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Journal of Chemical Physics / Volume 136 / Issue 2 / ARTICLES / Theoretical Methods and Algorithms
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J. Chem. Phys. 136, 024101 (2012); http://dx.doi.org/10.1063/1.3670417 (14 pages)

Electronic structure calculations in arbitrary electrostatic environments

Mark A. Watson, Dmitrij Rappoport, Elizabeth M. Y. Lee, Roberto Olivares-Amaya, and Alán Aspuru-Guzik

Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA

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(Received 3 November 2011; accepted 28 November 2011; published online 9 January 2012)

Modeling of electronic structure of molecules in electrostatic environments is of considerable relevance for surface-enhanced spectroscopy and molecular electronics. We have developed and implemented a novel approach to the molecular electronic structure in arbitrary electrostatic environments that is compatible with standard quantum chemical methods and can be applied to medium-sized and large molecules. The scheme denoted CheESE (chemistry in electrostatic environments) is based on the description of molecular electronic structure subject to a boundary condition on the system/environment interface. Thus, it is particularly suited to study molecules on metallic surfaces. The proposed model is capable of describing both electrostatic effects near nanostructured metallic surfaces and image-charge effects. We present an implementation of the CheESE model as a library module and show example applications to neutral and negatively charged molecules.

© 2012 American Institute of Physics

Article Outline

  1. INTRODUCTION
  2. THEORY AND IMPLEMENTATION
    1. Background
    2. The CheESE model
    3. Interpreting the environment potential
    4. Solving the nonlinear Schrödinger equation
    5. Obtaining the environment potential
  3. BENCHMARKS AND APPLICATIONS
    1. Computational details
    2. Specification of the boundary conditions
    3. Energy calculations with Φ fixed ( s ) = 0
    4. Energy calculations with Φ fixed ( s ) ≠ 0
    5. Molecular orbital tuning
  4. CONCLUSION

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KEYWORDS and PACS

Keywords

density functional theory, molecular electronic states

PACS

ARTICLE DATA

Digital Object Identifier
http://dx.doi.org/10.1063/1.3670417

PUBLICATION DATA

ISSN

0021-9606 (print)  
1089-7690 (online)

Publisher

$abstract.society.value is a Member of CrossRef American Institute of Physics

  1. L. Vogt, R. Olivares-Amaya, S. Kermes, Y. Shao, C. Amador-Bedolla, and A. Aspuru-Guzik, J. Phys. Chem. A 112, 2049 (2008). [Inspec] [MEDLINE] [CAS]
  2. I. S. Ufimtsev and T. J. Martinez, Comput. Sci. Eng. 10, 26 (2008).
  3. I. S. Ufimtsev and T. J. Martinez, J. Chem. Theory Comput. 5, 1004 (2009).
  4. R. Olivares-Amaya, M. A. Watson, R. G. Edgar, L. Vogt, Y. Shao, and A. Aspuru-Guzik, J. Chem. Theory Comput. 6, 135 (2010).
  5. M. Watson, R. Olivares-Amaya, R. G. Edgar, and A. Aspuru-Guzik, Comput. Sci. Eng. 12, 40 (2010).
  6. G. C. Schatz, Proc. Natl. Acad. Sci. U.S.A. 104, 6885 (2007). [MEDLINE]
  7. Advances in the Atomic-Scale Modeling of Nanosystems and Nanostructured Materials, Lecture Notes in Physics Vol. 795 , edited by C. Massobrio, H. Bulou, and C. Goyhenex (Springer, Heidelberg, 2010).
  8. Nanomaterials: Design and Simulation, Theoretical and Computational Chemistry Vol. 18, edited by P. B. Balbuena and J. M. Seminario (Elsevier, Amsterdam, 2007).
  9. Surface-Enhanced Raman Scattering: Physics and Applications, Topics in Applied Physics No. 103, K. Kneipp, M. Moskovits, and H. Kneipp (Springer, Berlin, 2006).
  10. R. Aroca, Surface Enhanced Vibrational Spectroscopy (Wiley, Chichester, 2006).
  11. E. C. Le Ru and P. G. Etchegoin, Principles of Surface-Enhanced Raman Spectroscopy and Related Plasmonic Effects (Elsevier, Amsterdam, 2008).
  12. P. L. Stiles, J. A. Dieringer, N. C. Shah, and R. P. Van Duyne, Annu. Rev. Anal. Chem. 1, 601 (2008). [MEDLINE]
  13. A. Campion and P. Kambhampati, Chem. Soc. Rev. 27, 241 (1998).
  14. A. Pecchia and A. D. Carlo, Rep. Prog. Phys. 67, 1497 (2004).
  15. W. Y. Kim, Y. C. Choi, S. K. Min, Y. Cho, and K. S. Kim, Chem. Soc. Rev. 38, 2319 (2009). [MEDLINE]
  16. H. Phillips, A. Prociuk, and B. D. Dunietz, J. Chem. Phys. 134, 054708 (2011)JCPSA6000134000005054708000001. [MEDLINE]
  17. S. Kuhn, G. Mori, M. Agio, and V. Sandoghdar, Mol. Phys. 106, 893 (2008). [Inspec]
  18. M. Tsutsui, M. Taniguchi, K. Yokota, and T. Kawai, Nat. Nanotechnol. 5, 286 (2010). [MEDLINE]
  19. P.-O. Löwdin, J. Chem. Phys. 19, 1396 (1951)JCPSA6000019000011001396000001. [ISI]
  20. R. McWeeny, in Advances in Quantum Chemistry, edited by J. R. Sabin, M. C. Zerner, E. Brändas, S. Wilson, J. Maruani, Y. G. Smeyers, P. J. Grout, and R. McWeeny (Academic, New York, 1998), Vol. 31, pp. 15–35.
  21. K. Kitaura, E. Ikeo, T. Asada, T. Nakano, and M. Uebayasi, Chem. Phys. Lett. 313, 701 (1999).
  22. M. S. Gordon, J. M. Mullin, S. R. Pruitt, L. B. Roskop, L. V. Slipchenko, and J. A. Boatz, J. Phys. Chem. B 113, 9646 (2009).
  23. Y. Okiyama, T. Nakano, K. Yamashita, Y. Mochizuki, N. Taguchi, and S. Tanaka, Chem. Phys. Lett. 490, 84 (2010).
  24. T. Fujita, T. Nakano, and S. Tanaka, Chem. Phys. Lett. 506, 112 (2011).
  25. J. Tomasi and M. Persico, Chem. Rev. 94, 2027 (1994).
  26. J. Tomasi, B. Mennucci, and R. Cammi, Chem. Rev. 105, 2999 (2005).
  27. A. Klamt and G. Schüürmann, J. Chem. Soc., Perkin Trans. 2 1993, 799.
  28. A. Klamt, J. Phys. Chem. 99, 2224 (1995).
  29. A. Warshel and M. Levitt, J. Mol. Biol. 103, 227 (1976). [MEDLINE]
  30. M. J. Field, P. A. Bash, and M. Karplus, J. Comput. Chem. 11, 700 (1990). [Inspec] [ISI] [CAS]
  31. H. M. Senn and W. Thiel, in Atomistic Approaches in Modern Biology, edited by M. Reiher (Springer, Berlin Heidelberg, 2007), Vol. 268, pp. 173–290.
  32. G. C. Schatz, Acc. Chem. Res. 17, 370 (1984). [ISI]
  33. M. Moskovits, Rev. Mod. Phys. 57, 783 (1985).
  34. M. Stockman, in Surface-Enhanced Raman Scattering, edited by K. Kneipp, M. Moskovits, and H. Kneipp (Springer, Berlin Heidelberg, 2006), Vol. 103, Chap. 3, pp. 47–65.
  35. A. Otto, J. Raman Spectrosc. 36, 497 (2005). [ISI]
  36. L. Zhao, L. Jensen, and G. C. Schatz, J. Am. Chem. Soc. 128, 2911 (2006). [MEDLINE] [CAS]
  37. S. M. Morton and L. Jensen, J. Am. Chem. Soc. 131, 4090 (2009). [MEDLINE] [CAS]
  38. S. K. Saikin, R. Olivares-Amaya, D. Rappoport, M. Stopa, and A. Aspuru-Guzik, Phys. Chem. Chem. Phys. 11, 9401 (2009).
  39. K. Yee, IEEE Trans. Antennas Propag. 14, 302 (1966).
  40. A. Taflove and S. C. Hagness, Computational Electrodynamics: The Finite-Difference Time-Domain Method, 3rd ed. (Artech House, Norwood, MA, 2005).
  41. D. J. Masiello and G. C. Schatz, Phys. Rev. A 78, 042505 (2008).
  42. D. J. Masiello and G. C. Schatz, J. Chem. Phys. 132, 064102 (2010)JCPSA6000132000006064102000001. [MEDLINE]
  43. J. M. McMahon, S. K. Gray, and G. C. Schatz, Phys. Rev. Lett. 103, 097403 (2009). [MEDLINE]
  44. J. M. McMahon, S. K. Gray, and G. C. Schatz, Nano Lett. 10, 3473 (2010).
  45. H. Chen, J. M. McMahon, M. A. Ratner, and G. C. Schatz, J. Phys. Chem. C 114, 14384 (2010).
  46. S. Corni and J. Tomasi, J. Chem. Phys. 116, 1156 (2002)JCPSA6000116000003001156000001. [ISI]
  47. S. Corni and J. Tomasi, in Surface-Enhanced Raman Scattering, Topics in Applied Physics Vol. 103, edited by K. Kneipp, M. Moskovits, and H. Kneipp (Springer, Berlin, Heidelberg, 2006), pp. 105–123.
  48. R. Olivares-Amaya, M. Stopa, X. Andrade, M. A. Watson, and A. Aspuru-Guzik, J. Phys. Chem. Lett. 2, 682 (2011).
  49. A. Castro, H. Appel, M. Oliveira, C. A. Rozzi, X. Andrade, F. Lorenzen, M. A.L. Marques, E. K.U. Gross, and A. Rubio, Phys. Status Solidi B 243, 2465 (2006)
    see http://www.tddft.org/programs/octopus/.
  50. P. Pulay, Chem. Phys. Lett. 73, 393 (1980).
  51. M. A. Watson, Y. Kurashige, T. Nakajima, and K. Hirao, J. Chem. Phys. 128, 054105 (2008)JCPSA6000128000005054105000001. [MEDLINE]
  52. L. E. McMurchie and E. R. Davidson, J. Comput. Phys. 26, 218 (1978).
  53. DALTON2011, a molecular electronic structure program (2011), see http://www.daltonprogram.org.
  54. A. D. Becke, J. Chem. Phys. 98, 5648 (1993).
  55. S. R. Kass, J. Am. Chem. Soc. 127, 13098 (2005).
  56. Y. C. Choi, W. Y. Kim, K.-S. Park, P. Tarakeshwar, K. S. Kim, T.-S. Kim, and J. Y. Lee, J. Chem. Phys. 122, 094706 (2005).
  57. W. Y. Kim and K. S. Kim, Acc. Chem. Res. 43, 111 (2010). [MEDLINE] [CAS]
  58. M. J. W. Boness, I. W. Larkin, J. B. Hasted, and L. Moore, Chem. Phys. Lett. 1, 292 (1967).
  59. J. C. Rienstra-Kiracofe, C. J. Barden, S. T. Brown, and H. F. Schaefer III, J. Phys. Chem. A 105, 524 (2001).
  60. W. Y. Kim and K. S. Kim, Acc. Chem. Res. 43, 111 (2010). [MEDLINE] [CAS]
  61. J. E. Sanhueza, O. Tapia, W. G. Laidlaw, and M. Trsic, J. Chem. Phys. 70, 3096 (1979)JCPSA6000070000006003096000001. [ISI] [CAS]
  62. A. D. Miller, I. Bezel, K. J. Gaffney, S. Garrett-Roe, S. H. Liu, P. Szymanski, and C. B. Harris, Science 297, 1163 (2002). [MEDLINE]

Figures (6) Tables (1)

Figures (click on thumbnails to view enlargements)

FIG.1
Geometry of the CheESE model showing the direction of the applied potential, ±V. We use a cuboid box, with the xy-plates representing the electrodes of a nano-device. The coordinate origin is equidistant from the two plates.

FIG.1 Download High Resolution Image (.zip file) | Export Figure to PowerPoint

FIG.2
Stabilization of the benzene (blue lines), benzene anion (red lines), and glycine (green lines) molecules due to CheESE image charges in the case Φfixed(s) = 0 with varying Δz. Part (a) compares the total energies, E tot sys , shown as dotted lines, with the reference free-space energies, shown as solid lines, for an xy-plate area of 200×200 bohr2. Parts (b)–(d) highlight the CheESE effect as the difference between E tot sys and the free-space energy for (b) benzene, (c) glycine, and (d) benzene anion, with two choices of plate area.

FIG.2 Download High Resolution Image (.zip file) | Export Figure to PowerPoint

FIG.3
Energies of neutral benzene (blue lines), benzene anion (red lines), and glycine (green lines), with an applied potential, V, as given in Eq. ( 39 ), an xy-plate area of 108×108 bohr2, and Δz = 54 bohr. The total CheESE energies, E tot sys , are shown as dashed lines, and the reference free-space energies are shown as solid lines.

FIG.3 Download High Resolution Image (.zip file) | Export Figure to PowerPoint

FIG.4
Energy changes for different applied potentials when including image charge effects in addition to a static field. Eimage, as given by Eq. ( 25 ), is shown for (a) neutral benzene, (b) glycine, and (c) benzene anion, using an xy-plate area of 108×108 bohr2, and Δz = 54 bohr.

FIG.4 Download High Resolution Image (.zip file) | Export Figure to PowerPoint

FIG.5
Energy profiles of the lowest lying molecular orbitals of (a) neutral benzene, (b) glycine, and (c) benzene anion, with an applied potential, V, an xy-plate area of 108×108 bohr2, and Δz = 54 bohr. Since there are no relevant orbital crossings, only the HOMO and LUMO are shown for the anion and glycine.

FIG.5 Download High Resolution Image (.zip file) | Export Figure to PowerPoint

FIG.6
Static field and image charge contributions (see main text for definitions) to the HOMO–LUMO gap for neutral benzene (blue line), glycine (green line), and benzene anion (red line) with varying applied potential, V, an xy-plate area of 108×108 bohr2, and Δz = 54 bohr.

FIG.6 Download High Resolution Image (.zip file) | Export Figure to PowerPoint

Tables

Table I. Energy differences in kcal/mol, according to Eqs. (24,25), giving the change, Estatic, to the total energy on applying a static field with potential V/a.u., and the additional CheESE image charge contribution, Eimage.

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