Bağlanma Enerjilerinin Doğru Tanımlanması için Uygun Bir Baz Setinin Seçilmesi: Bir İlk-İlkeler Yöntemi Çalışması

Ar2 and H2 dimerlerinin bağlanma enerjileri korelasyon- uyumlu ccpVXZ ve aug-cc-pVXZ baz setleri kullanılarak ikili ve üçlü pertürbatif çiftlenimli küme yöntemi ile incelendi. Baz seti noksanlık hatalarını azaltmak için tam baz limitine iki noktalı ekstrapolasyon tekniği uygulandı. Elde edilen teorik bağlanma enerjilerinin literatürdeki mevcut deneysel bağlanma enerjilerinden farkının hem Ar2 hem de H2 dimerleri için 1kcal/mol’den daha az olduğu gözlendi.

Selection of an Appropriate Basis Set for Accurate Description of Binding Energy: A First Principles Study

Binding energies of Ar2 and H2 dimers have been investigated using correlation consistent cc-pVXZ and aug-cc-pVXZ basis sets together with Coupled Cluster with Singles and Doubles with Perturbative Triples (CCSD(T)) method. Two point extrapolations to complete basis set limit has been applied to reduce basis set incompleteness (BSIE) error. Discrepancy of our theoretical binding energy values from current experimental binding energy values in literature both for Ar2 and H2 dimers observed to be less than 1kcal/mol.

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Lide, D. R. (ed.). 1998. Chemical Rubber Company handbook of chemistry and physics, CRC Press, Boca Raton, Florida, USA, 79th edition.
Halkier, A., Helgaker, T., Jorgensen, P., Klopper, W., Olsen, K. H. J., Wilson, A. K. 1998. Basis-set convergence in correlated calculations on Ne, N, and H2O. Chemical Physics Letters, 286(1998), 243-252.
Ruzzinsky, A., Perdew, J. P., Gabor, C. I. 2005. Binding energy curves from nonempirical density functionals II. van der Waals bonds in rare-gas and alkaline-earth diatomics. Journal of Physical Chemistry A, 109(2005), 11015-21.
[68] Schütz, M., Maschio, L., Karttunen, A. J., Usvyat, D. 2017. Exfoliation Energy of Black Phosphorus Revisited: A Coupled Cluster Benchmark. Journal of Physical Chemistry Letters, 8(2017), 1290- 1294.
Boschen, J. S., Theis, D., Ruedenberg, K., Windus, T. L . 2017. Correlation energy extrapolation by many-body expansion. The Journal of Physical Chemistry A, 121(2017), 836-844.
Olsson, M. A., Ryde, U. 2017. Comparison of QM/MM methods to obtain ligand-binding free energies. Journal of Chemical Theory and Computation, 13(2017), 2245-2253.
Elm, J., Kristensen, K. 2017. Basis set convergence of the binding energies of strongly hydrogen-bonded atmospheric clusters. 19(2017), 1122-1133.
Deible, M. J., Kessler, M., Gasperich, K. E., Jordan, K. D. 2015. Quantum Monte Carlo calculation of the binding energy of the beryllium dimer. Journal of Chemical Physics, 143(2015), 084116.
Tuma, C., Boese, A. D., Handy, N. C. 1999. Predicting the binding energies of H-bonded complexes: A comparative DFT study. Physical Chemistry Chemical Physics, 1(1999), 3939.
Sinnokrot, M. O., Valeev, E. F., Sherrill, C. D. 2002. Estimates of the ab initio limit for π− π interactions: the benzene dimer. Journal of American Chemical Society, 124(2002), 10887.
Lee, J. S. 2005. Accurate ab initio binding energies of alkaline earth metal clusters Journal of Physical Chemistry A, 109(2005), 11927- 11932.
Pieniazek, P. A., Krylov, A. I., Bradforth, S. E. 2007. Electronic structure of the benzene dimer cation. Journal of Chemical Physics, 127(2007), 044317.
Johll, H., Kang, H. C., Tok, E. S. 2009. Density functional theory study of Fe, Co, and Ni adatoms and dimers adsorbed on graphene. Physical Review B, 79(2009), 245416.
Yousaf, K. E., Brothers, E. N. 2010. Applications of Screened Hybrid Density Functionals with Empirical Dispersion Corrections to Rare Gas Dimers and Solids. Journal of Chemical Theory and Compution, 8(2010), 864-872.
Zadorozhnaya, A. A., Krylov, A. I. 2010. Ionization-Induced Structural Changes in Uracil Dimers and Their Spectroscopic Signatures. Journal of Chemical Theory and Compution, 6(2010), 705-717.
Kreutzer, J., Blaha, P., Schubert, U. 2016. Assessment of different basis sets and DFT functionals for the calculation of structural parameters, vibrational modes and ligand binding energies of Zr4O2(carboxylate)12 clusters. Computational and Theoretical Chemistry, 1084(2016), 162-168.
Song, X. D., Zhao, Y. F., Zhang, G. H., Zhang, P. X. 2011. Theoretical study on structures, binding energies and vibrational spectra of M+(H2O)2Ar(M = Cu, Ag, Au). Computational and Theoretical Chemistry 2011, 963, 290-293.
Johll, H., Tok, E. S., Kang, H. C. 2011. Structure and properties of pure and mixed transition metal dimers on graphene. International Journal of Nanotechnology, 8(2011), 825.
Miliordos, E., Apra, E., Xantheas, S. S. 2014. Benchmark theoretical study of the π–π binding energy in the benzene dimer. Journal of Physical Chemistry A, 118(2014), 7568-7578.
Pimienta Ian, S. O. 2015. Computational Study of Monosubstituted Azo(tetrazolepentazolium)- Based Ionic Dimers. Journal of Physical Chemistry A, 119(2015), 5826-5841.
Antony, J., Grimme, S. 2006. Density functional theory including dispersion corrections for intermolecular interactions in a large benchmark set of biologically relevant molecules. Physical Chemistry Chemical Physics, 8(2006), 5287-5293.
Simon, S., Duran, M., Dannenberg, J. J. 1996. How does basis set superposition error change the potential surfaces for hydrogen-bonded dimers?. Journal of Chemical Physics, 105(1996), 11024.
Almlöf, J. 1991. Atomic natural orbital (ANO) basis sets for quantum chemical calculations. Advances Quantum Chemistry, 22(1991), 301- 373.
Almlöf, J., Taylor, P. R. 1990. General contraction of Gaussian basis sets. II. Atomic natural orbitals and the calculation of atomic and molecular properties. Journal of Chemical Physics, 92(1990), 551.
Almlöf, J., Taylor, P. R. 1987. General contraction of Gaussian basis sets. I. Atomic natural orbitals for first- and second-row atoms. Journal of Chemical Physics. 86(1987), 4070.
Feller, D., Peterson, K. A. 1998. An examination of intrinsic errors in electronic structure methods using the EMSL computational results database and the G2 set. Journal of Chemical Physics. 108(1998), 154.
Peterson, K. A. 2003. Systematically convergent basis sets with relativistic pseudopotentials. I. Correlation consistent basis sets for the post-d group 13–15 elements. Journal of Chemical Physics, 119(2003), 11099-11112.
Balabanov, N. B., Peterson, K. A. 2005. Systematically convergent basis sets for transition metals. I. All-electron correlation consistent basis sets for the 3d elements Sc-Zn. Journal of Chemical Physics, 123(2005), 064107.
Hariharan, P. C., Pople, J. A. 1973. The influence of polarization functions on molecular orbital hydrogenation energies. Theoretical Chimimica Acta, 28(1973), 213-222.
Krishnan, R., Binkley, J. S., Seeger, R., Pople, J. A. 1980. Self-consistent molecular orbital methods. XX. A basis set for correlated wave functions. Journal of Chemical Physics. 72(1980), 650.
Hehre, W. J., Ditchfield, R., Pople, J. A. 1972. Self—Consistent Molecular Orbital Methods. XII. Further Extensions of Gaussian—Type Basis Sets for Use in Molecular Orbital Studies of Organic Molecules. Journal of Chemical Physics, 56(1972), 2257.
Gordon, M. S., Binkley, J. S., Pople, J. A., Pietro, W. J., Hehre, W. J. 1982. Self-consistent molecularorbital methods. 22. Small split-valence basis sets for second-row elements. Journal of American Chemical Society, 104(1982), 2797- 2803.
Binkley, J. S., Pople, J. A., Hehre, W. J. 1980. Selfconsistent molecular orbital methods. 21. Small split-valence basis sets for first-row elements. Journal of American Chemical Society, 102(1980), 939-947.
Hehre, W. J., Ditchfield, R., Stewart, R. F.; Pople, J. A. 1970. Self-Consistent Molecular Orbital Methods. IV. Use of Gaussian Expansions of Slater-Type Orbitals. Extension to Second-Row Molecules. Journal of Chemical Physics, 52(1970), 2769.
Hehre, W. J., Stewart, R. F., Pople, J. A. 1969. SelfConsistent Molecular-Orbital Methods. I. Use of Gaussian Expansions of Slater-Type Atomic Orbitals. Journal of Chemical Physics, 51(1969), 2657.
Peterson, K. A., Dunning, T. H. 2002. Accurate correlation consistent basis sets for molecular core-valence correlation effects: The second row atoms Al-Ar, and the first row atoms B-Ne revisited. Journal of Chemical Physics, 117(2002), 10548-10560.
Woon, D. E., Dunning, T. H. 1993. Gaussian basis sets for use in correlated molecular calculations. III. The atoms aluminum through argon. Journal of Chemical Physics, 98(1993), 1358-1371.
Woon, D. E., Dunning, T. H. 1993. Calculation of the electron affinities of the second row atoms: Al-Cl. Journal of Chemical Physics, 99(1993), 3730-3737.
Dunning, T. H., Peterson, K. A., Wilson, A. K. 2001. Gaussian basis sets for use in correlated molecular calculations. X. The atoms aluminum through argon revisited. Journal of Chemical Physics, 2001, 114(2001), 9244.
Dunning, T. H. 1971. Gaussian basis functions for use in molecular calculations. III. Contraction of (10s6p) atomic basis sets for the first-row atoms. Journal of Chemical Physics, 55(1971), 716-723.
Dunning, T. H. 1970. Gaussian Basis Functions for Use in Molecular Calculations. I. Contraction of (9s5p) Atomic Basis Sets for First-Row Atoms. The Journal of Chemical Physics, 53(1970), 2823.
Kendall, R. A., Dunning, T. H., Harrison, R. 1992. Electron affinities of the first-row atoms revisited. Systematic basis sets and wave functions. Journal of Chemical Physics, 1992, 96(1992), 6796.
Dunning, T. H. 1989. Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen. Journal of Chemical Phyics, 90(1989), 1007- 1023.
[28] Wahnon, P., Tablero, C. 2002. Ab initio electronic structure calculations for metallic intermediate band formation in photovoltaic materials. Physical Review B 65(2002), 165115.
Tsolakidis, A., Sanchez-Portal, D., Martin, R. M. 2002. Calculation of the optical response of atomic clusters using time-dependent density functional theory and local orbitals. Physical Review B, 66(2002), 235416.
Dunning, T. H. 2000. A Road Map for the Calculation of Molecular Binding Energies. Journal of Physical Chemistry A, 104(2000), 9062-9080.
Neese, F. 2003. A spectroscopy oriented configuration interaction procedure. Journal of Chemical Physics, 119(2003), 9428.
Neese, F. J. 2007. Calculation of the zero-field splitting tensor on the basis of hybrid density functional and Hartree-Fock theory. Chemical Physics, 127(2007), 164112.
Neese, F., Wennmohs, F., Hansen, A., Becker, U. 2009. Efficient, approximate and parallel Hartree–Fock and hybrid DFT calculations. A ‘chain-of-spheres’ algorithm for Hartree-Fock exchange. Chemical Phyics, 356(2009), 98-109.
P. Rani, P., Jindal, V. K. 2013. Designing band gap of graphene by B and N dopant atoms, RCS Advances, 3(2013), 802-812.
Zahid, F., Lake, R. R. 2010. Thermoelectric properties of Bi2Te3 atomic quintuple thin films. Applied Physics Letters, 97(2010), 212102.
A. Tkatchenko, A., Jr. DiStasio, R. A., Car, R., Scheffler, M. 2012. Accurate and efficient method for many-body van der Waals interactions. Physical Review Letters, 108(2012), 236402.
Ugeda, M. M., Brihuega, F., Guinea, J. M., GomezRodriguez. 10. Missing Atom as a Source of Carbon Magnetism. Physical Review Letters, 104(2010), 096804.
Setyawan, W., 2010. Curtarolo, S. Highthroughput electronic band structure calculations: Challenges and and tools Compuational Material Science, 49(2010), 299- 312.
Hafner, J. 2008. Ab-initio simulations of materials using VASP: Density-functional theory and beyond. Journal of Compuational Chemistry, 29(2008), 2044-2078.
Neese, F. 2012. The ORCA program system. Wires Compuational Molecular Science, 2(2012), 73-78.
Soler, J. M., Artacho, E., Gale, J. D., Garcia, A., Unquera, J. J., Ordejon, P., Sanchez-Portal, D. 2002. The SIESTA method for ab initio order- N materials simulation. Journal of Physics Condensed Matter, 14(2002), 2745-2779.
Giannozzi, P., Baroni, S., Bonini, N., Calandra, M., Car, R., Cavazzoni, C., Ceresoli, D., Chiarotti, G. L., Cococ cioni, M., Dabo, I., Dol Corso, A., De Groncoli, S., Fabris, S., Fratesi, G., Gebauer, R., Gerstmann, U., Gou goussis, C., Kokalj, A., Lazzeri, M., Martin-Samos, L., Marzari, N., Mauri, F., Mazzarello, R., Paolini, S., Pasquarello, A., Paulatto, L., Sbraccia, C., Seitsonen, A. P., Smogunov, A., Umari, P., Wentzcovitch, R. M. 2009. QUANTUM ESPRESSO: a modular and open-source software project for quantum simulation of materials. Journal of Physics Condensed Matter, 21(2009), 395502.
Kresse, G., Furthmuller, J. 1996. Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set. Physical Review B, 54(1996), 11169.
Karakaya, M., Sert, Y., Kurekci, M., Eskiyurt, B., Cirak, C. 2015. Theoretical and experimental investigations on vibrational and structural properties of tolazamide. Journal of Molecular Structure 1095(2015), 87-95.
Tkatchenko, A., Scheffler, M. 2009. Accurate molecular van der Waals interactions from ground-state electron density and free-atom reference data. Physical Review Letters, 102(2009), 073005.
Marzari, N., Vanderbilt, D. 1997. Maximally localized generalized Wannier functions for composite energy bands. Physical Review B, 57(1997), 12845.
Onida, G., Reining, L., Rubio, A. 2002. Electronic excitations: density-functional versus manybody Green’s-function approaches. Review of Modern Physics, 74(2002), 601.
Mete, E., Yilmaz, A., Danışman, M. F. 2016. A van der Waals density functional investigation of carboranethiol self-assembled monolayers on Au (111). Physical Chemistry Chemical Physics, 18(2016), 12920-12927.
Gece, G., Bigiç, S. 2010. A theoretical study on the inhibition efficiencies of some amino acids as corrosion inhibitors of nickel. Corrosion Science 55(2010), 3304-3308.
Gece, G. 2008. The use of quantum chemical methods in corrosion inhibitor studies. Corrosion Science 50 (2008), 2981-2992.
Boukhvalov, D. W., Katsnelson, M. I.;, Lichtenstein, A. I. 2008. Hydrogen on graphene: Electronic structure, total energy, structural distortions, and magnetism from first-principles calculations. Physical Review B, 77(2008), 035427.
Yoffe, A.D. 2001. Semiconductor quantum dots and related systems: Electronic, optical, luminescence and related properties of low dimensional systems. Advances in Physics. 50(2001), 1-208.
Nazarian, D., Camp, J.S, Chung, Y.G, Snurr, R.Q., Sholl, D.S. 2017. Large-Scale Refinement of Metal−Organic Framework Structures Using Density Functional Theory. Chemistry of Materials, 29(2017), 2521-2528.
Moreels, I., Lambert, K. D., Muyncuk Smeets, D., Nollet, T., Martins, J. C., Vanhaecke, F., Vantomme, A., Delerue, C., Allan, G., Hens, Z. 2009. Size-Dependent Optical Properties of Colloidal PbS Quantum Dots. ACS NANO, 3(2009), 3023.
Shi, H. L., Pan, H., Zhang, Y. W., Yakobson, B. I. 2013. Quasiparticle band structures and optical properties of strained monolayer MoS2 and WS2. Physical Review B, 87(2013), 155304.