new computers for our research. I was wondering if anyone could advise us regarding the hardware specifications needed to run heavy and time-expensive programs, specifically in...
  11. sams

    Coefficients of Secular Equations

    Dear Everyone, I would like to ask a question regarding the evaluation of the coefficients in Linear Combination of Atomic Orbitals (LCAO). In Molecular Quantum Mechanics book authored by Peter Atkins and Ronald Friedman (Fourth Edition ISBN 0199274983), we are trying to calculate the...
  12. sams

    A Computational Physics: Trivial & Non-Trivial Solutions, LCAO

    Dear Everyone, 1. Could anyone please explain what is meant by trivial and non-trivial solutions? 2. LCAO: Ψ = ∑crΦr Ψ: Molecular orbitals c: coefficients Φ: Atomic orbitals When we talk about basis sets, do we mean here the coefficients or the atomic functions? Thanks a lot...
  13. Mathamans

    Using what I've learned in the classroom for Graphical Data

    I'm a first-year undergraduate student in mathematics and physics. In my Chemistry Lab class we've recently completed a graphical representation of data assignment and it was interesting. My question is, what can I do in regards to mathematics and physics, or something interesting in general...
  14. D

    A How to find vibrational frequency for specific bond? (DFT)

    Hello, I performed an optimization and frequency calculation at the ub3lyp 6-311g level of theory. The compound has the formula C39H41PS2. Using Molden, I am having a hard time identifying the frequency corresponding to the stretching of a phosphorus carbon double bond present in the molecule. I...
  15. D

    A How can I tell Gaussian to read coordinates as Cartesian?

    Hello, I have been I am trying to optimize a molecule (crowded) with the chemical formula C60H52O18P4S4W2. The problem arises after 2 days, which means that the initial geometry was not a problem. " GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization...
  16. D

    A Why does my chosen basis set for W crash (DFT)?

    Hello, I am trying to optimize a molecule with the chemical formula C60H52O18P4S4W2. I have tried using different Basis Sets on my input file but I keep getting the following error: " Standard basis: Aug-CC-pV5Z (5D, 7F) Atomic number out of range in CCPV5Z. Error termination via Lnk1e in...
  17. EuclidPhoton

    Complex Geometric Theories and Molecules

    If QM is a statistical model to approximate something underlying space time we don't quite understand yet, and there is a complex geometry underlying space time, is it possible to find other ways to simplify molecular optimizations and electron interactions in computational chemistry using...
  18. Raazi

    Modeling Hydrophobic Interactions

    Hi, I am trying to design or find a simulator for hydrophobic/hydrophilic interactions which can be used in tandem with a multi-objective optimization framework such as Jmetal or etc... I am having trouble determining a generalized approach for modeling the contact angle from younge's equation...
  19. H

    Geometry Optimization in Computational Chemistry

    I've read an article about computational chemistry in which the authors were performing a geometry optimization. For this purpose, they firstly optimized the geometry at HF/6-311++G(d,p) level with full relaxation on the potentiel energy surface (what does that mean exactly ? Can we extract this...
  20. C

    Molecular Charge Density Analysis

    How would one go about estimating the relative position of the center of charge density (with respect to oxygen) in ruthenium oxide vs. silicon oxide? (Hypothetically) My real quandary is with the relative screening experienced by oxygen core electrons in silicon dixoide vs. ruthenium dioxide...
  21. \Theta

    Computational Chemistry in undergrad?

    Hey there folks! I'm a math/computer science major focusing on scientific computing and I was wondering what courses I would need to take in my undergrad to be able to help out in Computational/Theoretical Chemistry. I've taken general chem and taking P Chem soon, is this enough or are there...
  22. T

    Chemistry BS, Looking to go into computational chemistry

    Hi Physics forum. I am a BS in biochemistry, looking into going into computer programming with my chemistry degree. I got A's in Gen Chem I and II, Organic Chem, Analytical Chem, Physical Chem, but I sucked at Biochemistry and got a C-. I got a B in Calc II but I was good at the Integration...
  23. Q

    Does Organic Chemistry Have Strong Roots in Computational Chemistry?

    So I'm an undergraduate student in Chemistry in my junior year and I recently transferred schools for a better science program. The one I was at was very, well, easy. Like toddler easy. I never went to class and I aced everything. Here, they're far ahead and it's much more rigorous. I was...
  24. J

    Computational chemistry of oxidation inhibitors

    I am currently working on a project analysing inhibitors of a heme enzyme which oxidises an indole molecule. We have data on halogenated and non halogenated indoles (methyl, hydroxy, amino and nitro). I have split them into these two classes because the first group have a negative correlation...
  25. M

    Fortran Fortran Formatting Computational Chemistry

    Hi, I require specific formatting for a quantum chemistry calculation. But for some reason I can't seem to write using formatting. I have checked tutorials, but to no avail. Here is my toy program: program test_format implicit none real :: m write(*,*) 'Enter a number' read(*,*)...
  26. G

    Understanding the Importance of Hessian in Computational Chemistry Simulations

    Hi, First I hope it is okay to post the problem here(?). I have some general questions regarding the use of software for chemistry simulations - my questions are more fundamental than software specific. I would like to simulate a chemical reaction - so I should be searching for the saddle...