Chromophore-Dependent Intramolecular Exciton-Vibrational Coupling in the FMO Complex: Quantification and Importance for Exciton Dynamics.

In this paper, we adopt an approach suitable for monitoring the time evolution of the intramolecular contribution to the spectral density of a set of identical chromophores embedded in their respective environments. We apply the proposed method to the Fenna-Matthews-Olson (FMO) complex, with the objective to quantify the differences among site-dependent spectral densities and the impact of such differences on the exciton dynamics of the system. Our approach takes advantage of the vertical gradient approximation to reduce the computational demands of the normal modes analysis. We show that the region of the spectral density that is believed to strongly influence the exciton dynamics changes significantly in the timescale of tens of nanoseconds. We then studied the impact of the intramolecular vibrations on the exciton dynamics by considering a model of FMO in a vibronic basis and neglecting the interaction with the environment to isolate the role of the intramolecular exciton-vibration coupling. In agreement with the assumptions in the literature, we demonstrate that high frequency modes at energy much larger than the excitonic energy splitting have negligible influence on exciton dynamics despite the large exciton-vibration coupling. We also find that the impact of including the site-dependent spectral densities on exciton dynamics is not very significant, indicating that it may be acceptable to apply the same spectral density on all sites. However, care needs to be taken for the description of the exciton-vibrational coupling in the low frequency part of intramolecular modes because exciton dynamics is more susceptible to low frequency modes despite their small Huang-Rhys factors.

Effect of Infrared Pulse Excitation on the Bound Charge-Transfer State of Photovoltaic Interfaces.

The nature and dynamics of the bound charge-transfer (CT) state in the exciton dissociation process in organic solar cells are of critical importance for the understanding of these devices. It was recently demonstrated that this state can be probed by a new experiment in which an infrared (IR) push-pulse is used to dissociate charges from the bound excited state. Here we proposed a simple quantum dynamics model to simulate the excitation of the IR pulse on the bound CT state with model parameters extracted from quantum chemical calculations. We show that the pulse dissociates the CT state following two different mechanisms: one, fairly expected, is the direct excitation of higher energy CT states leading to charge separation; the other, proposed here for the first time, is a rebound mechanism in which the negative charge is transferred in the opposite direction to form the neutral Frenkel exciton state from where it dissociates.

Vibronic enhancement of excitation energy transport: Interplay between local and non-local exciton-phonon interactions.

It has been reported in recent years that vibronic resonance between vibrational energy of the intramolecular nuclear mode and excitation-energy difference is crucial to enhance excitation energy transport in light harvesting proteins. Here we investigate how vibronic enhancement induced by vibronic resonance is influenced by the details of local and non-local exciton-phonon interactions. We study a heterodimer model with parameters relevant to the light-harvesting proteins with the surrogate Hamiltonian quantum dynamics method in a vibronic basis. In addition, the impact of field-driven excitation on the efficiency of population transfer is compared with the instantaneous excitation, and the effect of multi-mode vibronic coupling is presented in comparison with the coupling to a single effective vibrational mode. We find that vibronic enhancement of site population transfer is strongly suppressed with the increase of non-local exciton-phonon interaction and increasing the number of strongly coupled high-frequency vibrational modes leads to a further decrease in vibronic enhancement. Our results indicate that vibronic enhancement is present but may be much smaller than previously thought and therefore care needs to be taken when interpreting its role in excitation energy transport. Our results also suggest that non-local exciton-phonon coupling, which is related to the fluctuation of the excitonic coupling, may be as important as local exciton-phonon coupling and should be included in any quantum dynamics model.

Quantum dynamics of a vibronically coupled linear chain using a surrogate Hamiltonian approach.

Vibronic coupling between the electronic and vibrational degrees of freedom has been reported to play an important role in charge and exciton transport in organic photovoltaic materials, molecular aggregates, and light-harvesting complexes. Explicitly accounting for effective vibrational modes rather than treating them as a thermal environment has been shown to be crucial to describe the effect of vibronic coupling. We present a methodology to study dissipative quantum dynamics of vibronically coupled systems based on a surrogate Hamiltonian approach, which is in principle not limited by Markov approximation or weak system-bath interaction, using a vibronic basis. We apply vibronic surrogate Hamiltonian method to a linear chain system and discuss how different types of relaxation process, intramolecular vibrational relaxation and intermolecular vibronic relaxation, influence population dynamics of dissipative vibronic systems.

The Effect of Interfacial Geometry on Charge-Transfer States in the Phthalocyanine/Fullerene Organic Photovoltaic System.

The dependence of charge-transfer states on interfacial geometry at the phthalocyanine/fullerene organic photovoltaic system is investigated. The effect of deviations from the equilibrium geometry of the donor-donor-acceptor trimer on the energies of and electronic coupling between different types of interfacial electronic excited states is calculated from first-principles. Deviations from the equilibrium geometry are found to destabilize the donor-to-donor charge transfer states and to weaken their coupling to the photoexcited donor-localized states, thereby reducing their ability to serve as charge traps. At the same time, we find that the energies of donor-to-acceptor charge transfer states and their coupling to the donor-localized photoexcited states are either less sensitive to the interfacial geometry or become more favorable due to modifications relative to the equilibrium geometry, thereby enhancing their ability to serve as gateway states for charge separation. Through these findings, we eludicate how interfacial geometry modifications can play a key role in achieving charge separation in this widely studied organic photovoltaic system.

Calculating High Energy Charge Transfer States Using Optimally Tuned Range-Separated Hybrid Functionals.

Recently developed optimally tuned range-separated hybrid (OT-RHS) functionals within time-dependent density functional theory have been shown to address existing limitations in calculating charge transfer excited state energies. The RSH success in improving the calculation of CT states stems from enforcing the correspondence of the frontier molecular orbitals (FMOs) to physical properties, where the highest occupied MO energy relates to the ionization potential and the lowest unoccupied MO energy relates to the electron affinity. However, in this work, we show that a less accurate description of CT states that involves non-FMOs is afforded by the RSH approach. In order to achieve a high quality description of such higher energy CT states, the parameter tuning procedure, which lies at the foundation of the RSH approach, needs to be generalized to consider the CT process. We demonstrate the need for improved description of such CT states in donor-acceptor systems, where the optimal tuning parameter is accounting for the state itself.

Ultrafast Charge-Transfer Dynamics at the Boron Subphthalocyanine Chloride/C60 Heterojunction: Comparison between Experiment and Theory.

Photoinduced charge-transfer (CT) processes play a key role in many systems, particularly those relevant to organic photovoltaics and photosynthesis. Advancing the understanding of CT processes calls for comparing their rates measured via state-of-the-art time-resolved interface-specific spectroscopic techniques with theoretical predictions based on first-principles molecular models. We measure charge-transfer rates across a boron subphthalocyanine chloride (SubPc)/C60 heterojunction, commonly used in organic photovoltaics, via heterodyne-detected time-resolved second-harmonic generation. We compare these results to theoretical predictions based on a Fermi's golden rule approach, with input parameters obtained using first-principles calculations for two different equilibrium geometries of a molecular donor-acceptor in a dielectric continuum model. The calculated rates (∼2 ps(-1)) overestimate the measured rates (∼0.1 ps(-1)), which is consistent with the expectation that the calculated rates represent an upper bound over the experimental ones. The comparison provides valuable understanding of how the structure of the electron donor-acceptor interface affects the CT kinetics in organic photovoltaic systems.

Donor-to-Donor vs Donor-to-Acceptor Interfacial Charge Transfer States in the Phthalocyanine-Fullerene Organic Photovoltaic System.

Charge transfer (CT) states formed at the donor/acceptor heterointerface are key for photocurrent generation in organic photovoltaics (OPV). Our calculations show that interfacial donor-to-donor CT states in the phthalocyanine-fullerene OPV system may be more stable than donor-to-acceptor CT states and that they may rapidly recombine, thereby constituting a potentially critical and thus far overlooked loss mechanism. Our results provide new insight into processes that may compete with charge separation, and suggest that the efficiency for charge separation may be improved by destabilizing donor-to-donor CT states or decoupling them from other states.

Dynamic and electronic transport properties of DNA translocation through graphene nanopores.

Graphene layers have been targeted in the last years as excellent host materials for sensing a remarkable variety of gases and molecules. Such sensing abilities can also benefit other important scientific fields such as medicine and biology. This has automatically led scientists to probe graphene as a potential platform for sequencing DNA strands. In this work, we use robust numerical tools to model the dynamic and electronic properties of molecular sensor devices composed of a graphene nanopore through which DNA molecules are driven by external electric fields. We performed molecular dynamic simulations to determine the relation between the intensity of the electric field and the translocation time spent by the DNA to pass through the pore. Our results reveal that one can have extra control on the DNA passage when four additional graphene layers are deposited on the top of the main graphene platform containing the pore in a 2 × 2 grid arrangement. In addition to the dynamic analysis, we carried electronic transport calculations on realistic pore structures with diameters reaching nanometer scales. The transmission obtained along the graphene sensor at the Fermi level is affected by the presence of the DNA. However, it is rather hard to distinguish the respective nucleobases. This scenario can be significantly altered when the transport is conducted away from the Fermi level of the graphene platform. Under an energy shift, we observed that the graphene pore manifests selectiveness toward DNA nucleobases.

Insights into electron tunneling across hydrogen-bonded base-pairs in complete molecular circuits for single-stranded DNA sequencing.

We report a first-principles study of electron ballistic transport through a molecular junction containing deoxycytidine-monophosphate (dCMP) connected to metal electrodes. A guanidinium ion and guanine nucleobase are tethered to gold electrodes on opposite sides to form hydrogen bonds with the dCMP molecule providing an electric circuit. The circuit mimics a component of a potential device for sequencing unmodified single-stranded DNA. The molecular conductance is obtained from DFT Green's function scattering methods and is compared to estimates from the electron tunneling decay constant obtained from the complex band structure. The result is that a complete molecular dCMP circuit of 'linker((CH(2))(2))-guanidinium-phosphate-deoxyribose-cytosine-guanine' has a very low conductance (of the order of fS) while the hydrogen-bonded guanine-cytosine base-pair has a moderate conductance (of the order of tens to hundreds of nS). Thus, while the transverse electron transfer through base-pairing is moderately conductive, electron transfer through a complete molecular dCMP circuit is not. The gold Fermi level is found to be aligned very close to the HOMO for both the guanine-cytosine base-pair and the complete molecular dCMP circuit. Results for two different plausible geometries of the hydrogen-bonded dCMP molecule reveal that the conductance varies from fS for an extended structure to pS for a slightly compressed structure.

Structural and dynamic properties of BaInGeH: a rare solid-state indium hydride.

BaInGeH was synthesized by hydrogenating the intermetallic compound BaInGe. The crystal structure determination from the powder neutron diffraction data of BaInGeD [P3m1, Z = 1, a = 4.5354(3) A, c = 5.2795(6) A] reveals the presence of hydrogen in tetrahedral voids defined by three Ba atoms and one In atom.

Theory of tunneling across hydrogen-bonded base pairs for DNA recognition and sequencing.

We present the results of first-principles calculations for the electron tunnel current through hydrogen-bonded DNA base pairs and for (deoxy)nucleoside-nucleobase pairs. Electron current signals either through a base pair or through a deoxynucleoside-nucleobase pair are a potential mechanism for recognition or identification of the DNA base on a single-stranded DNA polymer. Four hydrogen-bonded complexes are considered: guanine-cytosine, diaminoadenine-thymine, adenine-thymine, and guanine-thymine. First, the electron tunneling properties are examined through their complex band structure (CBS) and the metal contact's Fermi-level alignment. For gold contacts, the metal Fermi level lies near the highest occupied molecular orbital for all DNA base pairs. The decay constant determined by the complex band structure at the gold Fermi level shows that tunnel current decays more slowly for base pairs with three hydrogen bonds (guanine-cytosine and diaminoadenine-thymine) than for base pairs with two hydrogen bonds (adenine-thymine and guanine-thymine). The decay length and its dependence on hydrogen-bond length are examined. Second, the conductance is computed using density functional theory Green's-function scattering methods and these results agree with estimates made from the tunneling decay constant obtained from the CBS. Changing from a base pair to a deoxynucleoside-nucleobase complex shows a significant decrease in conductance. It also becomes difficult to distinguish the current signal by only the number of hydrogen bonds.

Vibrational property study of SrGa2H2 and BaGa2H2 by inelastic neutron scattering and first principles calculations.

Vibrational properties of the gallium hydrides SrGa2H2 and BaGa2H2 have been investigated by means of inelastic neutron scattering (INS) and first-principles calculations. The compounds contain Ga-H units being part of a two-dimensional polyanionic layer, [(GaH)(GaH)]2-. The INS spectra are composed of dispersed internal Ga-H bending and stretching modes at frequencies above 600 cm(-1) and external lattice modes at frequencies below 220 cm(-1). Frequencies of the internal modes are not susceptible to the metal countercation, indicating a strong integrity of the polyanionic layer as a building unit in the structures of SrGa2H2 and BaGa2H2. The Ga-H stretching modes have frequencies between 1200 and 1400 cm(-1), which is very low compared to molecular gallium hydrides. The weak Ga-H bond in SrGa2H2 and BaGa2H2 is balanced by Sr(Ba)-H interactions.

Vibrational properties of polyanionic hydrides SrAl2H2 and SrAlSiH: new insights into Al-H bonding interactions.

The vibrational properties of the recently discovered aluminum hydrides SrAl2H2 and SrAlSiH have been investigated by means of inelastic neutron scattering (INS) and first-principles calculations. Both compounds contain Al-H units being part of a two-dimensional polyanionic layer, [(AlH)(AlH)]2- and [Si(AlH)]2-, respectively. The INS spectrum of SrAlSiH is characterized by very weakly dispersed Al-H modes with well-resolved overtones, while SrAl2H2 yields a solid-state dispersed phonon spectrum. The frequency of the stretching mode of the Al-H unit in SrAlSiH is the hitherto lowest observed for a terminal Al-H bond. At the same time, SrAlSiH displays the highest decomposition temperature known for an aluminum hydride compound. It is proposed that the stability of solid-state aluminum hydrides correlates inversely with the strength of Al-H bonding.