Jorge M. Seminario

Analysis of a dinitro-based molecular device

A proposed dinitro device, Au-(2′-nitro-4-ethynylphenyl-4′-ethynylphenyl-5′-nitro-1-benzene thiolate)-Au is analyzed using a combination of density functional and Green function theories complemented with information from theoretical and experimental studies of a similar nitroamino device, Au-(2′-amino-4-ethynylphenyl-4′-ethynylphenyl-5′-nitro-1-benzenethiolate)-Au. The dinitro compound might also perform as a molecular memory but with different characteristics than those of the nitroamino, showing well-defined charge states; however, the neutral charge state of the nitroamino presents well-defined resonant tunneling characteristics and a larger intrinsic dipole moment. Density of states, transmission functions, and current–voltage characteristics for the neutral, anion, and dianion of the two molecules are compared. The effect of the bias potential is explicitly considered in the calculations as well as the effect of the contacts and the spin states of the open shell systems. The theoretical results for ...

Mechanism of carbon nanotubes unzipping into graphene ribbons

The fabrication of graphene nanoribbons from carbon nanotubes (CNTs) treated with potassium permanganate in a concentrated sulfuric acid solution has been reported by Kosynkin et al. [Nature (London) 458, 872 (2009)]. Here we report ab initio density functional theory calculations of such unzipping process. We find that the unzipping starts with the potassium permanganate attacking one of the internal C-C bonds of the CNT, stretching and breaking it. The created defect weakens neighboring bonds along the length of the CNT, making them energetically prone to be attacked too.

An ab initio approach to the calculation of current-voltage characteristics of programmable molecular devices

Molecular electronics can be developed if we are able to program a random arrangement of molecules or a field-programmable molecular random array. The ansatz that small molecules can be programmed needs to be demonstrated; this means characterizing the smallest molecular system with programmable features. We demonstrate that even two molecules in a series conformation can have multivalued responses and, thus, is able to be programmed; we also indicate how to extend this programmability to other molecular circuit conformations. Current programs for the calculation of current-voltage characteristics of electronic circuits, needed for such demonstrations, are only capable of predicting single-valued characteristics. We present results from our ab initio procedures that couple the molecular approaches with a practical analysis of molecular circuits having strong nonlinearities.

Scenarios for Molecular-Level Signal Processing

Several research efforts are being carried out in molecular electronics; both theory and experiment claim extraordinary findings for molecular devices. However, before practical molecular circuits can be implemented, we need to develop scenarios for information coding and transfer in molecular circuits able to operate at integration densities and speeds orders of magnitude higher than current ICs do. Initial attempts have been already proposed; however,a simple adaptation to methods being used in current microelectronics devices does not offer much hope at the atomistic and nanoscopic levels due to the large dissipation energy densities that would be generated. We have proposed two new paradigms to process and transmit information in molecular circuits that can defeat the heat dissipation problem. One is based on the characteristic vibrational behavior of molecules and clusters, and the other is based on the molecular electrostatic potentials. It is suggested that these two scenarios can be used for molecular signal processing and transfer in molecular circuits; a theoretical demonstration using computational techniques is presented for these two paradigms.

A molecular device operating at terahertz frequencies: theoretical simulations

This brief presents a molecular dynamics study on a molecular device proposed for terahertz signal processing. We conclude that signals following the movement of gold clusters attached to molecules can modulate vibrational modes in the terahertz spectrum of the internal coordinates defining molecular bonds. It is shown, that by using intensities involved in natural vibrational modes, which are experimentally recoverable in spectroscopy measurements, we can recover components due to couplings between local modes and, thus, provide a computational proof of the possibility of using molecular-vibrational modes for molecular electronics. The vibration of atoms can encode information that reflects local variations of electrical dipole and polarizability.

Molecular biosensor based on a coordinated iron complex

A sensor model based on the porphyrin nucleus of the soluble guanylate cyclase enzyme is modeled and tested with nitric oxide and carbon monoxide. Molecular oxygen is tested as a possible interferer. Geometries and electronic structures of the model are assessed by density functional theory. Vibrational circular dichroism (VCD), infrared, and Raman spectra are obtained for the iron complexes uncoordinated and coordinated with the gas moieties. The sensor is capable of detecting the ligands to different extents. Carbon monoxide is less detectable than nitric oxide due to the adopted position of the molecule in the sensor; carbon oxide is aligned with the iron atom, while nitric oxide and molecular oxygens bend with an angle detectable by the VCD. It is suggested that pollutants may be detected and measured with the proposed biosensors.

Polypeptides in alpha-helix conformation perform as diodes

Molecules that resemble a semiconductor diode depletion zone are those with an intrinsic electric dipole, which were suggested as potential electronic devices. However, so far, no single molecule has met such a goal because any electron donor-acceptor linker strongly diminishes any possibility of diode behavior. We find an intrinsic diode behavior in polypeptides such as poly(L-alanine) and polyglycine in alpha-helix conformation, explained in terms of molecular orbital theory using ab initio methods. The application of an antiparallel electric field with respect to the molecular dipole yields a gradual increase in current through the junction because the valence and conduction orbitals approach each other reducing their gap as the bias increases. However, a parallel field makes the gap energy increase, avoiding the pass of the electrons.

Molecular electrostatic potentials of DNA base-base pairing and mispairing

AbstractAn understanding of why adenine (A) pairs with thymine (T) and cytosine (C) with guanine (G) in DNA is very useful in the design of sensors and other related devices. We report the use of dissociation energies, geometries and molecular electrostatic potentials (MEPs) to justify the canonical (AT and CG) Watson-Crick pairs. We also analyze all mismatches in both configurations—cis and trans—with respect to their glycoside bonds. As expected, we found that the most stable pair configuration corresponds to CG, providing an energy criterion for that preferred configuration. The reason why A gets together with T is much more difficult to explain as the energy of this pair is smaller than the energy of some other mismatched pairs. We tested MEPs to see if they could shed light on this problem. Interestingly, MEPs yield a unique pattern (shape) for the two canonical cases but different shapes for the mismatches. A tunnel of positive potential surrounded by a negative one is found interconnecting the three H-bonds of CG and the two of AT. This MEP tunnel, assisted partially by energetics and geometrical criteria, unambiguously determine a distinctive feature of the affinity between A and T as well as that between G and C. FigureThe signature of pairing in DNA: A characteristic positive potential tunnel on a negative background is observed in DNA; this potential shape (left) is an indicator of why A pairs with T and C pairs with G, as this shape form is not observed in most of others H-bonds

Current–voltage–temperature characteristics of DNA origami

The temperature dependences of the current-voltage characteristics of a sample of triangular DNA origami deposited in a 100 nm gap between platinum electrodes are measured using a probe station. Below 240 K, the sample shows high impedance, similar to that of the substrate. Near room temperature the current shows exponential behavior with respect to the inverse of temperature. Sweep times of 1 s do not yield a steady state; however sweep times of 450 s for the bias voltage secure a steady state. The thermionic emission and hopping conduction models yield similar barriers of approximately 0.7 eV at low voltages. For high voltages, the hopping conduction mechanism yields a barrier of 0.9 eV and the thermionic emission yields 1.1 eV. The experimental data set suggests that the dominant conduction mechanism is hopping in the range 280-320 K. The results are consistent with theoretical and experimental estimates of the barrier for related molecules.

Encoding and transport of information in molecular and biomolecular systems

We have proposed possible scenarios based on molecular electrostatic potentials and molecular vibrational modes that can be combined to process and encode information in nanosized circuits. These two intrinsic properties determine how molecules interact or communicate to each other and to themselves. These scenarios may provide the solution to satisfy the urgent need for exponential growth of computational performance and eventually to radically change the way how computation is performed. Presently, the increase in computational power is achieved by scaling down the size of devices. However, already at the nanometer scale, the process of scaling down is seriously limited by physical laws regardless of what materials are used. These limitations lead us to compromise the speed of electronic devices against heat removal, which is one of the consequences of scaling-down. The new scenarios would allow computing with molecules in a molecular friendly fashion and eventually in a way similar to those in biological systems. The molecular potentials and vibronics would indeed address the heating issues, which are the overarching killers at future technology nodes