Questions tagged [spectroscopy]

For questions about or related to spectroscopy.

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27 votes
2 answers
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Is it right to neglect very small imaginary frequencies?

I'm running a DFT optimization (B3LYP/def2-TZVP) and frequencies in ORCA for a molecule. And I get one or two very small (1-6 cm^-1) imaginary frequencies which corresponds to a slight bend of the ...
Roman's user avatar
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23 votes
1 answer
2k views

How exactly does one compute the vibrational density of states from the output of a molecular dynamics simulation?

There are many things that can be done with the output of a molecular dynamics simulation, but one of the more powerful things is the ability to compute the vibrational density of states (or the ...
jheindel's user avatar
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17 votes
5 answers
3k views

Bond length from infrared spectra?

It's been taught by my lecturer that infrared (IR) spectra are widely used for chemical bonding determination. My question is: is it possible to calculate bond lengths according to the IR spectra? If ...
Rizky Arief S's user avatar
16 votes
3 answers
3k views

Can you estimate the electronic excited state lifetime of a molecule?

I want to estimate the lifetime of an electronic excited state. Lets assume there is only radiative coupling via spontaneous emission from this state to the ground state. I can optimize the excited ...
Hans Wurst's user avatar
15 votes
5 answers
2k views

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 ...
Omar Shehab's user avatar
14 votes
1 answer
180 views

What is the impact of the orientation of a molecule in cartesian coordinates to molecular properties?

According to my knowledge, each computational chemistry code optimizes a molecule keeping the input orientation of the molecule. The population and spectral analysis is performed on the optimized ...
Aritra Mukhopadhyaya's user avatar
13 votes
2 answers
641 views

How to export a calculated Raman spectrum in Q-Chem, as a Gaussian profile?

Does anyone know how to export a calculated Raman spectrum (my calculation was performed in Q-Chem) as a data-file, which can be used to plot the profile of a Gaussian-shape spectrum (in origin, excel,...
Dmitry Eremin's user avatar
13 votes
1 answer
256 views

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 ...
S R Maiti's user avatar
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13 votes
1 answer
153 views

Photoemission Spectra of Solids

I know that in non-periodic codes such as Gaussian the fluorescence spectra of molecule can be calculated in the following manner. Relax geometry TD-DFT to find excited state Relax excited state ...
Tristan Maxson's user avatar
13 votes
1 answer
922 views

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 ...
Aswin Alex's user avatar
12 votes
1 answer
838 views

How to determine which levels correspond to each other in LS coupling and jj-coupling?

In the LS coupling scheme, L, S and J are good quantum numbers; whereas in jj-coupling scheme, j1, j2 and J are good quantum numbers. I have learnt how to get the term symbols for LS coupling, and for ...
S R Maiti's user avatar
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12 votes
2 answers
606 views

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?
user779130's user avatar
12 votes
2 answers
690 views

Recommended code to do XAS/XES/RIXS calculations with?

I am a grad student looking to simulate several XAS/XES and potentially RIXS spectra for some strongly correlated metal-oxides. The materials in question will likely require solving the Bethe-Salpeter ...
Haru Fujimura's user avatar
11 votes
1 answer
122 views

Regarding oscillatory strength theoretical units to experimental ones

The output of Gaussian rotatory and oscillatory strength intensities, plus a gaussian/lorentzian fit, translates to a theoretical CD/UV-vis spectra. In order to try and compare with experimental ...
C. Alexander's user avatar
11 votes
0 answers
265 views

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....
Ademola Soyemi's user avatar
10 votes
3 answers
513 views

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, ...
Hans Wurst's user avatar
10 votes
2 answers
136 views

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 ...
Till's user avatar
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10 votes
2 answers
3k views

Is there a free online repository where I can download X-ray diffraction (XRD) data?

It's as the title of the question states. To be specific, I'm wondering if there are any free online repositories where I can download (.csv or .txt. or .xsl) files for x-ray diffraction (XRD) data.
jboy's user avatar
  • 1,131
10 votes
1 answer
280 views

Where did the "Computational Chemistry Comparison and Benchmark DataBase" find its scaling factors for vibrational specra?

I worked with gaussian to simulate vibrational IR and Raman spectra. For that purpose, I scaled the vibrational frequencies from my gaussian calculation with the scaling factors from this website: ...
Till's user avatar
  • 589
10 votes
1 answer
184 views

How can I simulate the work function given by Ultraviolet Photoelectron Spectrum (UPS)?

How can I simulate the work function given by Ultraviolet Photoelectron Spectrum (UPS) of a molecule or a molecular crystal? I thought it is an easy job: Just do a geometry optimization and get the ...
Y. Zhai's user avatar
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10 votes
1 answer
726 views

Understanding emission spectra using TDDFT calculation

I did a TDDFT calculation to get the emission spectra of my molecule. Here are the first five roots for the emission calculation: ...
Bikash Patra's user avatar
9 votes
1 answer
308 views

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: ...
Bruno's user avatar
  • 233
9 votes
1 answer
118 views

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 ...
Patrick's user avatar
  • 99
9 votes
1 answer
327 views

Phonon Calculations and Vibrational Modes

The Raman spectrum of a material shows certain 'active' modes for which we get experimental signatures. Phonon calculations are mostly used to calculate vibrational modes. How can we determine the ...
Shahid Sattar's user avatar
9 votes
2 answers
407 views

Is there an anisotropy factor (g factor) for TDDFT absorption and circular dichroism calculations?

Experimentally, anisotropy factor is calculated by dividing the CD (circular dichroism) spectra by the absorbance spectra and multiplying by a factor of 32980 (in order to get a dimensionless quantity)...
C. Alexander's user avatar
9 votes
1 answer
52 views

Approach for Higher Order Response Properties

There are three (at least that I'm aware of) commonly used approaches to obtain linear response properties (e.g electric polarizability, optical rotation, NMR shielding tensors) Sum over states: The ...
Tyberius's user avatar
  • 15.4k
8 votes
2 answers
1k views

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". ...
S R Maiti's user avatar
  • 6,741
8 votes
2 answers
2k views

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 ...
sarah bnm's user avatar
8 votes
1 answer
134 views

How are molecular rotational states modeled within the Born Oppenheimer Approximation for polyatomic molecules?

Molecular vibrational states associated with an adiabatic electronic state within the Born-Oppenheimer Approximation are typically defined by doing the harmonic approximation for the potential at an ...
Hans Wurst's user avatar
8 votes
1 answer
117 views

What phosphorescence material emits light for a 1 hour period?

I am looking for a phosphorescence material that emits light (400nm - 600nm). The trick is I need the material not to heat up when absorbing or discharging the light, so basically, I hope it maintains ...
Anwar Elhadad's user avatar
8 votes
1 answer
397 views

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 ...
Omar Shehab's user avatar
8 votes
0 answers
234 views

How to reproduce 2D small-angle X-ray scattering (SAXS) interferogram of water via ab-initio MD methods?

I am trying to reproduce the 2D SAXS interference pattern of bulk water via ab initio MD methods as shown in the figure below: The main aim is to recreate figure (a) via averaging MD configurations ...
mykd's user avatar
  • 2,282
8 votes
0 answers
109 views

How to classify ionic and covalent excited-states? [closed]

In spectroscopy it is common to describe excited-states as ionic or covalent. I understand the concept on a toy model e.g. $\ce{H2}$ with a minimal basis set \begin{align} \Phi_0 &= [\chi_A(1) + \...
Cody Aldaz's user avatar
  • 7,997
7 votes
2 answers
167 views

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_\...
benshi97's user avatar
  • 408
7 votes
1 answer
316 views

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,...
diamond999's user avatar
7 votes
1 answer
215 views

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 (...
Mika R.'s user avatar
  • 141
7 votes
1 answer
745 views

Is it possible to simulate the Raman spectra via Molecular Dynamics (MD) using the GROMACS package?

I'm new to molecular dynamics and DFT. The aim was to study the Raman spectra of a molecule in a medium. As we know the Raman spectra of a molecule change due to the induced polarization in the ...
Anoop A Nair's user avatar
  • 4,458
7 votes
1 answer
99 views

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 ...
quantum.puppy's user avatar
7 votes
0 answers
72 views

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 ...
Paulie Bao's user avatar
  • 3,813
7 votes
0 answers
153 views

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 ...
mykd's user avatar
  • 2,282
7 votes
0 answers
66 views

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 ...
mykd's user avatar
  • 2,282
7 votes
0 answers
51 views

How are nematic phases modelled? [closed]

Nematic phases in superconducting materials are studied in both angular-resolved photoelectron spectroscopy (ARPES) and second harmonic generation (SHG) experiments. What techniques, if any, are used ...
2ndQuantized's user avatar
  • 1,021
6 votes
2 answers
393 views

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{\...
L Maxime's user avatar
6 votes
2 answers
231 views

Excited state normal mode frequency doesn't match for NH3

I am trying to optimize the geometry of excited state NH3 and get the corresponding normal modes for excited states. I am trying to get the frequencies as mentioned in this reference. They claim to ...
madhusudana's user avatar
6 votes
1 answer
450 views

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 ...
John's user avatar
  • 63
6 votes
1 answer
113 views

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 ...
More Anonymous's user avatar
6 votes
0 answers
43 views

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 ...
ghawk's user avatar
  • 61
5 votes
2 answers
1k views

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,...
S R Maiti's user avatar
  • 6,741
5 votes
1 answer
2k views

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. ...
John T's user avatar
  • 574
5 votes
1 answer
244 views

GAMESS(US) Hessian calculation sometimes does not produce the IR intensities

I have noticed that for certain Hessian calculations that I run with GAMESS(US), the IR intensities are not produced in the log file. Below I have an example input card (without the molecule $DATA ...
Cavenfish's user avatar
  • 1,222