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74 Ying Luo et al.
all-trans-retinal
H
C COOH
COOH
CH
2
S
–H
H
2
NH
NCH SH
H
CH
2
O
+
cysteine
Figure 16 Nucleophilic addition-elimination reaction between all-trans-retinal and cysteine
amino acid
Second, fabricate two-dimensional gold nanostructure arrays on pit-patterned HOPG
surfaces [40] or semiconductor substrates by a dip-pen nanolithography (DPN)-based
strategy [41]. A two-step experiment was performed in [40] to produce two-dimensional
patterns of gold nanostructures on HOPG. First, nanometer-size etch pits were patterned
as regular arrays on HOPG using highly focused 25 keV Ga
+
ion bombardment. The
second step was to deposit gold onto the pit-patterned HOPG surfaces in vacuum. In
[41], the investigators developed a method for fabricating arrays of Au nanostructures
on a SiO
x
/Si surface based on DPN and wet chemical etching.
Finally, due to the strength of the thiol groups at the end of cysteine amino acids,
self-assembled monolayers of retinylidene cysteine molecules on gold nanopaticles can
be formed. For example, in [43] they show how the etched Au nanopatterns can be
used as templates to adsorb and assemble proteins from solution to form functionalized
inorganic/biological nanostructures and in [44] self-assembled monolayers on Au(111)
are formed by microcontact printing of dodecanethiol. The bonding of the sulfur head
group to the gold substrate is in the form of a metal thiolate (RS
−
) species [45]. This
is an extremely strong surface bond and the resulting monolayers are quite stable.
The formation of gold thiolate requires the loss of SH hydrogen but it has not been
determined whether this proton is lost as H
2
or H
2
O [46]. The presumed adsorption
chemistry is shown in the equation of Figure 17 [47]. In this way, retinal derivative
molecules are confined in a nano-size space and two-dimensional retinal nanostructure
arrays are formed as shown in Figure 18.
3.2. Simulation and analysis of retinal derivatives
To approximately infer how the gold substrates will affect the properties of retinal
molecules, simulations have been conducted to predict the properties of retinylidene
300 K, EtOH
Au + HS (CH
2
)
n
X
Au–S
–
(CH
2
)
n
X
–H
2
(+O
2
–H
2
O?)
Figure 17 Chemical reaction between molecules with thiol group and gold [47]
Bio-molecular devices for terahertz frequency sensing 75
Retinal
derivatives
Retinal
derivatives
HOPG
substrate
Pit etched
on HOPG
Gold contact
deposited in pit
Gold nanopaticles
Pit-templated HOPG
Figure 18 Two-dimensional nanopatterned N -retinylidene cysteine arrays
cysteine-gold molecules. While the long-range goal is to simulate retinylidene cysteine-
gold monolayers on gold clusters, initial investigations have been focused on the case
where one retinal isomeric molecule is connected to a gold atom via the link of a cysteine
molecule (N -retinylidene cysteine-gold molecule) and one such N-all-trans-retinylidene
cysteine-gold molecule is illustrated in Figure 19. Other retinylidene cysteine-gold
isomers simulated in this chapter are constructed in the same manner.
The THz characteristics of various retinylidene cysteine-gold molecular conformations
have been investigated at HF level using LANL2DZ basis set. The scaling factor 0.9
was applied to eliminate the systematic errors due to the method and basis set [48].
The very far infrared spectra (<30 cm
−1
)ofN -all-trans-retinylidene cysteine-gold and
its isomers are shown in Figures 20–22. It is clear that there are many more vibrational
modes in FIR spectra of retinal derivatives than those of isolated retinal isomers. The
strongest absorption peaks of N -9-cis-retinylidene cysteine-gold, N -11-cis-retinylidene
COOH
H
N
S
Au
CH
CH
2
Figure 19 An all-trans-retinal molecule connected with a cysteine amino acid molecule and
then a gold atom (N -all-trans-retinylidene cysteine-gold molecule)
76 Ying Luo et al.
Vibrational frequency (cm
–1
)
0.0
0 5 10 15 20 25 30
0.5
1.0
1.5
2.0
2.5
3.0
IR intensity (km/mol)
all-trans
9-cis-IR
Figure 20 FIR spectra of N -9-cis-retinylidene cysteine-gold and N -all-trans-retinylidene
cysteine-gold (<30 cm
−1
)
Vibrational frequency (cm
–1
)
0.0
051015202530
0.5
1.0
1.5
2.0
IR intensity (km/mol)
all-trans
11-cis-IR
Figure 21 FIR spectra of N -11-cis-retinylidene cysteine-gold and N -all-trans-retinylidene
cysteine-gold (<30 cm
−1
)
cysteine-gold and N-13-cis-retinylidene cysteine-gold molecule are quite distinguishable
from that of N-all-trans-retinylidene cysteine-gold, which shows that the spectra fidelity
of retinal isomers still exists in these retinal derivatives.
In addition, the PECs of the retinylidene cysteine-gold molecule were derived as
were done earlier for the isolated retinal. Geometric optimizations and calculations of
potential energies of molecules were performed at DFT using LANL2DZ basis set.
B3PW91 is used by the DFT level, which uses the Becke-3 hybrid exchange functional
and the Perdew–Wang 91 correlation functional. The PECs of rotation for N -all-trans-
retinylidene cysteine-gold around C9
==
C10, C11
==
C12, and C13
==
C14 double bonds are
Bio-molecular devices for terahertz frequency sensing 77
0.0
Vibrational frequency (cm
–1
)
0 5 10 15 20 25
30
0.5
1.0
1.5
2.0
2.5
3.0
IR intensity (km/mol)
all-trans
13-cis
Figure 22 FIR spectra of N -13-cis-retinylidene cysteine-gold and N -all-trans-retinylidene
cysteine-gold (<30 cm
−1
)
Torsional Angle (degree)
0.0
0
Energy of molecular sustem (eV)
20 40 60 80 100 120 140 160 180 200
0.2
0.4
0.6
0.8
1.0
1.2
1.4
1.6
1.8
9-cis-cysteine-gold
11-cis-cysteine-gold
13-cis-cysteine-gold
Figure 23 PECs of N -all-trans-retinylidene cysteine-gold molecule rotated around C9==C10,
C11==C12, and C13==C14 double bonds
shown in Figure 23. Besides the spectra fidelity, other observations from the simulations
of isolated retinal isomers can also be found from the simulations of retinal derivatives
isomers. For example, significant barriers are observed in PECs that are even larger
than those of isolated retinal. And another one is that the barrier for rotation around
the C9
==
C10 double bond of retinylidene cysteine-gold is still the largest and around
C13
==
C14 is still the smallest. The complete list of excitation energies of both isolated
retinal and retinylidene cysteine-gold is shown in Table 5. Excited states were calculated
with the time-dependent DFT (TDDFT) method. The excitation energies of the retinal
derivatives are smaller than those of corresponding isolated retinal isomers but still
relatively close to each other as isolated retinal isomers. According to the discussion
78 Ying Luo et al.
Table 5 Excitation energies calculated with TDDFT method (eV)
Isomers S
1
S
2
S
3
All-trans-retinal (Isolated) 3.0496 3.0646 3.8893
N-all-trans-retinylidene cysteine-gold 1.6606 1.8640 2.7852
9-cis-retinal (Isolated) 3.0708 3.0833 3.8894
N-9-cis-retinylidene cysteine-gold 1.6900 1.8780 2.7732
11-cis-retinal (Isolated) 3.049 3.0505 3.0991
N-11-cis-retinylidene cysteine-gold 1.6654 1.8745 2.7825
13-cis-retinal (Isolated) 3.0673 3.0991 3.9118
N-13-cis-retinylidene cysteine-gold 1.6594 1.8656 2.7506
above, it is reasonable to conclude that many properties of isolated retinal isomers are
preserved in retinal derivatives.
4. Directions for future work and conclusions
This chapter has presented a new bio-molecular electronic architecture that offers an
enhanced capability for sensing THz-frequency bio-signatures. This chapter also presents
modeling results that illustrate prototypical examples for the type of functional bio-
molecules needed for implementing this bio-molecular system. In the future, this work
will be used to guide new experimental investigations that focus on the measurement of
very far infrared spectra of retinal isomers and retinal isomer derivatives. The studies
presented in this chapter analyzed compound molecules of the type needed for realiz-
ing functional bio-molecular devices and derived their THz spectra and photo-induced
methods for controlling the THz-frequency characteristics through changes to energy
state and conformation. One possible fabrication approach for the construction of retinal-
based two-dimensional nanostructures was also presented. Future theoretical work will
consider such functional bio-molecules that are bonded to traditional nanoscale semicon-
ductor systems. The ultimate goal of this research is to define functioning bio-molecular
devices (e.g., light guiding structures) that can be used to achieve bio-signature sensing
and data processing in ultra-small integrated platforms.
References
[1] D. L. Woolard, Y. Luo, B. L. Gelmont, T. Globus, and J. O. Jensen, “Bio-Molecular inspired
electronic architectures for enhanced sensing of THz-frequency bio-signatures”, Int. J. High
Speed Electron, 16, no. 2, 609–637 (2006).
[2] D. L. Woolard, Y. Luo, B. L. Gelmont, T. Globus, and J. O. Jensen, “A bio-molecular
inspired electronic architecture: Bio-based device concepts for enhanced sensing”, invited
paper in Proc. SPIE Secur. Defense Symp., 5790, 180 (2005).
[3] D. L. Woolard, Y. Luo, B. L. Gelmont, T. Globus, J. O. Jensen, H-L Cui, and N. C. Seeman,
“Patent title: Bio-molecular inspired electronic architectures for enhanced sensing of THz-
frequency bio-signatures”, Patent submission to the legal office of U.S.Army Reserch Office,
March 2005.
Bio-molecular devices for terahertz frequency sensing 79
[4] D. Woolard, T. Globus, E. Brown, L. Werbos, B. Gelmont, and A. Samuels, “Sensitivity
Limits & Discrimination Capability of THz Transmission Spectroscopy as a Technique for
Biological Agent Detection,” in the proceedings to the 5
th
Joint Conference on Standoff
Detection for Chemical and Biological Defense, Williamsburg, VA, 24–28 September (2001).
[5] D. L. Woolard, T. Koscica, D. L. Rhodes, H. L. Cui, R. A. Pastore, J. O. Jensen, J. L. Jensen,
W. R. Loerop, R. H. Jacobsen, D. Mittleman, and M. C. Nuss, “Millimeter wave induced
vibrational modes in DNA as a possible alternative to animal tests to probe for carcinogenic
mutations,” J. Appl. Toxicol., 17, 243–246, May (1997).
[6] Dwight L. Woolard, William R. Loerop and Michael S. Shur (eds), Terahertz Sensing Tech-
nology, Volume 1: Electronic Devices and Advanced Systems Technology (World Scientific,
Singapore, 2003).
[7] Dwight L. Woolard, William R. Loerop and Michael S. Shur (eds), Terahertz Sensing
Technology, Volume 2: Emerging Scientific Applications & Novel Device Concepts (World
Scientific, Singapore, 2003).
[8] T. Globus, D. Woolard, M. Bykhovskaia, B. Gelmont, L. Werbos, and A. Samuels, “Milli-
meter and submillimeter wave spectroscopy of DNA and related materials (theory and
experiment),” Int. J. High Speed Electron. Syst. (IJHSES), 13, no. 4, 903–936, December
(2003).
[9] T. Globus, D. Theodorescu, H. Frirson, T. Kchromova, and D. Woolard, “Terahertz Spec-
troscopic Characterization of Cancer Cells,” accepted SPIE, Photonics West, San Jose,
California, January (2005).
[10] T. Globus, L. Dolmatova-Werbos, D. Woolard, A. Samuels, B. Gelmont, and
M. Bykhovskaia, “Application of Neural Network Analysis to Submillimeter-wave Vibra-
tional Spectroscopy of DNA Macromolecules,” in the proceedings to the 2001 ISSSR, June
12–15, Quebec City, Canada (2001).
[11] M. Bykhovskaia, B. Gelmont, T. Globus, D. L. Woolard, A. C. Samuels, T. Ha-Duong,
and K. Zakrzewska, “Prediction of DNA far IR absorption spectra basing on normal mode
analysis,” Theor. Chem. Acc., 106, 22–27 (2001).
[12] T. Globus, M. Bykhovskaia, D. Woolard, and B. Gelmont, “Sub-Millimeter Wave Absorp-
tion Spectra of Artificial RNA Molecules,” published in the proceedings to the Advanced
Workshop on Frontiers in Electronics (WOFE), St. Croix, Virgin Islands, 6–11 January
(2002).
[13] T. Globus, D. L. Woolard, A. C. Samuels, T. Khromova, and J. O. Jensen, “Sub-
millimeter Wave Fourier Transform Characterisation of Bacterial Spores, “ in the Proceed-
ings of the Int. Symp. Spectral Sensing Res., Santa Barbara, California, 2–6 June 2003,
file://F:\isssr2003\index.htm (2004).
[14] T. Globus, T. Khromova, D. Woolard, and B. Gelmont, “Terahertz Fourier transform char-
acterization of biological materials in solid and liquid phases,” presented at SPIE Photonic
East, Program on Chemical and Biological Sensors, Providence, RI, October 2003, in Proc.
SPIE, 5268–2, 10–18 (2004).
[15] T. Globus, M. Bykhovskaia, D. Woolard, and Boris Gelmont, “Submillimeter-wave absorp-
tion spectra of artificial RNA molecules,” invited to J. Phys. D, 36, 1314–1322 (2003).
[16] T. R. Globus, D. L. Woolard, T. Khromova, T. W. Crowe, M. Bykhovskaia, B. L. Gelmont,
J. Hesler and A. C. Samuels, “THz-Spectroscopy of biological molecules,” J. Biol. Phys.,
29, 89–100 (2003).
[17] Thomas W. Crowe, Tatiana Globus, Dwight L. Woolard, and Jeffery Hesler, “Terahertz
sources and detectors and their application to biological sensing,” invited to Phil. Trans. R.
Soc. Lond. A 362, 365–377 (2004).
[18] T. Globus, D. Woolard, T. Khromova, R. Partasarathy, A. Majewski, R. Abreu, J. Hesler,
S.-K. Pan, and G. Ediss, “Terahertz signatures of biological-warfare-agent simulants,” Proc.
SPIE Defense Secur. Symp., 5411–5, Orlando, FL, April (2004).
80 Ying Luo et al.
[19] D. Woolard, T. R. Globus, B. L. Gelmont, M. Bykhovskaia, A. C. Samuels, D. Cookmeyer,
J. L. Hesler, T. W. Crowe, J. O. Jensen, J. L. Jensen, and W. R. Loerop, “Submillimeter-Wave
Phonon Modes in DNA Macromolecules,” Phys. Rev. E, 65, 1903–1914, May (2002).
[20] V. K. Saxena, B. H. Dorfman, and L. L. Van Zandt, Phys. Rev.,A43, 4510–4516 (1991).
[21] L. L. Van Zandt and V. K. Saxena, in Structure & Functions, Volume 1: Nucleic Acids, Eds
R. H. Sarma and M. H. Sarma (Adenine Press, 1992) and references therein.
[22] T. Globus, D. L. Woolard, A. C. Samuels, B. L. Gelmont J. L. Hesler, T. W. Crowe, and
M. Bykhovskaia, “Submillimeter-wave FTIR spectroscopy of DNA macromolecules and
related materials,” J. Appl. Phys., 91, 6106–6113 (2002).
[23] E. R. Brown, D. L. Woolard, A. C. Samuels, T. Globus, and B. Gelmont, “Remote detection
of bioparticles in the THz region,” Proc. Int. Microw. Symp., Seattle, WA, June 2–6 (2002).
[24] D. L. Woolard, E. R. Brown, A. C. Samuels, T. Globus, B. Gelmont, and M. Wolski,
“Terahertz-frequency spectroscopy as a technique for the remote detection of biological
warfare agents,” presented to the special session on terahertz electronics, Proc. IEEE Int.
Microw. Symp., 8–13 June, Philadelphia, PA (2003).
[25] M. K. Choi, K. Taylor, A. Bettermann, and D. W. van der Weide, “Spectroscopy with elec-
tronic terahertz techniques for chemical and biological sensing,” pp. 35–48 in reference [7].
[26] D. W. van der Weide, M. K. Choi, K. Taylor, and A. Bettermann, “Sensing biomolecules
with microwave and terahertz frequencies,” invited to 16th International Zurich Symposium
on Electromagnetic Compatibility, Zurich, 13–18 February (2005).
[27] G. Markelz and S. E. Whitmire, “Terahertz applications to biomolecular sensing,” pp. 49–66
of reference [7].
[28] T. Globus, D. Woolard, M. Bykhovskaia, B. L. Gelmont, L. Werbos, and A. C. Samuels,
“THz-frequency spectroscopic sensing of DNA and related materials, p. 1–34 of
reference [7].
[29] E. R. Brown, J. E. Bjarnason, T. L. J. Chan, A. W. M Lee, and M. A. Celis, “Optical atten-
uation signatures of Bacillus subtillis in the THz region,” Appl. Phys. Lett., 84, 3438–3440
(2004).
[30] B. L. Gelmont, “Computational modeling of light induced transformations in organic
molecules,” U.S. ARO Interim (10/1/02–12/31/02) Progress Report on Research Grant
DAAD19-02-1-0439 (2003).
[31] M. J. Frisch, et al., Gaussian, Inc., Pittsburgh, PA (2002).
[32] J. B. Foresman and Æleen Frisch, Exploring Chemistry with Electronic Structure Methods,
2nd edn Gaussian, Inc., Pittsburgh, PA (1996).
[33] D. C. McKean, M. W. Mackenzie, A. R. Morrisson, J. C. Lavalley, A Janin, V. Fawcett,
and H. G. M. Edwards, Spectrochimica Acta, 41A, 3, 435–450 (1985).
[34] S. Yamamoto, H. Wasada and T. Kakitani, and T. Yamato, J. Molecul. Struct., 461–462,
463–471 (1999).
[35] S. Yamamoto, H. Wasada, and T. Kakitani, J. Molecul. Struct., 451, 151–162 (1998).
[36] F. L. Gervasio, G. Cardini, P. R. Salvi, and V. Schettino, Journal of Physical Chemistry A,
102, 2131–2136 (1998).
[37] M. Walther, B. Frischer, M. Schall, H. Helm, and P. Uhd Jepsen, Chemi. Phys. Lett., 332,
389–395 (2000).
[38] Æleen Frisch and M. J. Frisch, Gaussian 98 User’s Reference, 2nd edn Gaussian, Inc.,
Pittsburgh, PA (1999).
[39] R. E. Stratmann, G. E. Scuseria, and M. J. Frisch, J. Chem. Phys., 109, 8218–8224 (1998).
[40] Y Zhu, A. Schnieders, J. D. Alexander, and T. P. Beebe, Jr., Langmuir,
18, 5728–5733
(2002).
[41] H. Zhang, Z. Li, and C. A. Mirkin, Adv. Mater., 14, 1472 (2002); H. Zhang, S. W. Chung,
and C.A. Mirkin, Nano Lett., 3, 43 (2003).
[42] F. A. Carey, Organic Chemistry, p. 664. (1987).
Bio-molecular devices for terahertz frequency sensing 81
[43] H. Zhang, K. Lee, Z. Li, and C. A. Mirkin, “Biofunctionalized nanoarrays of inorganic
structures prepared by dip-pen nanolithography, ” Nanotechnol., 14, 10, 1113–1117 (2003).
[44] N. B. Larsen, H. Biebuyc, E. Delamarche, and B. Michel, “Order in microcontact printed
self-assembled monolayers”, J. Am. Chem. Soc., 119, 3017–3026 (1997).
[45] R. G. Nuzzo, B. R. Zegarski, and L. H. Dubois, J. Am. Chem. Soc., 109, 2358 (1987).
[46] Ulman, An introduction to Ultrathin Organic Films: From Langmuir-Blodgett to Self-
Assembly, Academic Press, Inc. (1991).
[47] L H. Dubois and R. G. Nuzzo, “Synthesis, structure, and properties of model organic
surfaces”, Annu. Rev. Phys. Chem., 43, 437–463 (1992).
[48] http://srdata.nist.gov/cccbdb/vsf.asp.
Molecular and Nano Electronics: Analysis, Design and Simulation
J. M. Seminario (Editor)
© 2007 Elsevier B.V. All rights reserved.
Chapter 3
Charge delocalization in (n, 0) model carbon
nanotubes
Peter Politzer, Jane S. Murray and Monica C. Concha
Department of Chemistry, University of New Orleans, New Orleans,
LA 70148, USA. ppolitze@uno.edu
1. Introduction
Carbon nanotubes are long cylindrical structures composed of hexagonal rings of carbon
atoms. These rings can have various orientations with respect to the tube axis, as can be
seen in the examples in Figure 1. The two extremes are when each ring has two sides
parallel to the axis, Figure 1(a), and perpendicular to it, Figure 1(b). An intermediate
case (one of many possibilities) is illustrated in Figure 1(c).
A system has been devised for labeling the different types of nanotubes in terms of
two positive integers (n m); it is explained in detail elsewhere [1–4]. Our present interest
is primarily in tubes having two sides of the carbon rings parallel to the axis; these are
in the category (n 0), with n being the number of rings around the circumference of
the tube. Thus Figure 1(a) shows an (8, 0). Tubes having two ring sides perpendicular
to the axis are labeled (n n); all others are (n m) with n =m.
The structures in Figure 1 are portions of “single-walled” nanotubes, meaning that
each is a single cylinder. It is also possible to have several coaxial tubes; these are
designated as “multi-walled.” We shall focus solely upon the former.
Another feature of nanotubes, in practice, is that they are normally closed at both
ends (capped) when synthesized. The caps can have various structures and shapes [2].
However, whereas the lateral sides of carbon nanotubes are composed entirely of six-
membered rings (except for possible defects), each cap must contain six five-membered
rings. This follows from Euler’s theorem: Any hexagonal framework can achieve com-
plete closure only through the introduction of exactly twelve pentagons [1, 2].
The unusual structural, electronic and mechanical properties of carbon nanotubes
have aroused enormous interest and stimulated a great deal of work, as well as proposed
applications in many different areas. For recent overviews, see White and Mintmire [3]
and Politzer et al. [4].
82
Charge delocalization in (n, 0) model carbon nanotubes 83
(a)
(b)
(c)
Figure 1 Portions of lateral surfaces of carbon nanotubes: (a) (8, 0); (b) (8, 8); (c) (8, 5)
A natural extension of all this activity has been to investigate the possibility of
nanotubes with other elemental compositions. The boron/nitrogen combination seemed
particularly promising because of B
x
N
x
being isoelectronic with C
2x
, as well as other
analogies between B/N and carbon compounds, such as the fact that solid boron
nitride exists in both graphite-like and diamond-like forms [5, 6]. B
x
N
x
[7, 8] and
C
x
B
y
N
z
[9, 10] nanotubes have indeed been prepared.
In this chapter, our emphasis will be upon the remarkable capacities of some (n,0)
model nanotubes for charge delocalization and transmission of electronic effects. We
will limit the discussion to all-carbon systems, although some C
x
B
y
N
z
are also of interest
in this respect. We became aware of these unique features in the course of computational
analyses of the electrostatic potentials and local ionization energies on model nanotube
surfaces [4, 11, 12]. We will therefore begin by providing some background relating to
these two properties.
2. Electrostatic potential
The nuclei and electrons of any system produce an electrostatic potential V (r)inthe
surrounding space; its value at any point r is given rigorously by Eq. (1):
Vr =
A
Z
A
R
A
−r
−
r
dr
r
−r
(1)