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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TDDFT Results - Excitation Energies
I ran some vertical excitation energy calculations, and I'm a little confused about the results. Would someone be able to help me to understand?
Here are my results:
I'm trying to understand the ...
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Is it possible to have a positive BSSE energy using the counterpoise method?
I've just learned about the counterpoise correction method for Basis Set Superposition Error (BSSE).
My understanding is that the BSSE energy represents an overbinding effect due to the incomplete ...
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Difficulty Finding Transition State for Singlet Oxygen Reaction with 1,3-Diphenylisobenzofuran (DPBF) Using QST2 in Gaussian
I'm currently trying to model the interaction between singlet oxygen (1O2) and 1,3 diphenylisobenzofuran (DPBF) using Gaussian 16 program package. The goal is to find the transition state (TS) for ...
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Determining bonding characteristics of a structure from PDOS
Recently, I have been working with PDOS. I can read and understand PDOS to some extent, but I am not an expert in it. These are some of the graphs I have been working on. Can someone explain how to ...
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Second derivative terms of DFT functional
Given the density functional to KSF matrix elements
$E^{XC} = \int dr f(r,R)$,
where $r$ and $R$ denotes electronic and nuclear coordinates, respectively.
Suppose we have an LDA functional, which can ...
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How to interpret molecular orbital (HOMO - LUMO) plots in Chem3D 22.0?
Recently, I have been trying to understand the origin of the difference in reactivity of alkynyl-boron(ate) complexes so I tried to generate a molecular orbital plot on Chem3D (Version 22.0.22 64bit) ...
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Comparing calculated DOS with experimental valence band spectra for oxidized platinum nanoparticles
I've been studying the electronic structure of platinum nanoparticles using DFT and have a question about comparing my calculated density of states (DOS) with experimental valence band spectra.
I ...
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How to rotate Octahdrals locally along with unit cell axis
I am curious about crystal field effects on a given atom by analysing $m_l$
projected DOS, the individual d-orbitals are given with respect to the Cartesian coordinates (not the lattice constants). So ...
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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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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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Can we use DFT to compute the potential energy of dynamic processes?
Suppose we want to determine the potential energy between a hydrogen atom and a surface, such as Cu(001), during hydrogen scattering on Cu(001) surface, assuming that the hydrogen atom does not change ...
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Energy Decomposition Analysis for SN2 involving ambident nucleophiles and an alkali metal counterion
I am wanting to perform an EDA on transition state structure of the nucleophilic attack of an ambident nucleophile (2 atoms that could be used in nucleophilic attack on the same molecule) on a benzyl ...
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Can geometry of a molecule change when the spin-orbit coupling is taken into account? [closed]
Cross-posted on MMSE.
Is there any evidence that spin-orbit coupling (SOC) leads to significant changes in atomic structure? Using DFT, I am getting different relaxed lattice constants when I take SOC ...
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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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Behavior of the Vosco-Wilk-Nusair correlation functional
Assumptions:
interacting system
uniform gas system
In the Kohn-Sham model, the exchange correlation functional is introduced to account for correlation energy $\epsilon_{xc} = \epsilon_{x} + \...
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What is the difference between zero-point and total energy of a molecule in the output of an ORCA FREQ calculation?
I am trying to find the enthalpies of formation for a couple organometallics in ORCA and as a first time user I am a bit bogged down in the terminology. The Gaussian manual has a section on these ...
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Effective Core Potentials and their "corresponding Pople" basis set
Reading through a handout from Yale shows the author correlating the ECP with Pople basis sets. The author of this says the corresponding basis set for SDD is 6-31G, Def2TZV as 6-311G, LANL2MB as STO-...
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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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Do we know the asymptotic behavior of density functional in DFT?
I was reading a book on DFT the other day, and the author included asymptotic behavior for $E_{xc}[\rho(r)]$.
Given that, do we know the asymptotic behavior for kinetic energy and/or total energy in ...
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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 ...
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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 ...
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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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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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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 ...
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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 ...
