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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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How to calculate dielectric constant of molecules using gaussian software in DFT studies? How to make input for these calculations?

I am trying to find the dielectric constant of my organic solar cell molecules, but I don't know how to make input files for these calculations. Can anybody please tell that which parameters should be ...
Muhammad Waqas's user avatar
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DFT : Usual way of computing exchange-correlation potential on a simple case H2 (RHF, LDA) [migrated]

The python code is at : https://github.com/MaximeLee/qmodelling/blob/main/examples/dft/H2_RHF_STO3G_V2.py I tried to do a DFT calculation for H2 Restricted Hartree-Fock with Local Density ...
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How to convert SMILES to 3D (with higher accuracy than RDKit)?

I am interested in assigning 3D coordinates to (atoms in) some 10K molecules that I have, currently represented by SMILES. This is because as have been shown by many chemoinformatics papers, 3D and 2D ...
jasperhyp's user avatar
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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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Input file details for rigid PES scan

I have a planar molecule and a hydrogen atom. I wish to perform single point energy calculation for different configurations of this system where I would place the hydrogen at a certain distance away ...
Arun's user avatar
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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 ...
farmaceut's user avatar
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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 ...
Kanghun Kim's user avatar
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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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Theoretical extent of exactness of IE/BG of Kohn-Sham DFT with exact XC functional

It is known that Kohn-Sham DFT with an exact XC functional theoretically exactly captures (the ionisation potential)(resp. the band gap) as (the HOMO energy level negated)(resp. the difference between ...
Kanghun Kim's user avatar
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Enthalpy of crystal solids using Density Functional Theory

I wanna see the feasibility of a chemical reaction $$A \rightarrow B +C$$ where A,B and C are crystal systems. Now I am using VASP in order to calculate the internal energy U, pressure and volume of ...
Parmeet Singh EP 066's user avatar
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How to define a chemical bond computationally?

I'm working with an amorphous system. With oxygen, my system has both covalent and ionic bond forming cations. I utilise the Wannier centre to define a covalent bond, and my theory is that if the ...
Raghvender's user avatar
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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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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 ...
brokaryote's user avatar
1 vote
1 answer
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Why do DFT calculations output molecular orbitals?

My understanding is that DFT finds the electron density which minimizes some energy functional. How does it make the connection from this optimized density to molecular orbitals?
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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 ...
Prasanta Bandyopadhyay's user avatar
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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 ...
Runa's user avatar
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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 ...
Runa's user avatar
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COSMO Segment charge density via NWChem [closed]

I'm struggling to get COSMO segment surface charge densities that I need to create the sigma profiles in COSMO-SAC. I am not a chemist by training, so please explain like I am five. I've read papers ...
mabounassif's user avatar
2 votes
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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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Physical origin of induction and dispersion energies

I am reading this book on non-covalent interactions. Chapter 1 states that there are 3 types of non-covalent interactions: Electrostatic interactions, which are just the coulomb interactions between ...
simulation_engine's user avatar
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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 ...
Gerard Puts's user avatar
6 votes
1 answer
137 views

How can I formally justify the description of an electronic excitation that includes only the relevant orbitals?

I am writing a small program to animate electronic transitions. To do this, I am animating a Rabi cycle for a single electron as it moves from an occupied into a virtual orbital. The on-resonance ...
MaxParadiz's user avatar
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In Kohn Sham DFT, what do we know theoretically about the exchange correlation energy?

As I understand Kohn Sham theory, it is proposed that the ground state energy for a molecule can be derived from the ground state of a fictitious set of non-interacting electrons moving in a ...
HenryH's user avatar
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2 answers
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Why wasn't Lu Jeu Sham awarded the 1998 Nobel Prize with Walter Kohn? [closed]

Reviewing part of the history behind computational chemistry for my thesis I could not understand why only Walter Kohn was awarded the 1998 Nobel Prize in Chemistry (with John Pople getting the other ...
HCSthe2nd's user avatar
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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) ...
thchem's user avatar
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4 votes
1 answer
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Confusion regarding DFT basics, i.e. the connection between Hohenberg–Kohn theorems, external potentials and the Kohn-Sham method

I have a question on the basics of DFT, which bases on the Hohenberg-Kohn theorem: there exist an unique mapping between the external potential, the electronic wave function and thus also the ...
aspiring_comp_chemist's user avatar
7 votes
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157 views

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 ...
HCSthe2nd's user avatar
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3 votes
1 answer
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What makes selectivity other than activation energy?

Selectivity and kinetics of reactions are somehow linked to the activation energies of reactions. However, there's something not totally clear in my mind about the selectivity. I will get a general ...
thchem's user avatar
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Oscillator Strength and Absorption Intensity in TDDFT

When I run a linear-response time-dependent DFT calculation in my favourite electronic structure program, for each excitation I'm given an oscillator strength, $f_i$, and transition dipole moment $$\...
user213305's user avatar
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small negative frequencies in DF T optimizations with organic molecules containing CF3 groups [duplicate]

When optimizing by DFT medium-sized organic molecules containing aromatic CF3 groups (for example, adducts involving takemoto's catalyst), the frequency calculation on optimized structures have always ...
saiwa's user avatar
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1 vote
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Dielectric polarization: how to identify what part of the total polarization (dipolar+electronic+ionic) I need (conceptual question, I use DFPT, VASP)

I am doing polarization calculations to get data for use in other calculations. To start with, I want to calculate the static dielectric constant. However, I'm a newbie to polarization and it is a ...
NTS's user avatar
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0 answers
125 views

How to choose the parameter to scan in finding transition state by using Gaussian 16?

I have problems in finding the TS of reaction dehydrogenation of an organic compound. I read many tricks to find the TS and see scan is an effective method. As I know we can use the product of the ...
Diem Huynh's user avatar
1 vote
0 answers
92 views

How to retrieve excited state molecular orbital coefficients in Gaussian?

Currently I am doing TD-DFT calculations in Gaussian and want to calculate transition dipole moment for $S_1$ transition manually. However, I do not manage to retrieve molecular orbital coefficients ...
aerospace's user avatar
2 votes
0 answers
34 views

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^\...
Jonny_92's user avatar
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are the exact and kohn-sham electron densities totally symmetric?

For any molecule with open or closed shells considering the electronic state to be the ground state: Is the exact electron density totally symmetric? is the Kohn-Sham electron density totally ...
Horse time's user avatar
5 votes
1 answer
128 views

Which quantum chemistry approximation to use?

I'm just getting started with quantum chemistry using some simple test problems. I have a few of the software packages installed (ASE, Psi4, GPAW etc) and everything is working - no issues with the ...
Alex I's user avatar
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3 votes
1 answer
319 views

Is it rigorous enough to change a DFT functional after geometry optimization to calculate excited state properties?

I have done the geometry optimization with the B3LYP functional, however, there is a need to calculate the excited state energy, so the CAM-B3LYP functional should be better suited for that. Do I need ...
aerospace's user avatar
0 votes
1 answer
184 views

What is the form of the Hamiltonian for solids?

For atoms, and even molecules, I can understand how the Hamiltonian would be constructed, but what of solids (as in, for electronic structure calculations)? Thank you for any help.
no_48102's user avatar
4 votes
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42 views

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 ...
Andrea's user avatar
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4 votes
1 answer
170 views

Gaussian16 Raman calculation from IR checkpoint file

I already did an IR frequency calculation for my molecule. Is there any possibility to just run a Raman frequency calculation with the chk file from my IR ...
Andrea's user avatar
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3 votes
0 answers
27 views

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 ...
Charlie A's user avatar
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1 answer
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Ab initio molecular properties which can be experimentally measured and don't require derivatives/gradients

I'm attempting to teach myself HF and DFT by implementing various algorithms, but I've run into a snag: many molecular properties which are experimentally measurable appear to require taking gradients,...
Eric J's user avatar
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0 answers
111 views

Chemical accuracy and room temperature

Chemical accuracy is $\pu{2E-2 eV}$ but room temperature $\pu{20 ^\circ C}$ is $\pu{2.5E-2 eV}$, so why is it not necessary to take into account thermal effects in DFT? I understood (maybe wrongly) ...
Jom's user avatar
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2 votes
0 answers
23 views

'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) ...
user2820579's user avatar
3 votes
1 answer
94 views

GGA functionals requiring second derivatives?

In "Lecture Notes in Quantum Chemistry II" from the European Summer School in Quantum Chemistry, the authors note that when discussing the LYP functional and other GGA functionals, that ...
Eric J's user avatar
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1 vote
1 answer
85 views

Quantum calculation of free energy change in neat conditions

I am slightly baffled by a seemingly simple situation: I want to calculate the free energy of association between a molecule $\ce{A}$ and the solvent $\ce{B}$ using quantum methods (e.g. DFT). From ...
Raphaël's user avatar
  • 1,608
1 vote
0 answers
54 views

Transition State search

I've been trying to find a transition state for the reaction of Pd + F2 with no luck. Has anyone ever tried a similar reaction, have they managed to get the TS? The reaction proceeds from the ...
Bryan's user avatar
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1 vote
1 answer
75 views

Why does DFT-D finds different optimized geometries for the same structure when using different input geometry files?

When I change c lattice parameter and optimize the structure with DFT-D, every time I get a significantly different geometry with different energy? Why is this happening with DFT-D?
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What are the rules for constructing Kohn-Sham orbitals?

I just recently began to study quantum chemistry and need some clarification for the construction of Kohn-Sham orbitals. Consider a system of several atoms. Let there be $N$ electrons in this system. ...
Disciple's user avatar
  • 117
7 votes
2 answers
1k views

High-temperature DFT

Why is it so difficult to perform DFT calculations that consider temperature? I have seen that time-dependent DFT is needed to model systems at high temperature. Why is this the case? What about ...
Wychh's user avatar
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