Analysis of the vibrational properties of crotonaldehyde: DFT vs MD

Main Article Content

Ricardo Ruvalcaba
https://orcid.org/0000-0002-8232-8127
Jonathan Guerrero-Sánchez
https://orcid.org/0000-0003-1457-9677
Noboru Takeuchi

Abstract

Molecular dynamics (MD) and density functional theory (DFT) are currently the most widely used theories in computational materials science. Both have different scopes and applications, but they converge in certain areas. The present work makes a comparison and contrast between the accuracy of both theories to model the infrared spectrum of a simple but representative organic molecule: crotonaldehyde. An analysis of the energies, bond distances, and vibrational frequencies and intensities is carried out to determine the advantages and disadvantages of each theory in this calculation frame.

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How to Cite
Ruvalcaba, R., Guerrero-Sánchez, J., & Takeuchi, N. (2022). Analysis of the vibrational properties of crotonaldehyde: DFT vs MD. Mundo Nano. Interdisciplinary Journal on Nanosciences and Nanotechnology, 15(29), 1e-14e. https://doi.org/10.22201/ceiich.24485691e.2022.29.69707
Section
Research articles

References

ATSDR. (s. f.). Toxfaqs™—Letter a | toxic substance portal | atsdr. (Consultado, noviembre 1, 2021). https://wwwn.cdc.gov/TSP/ToxFAQs/ToxFAQsLanding.aspx

Bhoskar, Ms. T., Kulkarni, Mr. O. K., Kulkarni, Mr. N. K., Patekar, Ms. S. L., Kakandikar, G. M. y Nandedkar, V. M. (2015). Genetic algorithm and its applications to mechanical engineering: A review. Materials Today: Proceedings, 2(4-5): 2624-2630. https://doi.org/10.1016/j.matpr.2015.07.219

Blöchl, P. E. (1994). Projector augmented-wave method. Physical Review B, 50(24): 17953-17979. https://doi.org/10.1103/PhysRevB.50.17953

Braun, E. (2016). Open source code: Calculating an ir spectra from a lammps simulation. Zenodo. https://doi.org/10.5281/ZENODO.154672

Car, R. y Parrinello, M. (1985). Unified approach for molecular dynamics and density-functional theory. Physical Review Letters, 55(22): 2471-2474. https://doi.org/10.1103/PhysRevLett.55.2471

Cataldo, F., Iglesias-Groth, S. y Manchado, A. (2010). Low and high temperature infrared spectroscopy of c 60 and c 70 fullerenes. Fullerenes, Nanotubes and Carbon Nanostructures, 18(3): 224-235. https://doi.org/10.1080/15363831003782940

De Groot, M. S. y Lamb, J. (1957). Ultrasonic relaxation in the study of rotational isomers. Proceedings of the Royal Society of London. Series A. Mathematical and Physical Sciences, 242(1228): 36-56. https://doi.org/10.1098/rspa.1957.0152

Gallezot, P. y Richard, D. (1998). Selective hydrogenation of α,β-unsaturated aldehydes. Catalysis Reviews, 40(1-2): 81-126. https://doi.org/10.1080/01614949808007106

Haley, B. (2016). LAMMPS structure generator. https://doi.org/https://doi.org/10.4231/D34B2X60F

Haubrich, J., Loffreda, D., Delbecq, F., Sautet, P., Krupski, A., Becker, C. y Wandelt, K. (2009). Adsorption of α,β-unsaturated aldehydes on pt(111) and pt−sn alloys: Ii. crotonaldehyde. The Journal of Physical Chemistry C, 113(31): 13947-13967. https://doi.org/10.1021/jp903473m

Honorio, T. (2019). Monte Carlo molecular modeling of temperature and pressure effects on the interactions between crystalline calcium silicate hydrate layers. Langmuir, 35(11): 3907-3916. https://doi.org/10.1021/acs.langmuir.8b04156

Hunter, J. D. (2007). Matplotlib: A 2d graphics environment. Computing in Science y Engineering, 9(3): 90-95. https://doi.org/10.1109/MCSE.2007.55

Infrared: Interpretation. (2013, octubre 2). Chemistry LibreTexts. https://chem.libretexts.org/Bookshelves/Physical_and_Theoretical_Chemistry_Textbook_Maps/Supplemental_Modules_(Physical_and_Theoretical_Chemistry)/Spectroscopy/Vibrational_Spectroscopy/Infrared_Spectroscopy/Infrared%3A_Interpretation

Karhánek, D. (2020). Dakarhanek/vasp-infrared-intensities: Vasp-infrared-intensities (v1.0) [Computer software]. Zenodo. https://doi.org/10.5281/ZENODO.3930989

Kong, L. T. (2011). Phonon dispersion measured directly from molecular dynamics simulations. Computer Physics Communications, 182(10): 2201-2207. https://doi.org/10.1016/j.cpc.2011.04.019

Kresse, G. y Furthmüller, J. (1996). Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set. Physical Review B, 54(16): 11169-11186. https://doi.org/10.1103/PhysRevB.54.11169

Leach, A. R. (2001). Molecular modelling: Principles and applications, Chapter 4: Empirical Force Field Models: Molecular Mechanics, 2a ed. Prentice Hall, 165-247.

Lee, J. W., Nilson, R. H., Templeton, J. A., Griffiths, S. K., Kung, A. y Wong, B. M. (2012). Comparison of molecular dynamics with classical density functional and Poisson–Boltzmann theories of the electric double layer in nanochannels. Journal of Chemical Theory and Computation, 8(6): 2012-2022. https://doi.org/10.1021/ct3001156

Lindenmaier, R., Williams, S. D., Sams, R. L. y Johnson, T. J. (2017). Quantitative infrared absorption spectra and vibrational assignments of crotonaldehyde and methyl vinyl ketone using gas-phase mid-infrared, far-infrared, and liquid raman spectra: S-cis vs s-trans composition confirmed via temperature studies and ab initio methods. The Journal of Physical Chemistry A, 121(6): 1195-1212. https://doi.org/10.1021/acs.jpca.6b10872

Magnasco, V. (2013). Post-hartree–fock methods. En Elementary molecular quantum mechanics. Elsevier, 681-722. https://doi.org/10.1016/B978-0-444-62647-9.00016-6

Momma, K. y Izumi, F. (2011). Vesta 3 for three-dimensional visualization of crystal, volumetric and morphology data. Journal of Applied Crystallography, 44(6): 1272-1276. https://doi.org/10.1107/S0021889811038970

Oukhrib, R., Abdellaoui, Y., Berisha, A., Abou Oualid, H., Halili, J., Jusufi, K., Ait El Had, M., Bourzi, H., El Issami, S., Asmary, F. A., Parmar, V. S. y Len, C. (2021). DFT, Monte Carlo and molecular dynamics simulations for the prediction of corrosion inhibition efficiency of novel pyrazolylnucleosides on Cu(111) surface in acidic media. Scientific Reports, 11(1): 3771. https://doi.org/10.1038/s41598-021-82927-5

Perdew, J. P., Burke, K. y Ernzerhof, M. (1996). Generalized gradient approximation made simple. Physical Review Letters, 77(18): 3865-3868. https://doi.org/10.1103/PhysRevLett.77.3865

Pittalis, S., Proetto, C. R., Floris, A., Sanna, A., Bersier, C., Burke, K. y Gross, E. K. U. (2011). Exact conditions in finite-temperature density-functional theory. Physical Review Letters, 107(16): 163001. https://doi.org/10.1103/PhysRevLett.107.163001

Plimpton, S. J. y Thompson, A. P. (s.f.). Pair_style lj/cut/coul/cut command—Lammps documentation. Retrieved November 1, 2021, from https://docs.lammps.org/pair_lj_cut_coul.html

Pribram-Jones, A., Grabowski, P. E. y Burke, K. (2016). Thermal density functional theory: Time-dependent linear response and approximate functionals from the fluctuation-dissipation theorem. Physical Review Letters, 116(23): 233001. https://doi.org/10.1103/PhysRevLett.116.233001

PubChem. (s. f.-a). Crotonaldehyde. (Consultado, noviembre 1, 2021). https://pubchem.ncbi.nlm.nih.gov/compound/447466

PubChem. (s. f.-b). Hazardous substances data bank (Hsdb): 2871. (Consultado, noviembre 1, 2021). https://pubchem.ncbi.nlm.nih.gov/source/hsdb/2871# section=Human-Health-Effects

Qin, W., Li, X., Bian, W.-W., Fan, X.-J. y Qi, J.-Y. (2010). Density functional theory calculations and molecular dynamics simulations of the adsorption of biomolecules on graphene surfaces. Biomaterials, 31(5): 1007-1016. https://doi.org/10.1016/j.biomaterials.2009.10.013

Rogge, S. M. J., Goeminne, R., Demuynck, R., Gutiérrez‐Sevillano, J. J., Vandenbrande, S., Vanduyfhuys, L., Waroquier, M., Verstraelen, T. y Van Speybroeck, V. (2019). Modeling gas adsorption in flexible metal-organic frameworks via hybrid monte carlo/molecular dynamics schemes. Advanced Theory and Simulations, 2(4): 1800177. https://doi.org/10.1002/adts.201800177

Rohatgi, A. (s. f.). Webplotdigitizer. (Consultado, noviembre 1, 2021). https://automeris.io/WebPlotDigitizer/

Smith, B. (s. f.). Alcohols—The rest of the story. Spectroscopy Online. (Consultado, noviembre 1, 2021). https://www.spectroscopyonline.com/view/alcohols-rest-story-alf3

Software for Chemistry y Materials. (2021). ReaxFF – Force field format specification. https://www.scm.com/doc/ReaxFF/ffield_descrp.html

Thompson, A. P., Aktulga, H. M., Berger, R., Bolintineanu, D. S., Brown, W. M., Crozier, P. S., in ’t Veld, P. J., Kohlmeyer, A., Moore, S. G., Nguyen, T. D., Shan, R., Stevens, M. J., Tranchida, J., Trott, C. y Plimpton, S. J. (2022). LAMMPS – a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales. Computer Physics Communications, 271: 108171. https://doi.org/10.1016/j.cpc.2021.108171

Van Duin, A. C. T., Dasgupta, S., Lorant, F. y Goddard, W. A. (2001). ReaxFF: A reactive force field for hydrocarbons. The Journal of Physical Chemistry A, 105(41): 9396-9409. https://doi.org/10.1021/jp004368u

Wiley, J. y Sons, Inc. (s.f.). Crotonaldehyde—Ftir—Spectrum—Spectrabase. (Consultado, noviembre 1, 2021). https://spectrabase.com/spectrum/69ZANaBjwub

Wu, X., Vanderbilt, D. y Hamann, D. R. (2005). Systematic treatment of displacements, strains, and electric fields in density-functional perturbation theory. Physical Review B, 72(3): 035105. https://doi.org/10.1103/PhysRevB.72.035105

Zhang, L., Zhou, M., Wang, A. y Zhang, T. (2020). Selective hydrogenation over supported metal catalysts: From nanoparticles to single atoms. Chemical Reviews, 120(2): 683-733. https://doi.org/10.1021/acs.chemrev.9b00230