Abstract
This protocol is intended to provide chemists and physicists with a tool for predicting the charge carrier mobilities of π-stacked systems such as organic semiconductors and the DNA double helix. An experimentally determined crystal structure is required as a starting point. The simulation involves the following operations: (i) searching the crystal structure; (ii) selecting molecular monomers and dimers from the crystal structure; (iii) using density function theory (DFT) calculations to determine electronic coupling for dimers; (iv) using DFT calculations to determine self-reorganization energy of monomers; and (v) using a numerical calculation to determine the charge carrier mobility. For a single crystal structure consisting of medium-sized molecules, this protocol can be completed in ∼4 h. We have selected two case studies (a rubrene crystal and a DNA segment) as examples of how this procedure can be used.
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References
Podzorov, V. Organic single crystals: addressing the fundamentals of organic electronics. MRS Bull. 38, 15–27 (2013).
Li, Y. & Zou, Y. Conjugated polymer photovoltaic materials with broad absorption band and high charge carrier mobility. Adv. Mater. 20, 2952–2958 (2008).
Sun, Y., Wu, Q. & Shi, G. Graphene based new energy materials. Energ. Environ. Sci. 4, 1113–1132 (2011).
Hirakawa, T. & Kamat, P.V. Charge separation and catalytic activity of Ag@TiO2 core-shell composite clusters under UV-irradiation. J. Am. Chem. Soc. 127, 3928–3934 (2005).
Thompson, T.L. & Yates, J.T. Jr . TiO2-based photocatalysis: surface defects, oxygen and charge transfer. Top. Catal. 35, 197–210 (2005).
Yoon, B. et al. Charging effects on bonding and catalyzed oxidation of CO on Au8 clusters on MgO. Science 307, 403–407 (2005).
Jortner, J., Bixon, M., Langenbacher, T. & Michel-Beyerle, M.E. Charge transfer and transport in DNA. Proc. Natl. Acad. Sci. 95, 12759–12765 (1998).
Lewis, F.D., Letsinger, R.L. & Wasielewski, M.R. Dynamics of photoinduced charge transfer and hole transport in synthetic DNA hairpins. Acc. Chem. Res. 34, 159–170 (2001).
Valis, L. et al. Base pair motions control the rates and distance dependencies of reductive and oxidative DNA charge transfer. Proc. Natl. Acad. Sci. 103, 10192–10195 (2006).
Orton, J.W. & Blood, P. The Electrical Characterization of Semiconductors: Measurement of Minority Carrier Properties. (Academic Press, London, 1990).
Pernegger, H. et al. Charge-carrier properties in synthetic single-crystal diamond measured with the transient-current technique. J. Appl. Phys. 97, 073704 (2005).
Schroder, D.K. Semiconductor Material and Device Characterization (John Wiley & Sons, 2006).
Ling, M.M., Reese, C., Briseno, A.L. & Bao, Z. Non-destructive probing of the anisotropy of field-effect mobility in the rubrene single crystal. Synthetic Met. 157, 257–260 (2007).
Lee, J.Y., Roth, S. & Park, Y.W. Anisotropic field effect mobility in single crystal pentacene. Appl. Phys. Lett. 88, 252106 (2006).
Sundar, V.C. et al. Elastomeric transistor stamps: reversible probing of charge transport in organic crystals. Science 303, 1644–1646 (2004).
Grozema, F.C. & Siebbeles, L.D.A. Mechanism of charge transport in self-organizing organic materials. Int. Rev. Phys. Chem. 27, 87–138 (2008).
Yang, X.D., Wang, L.J., Wang, C.L., Long, W. & Shuai, Z.G. Influences of crystal structures and molecular sizes on the charge mobility of organic semiconductors: oligothiophenes. Chem. Mater. 20, 3205–3211 (2008).
Yang, X.D., Li, Q.K. & Shuai, Z.G. Theoretical modelling of carrier transports in molecular semiconductors: molecular design of triphenylamine dimer systems. Nanotechnology 18, 424029 (2007).
Cornil, J., Brédas, J.L., Zaumseil, J. & Sirringhaus, H. Ambipolar transport in organic conjugated materials. Adv. Mater. 19, 1791–1799 (2007).
Zhang, X.-Y. & Zhao, G.-J. Anisotropic charge transport in bisindenoanthrazoline-based n-type organic semiconductors. J. Phys. Chem. C 116, 13858–13864 (2012).
Zhang, M.-X., Chai, S. & Zhao, G.-J. BODIPY derivatives as n-type organic semiconductors: isomer effect on carrier mobility. Organic Electronics 13, 215–221 (2012).
Zhang, M.X. & Zhao, G.J. Modification of n-type organic semiconductor performance of perylene diimides by substitution in different positions: two-dimensional π-stacking and hydrogen bonding. ChemSusChem 5, 879–887 (2012).
Liu, D. et al. Anisotropic charge injection and transport in the cross stacking crystal of distyrylbenzene derivative and a possible new device structure. Chem. Phys. Lett. 514, 174–180 (2011).
Jiang, L., Dong, H.L. & Hu, W.P. Organic single crystal field-effect transistors: advances and perspectives. J. Mater. Chem. 20, 4994–5007 (2010).
Chai, S., Wen, S.H., Huang, J.D. & Han, K.L. Density functional theory study on electron and hole transport properties of organic pentacene derivatives with electronwithdrawing substituent. J. Comput. Chem. 32, 3218–3225 (2011).
Wen, S.-H. et al. First-principles investigation of anistropic hole mobilities in organic semiconductors. J. Phys. Chem. B 113, 8813–8819 (2009).
Wen, S.-H., Deng, W.-Q. & Han, K.-L. Ultra-low resistance at TTF–TCNQ organic interfaces. Chem. Commun. 46, 5133–5135 (2010).
Brédas, J.-L., Norton, J.E., Cornil, J. & Coropceanu, V. Molecular understanding of organic solar cells: the challenges. Acc. Chem. Res. 42, 1691–1699 (2009).
Geng, H. et al. Toward quantitative prediction of charge mobility in organic semiconductors: tunneling enabled hopping model. Adv. Mater. 24, 3568–3572 (2012).
Ryno, S.M., Risko, C. & Bredas, J.L. Impact of molecular packing on electronic polarization in organic crystals: the case of pentacene vs TIPS-pentacene. J. Am. Chem. Soc. 136, 6421–6427 (2014).
Shuai, Z., Geng, H., Xu, W., Liao, Y. & André, J.-M. From charge transport parameters to charge mobility in organic semiconductors through multiscale simulation. Chem. Soc. Rev. 43, 2662–2679 (2014).
Shuai, Z., Wang, L. & Li, Q. Evaluation of charge mobility in organic materials: from localized to delocalized descriptions at a first-principles level. Adv. Mater. 23, 1145–1153 (2011).
Wang, L. et al. Computational methods for design of organic materials with high charge mobility. Chem. Soc. Rev. 39, 423–434 (2010).
Marcus, R.A. On the theory of oxidation–reduction reactions involving electron transfer. I. J. Chem. Phys. 24, 966–978 (1956).
Hush, N.S. Adiabatic rate processes at electrodes. I. energy–charge relationships. J. Chem. Phys. 28, 962–972 (1958).
Valeev, E.F., Coropceanu, V., da Silva Filho, D.A., Salman, S. & Brédas, J.-L. Effect of electronic polarization on charge-transport parameters in molecular organic semiconductors. J. Am. Chem. Soc. 128, 9882–9886 (2006).
Yu, G. et al. Structures, electronic states, photoluminescence, and carrier transport properties of 1,1-disubstituted 2,3,4,5-tetraphenylsiloles. J. Am. Chem. Soc. 127, 6335–6346 (2005).
Senthilkumar, K., Grozema, F.C., Bickelhaupt, F.M. & Siebbeles, L.D.A. Charge transport in columnar stacked triphenylenes: effects of conformational fluctuations on charge transfer integrals and site energies. J. Chem. Phys. 119, 9809–9817 (2003).
Chu, T.-S., Zhang, Y. & Han, K.-L. The time-dependent quantum wave packet approach to the electronically nonadiabatic processes in chemical reactions. Int. Rev. Phys. Chem. 25, 201–235 (2006).
Coropceanu, V. et al. Charge transport in organic semiconductors. Chem. Rev. 107, 926–952 (2007).
Deng, W.-Q. & Goddard, W.A. Predictions of hole mobilities in oligoacene organic semiconductors from quantum mechanical calculations. J. Phys. Chem. B 108, 8614–8621 (2004).
Demiralp, E. & Goddard, W.A. Conduction properties of the organic superconductor based on Hubbard–unrestricted-Hartree-Fock band calculations. Phys. Rev. B 56, 11907–11919 (1997).
Wang, C., Wang, F., Yang, X., Li, Q. & Shuai, Z. Theoretical comparative studies of charge mobilities for molecular materials: Pet versus bnpery. Organic Electronics 9, 635–640 (2008).
te Velde, G. et al. Chemistry with ADF. J. Comput. Chem. 22, 931–967 (2001).
Frisch, M.J. et al. Gaussian 09, Revision C01. (Gaussian, Inc., 2009).
Burke, K., Perdew, J.P. & Wang, Y. in Electronic Density Functional Theory 81–111 (Springer, 1998).
Becke, A.D. Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 98, 5648–5652 (1993).
Lewis, F.D. et al. Crossover from superexchange to hopping as the mechanism for photoinduced charge transfer in DNA hairpin conjugates. J. Am. Chem. Soc. 128, 791–800 (2006).
Renaud, N., Berlin, Y.A. & Ratner, M.A. Impact of a single base pair substitution on the charge transfer rate along short DNA hairpins. Proc. Natl. Acad. Sci. 110, 14867–14871 (2013).
Messer, A. et al. Electron spin resonance study of electron transfer rates in DNA: determination of the tunneling constant β for single-step excess electron transfer. J. Phys. Chem. B 104, 1128–1136 (2000).
Cai, Z., Gu, Z. & Sevilla, M.D. Electron spin resonance study of the temperature dependence of electron transfer in DNA: competitive processes of tunneling, protonation at carbon, and hopping. J. Phys. Chem. B 104, 10406–10411 (2000).
Elias, B., Genereux, J.C. & Barton, J.K. Ping-pong electron transfer through DNA. Angew. Chem. Int. Edit. 47, 9067–9070 (2008).
Renaud, N., Berlin, Y.A., Lewis, F.D. & Ratner, M.A. Between superexchange and hopping: an intermediate charge-transfer mechanism in poly(A)-poly(T) dna hairpins. J. Am. Chem. Soc. 135, 3953–3963 (2013).
Novoa, J.J. & Sosa, C. luation of the density functional approximation on the computation of hydrogen bond interactions. J. Phys. Chem. 99, 15837–15845 (1995).
Stephens, P.J., Devlin, F.J., Chabalowski, C.F. & Frisch, M.J. Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields. J. Phys. Chem. 98, 11623–11627 (1994).
Nan, G.J., Yang, X.D., Wang, L.J., Shuai, Z.G. & Zhao, Y. Nuclear tunneling effects of charge transport in rubrene, tetracene, and pentacene. Phys. Rev. B 79 (2009).
Zeis, R. et al. Field effect studies on rubrene and impurities of rubrene. Chem. Mater. 18, 244–248 (2006).
Ling, M.-M., Reese, C., Briseno, A.L. & Bao, Z. Non-destructive probing of the anisotropy of field-effect mobility in the rubrene single crystal. Synthetic. Met. 157, 257–260 (2007).
Park, M.J., Fujitsuka, M., Kawai, K. & Majima, T. Direct measurement of the dynamics of excess electron transfer through consecutive thymine sequence in DNA. J. Am. Chem. Soc. 133, 15320–15323 (2011).
Briseno, A.L. et al. Patterning organic single-crystal transistor arrays. Nature 444, 913–917 (2006).
Podzorov, V., Sysoev, S.E., Loginova, E., Pudalov, V.M. & Gershenson, M.E. Single-crystal organic field effect transistors with the hole mobility ∼8cm2/Vs. Appl. Phys. Lett. 83, 3504–3506 (2003).
da Silva Filho, D.A., Kim, E.G. & Brédas, J.L. Transport properties in the rubrene crystal: electronic coupling and vibrational reorganization energy. Adv. Mater. 17, 1072–1076 (2005).
Acknowledgements
We acknowledge support from the National Basic Research Program of China (2013CB834604) and National Natural Science Foundation of China (91333116 and 21321091).
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W.-Q.D. and L.S. contributed equally to this work and performed the research; J.-D.H., S.C. and S.-H.W. performed the calculations; K.-L.H. conceived and supervised the work; all authors co-wrote the manuscript.
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Supplementary information
Supplementary Text and Figures
Supplementary Note (PDF 188 kb)
Supplementary Data 1
A zip file containing the crystal files download from the online database (“DNA-4HW1.ent” and “Rubrene.cif”) A zip file containing the matlab code (“mobility.m”), the corresponding parameters file (“input. txt”) and the help information (example-input.txt). (ZIP 127 kb)
Supplementary Data 2
A zip file containing the matlab code (“mobility.m”), the corresponding parameters file (“input. txt”) and the help information (example-input.txt). (ZIP 2 kb)
Supplementary Data 3
A zip file containing four types of the molecular dimers chosen from rubrene crystal (“rubrene-L.mol”, “rubrene-P.mol”, “rubrene-T1.mol” and “rubrene-T2.mol”) and four types of the molecular dimers chosen from DNA-4HW1 (“adenine-dimer-1.mol”, “adenine-dimer-2.mol”, “thymine-dimer-1.mol” and “thymine -dimer-2.mol”). (ZIP 11 kb)
Supplementary Data 4
A zip file containing the ADF-output files for each of the molecular dimers. (ZIP 596 kb)
Supplementary Data 5
Gaussian-output files for each molecular monomer. (ZIP 724 kb)
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Deng, WQ., Sun, L., Huang, JD. et al. Quantitative prediction of charge mobilities of π-stacked systems by first-principles simulation. Nat Protoc 10, 632–642 (2015). https://doi.org/10.1038/nprot.2015.038
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DOI: https://doi.org/10.1038/nprot.2015.038
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