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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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 ...
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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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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 ...
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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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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 ...
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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 ...
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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 ...
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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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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 ...
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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 ...
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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 $$\...
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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 ...
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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 ...
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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 ...
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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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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 ...
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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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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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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 ...
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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 ...
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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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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) ...
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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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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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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 ...
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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 ...
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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. ...
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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 ...
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Does the amount of solvent interaction energy depend on the absolute gas phase energy?

I've been performing Gaussian 16 DFT optimization and single-point energy calculations on different conformers of a rather large organic molecule. My first series of calculations was without solvent ...
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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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I'd like to model some compounds with DFTB, but some elements don't have parameter files in the official site. Is there a workaround?

I was reading a bit about this technique, Density Functional based Tight binding (DFTB). It's claimed it can provide a speed improvement of several fold when compared to plain DFT, still giving ...
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Would there be need for periodic DFT if we are able to get all the forcefields of all the elements in the periodic table in ReaxFF?

Since ReaxFF combines the advantages of DFT and Classical MD, would there be any need for periodic DFT calculations if we can have all the forcefields of all the elements of all the possible systems?
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Is there any software that can do geometry optimization using machine learning?

DFT is a computational tool that is used in optimizing and calculating the electronic structure properties of molecules. Are there any machine learning codes that can do something similar in a ...
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Trouble understanding equation from density functional theory

In the review by Oliviera et. al., I do not understand how the authors get equation 14: \begin{equation} E[\rho]=\sum_i^Mn_i\langle\Psi_i|-\frac{1}{2}\nabla^2+v_{ext}(\vec{r})+\frac{1}{2}\int\frac{\...
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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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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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Is this approximate equivalence table between Pople's basis sets and Jensen's DFT attuned polarization consistent basis sets (pcseg-n) correct?

I have some calculations results I runned previously using Pople's basis sets, mostly 6-311+G(d), under Gaussian09. These days I read some texts on Frank Jensen's family of polarization consistent, ...
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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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