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J. Phys. Chem. C 2007, 111, 8366-8371
Molecular Dynamics Simulations of the Vibrational Signature Transfer from a Glycine Peptide Chain to Nanosized Gold Clusters Ling Miao† and Jorge M. Seminario*,†,‡ Department of Chemical Engineering and Department of Electrical and Computer Engineering, Texas A&M UniVersity, College Station, Texas 77840 ReceiVed: December 21, 2006; In Final Form: March 30, 2007
Molecular dynamics simulations are used to study a glycine polypeptide chain connected to gold nanoclusters. This system is used as a proof of concept for the development of scenarios for the transmission of signals encoded into molecular vibrations (vibronics) instead of the standard encoding in electron currents (electronics). We demonstrate theoretically that, although a linear polypeptide is not energetically stable thus not suitable to be connected to gold clusters, a prerelaxed polypeptide can stay connected to the nanosized gold electrodes showing a final stable structure, which is important for the design and development of molecular vibronics systems. The frequency analysis shows an observable change of the vibrational characteristics of the nanogold cluster due to the peptide presence, suggesting that such system can also be used as a sensor device for molecule detection.
1. Introduction Current microelectronics technology is dominated by the so-called silicon complementary metal-oxide-semiconductor (CMOS).1-3 Transistors in this technology are switches where the charge current through a semiconductor channel is controlled by a metal gate separated by a thin insulator from the channel. These transistors are always paired (complementary), one doped with positive impurities and the other with negative ones, allowing extreme savings in energy because this arrangement makes it so that that the channels only conduct during a state change, i.e., at the frequency of operation (or clock frequency). The great advantage of this technology is the ability to scaledown; making everything smaller in an integrated circuit allows for faster and denser systems. However, as transistors reach the nanometer scale, several problems become an obstacle for a direct scale-down process. Arranging so many transistors (e.g., in microprocessors, 400 million in one cm2) creates a problem of heat removal; on the other hand, having shorter channels lengths than the present ones, ∼30 nm, yields strong current leakages that make it difficult to discriminate between the ON and OFF states needed for binary logic and needles to mention fabrication costs.4-6 Several other fundamental chemical and physical limits of CMOS transistors may be reached in the further downscaling of silicon based electronics.5,7,8 Although it is hoped that molecular electronics, based on one or a small number of molecules, may complement the conventional silicon electronics, the electron currents cannot be scaled down further in small structures due to the strong perturbation that electrons impinge on nanostructures and the associated heat.9,10 Several other possible alternatives of encoding information that do not use the electron charges and currents have been proposed, such as, molecular potentials,9,11,12 spin states,13,14 vibronic states,8,15 and plasmonic states.16,17 It has been demonstrated that the atomic vibrational continuous motion externally imposed at one end of a molecule can be * To whom correspondence should be addressed. † Department of Chemical Engineering. ‡ Department of Electrical and Computer Engineering.
propagated along linear or almost linear molecules, such as DNA, proteins, and other organic molecules. It was found that a vibrational wave is able to propagate along a polypeptide molecule for more than 168 Å3 when a periodic signal of arbitrary shape is continuously used to drive one atom at one end of a long molecule.1,15,18 Signals of very low energy ∼0.5 eV were used revealing a potential scenario for molecular vibronics. In previous work, we demonstrated that signal transmission occurs along relatively short polypeptides, such as glycine-58, whose terminals are assumed to be fixed in order to mimic a cluster-connected system.19 Molecular dynamics simulations were used to obtain feasible information of the geometric and dynamic properties of the system, and results were analyzed using digital signal processing (DSP) techniques. In this work, we study a much longer polypeptide molecule contacted to gold clusters. The molecule is equilibrated together with its two contacts attached through organic thiols, which are known to chemisorb on gold as thiolates after deprotonation of the S-H bonds. This process has been widely used in forming self-assembled monolayers (SAM) on gold surfaces.20,21 We test the stability of the system using molecular dynamics simulation techniques at 100 and 300 K. These results will be used to develop a peptide based vibronics and for the investigation of vibronic signal transmission along peptides. 2. Methodology and Preliminary Settings 2.1. Force Fields. The CHARMM all-hydrogen parameter force field22 was employed to model the bonded and nonbonded interactions of the polypeptide atoms. The interaction energy consists of intramolecular potential energies only due to the onemolecule system. The bond stretching, angle bending, and dihedral angle torsion terms are included to represent the bonded potential energy, together with the nonbonded van der Waals (vdW), and electrostatic potential terms. The interactions between the molecule and the Au atoms are described by Au-S and S-C bond stretching, the Au-S-C angle bending, and the vdW forces of Au-S and Au-C. Only the Au atoms close to the S atom are taken into account for the Au-S bonded
10.1021/jp068797p CCC: $37.00 © 2007 American Chemical Society Published on Web 05/22/2007
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Figure 1. Schematic drawing of methanethiolate capped glycine binding with the Au clusters. Section in brackets shows one residue. Gly1000 is composed of 1000 glycine residues with a total length of about 3.8 nm. Gly1000 is chemically a very soft molecule due to the lack of side groups on the R carbon (the one in between the CO group and the N atom).
TABLE 1: Force Field Potentials and Parameters Used in This Work potential type
functional form
potential type
functional form
bond potential
U(r) ) k(r -
valence angle potential
U(θ) ) k(θ - θ0)2
Lennard-Jones potential per interaction ij
dihedral angle potential
U(φ) ) A[1 + cos(mφ - δ)]
Lennard-Jones potential at each atom i
improper dihedral angle potential
U(φ) ) k(φ - φ0)2
Sutton-Chen potential at each atom i
r0)2
Coulomb potential
1 qiqj 4π0 rij σ 12 σ Uij (r) ) 4 rij rij σ 12 Ui (r) ) 2 j*i rij U(rij) )
[( ) ( ) ] 6
[ ( ) ∑( ) ] [∑ ( ) x∑ ( ) ] ∑
1 Ui (r) ) 2
σ
j*i
n
rij
σ
j*i
6
rij
σ
- 2C
m
rij
j*i
Atom types used in the simulations. Color coded as H (white), N (blue), C (light blue), and O (red). bond potential parameters bond type NH1-H NH1-CT2 C-O C-NH1 bond type H-NH1-CT2 NH1-CT2-HB HB-CT2-HB HB-CT2-HB NH1-CT2-C HB-CT2-C bond type H-NH1-CT2-HB H-NH1-CT2-C O-C-NH1-H O-C-NH1-CT2 C-NH1-CT2-HB C-NH1-CT2-C HB-CT2-C-O HB-CT2-C-NH1
k (kcal mol-1 Å-2) 440.00 220.00 620.00 370.00 k (kcal/mol/rad2) 35.00 48.00 35.00 50.00 50.00 50.00 A (kcal/mol) 0.0 0.0 2.5 2.5 0.0 0.2 0.0 0.0
bond type
k (kcal/mol/rad2)
C-CT2-NH1-O NH1-C-CT2-H
20.00 120.00
bond type
(kcal/mol)
Au-C
0.1965
k (kcal mol-1 Å-2) 250.00 300.00 434.68 96.00
r0 (Å) bond type 0.9970 CT2-C 1.4300 CT2-HB 1.2300 S-CT2 1.3450 S-Au valence angle potential parameters θ0(°) bond type 117.0 O-C-NH1 108.0 CT2-C-O 115.0 CT2-C-NH1 109.5 C-NH1-H 107.0 C-NH1-CT2 109.0 Au-S-CT2 dihedral angle potential parameters m δ (°) bond type 1 0 NH1-CT2-C-O 1 0 NH1-CT2-C-NH1 2 180 HB-CT2-C-O 2 180 HB-CT2-C-NH1 1 0 CT2-C-NH1-H 1 180 CT2-C-NH1-CT2 1 0 HB-CT2-NH1-H 1 0 HB-CT2-C-NH1 improper dihedral angle potential parameters φ (°)
bond type
0 C-CT2-NH1-O 0 C-CT2-CT2-O van der Waals potential parameters σ (Å)
bond type
3.252 Au-S quantum Sutton-Chen potential parameters
r0 (Å) 1.4900 1.0800 1.9020 2.3900
k (kcal/mol/rad2) 80.00 80.00 80.00 80.00 50.00 46.35 A (kcal/mol) 0.0 0.6 0.0 0.0 2.5 1.6 0.0 0.0
θ0(°) 122.5 121.5 116.5 123.0 120.0 104.0 δ (°) 0 0 0 0 180 0 0 0
m 1 1 1 1 2 1 1 1
k (kcal/mol/rad2)
φ (°)
20.00 120.00
0 0
(kcal/mol)
σ (Å)
0.3485
2.993
bond type
(kcal/mol)
σ(Å)
n
m
C
Au-Au
0.180
4.0651
11
8
53.581
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Figure 2. Shape of gly1000 after 100ps of MD simulation.
Miao and Seminario interactions, whereas the interactions between S and other surrounding Au atoms are modeled by Lennard-Jones (LJ) potential. The S-Au binding has been modeled from quantum mechanical calculations by Sellers et al.,23 where two stable chemisorption modes were found depending on the hybridization mode of sulfur. Both modes are expected to be readily accessible at room-temperature due to their small energy difference. In this work, we adopt the force parameters for the sp3 hybridization mode of S, as listed in Table 1. The nonbonded LJ parameters of Au-S and Au-C calculated from mixing rules are also listed in Table 1. The Au-Au interactions are described by a modified Sutton-Chen potential24 reported to be closer to experimental values than the ones predicted from the original Sutton-Chen potential parameters. In this potential, and σ have the same meaning (except for a constant value) as in the Lennard-Jones potential, i.e., as a cohesive energy and as a length parameter, respectively. Notice that for each atom, i, their interactions with the other atoms j are summed up for the sake of comparison; thus, the repulsive term is physically similar to the repulsive term in the Lennard-Jones potential, but the
Figure 3. (a) Snapshot of the detachment of the gly1000 terminal from the Au cluster. (b) Snapshot of the gly1000-Au system after 600 ps equilibration. The bright green dots are Au atoms.
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Figure 4. Total energy variation (in 105 kcal/mol) of gly1000 attached to the Au clusters versus time (in 10 ps). Notice that the molecule and Au cluster separate at ∼32 ps marked by the red arrow.
attractive (negative) term has been square rooted with C as a scaling parameter between attractive and repulsive terms. 2.2. Sample Preparation. Eight layers of Au FCC clusters (approximately 3.3 × 3.3 × 1.6 nm3) are connected to each side of the molecule. We construct gly1000 polypeptide, a soft polypeptide with 1000 glycine residues. The bracket part in Figure 1 shows the main repetitive unit or residue of the molecule. The polypeptide is capped by methylenethiol and connected to gold nanoclusters. Several experiments and theoretical calculations suggest that, after deprotonation of the S-H bond, methylenethiol molecules adsorb on the Au surface,25-27 as a methylenethiolate, as shown in Figure 1. All of the MD simulations have been performed using the DL_POLY program.28 The system is simulated under canonical (constant NVT) ensemble using the Verlet leapfrog algorithm.29 A time step of 1 fs is used in all simulations without using periodic boundary conditions. 3. Results and Discussion 3.1. Equilibration of a Peptide Molecule. The linear gly1000 is first relaxed during 100 ps at 100 K. We find that right after the simulation process begins, the molecule bends. The linear morphology becomes a sinuous curve and the molecule quickly falls down or collapses toward the center of the chain. Figure 2 shows a snapshot of gly1000 after 100 ps. This geometry evolution is expected because, unless the two ends of the molecules are held by strong forces, a straight long polypeptide is not energetically favored. Further runs of the molecular dynamics simulation shows that an isolated gly1000 collapses to a disordered body. 3.2. Equilibration of Peptide-Au System. We then study a peptide attached to a gold cluster. A linear gly1000 is used to connect with Au clusters on both sides. The simulation shows that gly1000 quickly detaches from the Au cluster by pulling a few of gold atoms away from the cluster as shown in Figure 3a. Then, the molecule bends and contracts, exhibiting a wavy geometry. However, due to the few Au atoms that are pulled by the peptide, the morphology change of the gly1000 does not behave as the lone glycine where no Au atoms are involved. When the Au clusters are attached, the contraction of
Figure 5. Snapshot of gly1000 terminal connected to gold clusters at 100 K after 700 ps of equilibration runs.
the gly1000 is not observed immediately. The geometry evolution is relatively much slower. Furthermore, Figure 3b shows that, even after 600 ps of equilibration time, the peptide does not contract into a disorganized body as seen previously when no gold clusters are attached. Figure 4 shows the total energy variation during the first 183 ps. The change in the slope of the total energy appears when gly1000 separates from the Au cluster, roughly at about 32 ps indicated by the red arrow in Figure 4. Once the peptide and Au cluster disconnect, the total energy variation becomes much smaller and the system evolves toward equilibration. 3.3. Reconnection of the Au Cluster and Peptide. Since it is obvious that a straight gly1000 is energetically unfavorable and it is not able to stay connected with the Au clusters, we investigate the possibility of reconnecting the clusters to the detached gly1000 by moving the Au clusters toward both ends of the molecule after they are separated. This is anyway a more realistic situation; once we have the gly100 equilibrated, we approach it to the clusters. After equilibration for 700 ps, we observe that, unlike the case of the straight gly1000, a detached gly1000 from the clusters can be reconnected to the Au clusters without breaking up again; therefore, in this case, gly1000 attaches perfectly well to the Au clusters on both sides as shown in Figure 5 (at one of the ends). 3.4. Spectral Analysis. The atomic conformations of the Au clusters obtained from simulations are used as input data for the vibrational frequency calculations using Fourier transforms.30 Although the dynamic features of molecular devices can be
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Miao and Seminario
Figure 7. Vibrational frequency of equilibrated Au bulk, Au cluster, and gly1000 connected Au cluster at 300 K.
which can be obtained from the Fourier transform of the velocity autocorrelation function (VACF)31
I(ω) )
∫-∞∞ VACF exp(-iωt) dt
where
VACF )
Figure 6. (a) Vibrational spectra of an equilibrated Au bulk, the Au cluster, and the Au cluster when connected to the gly1000. (b) Snapshots of bulk gold, (c) gold cluster, and (d) gold cluster when connected to the gly1000. The same production time is used for the three samples but the equilibration times are different. Considering the total mass of the cluster, the peptide is just roughly half.
represented by continuous time signals, the time-domain data available for the spectral calculations are discrete-time signals and must be processed in order to obtain frequency spectra,
〈Vi(t0)‚Vi(t0 + t)〉 〈Vi(t0)‚Vi(t0)〉
and Vi(t0) and Vi(t0 + t) are the atomic velocities at a reference time t0 relative time t0 + t through the simulation. Figure 6 shows the spectral intensity of the Au bulk and the Au cluster before and after connecting the gly1000 molecule. Before connecting the cluster to the gly1000, the Au cluster shows two main vibrational modes, which correspond to the acoustic and optical vibrations existing in Au bulk. From this figure, we observe that the acoustic peak of the Au cluster appears at the same frequency as in the Au bulk, whereas the optical peak shifts to a higher frequency. Certain behaviors of nanoclusters have been observed in Au and other metals.32-36 It is discussed that the high-frequency peak shift is mostly due to the inner atoms of the nanocluster. The shortening of the nearest neighbor distance of inner atoms stiffens the force constants and results in a disharmonic optical vibration with a higher frequency. The connection to gly1000 and thereafter the contracting force from the molecule increases the interatomic Au nearest neighbor distance and rearranges the lattice structure. As can been seen from the snapshots in Figure 6, the connected cluster shape and structure (Figure 6d) is different from the one before the attachment (Figure 6c) to gly1000, where a rectangular FCC structure (Figure 6b) is mostly maintained. The evolution from a mostly perfect lattice structure toward a semiamorphous rod induces severe reduction of intensity on the vibrational peaks. However, we observe that the lower frequency modes (frequencies of less than 1.5 THz) are slightly enhanced as compared to the free cluster. This can be explained by the softening of the atomic constants of the Au surface atoms that are near to the polypeptide, which strongly affect the local density of states of the surface atoms at low frequencies.33
Simulations of the Vibrational Signature Transfer 3.5. Effects of Temperature. We performed earlier calculations at 100 K in order to avoid mixing with other effects related to the force field. Once all effects were carefully analyzed, we increase the temperature of the sample to 300 K. The results are shown in Figure 7. Practically the same features observed at 100 K still were observed at 300 K. The amplitude of the peaks decreases strongly with the increase of the temperature, but most of the qualitative features persists, especially in the bulk and the cluster alone, where the persistence of lattice structure significantly depends on temperature. However, temperature has less effect on the frequency shifts once Au is connected to the peptide, because the deformation of the cluster is thus mainly caused by the peptide rather than by the change of temperature. 4. Conclusions We have developed a simulation procedure to model linear molecules attached to two terminals. Before applying any signals to this system, it is very important to understand its stability at ambient conditions. Our calculations show that a linear isolated polypeptide is not energetically favorable and cannot stay connected with the Au clusters. However, it is possible to connect the polypeptide with the Au cluster at room-temperature if the molecule is prerelaxed. The frequency analysis of the Au cluster before and after connecting with polypeptide indicates a significant change on the frequency of the cluster upon the appearance of the molecule, where the peptide, rather than temperature, is mainly responsible for the changes. This theoretical study is toward the design and implementation of a biomolecule-based vibronics able to transport high-frequency signals taking advantage of the delocalized molecular vibrational modes. Our results also suggest that small gold clusters can be used for sensing as they are strongly affected when the polypeptide molecule is attached to the cluster. Correlations between the effects on the frequency spectrum would allow us in the future determine the nature of a signal injected to the linear chains attached to metallic or other clusters. Acknowledgment. We thank the Defense Threat Reduction Agency (DTRA) and the Army Research Office (ARO) for their support to this project. References and Notes (1) Seminario, J. M.; Yan, L.; Ma, Y. Proc. IEEE 2005, 93, 17531764. (2) Seminario, J. M.; Cordova, L. E.; Derosa, P. A. Proc. IEEE 2003, 91, 1958-1975. (3) Seminario, J. M.; Yan, L.; Ma, Y. J. Phys. Chem. A 2005, 109, 9712-9715. (4) Chau, R.; Datta, S.; Doczy, M.; Doyle, B.; Jin, B.; Kavalieros, J.; Majumdar, A.; Metz, M.; Radosavljevic, M. IEEE Trans. Nanotechnol. 2005, 4, 153-158. (5) Zhirnov, V. V.; Cavin, R. K.; Hutchby, J. A. Proc. IEEE 2003, 11, 1934-1939.
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