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 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 ...
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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 ...
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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 ...
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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 ...
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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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Will hydrogen spillover be feasible on β12 borophene

Considering the fact that atomic hydrogen spillover has only been established to take place on reducible metal oxide supports, what is the possibility of spillover from palladium nanoparticles to 2D ...
3 votes
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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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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 ...
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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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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 ...
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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 ...
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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 ...
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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 ...
3 votes
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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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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 ...
6 votes
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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 ...
7 votes
1 answer
648 views

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 $$\...
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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 ...
2 votes
2 answers
177 views

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 ...
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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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2 answers
351 views

Strange "far out" orbitals in HF and DFT calculations. Why do they occur?

I calculated some orbitals and I get quite strange results with orbital geometries I wouldn't expect from MO theory. A more experienced colleague just said: "That's always the case with big basis sets,...
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 ...
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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 ...
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 ...
1 vote
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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 ...
14 votes
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Why is Density Functional Theory notoriously bad at describing oxygen molecules?

I read in several papers that DFT is notoriously bad at describing free oxygen molecules but in none of them an explanation or reference concerning the problem has been provided. I guess this has ...
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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 ...
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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 ...
12 votes
2 answers
2k views

There are no wavefunctions in DFT

I have seen this phrase several times across DFT textbooks. However, I am not sure if it still holds. Was there a change or a theorem that proved it otherwise? Several programs display wavefunctions ...
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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 ...
2 votes
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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^\...
3 votes
1 answer
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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 ...
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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 ...
38 votes
4 answers
5k views

DFT Functional Selection Criteria

I have a very very general question: In DFT functional selection , mostly people speak about the most recent ones. For example my professor always asks: " which DFT Functional did you select ? " ...
3 votes
1 answer
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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 ...
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1 answer
143 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.
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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 ...
4 votes
1 answer
127 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 ...
3 votes
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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 ...
1 vote
1 answer
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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 ...
3 votes
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,...
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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) ...
2 votes
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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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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 ...
4 votes
1 answer
3k views

How to calculate the energy of a single proton? [closed]

Using e.g. the VWN5 functional, what is a simple way to calculate the energy of a single proton? Of course, it is not possible to perform a calculation of a proton in isolation, as it bears no ...
19 votes
3 answers
633 views

Do modern dispersion-corrected DFT methods give more accurate molecular geometries?

I was discussing with a colleague the use of modern dispersion-corrected density functionals. I take it almost as a given that the methods generally produce "better" (for some definition) geometries, ...
1 vote
1 answer
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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. ...