Abstract
The interactions that occur within hemeproteins are important for biological systems and they are of interest for understanding living systems. In this way, it is important to know the vibrational and electrostatic interactions in this system. In this article, a study is made using a new approach to describe the interaction between iron ions and carbon monoxide inside spherical cavities that mimic volumes of protein cavities in three different media (vacuum, water and ice). We use an alternative trial wavefunction as an ansatz in the Variational Method for the calculation of the energy for a confined ion–dipole system. This trial function is inspired by Supersymmetric Quantum Mechanics. One of the results obtained is the value of the ground state energy of this interaction in a vacuum inside a spherical cavity of radius approximately equal to 12 Bohr radius obtained by the Variational Method. This result is compared with the energy value obtained by the second order Moller–Plesset perturbative method and there is a difference of approximately 1.9 10\(^{-3}\) hartree (3.87\( \%\)).
Graphical abstract
Similar content being viewed by others
Data Availability Statement
This manuscript has associated data in a data repository. [Authors’ comment: The datasets generated during and/or analysed during the current study are available from the corresponding author on reasonable request.]
References
D. Shapiro, R.A. Goldbeck, D. Che, R.M. Esquerra, S.J. Paquette, D.S. Kliger, Biophys. J. 68, 326 (1995)
B. Kushkuley, S.S. Stavrov, Biophys. J. 70, 1214 (1996)
M. Tsubaki, R.B. Srivastava, N.T. Yu, Biochemistry 21, 1132 (1982)
T.G. Spiro, A.V. Soldatova, G. Balakrishnan, Coord. Chem. Rev. 257, 511 (2013)
C.E. Martin, C.S. Castan, F.J.L. Garriga, A.B.C. Badia, Drug Discov. Today Technol. 17, 22 (2015)
Y. Sun, W. Zeng, A. Benabbas, X. Ye, I. Denisov, S.G. Sligar, J. Du, J.H. Dawson, P.M. Champion, Biochemistry 52, 5941 (2013)
C. Weber, D.J. Cole, D.D. O’Regan, M.C. Payne, Proc. Natl. Acad. Sci. 111, 5790 (2014)
L.A. Solomon, J.B. Kronenberg, H.C. Fry, J. Am. Chem. Soc. 139, 8497 (2017)
O. González-Blanco, V. Branchadell, J. Chem. Phys. 110, 778 (1999)
R.M. Sosa, P. Gardiol, G. Beltrame, Int. J. Quantum Chem. 69, 371 (1998)
P.W. Villalta, D.G. Leopold, J. Chem. Phys. 98, 7730 (1993)
E. Ley-Koo, Rev. Mex. de FÃsica 64, 326 (2018)
R.L. Koder, J.R. Anderson, L.A. Solomon, K.S. Reddy, C.C. Moser, P.L. Dutton, Nature 458, 305 (2009)
F. Nastri, M. Chino, O. Maglio, A. Bhagi-Damodaran, Y. Lu, A. Lombardi, Chem. Soc. Rev. 45, 5020 (2016)
C.W. Rausch, M. Feola, Extra pure semi-synthetic blood substitute (1992), US Patent 5,084,558
K. Yamada, K. Yokomaku, M. Kureishi, M. Akiyama, K. Kihira, T. Komatsu, Sci. Rep. 6, 36782 (2016)
F.R. Silva, E. Drigo Filho, Chem. Phys. Lett. 498, 198 (2010)
L.I. Schiff, Quantum Mechanics 1968 (McGraw-Hill, New York, 1968)
H.D.O. Batael, E. Drigo Filho, Theoretical Chemistry Accounts 137 (2018)
F. Cooper, A. Khare, U. Sukhatme, Phys. Rep. 251, 267 (1995)
E. Drigo Filho, R.M. Ricotta, Phys. Lett. A 320, 95 (2003)
L.E. Gendenshtein, I.V. Krive, Phys. Uspekhi 28, 645 (1985)
M. Frisch, G. Trucks, H. Schlegel, G. Scuseria, M. Robb, J. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. Petersson et al., Inc., Wallingford CT (2009)
S.A. Cruz, R. Colín-Rodríguez, Int. J. Quantum Chem. 109, 3041 (2009)
F. Weinhold, J. Chem. Phys. 54, 530 (1971)
R. Colín-Rodríguez, S.A. Cruz, J. Phys. B Atomic Mol. Opt. Phys. 43, 235102 (2010)
R. Colín-Rodríguez, C. Díaz-García, S. Cruz, J. Phys. B Atomic Mol. Opt. Phys. 44, 241001 (2011)
G.M. Longo, S. Longo, D. Giordano, Plasma Sources Sci. Technol. 24, 065019 (2015)
J.F. da Silva, F.R. Silva, E. Drigo Filho, Int. J. Quantum Chem. 116, 497 (2016)
L. Infeld, T. Hull, Rev. Mod. Phys. 23, 21 (1951)
C.S. Jia, J.Y. Wang, S. He, L.T. Sun, J. Phys. A Math. Gen. 33, 6993 (2000)
C. Sukumar, J. Phys. A Math. Gen. 18, 2917 (1985)
R. Dutt, A. Khare, U.P. Sukhatme, Am. J. Phys. 56, 163 (1988)
G. Borges, E. Drigo Filho, R. Ricotta, Phys. A Stat. Mech. Appl. 389, 3892 (2010)
M. Ioffe, E. Kolevatova, D. Nishnianidze, Phys. Lett. A 380, 3349 (2016)
D. Cevik, M. Gadella, S. Kuru, J. Negro, Phys. Lett. A 380, 1600 (2016)
E. Drigo Filho, R.M. Ricotta, Phys. Lett. A 269, 269 (2000)
G.R.P. Borges, E. Drigo Filho, Int. J. Mod. Phys. A 16, 4401 (2001)
J.N. Israelachvili, Intermolecular and Surface Forces (Academic Press, Cambridge, 2011)
Appendix. A table of dipole moments, Vol. 30 (The Royal Society of Chemistry, 1934), https://doi.org/10.1039/TF93430BB00I
M. Milani, A. Pesce, Y. Ouellet, S. Dewilde, J. Friedman, P. Ascenzi, M. Guertin, M. Bolognesi, J. Biol. Chem. 279, 21520 (2004)
J. Liang, C. Woodward, H. Edelsbrunner, Protein Sci. 7, 1884 (1998)
I. Boron, J.P. Bustamante, K.S. Davidge, S. Singh, L.A. Bowman, M. Tinajero-Trejo, S. Carballal, R. Radi, R.K. Poole, K. Dikshit et al., F1000Research 4 (2015)
S.S. Stavrov, Biomed. Spectrosc. Imaging 3, 261 (2014)
S. Sonavane, P. Chakrabarti, PLoS Comput. Biol. 4, e1000188 (2008)
V. Barone, M. Cossi, J. Phys. Chem. A 102, 1995 (1998)
R. Improta, V. Barone, G. Scalmani, M.J. Frisch, J. Chem. Phys. 125, 054103 (2006)
P. Bohleber, N. Wagner, O. Eisen, Cold Reg. Sci. Technol. 83, 13 (2012)
C.G. Malmberg, A.A. Maryott, J. Res. Natl. Bur. Stand. 56, 1 (1956)
M.M. Gonzalez, K. Bravo-Rodriguez, R. Suardiaz, J.M.G. de la Vega, L.A. Montero, E. Sanchez-Garcia, R. Crespo-Otero, Theoretical Chemistry Accounts 134, (2015)
D.L. Nelson, A.L. Lehninger, M.M. Cox, Lehninger Principles of Biochemistry (Macmillan, New York, 2008)
Acknowledgements
We would like to thank Gridunesp for making the Gaussian 09 software available and, also, we thank Capes and FAPESP (2017/01757-9) for their financial support.
Author information
Authors and Affiliations
Contributions
All the authors were involved in the preparation of the manuscript. All the authors have read and approved the final manuscript.
Corresponding author
Additional information
Guest editors: C.N. Ramachandran, Vincenzo Aquilanti, Henry Ed Montgomery and N. Sathyamurthy.
Rights and permissions
About this article
Cite this article
da Silva, J.F., Caruso, Í.P. & Drigo Filho, E. Interaction between iron ion and dipole carbon monoxide inside spherical cavities. Eur. Phys. J. D 75, 22 (2021). https://doi.org/10.1140/epjd/s10053-020-00018-y
Received:
Accepted:
Published:
DOI: https://doi.org/10.1140/epjd/s10053-020-00018-y