Molecular Dynamics Studies on the Selective Deposition of 3(5)-(9-Anthryl) Pyrazole onto Self-assembled Monolayers†

doi:10.7503/cjcu20150781

Abstract

Abstract:

The site-selective deposition behavior of 3(5)-(9-anthryl) pyrazole(ANP) onto self-assembled monolayers(SAMs) patterned substrate was studied via the equilibrium and steered molecular dynamics methods. Two kinds of different densely packed SAMs were constructed on silicon oxide substrates as the patterned templates, which represent liquid expanded(LE) and liquid condensed(LC) phases. Equilibrium molecular dynamics(MD) simulations showed that the packing density of alkyl chains on the substrate could influence the deposition behavior of the ANP molecules. On the LE covered SAM, the small molecule would submerge deeply into the alkyl chains film, while ANP molecule would deposit on the surface of LC film. Steered molecular dynamics showed that ANP molecule was hindered from the densely packed LC film. However, there was less hindrance for ANP to submerge into the LE film. Using umbrella sampling and the weighted histogram analysis method, the potential of mean force(PMF) of the deposition process of ANP onto the two patterned templates was calculated. From the PMF curves, the favorite deposition location of ANP onto the two SAMs was determined, which agreed well with that obtained from equilibrium MD simulations. The binding energies between ANP and the two SAMs can be estimated based on PMF, which could be used to explain the site-selective deposition of ANP on different densely packed SAMs.

Key words: Self-assembled monolayers(SAM), Site-selective deposition, Steered molecular dynamics, Umbrella sampling, 3(5)-(9-Anthryl)pyrazole, Low intensity liquid expanded phase, High intensity liquid condensed phase, Potential of mean force

CLC Number:

O641

TrendMD:

ZHANG Luge, XUE Zexu, ZHANG Chong, YAN Hui. Molecular Dynamics Studies on the Selective Deposition of 3(5)-(9-Anthryl) Pyrazole onto Self-assembled Monolayers^†[J]. Chem. J. Chinese Universities, 2016, 37(3): 505.

Figures/Tables 9

Fig.1 Chemical structure of 3(5)-(9-anthryl) pyrazole(ANP)

Fig.2 Configurations of ANP deposited on LC(A, A') and LE(B, B') phases at the initial(A, B) and the end(5 ns, A', B') of the MD simulation

Fig.3 Time profiles of the vertical distance between the COM(center of mass) of the ANP molecule and the surface of the SiO2 substratea. LC phase; b. LE phase.

Fig.4 Number density profiles of components for LC and LE systemsa. SiO2; b. LC; c. LE; d. LC-ANP; e. LE-ANP. Values for ANP atoms were multiplied by 10 for clarity.

Fig.5 Results from simulations started with different initial configurations for the LE system(A) Time profiles of distance; (B) number density profiles (values for ANP atoms were multiplied by 10 for clarity).

Fig.6 Distance profiles of force using different pulling ratesVertical shifts of 200, 400 and 700 units were imposed for profiles at rates of 0.005, 0.0025 and 0.001 nm/ps, respectively. V/(nm·ps-1): a. 0.001; b. 0.0025; c. 0.005; d. 0.01.

Fig.7 Configurations at different time during the SMD simulation for the LC systemTime/ps: (A) 0; (B) 300; (C) 460; (D) 600.

Fig.8 Time profiles of the external force applied on ANP(A) and time profiles of the vertical

Fig.9 Potential of mean force along the reaction coordinate for ANP molecules deposited onto each SAMa. LC phase; b. LE phase.

References 35

[1]	Gaal M., Gadermaier C., Plank H., Moderegger E., Pogantsch A., Leising G., List E., Adv. Mater., 2003, 15(14), 1165—1167
[2]	Koide Y., Wang Q., Cui J., Benson D. D., Marks T. J., J. Am. Chem. Soc., 2000, 122(45), 11266—11267
[3]	Cheek B. J., Steel A. B., Torres M. P., Yu Y., Yang H., Anal. Chem., 2001, 73(24), 5777—5783
[4]	Lingerfelt B. M., Mattoussi H., Goldman E. R., Mauro J. M., Anderson G. P., Anal. Chem., 2003, 75(16), 4043—4049
[5]	Hao J., Lu N., Wu Q., Hu W., Chen X., Zhang H., Wu Y., Wang Y., Chi L. F., Langmuir,2008, 24(10), 5315—5318
[6]	Hirtz M., Fuchs H., Chi L. F., J. Phys. Chem. B, 2008, 112(3), 824—827
[7]	Chen X. D., Rogach A. L., Talapin D. V., Fuchs H., Chi L. F., J. Am. Chem. Soc., 2006, 128(30), 9592—9593
[8]	Hao J., Lu N., Li L., Hirtz M., Gao L., Wang W., Du C., Fuchs H., Chi L. F., Soft Matter, 2010, 6(21), 5302—5304
[9]	Gao L., Lu N., Hao J., Hu W., Shi G., Wang Y., Chi L. F., Langmuir,2009, 25(6), 3894—3897
[10]	Gleiche M., Chi L. F., Fuchs H., Nature,2000, 403(6766), 173—175
[11]	Gleiche M., Chi L. F., Gedig E., Fuchs H., Chem.Phys.Chem,2001, 2(3), 187—191
[12]	Choi J. M., Jeong S. H., Hwang D. K., Im S., Lee B. H., Sung M. M., Org. Electron., 2009, 10(1), 199—204
[13]	Steudel S., Janssen D., Verlaak S., Genoe J., Heremans P., Appl. Phys. Lett., 2004, 85(23), 5550—5552
[14]	Hirtz M., Kumar N., Franke J. H., Hao J., Lu N., Fuchs H., Chi L. F., J. Colloid Interf. Sci., 2013, 389(1), 206—212
[15]	Xu Z., Hirtz M., Yuan S. L., Liu C. B., Chi L. F., Chem. Phys. Lett., 2011, 507(1—3), 138—143
[16]	Zhang C., Xu Z., Yan H., Gao F., Yuan S. L., Chem. Phys. Lett., 2013, 571, 38—43
[17]	Zhang C., Du C., Yan H., Yuan S. L., Chi L. F., RSC Adv., 2013, 3(35), 15404—15410
[18]	Shevade A. V., Zhou J., Zin M. T., Jiang S. Y., Langmuir,2001, 17(24), 7566—7572
[19]	Izrailec S., Stepaniants S., Isralewitz B., Kosztin D., Lu H., Molnar F., Wriggers W., Schulten K., Steered Molecular Dynamics Springer-Verlag, Berlin, 1998
[20]	Torrie G. M., Valleau J. P., J. Comput. Phys., 1977, 23(2), 187—199
[21]	He Z. J., Zhou J., Acta Chim. Sinica, 2011, 69(24), 2901—2907
	(贺仲金, 周健. 化学学报, 2011, 69(24), 2901—2907)
[22]	He J., Feng X. Z., Shao G. X., Cai W. S., Chem. J. Universities Chinese, 2015, 36(1), 110—115
	(何佳, 冯喜增, 邵学广, 蔡文生. 高等学校化学学报, 2015, 36(1), 110—115)
[23]	Zhang J. L., Zheng Q. C., Zhang H. X., J. Phys. Chem. B, 2010, 114(21), 7383—7390
[24]	Sun W. Q., Zhang J. L., Zheng Q. C., Sun Z. W., Zhang H. X., Acta Phys. Chim. Sinica, 2013, 29(4), 843—848
	(孙维琦, 张继龙, 郑清川, 孙志伟, 张红星. 物理化学学报, 2013 29(4), 843—848)
[25]	Kumbia S., Bouzida D., Swendsen R. H., Kollman P. A., Rosenberg J. M., J. Comput. Chem., 1992, 13(8), 1011—1021
[26]	Hozumi A., Asakura S., Fuwa A., Shirahata N., Kameyama T., Langmuir,2005, 21(18), 8234—8242
[27]	Janssen D., DePalma R., Verlaak S., Heremans P., Dehaen W., Thin Solid Films, 2006, 515(4), 1433—1438
[28]	Jorgensen W. L., Maxwell D. S., Tirada-Rives J., J. Am. Chem. Soc., 1996, 118(45), 11225—11236
[29]	Hess B., Kutzner C., van der Spoel D., Lindahl E., J. Chem. Theory Comp., 2008, 4(3), 435—477
[30]	Schmidt M. W., Baldridge K. K., Boatz J. A., Elbert S. T., Gordon M. S., Jensen J. H., Koseki S., Matsunaga N., Nguyen K. A., Su S. J., Windus T. L., Dupuis M., Montgomery J. A., J. Comput. Chem., 1993, 14(11), 1347—1363
[31]	Lorenz C. D., Webb III E. B., Stevens M. J., Chandross M., Grest G. S., Tribol. Lett., 2005, 19(2), 93—98
[32]	Berendsen H. J. C., Postma J. P. M., van Gunsteren W. F., DiNola A., Haak J. R., J. Chem. Phys., 1984, 81(8), 3684—3690
[33]	Hess B., Bekker H., Berendsen H. J. C., Fraaije J. G. E. M., J. Comput. Chem., 1997, 18(12), 1463—1472
[34]	Essman U., Perera L., Berkowitz M. L., Darden T., Lee H., Pedersen L. G., J. Chem. Phys., 1995, 103(19), 8577—8593
[35]	Humphrey W., Dalke A., Schulten K., J. Mol. Graph. Model., 1996, 14(1), 33—38