Seung Kyu Min

Fast DNA sequencing with a graphene-based nanochannel device.

Devices in which a single strand of DNA is threaded through a nanopore could be used to efficiently sequence DNA. However, various issues will have to be resolved to make this approach practical, including controlling the DNA translocation rate, suppressing stochastic nucleobase motions, and resolving the signal overlap between different nucleobases. Here, we demonstrate theoretically the feasibility of DNA sequencing using a fluidic nanochannel functionalized with a graphene nanoribbon. This approach involves deciphering the changes that occur in the conductance of the nanoribbon as a result of its interactions with the nucleobases via π-π stacking. We show that as a DNA strand passes through the nanochannel, the distinct conductance characteristics of the nanoribbon (calculated using a method based on density functional theory coupled to non-equilibrium Green function theory) allow the different nucleobases to be distinguished using a data-mining technique and a two-dimensional transient autocorrelation analysis. This fast and reliable DNA sequencing device should be experimentally feasible in the near future.

Near-field focusing and magnification through self-assembled nanoscale spherical lenses

It is well known that a lens-based far-field optical microscope cannot resolve two objects beyond Abbe’s diffraction limit. Recently, it has been demonstrated that this limit can be overcome by lensing effects driven by surface-plasmon excitation, and by fluorescence microscopy driven by molecular excitation. However, the resolution obtained using geometrical lens-based optics without such excitation schemes remains limited by Abbe’s law even when using the immersion technique, which enhances the resolution by increasing the refractive indices of immersion liquids. As for submicrometre-scale or nanoscale objects, standard geometrical optics fails for visible light because the interactions of such objects with light waves are described inevitably by near-field optics. Here we report near-field high resolution by nanoscale spherical lenses that are self-assembled by bottom-up integration of organic molecules. These nanolenses, in contrast to geometrical optics lenses, exhibit curvilinear trajectories of light, resulting in remarkably short near-field focal lengths. This in turn results in near-field magnification that is able to resolve features beyond the diffraction limit. Such spherical nanolenses provide new pathways for lens-based near-field focusing and high-resolution optical imaging at very low intensities, which are useful for bio-imaging, near-field lithography, optical memory storage, light harvesting, spectral signal enhancing, and optical nano-sensing.

Comprehensive Energy Analysis for Various Types of π-Interaction

We have investigated various types of π-interactions, where one of the interacting π-systems is represented by an aromatic benzene molecule. The system includes Rg-π, CH-π, π-π(D), π-π(T), H-π(T), π(+)-π(D), π(+)-π(T), H(+)-π(T), π(+2)-π(D), M(+)-π, and M(+2)-π complexes, where Rg denotes a rare gas or noble atom, M denotes a metal, and D/T indicates displaced-stacked/T-shaped structure. The microsolvation effect is also considered. We note that the interaction between a cationic π system and a neutral π system (πcation-π interaction) is so far ambiguously considered as either π-π or cation-π interaction. In terms of total binding energy, the πcation-π interaction is weaker than the cation-π interaction, but much stronger than the π-π interaction. When the hydrophilic (N-H)(+) or (C-H)(+) group in a singly charged π(+) system (as in protonated histidine, arginine, pyridine, or dimethyl imidazolium) interacts with a π-system, the complex favors a T-shaped form [π(+)-π(T) complex]. However, in the presence of polar solvating molecules or counteranions, these species interact with the (N-H)(+)/(C-H)(+) group, while the π(+) system interacts with the neutral aromatic ring. Then, the displaced-stacked form [π(+)-π(D) complex] is favored or otherwise nearly isoenergetic to the π(+)-π(T) form. The π(+)-π systems are stabilized mainly by both dispersion and electrostatic energies. Ternary diagrams using either attractive energy components or both attractive and repulsive energy components show that the π(+)-π(D) complexes have more contribution from dispersion energy but less contribution from induction energy than the π(+)-π(T) complexes, while both complexes have similar percentage contributions from electrostatic and exchange energy components. In particular, the π(+)-π(D) complexes are found to be distinctly different from the π-π complexes and the non-π organic or metallic cation-π complexes.

Complete basis set limit of Ab initio binding energies and geometrical parameters for various typical types of complexes

Using basis‐set extrapolation schemes for a given data set, we evaluated the binding energies and geometries at the complete basis set (CBS) limit at the levels of the second order Møller–Plesset perturbation theory (MP2) and the coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)]. The systems include the hydrogen bonding (water dimer), aromatic interaction (benzene dimer), π–H interaction (benzene–water), cation–water, anion–water, π–cation interaction (cation–benzene), and π–anion interaction (anion–triazine). One extrapolation method is to exploit both BSSE‐corrected and BSSE‐uncorrected binding energies for the aug‐cc‐pVNZ (N = 2, 3, 4, …) basis set in consideration that both binding energies give the same CBS limit (CBSB). Another CBS limit (CBSC) is to use the commonly known extrapolation approach to exploit that the electron correlation energy is proportional to N−3. Since both methods are complementary, they are useful for estimating the errors and trend of the asymptotic values. There is no significant difference between both methods. Overall, the values of CBSC are found to be robust because of their consistency. However, for small N (in particular, for N = 2, 3), CBS  NB is found to be slightly better for water–water interactions and cation–water and cation–benzene interactions, whereas CBS  NC is found to be more reliable for bezene–water and anion–water interactions. We also note that the MP2 CBS limit value based on N = 2 and 3 combined with the difference between CCSD(T) and MP2 at N = 2 would be exploited to obtain a CCSD(T)/CBS value for aromatic–aromatic interactions and anion–π interactions, but not for cationic complexes.

Chromium Porphyrin Arrays As Spintronic Devices

Spintronic devices are very important for futuristic information technology. Suitable materials for such devices should have half-metallic properties so that only one spin passes through the device. In particular, organic half metals have the advantage that they may be used for flexible devices and have a long spin-coherence length. We predict that the one-dimensional infinite chromium porphyrin array, which we call Cr-PA(∞), shows half-metallic behavior when the spins on the chromium atoms are in a parallel alignment. Since the chromium atoms are separated by a large distance (>8 Å), the coupling between spins is small and thus their directions can be readily controlled by an external magnetic field. In the ferromagnetic state, the band gap for major spin electrons is 0.30 eV, while there is no band gap for the minor spin electrons, thus reflecting the half-metallic property. This unique property originates from the high spin state of Cr which results in the spin asymmetry of the conduction band in Cr-PA(∞). Electron transport of Cr-PA(1,2,3) is calculated with the nonequilibrium Green function technique in the presence of Au electrodes. It turned out that the spin-filtering ability appears from the dimeric Cr-PA(2). Thus, a new organometallic framework for designing a spin filter is proposed. Though many others have designed novel spintronic devices, none of them are realized due to the lack of a practical fabrication method at present. However, the porphyrin-based spintronic device provides a synthesizable framework.

Noncovalent Interactions of DNA Bases with Naphthalene and Graphene

The complexes of a DNA base bound to graphitic systems are studied. Considering naphthalene as the simplest graphitic system, DNA base-naphthalene complexes are scrutinized at high levels of ab initio theory including coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)] at the complete basis set (CBS) limit. The stacked configurations are the most stable, where the CCSD(T)/CBS binding energies of guanine, adenine, thymine, and cytosine are 9.31, 8.48, 8.53, 7.30 kcal/mol, respectively. The energy components are investigated using symmetry-adapted perturbation theory based on density functional theory including the dispersion energy. We compared the CCSD(T)/CBS results with several density functional methods applicable to periodic systems. Considering accuracy and availability, the optB86b nonlocal functional and the Tkatchenko-Scheffler functional are used to study the binding energies of nucleobases on graphene. The predicted values are 18-24 kcal/mol, though many-body effects on screening and energy need to be further considered.

Structure and spectral features of H+(H2O)7: Eigen versus Zundel forms.

The two dimensional (2D) to three dimensional (3D) transition for the protonated water cluster has been controversial, in particular, for H(+)(H(2)O)(7). For H(+)(H(2)O)(7) the 3D structure is predicted to be lower in energy than the 2D structure at most levels of theory without zero-point energy (ZPE) correction. On the other hand, with ZPE correction it is predicted to be either 2D or 3D depending on the calculational levels. Although the ZPE correction favors the 3D structure at the level of coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)] using the aug-cc-pVDZ basis set, the result based on the anharmonic zero-point vibrational energy correction favors the 2D structure. Therefore, the authors investigated the energies based on the complete basis set limit scheme (which we devised in an unbiased way) at the resolution of the identity approximation Moller-Plesset second order perturbation theory and CCSD(T) levels, and found that the 2D structure has the lowest energy for H(+)(H(2)O)(7) [though nearly isoenergetic to the 3D structure for D(+)(D(2)O)(7)]. This structure has the Zundel-type configuration, but it shows the quantum probabilistic distribution including some of the Eigen-type configuration. The vibrational spectra of MP2/aug-cc-pVDZ calculations and Car-Parrinello molecular dynamics simulations, taking into account the thermal and dynamic effects, show that the 2D Zundel-type form is in good agreement with experiments.

The exact forces on classical nuclei in non-adiabatic charge transfer

The decomposition of electronic and nuclear motion presented in Abedi et al. [Phys. Rev. Lett. 105, 123002 (2010)] yields a time-dependent potential that drives the nuclear motion and fully accounts for the coupling to the electronic subsystem. Here, we show that propagation of an ensemble of independent classical nuclear trajectories on this exact potential yields dynamics that are essentially indistinguishable from the exact quantum dynamics for a model non-adiabatic charge transfer problem. We point out the importance of step and bump features in the exact potential that are critical in obtaining the correct splitting of the quasiclassical nuclear wave packet in space after it passes through an avoided crossing between two Born-Oppenheimer surfaces and analyze their structure. Finally, an analysis of the exact potentials in the context of trajectory surface hopping is presented, including preliminary investigations of velocity-adjustment and the force-induced decoherence effect.

Two Dimensional Molecular Electronics Spectroscopy for Molecular Fingerprinting, DNA Sequencing, and Cancerous DNA Recognition

Laser-driven molecular spectroscopy of low spatial resolution is widely used, while electronic current-driven molecular spectroscopy of atomic scale resolution has been limited because currents provide only minimal information. However, electron transmission of a graphene nanoribbon on which a molecule is adsorbed shows molecular fingerprints of Fano resonances, i.e., characteristic features of frontier orbitals and conformations of physisorbed molecules. Utilizing these resonance profiles, here we demonstrate two-dimensional molecular electronics spectroscopy (2D MES). The differential conductance with respect to bias and gate voltages not only distinguishes different types of nucleobases for DNA sequencing but also recognizes methylated nucleobases which could be related to cancerous cell growth. This 2D MES could open an exciting field to recognize single molecule signatures at atomic resolution. The advantages of the 2D MES over the one-dimensional (1D) current analysis can be comparable to those of 2D NMR over 1D NMR analysis.

Is the Molecular Berry Phase an Artifact of the Born-Oppenheimer Approximation?

We demonstrate that the molecular Berry phase and the corresponding nonanalyticity in the electronic Born-Oppenheimer wave function is, in general, not a true topological feature of the exact solution of the full electron-nuclear Schrödinger equation. For a numerically exactly solvable model we show that a nonanalyticity, and the associated geometric phase, only appear in the limit of infinite nuclear mass, while a perfectly smooth behavior is found for any finite nuclear mass.