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Molecular Dynamics Simulation of Self-Assembled Layer-by-Layer Structures of Chiral Molecules on Substrate Kun-qian Yu, Ze-sheng Li,* and Jia-zhong Sun Institute of Theoretical Chemistry, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun, Jilin, 130023, People’s Republic of China Received July 20, 2001. In Final Form: November 7, 2001 A molecular dynamics (MD) simulation has been carried out to investigate the morphology and structure of monolayer and multilayer of chiral molecule N-stearoy-L-glutamic acid (C18-L-Glu) self-assembled on a mica surface. Energy changes during the MD run have been analyzed. The results show that hydrogenbonding effects are the major driving forces in the layer formation of C18-L-Glu on a mica surface. On the basis of the simulation results, we proposed a multilayered model for the self-assembling of C18-L-Glu on a mica surface.
Introduction Self-assembled layers of small molecules, polymers, and proteins have attracted much attention in both experimental and theoretical fields for a long time. Self-assembly has been shown to provide a viable means of controlling the physical and chemical properties of solid surfaces.1,2 In recent years, many research activities have been devoted to the development of thin films composed of functional molecules for optical, mechanical, electronic, or biochemical applications.3-9 In this area a predominant theme is the correlation of the thin film microstructure to its macroscopic physical properties. Recent studies have reported the formation of superstructures driven by hydrogen bonding. Different experimental techniques such as neutron reflection, surface force apparatus and atomic force microscopy (AFM) have been used to study thin films over last three decades.10-17 * To whom correspondence may be addressed. Fax: 86-4318945942. E-mail:
[email protected];
[email protected]. (1) Sapp, S. A.; Mitchell, D. T.; Martin, C. R. Chem. Mater. 1999, 11, 1183. (2) Elghanian, R.; Storhoff, J. J.; Mucic, R. C.; Letsinger, R. L.; Mirkin, C. A. Science 1997, 277, 1078. (3) Jolliffe, K. A.; Timmerman, P.; Reinhoudt, D. N. Angew. Chem., Int. Ed. 1999, 38, 933. (4) Lehn, J.-M. Supramolecular Chemistry: Concept and Perspectives; VCH: Weinheim, 1995. (5) Scheibler, L.; Dumy, P.; Boncheva, M.; Leufgen, K.; Mathieu, H.-J.; Mutter, M.; Vogel, H. Angew. Chem., Int. Ed. 1999, 38, 696. (6) Weinbach, S. P.; Kjaer, K.; Bouwman, W. G.; Gru¨bel, G.; Legrand, J-F.; Als-nielsen, J.; Lahav, M.; Leiserowitz, L. Science 1994, 264, 1566. (7) Maoz, R.; Matlie, S.; Dimasi, E.; Ocko, B. M.; Sagiv, J. Nature 1996, 384, 150. (8) Bain, C. D.; Troughton, E. B.; Tao, Y.; Evall, J.; Whitesides, G. M.; Nuzzo, R. G. J. Am. Chem. Soc. 1989, 111, 321. (9) Salditt, T.; An, Q.; Plech, A.; Peisl, J.; Eschbaumer, C.; Weidl, C. H.; Schubert, U. S. Thin Solid Films 1999, 354, 208. (10) Yang, W.; Chai, X.; Chi, L.; Liu, X.; Cao, Y.; Lu, R.; Jiang, Y.; Tang, X.; Fuchs, H.; Li, T. J. Chem. Eur. J. 1999, 5, 1144. (11) Cao, Y. W.; Chai, X. D.; Li, T. J.; Smith, J.; Li, D. Q. Chem. Commun. 1999, 1605. (12) Martı´n, T.; Obst, U.; J. R., Jr. Science 1998, 281, 1842. (13) Vollmer, M. S.; Clark, T. D.; Steinem, C.; Ghadiri, M. R. Angew. Chem., Int. Ed. 1999, 38, 1598. (14) Beijer, F. H.; Kooijman, H.; Spek, A. L.; Sijbesma, R. P.; Meijer, E. W. Angew. Chem., Int. Ed. 1998, 37, 75. (15) Lange, R. F. M.; Lowe, J. K. L.; Meijer, E. W. Science 1997, 278, 1601. (16) Ostrander, J. W.; Mamedov, A. A.; Kotov, N. A. J. Am. Chem. Soc. 2001, 123, 1101.
Computer simulation studies can provide a microscopic picture of such phenomena at the molecular level.18-29 In earlier attempts to study such systems using MD simulation with much simplified models, important contributions to the understanding of the self-assembling processes involved have been made. The self-assembled monolayer (SAM) of n-hexadecanethiol chemisorbed on a gold(111) surface has been investigated to probe the atomic-scale behavior by molecular dynamics simulations for its welldefined structure. In this paper, we preformed molecular dynamics simulations on a much more complicated system: self-assembled layer-by-layer structures of the chiral molecule C18-L-Glu on a mica surface. In the present work, an atomic model for the intra-adsorbate and adsorbate-substrate interaction is combined with unit cell geometries and surface packing densities as obtained by AFM, to yield insight into the energetics and structures of chiral molecule C18-L-Glu layers. We find that the hydrogen bond is the most important factor in determining the structure of the layer-by-layer structure. The simulated results can satisfactorily describe some phenomena observed by experiments. The chiral molecule C18-L-Glu is able to form an extremely stable asymmetric multilayered structure with very long-range order on a mica surface.30 The organization of C18-L-Glu molecules on a mica surface was revealed by AFM at the molecular level. On the surface of the structure, (17) Schmit, H.; Badia, A.; Dickinson, L.; Reven, L.; Lennox, R. B. Adv. Mater. 1998, 10, 475. (18) Mar, W.; Klein, M. L. Langmuir 1994, 10, 188. (19) Chiu, S. W.; Jakobosson, E. J. Chem. Phys. 2001, 114, 5435. (20) Bishop, A. R.; Girolami, G. S.; Nuzzo, R. G. J. Chem. Phys. 2000 104, 754. (21) Siepmann, J. I.; McDonald, I. R. Langmuir 1993, 9, 2351. (22) Vekhter, B.; Berry, R. S. J. Chem. Phys. 1999, 110, 2195. (23) Hautman, J.; Klein, M. L. J. Chem. Phys. 1990, 93, 7483. (24) Bandyopadhyay, S.; Shelly, J. C.; Tarek, M.; Moore, P. B.; Klein, M. L. J. Phys. Chem. B 1998, 102, 6318. (25) Chalaris, M.; Samios, J. J. Phys. Chem. B 1999, 103, 1161. (26) Vekhter, B.; Berry, R. S. J. Chem. Phys. 1999, 110, 2195. (27) Tupper, K. J.; Brenner, D. W. Langmuir 1994, 10, 2335. (28) Sankararamakrishnan, R.; Weinstein, H. Biophys. J. 2000, 79, 2331. (29) Tarek, M.; Tu, K.; Klein, M. L.; Tobias, D. J. Biophys. J. 1999, 77, 964. (30) Zhang, Y. J.; Song, Y.; Zhao, Y.; Li, T. J. Submitted for publication in J. Chem. Phys.
10.1021/la0155045 CCC: $22.00 © 2002 American Chemical Society Published on Web 01/15/2002
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Figure 1. (left) 5 × 4 unit cell mica surface. The cell parameters are a ) 5.231 Å, b ) 9.065 Å, and θ ) 90°. The white lines correspond to the observed lines arranged in the mica AFM image (right) and every unit cell corresponds to two spots in the AFM image.
Figure 2. Running averages of total energy, potential energy, kinetic energy, temperature, nonbond energy, and valence energy during the 2500 ps long time simulation of the model for the first layer on mica. The energies stabilized after less than 1000 ps, which means the system is well equilibrated. In the first 1000 ps of the MD run, nonbond energy (mainly intramolecular interaction) decreases sharply but valence energy increases little.
large areas of hydrophilic and hydrophobic surfaces with different heights can be found. Within every layer, molecules can pack closely due to the formation of a lateral hydrogen bonding network between molecules. This kind of hydrogen bonding network can be considered as a simple model of β-sheet structures as secondary structure elements in proteins.
Models and Simulation Methods Atomic molecular dynamics (MD) calculations have been carried out to simulate the formation of layer-by-layer structures of C18-L-Glu molecules on a mica surface. All the modeling and simulations are preformed by Cerius2 software packag on an SGI origin200.
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Figure 3. Time profiles of several energy components of the model system during the simulation for the first layer on the mica. The fluctuation of H bond energy is between -22 and -38 kcal/mol, which means about four to six hydrogen bonds are formed in a unit cell. There are three hydrogen donators in a C18-L-Glu molecule, then at most three hydrogen bonds can be formed for a C18-L-Glu molecule.
Ideally, our simulation should include the adsorption from the solution and the attendant formation of the lamellar structures. Because such a complete study is presently ruled out by the rather short time scales accessible with MD, we start from an initial structure, which is already close to the equilibrium structure, whose unit cell symmetry and dimensions are deduced from AFM images. We modeled the layers of C18-L-Glu molecules on mica as two-dimensional periodic systems. A mica surface model was constructed as shown in Figure 1(left). To use the Berchart1.01-Dreiding2.1 force field, we substitute K by Na and Mg by Ca in the mica model. The parameters of the surface unit cell were u ) 5.231 Å, v ) 9.065 Å, and θ ) 90°. N-Stearoyl-L-gutamic acid (C18-L-Glu) molecule was built and energy minimized. We put two C18-L-Glu molecules on every mica unit cell with the carboxyl groups of C18-L-Glu touching the mica surface to model the first layer, and the distances between every molecule were 5.23 Å. The structures were energy minimized until full convergence with the two-dimensional cell parameters.
After molecular dynamics simulation was performed on the model of the first layer, we put another two C18-L-Glu molecules on every unit cell with the methyl groups near the methyl groups of the first layer to model the second layer. Then the same procedure was done to the second layer model as to the first layer. Constant number, constant volume, and constant temperature (NVT) ensemble molecular dynamics simulations were performed for 2500 ps at 300 K for both the models of the first layer and second layer of C18-L-Glu molecules on mica surface. The equations of motion were integrated by using the “velocity Verlet” algorithm, and a time step of 0.001 ps was used for the integration. The system was maintained at the desired temperature by the Nose-Hoover thermal bath method. During the simulation of the first layer, motions of the mica atoms were fixed. Then after the second layer was built on the final structure of the simulation of the first layer, MD simulation was performed, with the motions of mica atoms
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Figure 4. Running averages of energy components during the 2500 ps run for the first layer model. Except for bond energy and angle energy, hydrogen bond energy is the biggest energy component in absolute value, showing that the hydrogen bond plays a most important role in the self-organization of the layered structure. The average value of the H bond is -33 kcal/mol; about 2.5 hydrogen bonds are formed in every C18-Glu molecule.
and molecules of the first layer all fixed to reduce the computational costs. Force field Berchart1.01-Dreiding2.1 was loaded in the simulation. Energy terms such as bond, angle, torsion, inversion, van der Waals, and hydrogen bond energies were included in the energy expression setup. Parameters for the hydrogen bond energy expression were modified. In the Lennard-Jones (LJ12-10) function, Do was set to 7.0 kcal/mol and Ro was set to 3.0 Å for O-H‚‚‚H, and Do was set to 5.0 kcal/mol and Ro to 3.0 Å for N-H‚‚‚O. The cutoff radius of the van der Waals interaction was set to 0.9 nm. Results and Discussions I. Monolayer Model. The running averages of total energy, kinetic energy, potential energy, and temperature are shown in Figure 2 for the first layer model. As can be seen from the figure, the various energies became stable after about 1000 ps, which means that the system was
well equilibrated for the 2500 ps simulation run. In the first 1000 ps of the MD run, nonbond energy (mainly intramolecular interaction) decreases sharply, but valence energy increases a little. Time profiles and running averages of several energy components of the model system during the simulation are shown in Figure 3 and Figure 4, respectively. The fluctuation of hydrogen bond energy is between -22 and -38 kcal/mol, which means about four to six hydrogen bonds are formed in a unit cell. There are three hydrogen donators in a C18-L-Glu molecule, and then at most three hydrogen bonds can be formed for each molecule since there are enough hydrogen acceptors in the system. From the running averages of the energy components, we can see that except for bond energy and angle energy which are valence energies, hydrogen bond energy is the biggest energy component in absolute value of the intermolecular interaction (nonbond energy), showing that the hydrogen bond plays a most important role in the self-organization of the layered structure. The
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Figure 5. A snapshot of the first layer on mica (a) at 0 ps, namely, the initial structure of the simulation after a molecular mechanics energy minimization, and (b) at 2500 ps. The C18-L-Glu developed a tilt angle of about 30° when adjusting its position for carboxyl II to fit the mica lattice. The end carbon of the alkyl chain is colored pink.
Figure 6. Snapshot of the first layer model with top view at 2500 ps (the last carbon atom of C18-L-Glu is pink) and an AFM image of the smooth area of C18-l-Glu molecules on a mica surface.
average value of hydrogen bond energy is -33 kcal/mol, about 2.5 hydrogen bonds formed in every C18-Glu molecule on average. The average value of van der Waals energy is 15 kcal/mol, which is much smaller than the attraction energy provided by hydrogen bonds. So hydrogen bond energy can provide sufficient driving force for the C18-LGlu molecules to form a stable thin film structure on the mica surface. Snapshots of the first layer model at 0 ps after energy minimization to full convergence and at 2500 ps are shown in Figure 5. The molecules in the first layer form smooth surface areas in the AFM images. Until 1000 ps, torsion energy and van der Waals energy kept on decreasing while angle energy increased a little, and at this point the hydrogen bond energy reached its lowest value. During this time period, the tilt angle of the first layer changed from about 5° at 0 ps to about 30° at 1000 ps. There were some gauche defects in the initial structure of C18-L-Glu molecules, but after the energy minimization, all were in the trans configuration and the gauche defects that appeared in the following 2500 ps simulation runs were very scarce. We also found that the gauche defects were mostly located at the end of the chain, and the interior of the monolayer was essentially defect-free. Such phenomena can be explained since a single gauche defect is unlikely to exist in the middle of the chain because in a densely packed layer system, the bend formed by a gauche bond in the middle of the chain would be energetically prohibitive. This is similar to what Wen Mar etc. found for the configuration of n-hexadecanethiol monolayer chemisorbed on a gold surface.18 They pointed out that a way to accommodate gauche defects within the layer is to form a “kink”, i.e., a pair of gauche defects, for such a conformation can preserve the essential linearity of the molecule. Since experimental data suggested that a
Figure 7. Chiral molecule of N-stearoyl-L-glutamic acid (C18L-Glu). The carboxyl I group is attached to the chiral center directly, and the carboxyl II group is linked by two -CH2groups to the chiral center. The carboxyl II group can move more freely than carboxyl I group and can adjust the location of molecule to match the crystal lattice of mica well in order to form hydrogen bonds between C18-L-Glu and mica.
periodical pattern of an alternation of two different heights of 0.9 and 3.1 nm formed by C18-L-Glu, we first put the C18-Glu molecules with a large tilt angle (about 80° normal to mica surface) as to form a layer of 0.9 nm, but the big van der Waals interaction between the C18-L-Glu molecules forced the molecules to stand up quickly during the mechanics minimization, so we deduce that it is not possible to contain C18-L-Glu in a single 0.9 nm thick layer from our simulation result. A snapshot at 2500 ps is shown in Figure 6 with a top view together with an AFM image of the smooth area formed by C18-L-Glu molecules on a mica surface. From the figure we can see molecules in this layer formed a linear alignment and there is a period composed of the adjacent two lines. After the first layer had grown at the mica surface, the mica surface became highly hydrophobic with the hydrophobic lines composed of hydrocarbon
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Figure 8. Running averages of energy components during the 2500 ps run for the second layer model. During the simulation run, valence energy (including angle energy, torsion energy, and inversion energy) increases slightly and nonbond energy (including van der Waals energy and hydrogen bond energy) keeps on decreasing.
chains aligned parallel to each other. As we have pointed out before, hydrogen bonds play an important role in the structure of the self-assembled molecules. When C18-LGlu molecules were applied to the hydrophilic surface of mica, the free carboxyl group of C18-L-Glu in the chiral aggregate interacts with the domains of oxygen ions and the hydrophobic hydrocarbon chains extend upward. At this time, the chiral aggregates will be broken to form a layered structure. Most importantly, two carboxyl groups in the molecule C18-L-Glu are at different steric positions (Figure 7). One of them (carboxyl I) is attached to the chiral center directly and the other (carboxyl II) is linked by two -CH2- groups to the chiral center. Carboxyl I can form hydrogen bonds between the molecules in the same layer due to their relatively close positions. Carboxyl II can move more freely than carboxyl I and can adjust the location of the molecule to match the crystal lattice of mica well in order to form hydrogen bonds between C18L-Glu and mica. The driving force for the formation of stable layered structure is believed to be the capacity for establishing amide-amide hydrogen bond and carboxyl I-carboxyl I hydrogen bond networks in the same layer. The hydrogen-bonded structure of amino acid amphiphiles may resemble the β-sheet structure of protein to some extent.
II. Multiple Layers Model. The molecules in the second layer form rough surface areas observed in AFM images. The running average of the energy components during the MD simulation run is shown in Figure 8. During the simulation run valence energy (including angle energy, torsion energy, and inversion energy) increases slightly and nonbond energy (including van der Waals energy and hydrogen bond energy) keeps on decreasing. In the last 500 ps of the 2500 ps simulation, changes of the energy components become less than 0.5 kcal/mol, and the nonbond energies (including van der Waals energy and hydrogen bond energy) become stable. From Figure 8 we can see that it takes much longer for the energy components of the second layer to equilibrate than those of the first layer, especially for the hydrogen bond energy. We think that it is easier for the C18-L-Glu molecules in the first layer to form stable hydrogen bond networks than in the second layer due to the excessive hydrogen bond acceptors in mica surface. For the second layer it is only possible for the hydrogen bonds to be formed between the C18-L-Glu molecules in the same layer. The subsequent layers deposited in a multilayer appear to contain a modest concentration of conformational/orientational defects compared with the first layer as deduced from the torsion
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Figure 9. Snapshots with a side view at 0 ps (left) and 2500 ps (right) during the MD simulation run of the second layer model. To form hydrogen bonds in the same layer for the amide group and carboxyl group, C18-L-Glu adopted a fully extended conformation.
Figure 10. Skeletal model of the layer-by-layer asymmetric structure formed by C18-L-Glu on a mica surface, viewed at the cross section. The height of 3.1 nm obtained by cross-sectional analysis corresponds to the fully extended C18-L-Glu molecules, and the height of 0.9 nm corresponds to the difference of two tilted layers between one extended layer.
energy and inversion energy of the second layer, which are slightly higher than those of the first layer. Figure 9 shows snapshots of the multilayered structure with side views at 0 and 2500 ps during the MD simulation. At the beginning of the simulation, the second layer of C18-L-Glu molecules uses the final configuration of the first layer model simulation run, which has a tilted angle vertical to the mica surface. After a 2500 ps MD run, the molecules in the second layer stand up, which we think makes it easier for the carboxyl II to form an intermolecular hydrogen bond network. Cross-sectional analysis shows two steps with heights of about 0.9 and 3.1 nm in the layered structure of C18L-Glu on mica surface. These data suggest that a periodical pattern of an alternation of two different heights of 0.9 and 3.1 nm is formed by C18-L-Glu on mica surface. As we
have pointed out before, it is not possible for the C18-L-Glu molecules to form a single layer of 0.9 nm thick, so we suggest a packing pattern as shown in Figure 9 for C18L-Glu molecules assembling on a mica surface. The layer with a height of 3.1 nm corresponds to the fully extended C18-L-Glu molecules. The height of 0.9 nm corresponds to the difference between the length of two tilted layers that are stacked upon each other and that of a neighboring extended layer (see Figure 10). In the fully extended layer, hydrogen bonds are all formed in the same layer, so we think it may become difficult for another layer to grow on it. If no other layer of C18-L-Glu molecules assembled on it, then the fully extended layer forms the rough areas in the AFM images. However, if another layer of C18-L-Glu molecules assembled on the fully extended layer, with the carboxyl II groups in each layer face to face, we think the situation would be something like the first layer and the mica surface. The fully extended layer and the other layer may finally develop a tilted angle for the carboxyl II groups to form an interlayer hydrogen bond network and the carboxyl I groups to form an intralayer hydrogen bond network. The methyl groups in the other layer form the smooth areas observed in the AFM images Acknowledgment. This work was supported by the National Science Foundation of China (Grant No. 29892168 and No. 20073014), the Doctor Foundation by the Ministry of Education, the Foundation for University Key Teacher by the Ministry of Education, and the Key Subject of Science and Technology by the Ministry of Education of China. LA0155045
