Bio-molecular architectural concept and bio-component studies

Bio-molecular architectural concept and bio-component studies

The novelty of the bio-inspired architecture to be presented here lies in the strategic use of integrated biological elements to achieve higher-level function and spectral data processing within a nanoscale and molecular-level architecture. As discussed at length in Section 1, fundamental absorption/emission properties present in known biological materials (e.g., DNA, RNA, etc.) can provide new insight for a novel approach to nanoscale device functionality and integrated molecular-level sensing and data processing. Specifically, DNA and RNA macromolecules have been shown to exhibit spectral absorption characteristics with multiple absorption peaks that might be used to selectively filter and control transmission frequency channels at very long wavelengths. In addition, the absorption characteristics of such bio-molecules are known to be strongly dependent on molecular conformations. As all bio-molecules can be elevated to excited-state conformations through optical or THz-frequency excitation, this process can be used to define ETO molecular function. Therefore, it should be possible to utilize existing and the future artificially designed bio-molecular elements to realize optical or THz-frequency controlled filters of long wavelength electromagnetic signals.

Bio-molecular inspired architecture for sensing

A very simple example of the proposed concept is illustrated in Figure 4 where a hypothetically tunable DNA-based filter (i.e., the THz-frequency spectral absorption peak is influenced by the photonic emission at frequency f2 as depicted in the inset) can be used to establish feedback, and as will be shown later, clocking/register function. As conceptualized here, the ETO-based architecture utilizes two emission sources (i.e., at frequencies f1 and f2_, a single detector (i.e., sensitive to radiation at frequency f1_ and a

direct-current driven circuit. This particular bio-electronic element, as defined, will allow for defining functionality through the coupling of multiple-frequency channels that in turn control a direct-current pulse that periodically flows through the circuit connecting detector D1 to emitter E2. One important advantage of this architecture is that it is possible to realize gating and feedback within densely packed bio-molecular components while at the same time providing for isolation between other system elements (i.e., by utilizing alternative transmission frequencies for nearby units). Also note that these types of bio-molecular components might also be integrated with other inorganic molecules and to traditional semiconductor devices to enable functional control and data processing at the nanoscale. Most importantly, as this basic architecture is intrinsically linked to species-specific spectral absorption features, these bio-electronic systems can be engineered into sensing arrays that detect the presence of target bio-agents. This approach also solves a critical sensing problem, as this type of bio-architecture allows for the nanoscale modification of the electronic and/or conformational state of the target agent – here it is assumed that the target molecule will be captured into the system via engineered ligand bonding sites. Therefore, this bio-electronic architecture allows for a new MS3 approach that can expand the amount of available spectral signature information and greatly improve detection, identification, and characterization capabilities.

The control element of the nano-circuit defined in Figure 4 is to utilize the ETO characteristics of biomolecules – e.g., the THz-frequency spectral absorption will be modified through optical excitation. For example, consider an arbitrary DNA fragment that exhibits a conformation and typical absorption profile around a phonon-induced resonance as shown in Figure 5(A). Here, the resulting spectral absorption is defined by the ground-state conformation of the molecule as shown in the top of Figure 5(A). When subjected to an adequate external excitation (i.e., energy and polarization), the molecule can experience a charge (or potential) redistribution that is accompanied by changes in the conformation and spectral characteristics. If the proper modeling tools are available, it should be possible to identify naturally occurring or artificially engineered bio-molecules that under proper excitations assume excited-state conformations with modified spectral characteristics of the type as shown at the bottom of Figure 5(A). Indeed, simulation studies [30] on small test molecules have already been used to demonstrate this basic effect in the cis-2- and trans-2-isomers of butene. Figure 5(B) shows these two isomers (i.e., which can occur via a rotation around the center bond) along with the discrete (no broadening) THz-frequency absorption spectrum which displays the dramatic changes of the type needed for defining the new bio-molecular architecture. This ETO effect will allow for defining multi-frequency communications and for defining bio-molecular architectures that enable logic and signal processing type functionality.

2.2. Bio-component modeling and simulation

The successful implementation of bio-molecular architectures of the type described in the last sub-section requires the identification of bio-molecules that can be controllably induced (i.e., through optical and/or THz radiation) into alternative geometric conformations. Furthermore, these molecules must exhibit significant variations in their THz-frequency absorption characteristics, as to make the approach useful for processing and collecting bio-signatures. The sub-sections that follow will present a theoretical analysis of two bio-molecules that demonstrate these required ETO-based characteristics. Specifically, the investigations that follow will consider the optically induced isomers of butene and retinal. Here, the results will show that optical control of spectral characteristics is possible, with the smaller butene molecule exhibiting infrared absorption signatures and the larger retinal molecule that demonstrates similar properties in the THz regime.

2.2.1. Simulation and analysis of butene isomers

In the initial study, the cis-trans isomers of butene have been chosen because they are very well known and simple examples of a ground- and metastable-state pair with significantly different geometries. The cis-trans isomers are geometric isomers, a type of stereoisomerism in which atoms or groups display orientation differences around a double bond, such as trans-2- and cis-2-butene as was shown earlier in Figure 5(B). This work demonstrated molecular isomers that yield different sets of vibrational frequencies.

In this case to be studied, photo-induced transitions bring about the conversion from one geometric shape (i.e., trans-2-butene) to another (i.e., cis-2-butene) through rotation about a double bond and the conversion is also called isomerization. The analysis presented here includes calculations of the optimized energies, vibrational frequencies, and infrared intensities that were carried out at the Hartree–Fock (HF) level within the split valence polarized 6-31G(d) basis set in the Gaussian 98 package [31]. The energies of the excited states were found within the single configuration interaction approach (CIS), where one models the first excited state as combinations of a single substitution from the highest occupied molecular orbital (HOMO) to the lowest unoccupied molecular orbital (LUMO). Vibrational frequencies were then computed by determining the second derivatives of the potential energy with respect to the Cartesian nuclear coordinates and then transforming to mass-weighted coordinates. Due to the fact that electron correlation is neglected, the frequencies computed using the HF approximation are known to be overestimated by approximately 10–12%. Furthermore, because a medium-sized basis set was used, the derived values can be expected to deviate even more from experiments, i.e., by approximately 15% in total [32]. Therefore, a scaling was performed on the originally calculated frequencies by an empirical factor of 0.893 to eliminate known systematic errors in the physical model. To monitor the process of isomerization from trans-2-butene to cis-2-butene, the torsional angle _, defined as the dihedral angle of the plane of C1–C2–C3 and the plane of C2–C3–C4 around the double bond in the C1–C2==C3–C4 chain associated with the molecule given in Figure 6(A), was taken to be the reaction coordinate. The potential energy (PE) curves associated with the isomerization process for the ground (S0_ and the first excited singlet state (S1) of 2-butene are shown in Figure 6(B), along with the next two excited states S2 and S3. Here it is important to note that the trans-2 geometry (i.e., _ = 180_) is the natural-state and the cis-geometry (i.e., _ = 0_) is the metastable-state. Without external excitations, the large PE barrier 1.98 eV in the ground state prevents the transition from trans-2-butene to cis-2-butene. It is also clear from Figure 6(B) that there is no barrier in the first excited singlet state S1, which is ideal for an ultra-fast switching between the trans- and cis- isomers. Potential energy curves can be used to illustrate this optically induced isomerization process by following the superimposed arrows. The process begins with a required optical excitation (∼8_46 eV, 146 nm) of the “electronic-state” of the trans-geometry from S0 to S1. This is followed by a non-radiative decay to the S1 PE valley minimum, which corresponds to a 90_ rotation about the reaction coordinate. At this point, the molecule undergoes an “electronic” radiative decay from S1 to S0. This is followed by a second non-radiative decay to the cis-geometry, which corresponds to a second 90_ rotation about the reactive coordinate. At this point, butene will remain in the metastable cis-2 geometry until thermal relaxation of the system back to the ground state. To estimate the probability that the excited trans-2-butene will follow the isomerization process described above, instead of relaxing back to its own ground state, we investigate the molecular dynamics of butene in the first singlet excited state S1 by combining the theory of Newton’s Dynamics and standard quantum chemistry software Gaussian 98. We began the investigation from cis-geometry (_ = 0__ and calculated the time for the excited cis-geometry to achieve the energy minimum (_ = 90__ and the excited trans-geometry (_ = 180__ of S1. The calculation procedure is as follows: (i) we calculated the potential energy of the ground state and the excitation energy of S1 of the optimized cis-butene using Gaussian 98 package and by adding the two energies we got the potential energy of the excited cis-butene. Note that we took this potential energy as the total energy of butene ( i.e. we assume the kinetic energy of excited cis-butene is 0). To initiate the rotation, we actually started from a very small _ with a very small initial velocity. (ii) For every 10_, we calculated 20 points (i.e., we performed Gaussian 98

calculation every 0_5_). For every point, we calculated the ground-state energy without optimization and the corresponding excitation energy; thus we got the potential energy of the excited state. By subtracting the potential energy from the total energy, we got the kinetic energy. Then we used the energies of 20 points to calculate the time for butene to rotate 10_ by integrating Newton’s equations. The relation between the potential energies of excited states and time is given in Figure 7, and for demonstrative purposes, the PE curves of the ground state S0 is presented on the same graph. We can see that the time for excited trans-2-butene to relax to the valley minimum is about 100 fs and symmetrically it takes almost the same time to go from the minimum to cis-2-butene. On the other hand, according to the spontaneous emission theory the time for excited trans-2-butene to relax back to ground state is about 5_9×103 s. So the isomerization process will be significantly probable. In Figure 8, we demonstrate how the dihedral angle of C1–C2==C3–C4 double bond, or the geometric structure of butene, will change with time. The lowest vibrational frequencies and the associated IR intensities that were calculated for trans-2-butene and cis-2-butene are compared in Figure 9. These results indicate a significant difference in spectral signatures of the two molecular conformations and one that has the general quantitative characteristics needed by the previously discussed bio-molecular architecture.