Questions tagged [spectroscopy]

For questions about spectroscopy.

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5
votes
1answer
53 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. ...
5
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0answers
36 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 ...
6
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0answers
40 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 ...
4
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0answers
36 views

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?
9
votes
1answer
61 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 ...
5
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1answer
180 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 ...
7
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2answers
97 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_\...
13
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1answer
303 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 ...
9
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2answers
158 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, ...
12
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2answers
121 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?
10
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2answers
86 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 ...
8
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1answer
180 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: ...
13
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1answer
124 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 ...
8
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1answer
84 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 ...
15
votes
3answers
529 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 ...
6
votes
2answers
189 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 ...
10
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2answers
109 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.
7
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0answers
55 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 ...
9
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1answer
103 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: ...
5
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1answer
66 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 ...
7
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0answers
39 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 ...
9
votes
1answer
102 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: ...
8
votes
1answer
110 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 ...
15
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1answer
233 views

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 ...
9
votes
1answer
70 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 ...
13
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1answer
97 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 ...
6
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0answers
39 views

How are nematic phases modelled?

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 ...
6
votes
1answer
136 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 ...
16
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1answer
304 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 ...
7
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0answers
84 views

How to classify ionic and covalent excited-states?

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) + \...
8
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1answer
81 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 ...
8
votes
1answer
34 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 ...
17
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5answers
2k 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 ...
11
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1answer
98 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 ...
9
votes
1answer
70 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)...
12
votes
1answer
95 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 ...
13
votes
2answers
447 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,...