Questions tagged [spectroscopy]
For questions about or related to spectroscopy.
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The theoretical electron momentum profiles using Gaussian16
I am trying to calculate theoretical electron momentum profiles (TMP) of individual orbitals of a molecule using Gaussian16 for theoretical calculation of electron momentum spectroscopy. I there a ...
Arka
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Xray spectroscopy of elemental Cobalt
Can anyone please share the image of elemental cobalt Xray spectroscopy image? Particularly I would like to see how it shows within 50-200 eV range (or close to this range).
I have found some ...
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What would be the best tool to simulate FTIR spectra of molecules?
I tried to simulate a spectrum of a porphyrin using the orca 5.0.4 program, calculating the frequencies and simulating the spectrum with the orca_mapspc program from the orca package, however the ...
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How to check whether spin orbit coupling is strong or weak?
I am doing spin-orbit coupling (SOC) calculations using VASP. I had done a magnetic anisotropy calculation, but I do not know how to check whether the SOC is weak or strong. Any help would be highly ...
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Help regarding SLME calculation
Information
Paper - https://www.sciencedirect.com/science/article/abs/pii/S1566119918302787
Github Link - https://github.com/ldwillia/SL3ME
Question - I have been studying solar cell materials. I ...
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Algorithm for finding the v=1 state of an H2O molecule
In the context of simulating the dissociation dynamics of an H₂O molecule on a metal surface, what algorithm is employed for generating the initial state of a tri-atomic non-linear molecule, such as H₂...
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How may I solve the radial Schrödinger equation?
I want to solve the radial Schrodinger equation for a Carbon atom with all six electrons.
The equation I want to solve is for $r>0$: $$[\frac{-\hbar^2}{2m}\frac{\partial^2}{\partial r^2}+ \frac{\...
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How does dimer and monomer zero point energy affect dissociation energy?
This paper by Xinchuan Huang et al. gives a calculation for the dissociation energy of a water dimer. The electronic dissociation energy (what they call $D_e$) is around 21 kJ/mol, and this is ...
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How do I calculate XPS spectra for molecules to match experimental spectra?
I am trying to calculate the XPS spectra using the ICORELEVEL method in VASP, both using initial and final state approaches, for C1s and F1s electrons. My systems are single molecules.
However, my ...
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Normal coordinate analysis in TRAVIS
I have run a few AIMD calculations of some impurities trapped in a solid using CP2K and TRAVIS to simulate the resulting infrared spectrum. While the infrared spectrum was simulated well, there is no ...
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Why are some point groups for single atoms listed as Oh in the CCCBDB?
Does anyone know why the CCCBDB database lists the tin cation and antimony atom as having the Oh point group (please see the screenshot below from CCCBDB when I look at "All molecules sorted by ...
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How to Find the Huang-Rhys factor from the Intensity Vs Wavelength plot (PL plot)?
How can I find the HR factor like we calculate the Debye waller factor as - log(IZpl/Itotal), from the intensity profile of the PL spectra.
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Calculating vertical excitation energies at the DLPNO-STEOM-CCSD Theory level
I want to calculate the vertical excitation energy using the DLPNO-STEOM-CCSD method, on molecules previously optimized using TD-DFT. the parameters being used are as follows:
...
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Script to draw one-dimensional PES comparing harmonic and anharmonic vibrational modes
This is an extension of a question I asked a little while ago: Software to draw one-dimensional PES including vibrational energy levels. I am asking the followup here based on advice received after ...
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2D Infrared spectroscopy for bulk systems using molecular dynamics
There are some questions and answers (1,2) on this site regarding simple infrared and vibrational density of states calculations with molecular dynamics and there any simple algorithmic descriptions ...
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Determination of fluorescence lifetime by using oscillator strength?
$$k_r=2.88\times10^{-9}n^2\langle\tilde{v}\rangle_\text{av}^2 \int\varepsilon_{\tilde{v}}d\tilde{v}$$
$$f=4.32\times10^{-9}\int\varepsilon_{\tilde{v}}d\tilde{v}$$
I plan to use the above equations to ...
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Which component of the dielectric tensor is used in generating EELS in TDDFT? [closed]
Electron Energy Loss Spectroscopy (EELS) comes from the imaginary part of the inverse dielectric function $-\text{Im}[\varepsilon^{-1}(q, \omega)]$. If the dielectric function is actually a tensor and ...
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How to assign UV-vis maximum absorption wavelength theoretically by using td-DFT?
I'm currently working on the simulation of Uv-vis absorption spectra of some organic compounds, while performing TD-Dft the log file that we got contains the values of deltaE of the transition,...
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What is the lifetime of propane at standard conditions transitioning from an excited rotational state back to ground state? [closed]
I am a retired microwave engineer (88 yrs old) and have not had the opportunity to study or learn anything about quantum physics. I designed and built radars for the military.
We found a claim that ...
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Spin-Orbit coupling effects in topological insulator Bi2Se3
I'm currently trying to understand this paper explaining the origin of band inversion in the topological insulator Bi2Se3. In Fig. 2 (see below) they explain by means of 4 steps how certain atomic (...
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What is the bond length of O2--?
I need the bond length in Å for $\ce{O_2^{--}}$ from this geometry database page (type "O2--" for the input).
I get a bunch of possible values. I don't know much about those yet but after ...
iwab
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Check whether a simple molecule is Raman-active or IR-active using PySCF
I am trying to write a python code that checks the dipole moment and the polarisability of a certain molecule in order to determine if it will be Raman-active or IR-active.
Raman-active molecules are ...
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How to plot emission spectrum using gaussian? [closed]
I'm trying to learn how to plot emission spectrum for my system, but, as an initial test case, I'm trying to do this for methane.
I calculated the optimized geometry of the ground state, then I ...
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How are the simulated powder diffraction patterns calculated in CCDC Mercury?
From my understanding, programs like CCDC Mercury and VESTA are able to extract some information from imported .CIF files of molecules but then complete calculations to output a simulated X-ray ...
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List of properties of molecules categorized by the number of atoms?
Is there an online database having information on molecules with a certain number of atoms? For example, properties of tri-atomic molecules?
There is this table that I got from NIST which gives a few, ...
- 1,105
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Vertical transition, 0-0 transition, and experimental spectra
I am currently working on a machine learning with spectroscopy. I had learnt about the Franck-Condon principle and the vibronic coupling in photochemistry courses in my undergraduate lectures. However,...
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Determining bond angle from infrared spectra?
Looking at some historical data about water, I noticed that people were determining bond angles from infrared spectra. How is this done? Aside from having a bunch of absorption frequencies indicating ...
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Slope of the potential when both molecules "touch"?
My aim is to model the potential energy surface for two colliding H2 molecules. More specifically, I needed the order of magnitude of the slope of the potential at the moment when two colliding H2 ...
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How much does it cost (RAM and CPU) to calculate the energy of H2?
I have recently come across this very intriguing paper “The Fundamental Vibration of Molecular Hydrogen”.
I have asked the authors the following naïve questions directly via email:
What was the ...
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What's the point of doing high accuracy spectroscopy calculations?
I am currently reading Dickenson et al. (2013) The Fundamental Vibration of Molecular Hydrogen.
I am trying to understand why this calculation is important for the field beyond basic scientific ...
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EPR spectrum simulation [closed]
Can anyone recommend code (preferably open-source) for the simulation of EPR spectra from electronic structure calculations?
I found EasySpin:
EasySpin is an open-source MATLAB toolbox for simulating ...
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Calculating Core-Level Binding Energies (XPS) using DFT
I'm pretty new to DFT calculations but I'm trying to learn how to do X-ray photoelectron spectroscopy (XPS) calculations, particularly for open-shell molecular systems in common non-periodic DFT codes....
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Different types of transition dipole moment in ORCA output
In the ORCA output for a TD-DFT calculation, there are two types of spectra printed. One is called "transition electric dipole moment" and "transition velocty dipole moment".
...
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How does the VIBRA module of SIESTA compute IR intensities? [closed]
I am working with Fluoro-Graphene (let's assume a fully relaxed monolayer on the XY plane with 16C-1F cell where the F is "covalently" bound to the graphene on top of it with respect to the ...
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XANES simulation software/code besides FEFF for Pt L3 edge?
I need to generate the XANES region spectra of the Pt L3 edge of a theoretical Pt6 crystal with adsorbed atoms/molecules, such as $\ce{Pt(H^*), Pt(O^*), Pt(OH^*),Pt(CO^*)}$. It is for generating ...
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RAMAN calculation with SIESTA and ASE-SIESTA
I have been using the ASE-SIESTA-PyNAO module to attempt some RAMAN/IR mode calculations on graphene (if anyone has any experience with this please send me a message maybe we can chat about it). At no ...
- 1,411
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Are there any benchmark test sets for UV-vis absorption maxima?
In computational chemistry, I have come across many test sets which are used to benchmark a new method. For example, the G2 test set for thermochemical calculations (heats of formation). There is the ...
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How to calculate electronic circular dichroism (ECD) spectra from MCTDH? [closed]
Electronic circular dichroism (ECD) spectra is commonly used in organic chemistry to characterize chiral molecules. Here the question is how to simulate ECD spectra using MCTDH (Multi-configurational ...
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What is the equilibrium bond length for a Lennard-Jones potential?
If I have $\epsilon$ and $\sigma$ can I calculate equilibrium distance $r_e$ in one run? What I have tried is to put $V = \epsilon$ and bring out the $r$ from the formula, but it seems not solvable. ...
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How to analyse structure factors calculated from a mixture of isotropic amorphous substrates
I am looking for a way to computationally analyse the interactions between two molecular species (as solute and solvent) in an isotropic mixture using X-ray scattering. Is there a guideline as to how ...
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How to calculate small and wide-angle X-ray scattering spectra for the hydration shell restricted by a distance radius criteria
My main aim is to extract the SWAXS spectra for the hydration shell surrounding a solvated molecule and I am unfamiliar with the idea of excluded solvent volume. I tried looking online but many ...
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Calculating emission spectrum of organic compounds by DFT. Can someone elaborate in terms of calculating it for aggregatrion induced emission? [closed]
I am planning for the calculation of emission spectra of organic compounds showing the phenomenon of aggregation-induced emission (AIE). Can someone help me get started?
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Package for computing properties of excited vibrational states
We're starting to develop some calculations of the hyperfine parameters (electric field gradient, spin-rotation coupling, spin-spin coupling) with CFOUR, and we reached a limitation of the public ...
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Emission and absorption UV-Visible spectrum using GAUSSIAN-09
I am currently studying the UV-visible spectrum of ethylene using GAUSSIAN-09. I optimized the ground state(# opt b3lyp/6-31g geom=connectivity) then used the ...
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What quantity to perform CBS extrapolation on for adsorption/binding energies?
When calculating complete basis set extrapolations for quantities, such as adsorption energies or binding energies, which depend on the difference between three quantities (i.e. $E_\textrm{prop} = E_\...
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GUI for DFT calculations
I am a beginner in DFT. Can someone suggest a good DFT software with a GUI for simulating dipole moments and optical absorption spectra in an organic crystal? I have tried the Burai GUI of Quantum ...
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Transformation between two different sets of molecular vibrational normal coordinate systems
Lets assume we have $N$ Atoms and we treat them within the Born-Oppenheimer Approximation. We can calculate the adiabatic electronic groundstate potential. Lets assume we observe two local minima, ...
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Is there some free software to do Frank-Condon analysis?
I know Gaussian 16 can do it, but are there some free programs that can?
For simple excited state calculations using TD-DFT, we can use NWChem and Octopus. Can these do Franck-Condon factors?
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How to create a differential spectrum from two simulated spectra, calculated by two different basis sets?
In my bachelor thesis, I compare simulated IR-spectra computed by different basis sets. The simulated spectra from sets like cc-pVTZ and cc-pVQZ are too similar to compare them by plotting them next ...
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Problem obtaining a Raman spectra of a graphene structure
I am trying to obtain the Raman spectra of a graphene structure using Gaussian. I used the input below, but when I did it, I got this error:
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