Questions tagged [density-functional-theory]
Density functional theory (DFT) is a quantum mechanical model used to estimate the electronic structure of molecules and condensed matter. In broad terms, DFT works by treating all the electrons in the system as a single electron density, and computing physical quantities of interest as functionals of that electron density. (from Physics.SE)
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Density Functional Theory with Generalized Gradient Approxmations (GGA) - What Happens if the Electron Density Shows a "Kink" at the Ion Position?
My question may be stupid, so please correct me if you find anything which is obviously erroneous.
In the following I will place a question mark (?) besides points/steps I consider doubtful.
My ...
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Changing the level of theory for organometallic compounds
I'm finishing my Ph.D. in Inorganic Chemistry and having a debate with my supervisor. The work in question have two organometallic compounds A and B. The structures are based on X-Ray Diffraction, so ...
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Warning during geometry optimization via Gaussian
I have some recurrent problem with my DFT calculations [functional: hseh1pbe; basis:6-31+g(d,p), object: porphyrin derivative]. During the MO setting I get:
**** Warning!!: The largest alpha MO ...
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Are there examples of publications using DFT instead of HF as a coupled-cluster reference?
I have been searching for a while, and only managed to find an article by M. Saitow,[1] where CAM-B3LYP orbitals are used. I was wondering if this has been done elsewhere.
It was recommended to me by ...
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How to define the initial guess for the electron density?
This is a technical question. If I have a one-dimensional box of length L, and an electron density existing in the box and integrating to N electrons. And if I want to determine the electron density ...
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Paper Data Replication
I read a paper recently - Here. I found the concept of Electride materials very interesting and wanted to mess around with them myself. I tried to replicate the partial electron density plots shown in ...
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N2 HOMO-LUMO Gap calculation
I am thinking about calculating the HOMO-LUMO energy gap for $\ce{N2}$ molecule.
I thought I could model this as a particle in a box problem to find $E_\text{HOMO}$ and $E_\text{LUMO}$.
The formula I ...
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How to Validate Choice of DFT Functionals and Basis Sets for atomic charge calculation of Fluorocarbons
I need to calculate the charges (electron densities) on each atom of a set of partially fluorinated hydrocarbon molecules by NPA. The question arises:
What is the currently accepted / best practice ...
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Laplacian of the Hartree Fock second-order reduced density matrix
I am attempting to replicate and understand the Colle-Salvetti method for approximating the electron correlation energy.[1] I have successfully replicated the method, but there is one part of the ...
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Ab initio MD simulations in VASP
I'm not sure if this is an appropriate question for Chemistry.SE, but I'm taking a stab. I'm running ab initio MD calculations in VASP and I'm trying to optimize different input tags. On the VASP ...
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Calculation of rate constant for bimolecular reaction from Gaussian DFT calculations
I am working with a bimolecular reaction for which I have computed the energy profile. I have output files for TS and reactants which I intend to use for rate constant calculations. From TST we have:
...
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Simulation of electronic potential from nanoparticles interacting with molecules
I work with SERS, where the Raman signal gets enhanced by the electric field of the nanoparticles. Now I like to simulate this kind of spectrum with Gaussian. I found a paper[1], where it looks very ...
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DFT: Can the calculated enthalpy of two systems that aren't isoelectronic be compared?
As a simple example, say I wish to calculate the product of a reaction between methyl iodide and triethylamine, then compare it with the product of benzyl iodide and triethylamine. My goal is to ...
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Semi-numeric or analytic Hessian for DFT (GAMESS)
I'm trying to understand what parameter in the $FORCE group is better to use in computing vibrational frequencies (NVIB=2) of ...
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Signs of Exchange and Correlation Potentials
The exchange and correlation potentials refer to those defined in density functional theory. (See also http://en.wikipedia.org/wiki/Local-density_approximation)
Define the exchange potential as $V_{x}...
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Modelling barrier-less reactions
I am currently exploring a few dissociative reactions whose PES is barrierless (no first order saddle point). I have found a few approaches in literature like flexible nudged elastic band theory, ...
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What is the physical significance of the damping function in calculation of vdW interaction energy?
In order to take care for the singularity (also removing the double counting of exchange-correlation) obtained with this expression,
$$E_\mathrm{vdW} = \frac{C^6}{R^6}$$
many type of damping functions ...
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Can AMBER as low-layer be used to model reaction mechanisms using ONIOM? If yes, do you need to parameterize the intermediates and Transition states?
I'm debating moving from (M06-2X:PM7:UFF) to (M06-2X:PM7:AMBER) for modelling a reaction mechanism in an enzyme. I've already examined the errors introduced by my partitioning and whether they cancel ...
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Best way of studying protonation in non-polar solutions with ~100ppm of water present using computational methods?
I am currently looking at the mechanism of the formation of storage deposits in jet fuel. Interestingly, the concentration of acids in the fuel correlates strongly with the total insolubles formed ...
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What are the cheapest basis sets able to model intermolecular dipole interactions inside a metal complex and give good relative energies, with DFT?
As a example, If I have a square planar complex of a cation with both a weakly polar ligand (X) and strongly polar ones, like ammonia and water I expect a bit of stabilization due to formation of a ...
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How to do RPA (Random Phase Approximation) in VASP?
I'm new to VASP and as such don't know much of its intricacies yet. I want to find out the interlayer binding energy of a given molecule and to do that I already opted for the use of different ...
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How to find a full electron basis set that approximate a given ECP basis set?
In computational chemistry of transition metals, there are many popular basis sets, from pople+LANL2DZ mixed basis sets, to Ahlrich and Karlsruhe basis sets like def-SVPD, def2-TZVPPD. Often the ECP ...
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Q-chem equivalent solvent settings for Gaussian NMR ab inito methods
I'm attempting to use Q-Chem 5.0 to replicate CHESHIRE-esque http://cheshirenmr.info/ ab initio calculations of chemical shift values. Unfortunately Gaussian seems to be the predominant tool in this ...
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calculate SPE using dummy/ghost atoms in NWChem
I have been making some failed attempts to calculate interaction energy of 2 monomers using a dummy/ghost atom in NWChem6.5.
The code I was using to calculate the interaction energy is:
...
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What exactly does setting the net charge in a DFT calculation do?
In the implementations of DFT using Gaussian basis sets, it is common to set the net charge. What exactly does this do? The Gaussian (program) manual, for instance, says that it introduces a ...
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PAW vs USPP: Pseudopotentials in commercial DFT codes
What is the difference between USPP (ultra-soft pseudopotential) and PAW (projector augmented wave) in commercial DFT codes?
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Which Basis Set is suitable For Mercury-complex in DFT calculations?
Which Basis Set is suitable For Mercury-complex in DFT calculations? Please provide the answers with any journal reference.
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Gaussian16 optical rotation calculation using a deuterated species
I am running into issues preparing an input file for DFT calculations. Currently, I am trying to submit an optical rotation calculation for an alpha-deuterated benzyl bromide (1 deuterium on the ...
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What is the meaning and unit of the integral in the local density approximation (LDA)?
According to Parr and Weitao (1995), the Dirac exchange-energy formula (1930) comes from
[I am looking only at the last line of the equation and the rest for completeness]
It's an energy, so I'd ...
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Exploiting 8-fold symmetry of ERI tensor for building Coulomb and Exchange matrices
I'm trying to write a restricted Hartree Fock code in Fortran that reads in a file of zeroth-iteration 1 and 2 electron integrals (FCIDUMP format) and uses them to do the SCF procedure from an initial ...
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Comparing geometries and substrates calculated with DFT for different pathways
As DFT calculation is an excellent tool for confirming and understanding experimental results, I got deep into this field as organic chemist. I successfully isolated interesting transition states (TS) ...
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Spurious term in Thomas-Fermi-Hartree energy functional
I am quite a beginner in DFT and I am studying the theory behind the computational tools. I have some doubts about the Coulumb approximate functional term:
$$U[n] = \frac{1}{2} \int d^3 r \int d^3 r^\...
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'Ab initio' couplings for DNA used in charge transport
I came across a publication by Senthilkumar et al. [1] in order to compute charge transfer through the DNA. Table 3, for instance, gives the coupling between bases along the leading (or retarded) ...
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Generate Surface with CubeFile from Gaussian in VMD or other free programm
I asked a question before, about how to save a mapped surface from GaussView. I don't get an answer, so I get much deeper in my internet research about it again.
Now I want to try to create a mapped ...
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How to extract a image (vector graphic) from a surface EPS plot with GaussView?
I am quiet new to this field of chemistry. I work with GaussView and I created a surface plot for my molecule with the cube and surface generator. This works very well. Now I like to save and copy ...
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Is Tkatchenko's MBD-NL method self-consistent?
I have a question regarding Tkatchenko's [1] new nonlocal many-body dispersion method (MBD-NL). Does anyone know if it's a self-consistent method? I read this paper many times but I'm still not sure.
...
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How to account for solvation of a molecule explicitly in quantum calculation?
I'm looking for a way to account for hydrogen bonds formed with my molecule in aqueous solution explicitly in DFT calculation. I'll do it in order to compare stability of two structures in water. As ...
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DFT Exchange-Correlation Two Electron Integrals
Are there any electronic structure programs that print the exchange-correlation (XC) integrals for a given DFT functional? These integrals are of the form $$\langle pq|w|rs\rangle$$
where $w$ is an XC ...
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Natural orbital population analysis in Gaussian
Within (restricted) density functional theory and Hartree-Fock, respectively the Kohn-Sham orbitals and spin orbitals are the natural orbitals, with occupation numbers either 2 or 0.
As I understood, ...
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How to calculate the magnetic exchange coupling in a charged radical complex?
I have a neutral complex with two magnetic centers. For this case it is easy to calculate the exchange coupling as the broken symmetry state is converged properly. But when I am making the complex ...
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Determining global minimum structures for ion-water clusters
What is the best way to find the global minimum structure(or get close to it) for an ion and N waters? (i.e. ion cluster in vacuum)
For example, consider Flouride ion cluster with N=5 waters.
I want ...
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Units on rate constants from transition state theory and DFT
I am using density functional theory (DFT) to compute the energy profile and, by extension, kinetic parameters for a catalytic process. I know that the rate constant from transition state theory (TST) ...
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How to model iso-surface of molecular orbitals of singlet and triplet excited states
I've modelled the iso-surface of the highest occupied molecular orbital of a molecule with DFT in Gaussian.If I were to model the iso-surface of the molecular orbital of the singlet and triplet ...
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How to find the global minima of a supramolecular complex in computational chemistry?
So this is more of a complex problem, and my masters thesis could greatly benefit if I find an answer to this.
Essentially, I have a supramolecular inclusion complex. There is this molecule A (the ...
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Define a rate-determining step and an energy barrier for a multi-step reaction profile
I am currently making reaction profile by means of DFT calculations. I am able to correctly draw a whole reaction profile.
However, I am struggling to find what exactly is the energy barrier of a ...
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How to obtain reliable ligand binding energy in QM manner?
I wish to compute the binding energy of the ligand to the known cavity of the receptor.
My idea was to:
Perform docking to the recognized binding site using AutoDock Vina
Export bound ligands and ...
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Rationalisation of stabilising dispersion interactions in HgS via QM
It is well-known that mercury(II) sulfide, HgS, is extremely inert- for example, it has one of the lowest solubilities of nearly all known compounds in water(check Wikipedia). There are two well-known ...
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How to increase basis set while running cluster calculations
I am running (opt+freq)DFT calculations using 6-311G(d) basis set on polymers with different number of monomer units. Upto 2 monomer units optimization is converged but for 4 units max displacement ...
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Validating Resultant Structures of Computational Quantum Chemistry Optimisations
I have tried finding sources (publications, websites, blogs) that outline the logic of accepting the resultant structure of optimisation. I understand using a Hessian to determine if the structure is ...
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Using 3 layer ONIOM(M06-2X:PM7:UFF) over 2 layer ONIOM(M06-2X:AMBER) or 2 layer ONIOM(M06-2X:OPLS) to study enzymatic aldehyde reduction
I'm trying to model the reaction mechanism of an enzymatic steroid reduction. Experimental research proposes a large variety of intermediates, which I believe would each require separate ...