Nonorthogonality Problem and Effective Electronic Coupling Calculation: Application to Charge Transfer in π-Stacks Relevant to Biochemistry and Molecular Electronics

Enhancing Charge Transport Using Boron and Nitrogen Substitutions into Triphenylene-Based Discotic Liquid Crystals

The substitution of p-block heteroatoms into polyaromatic hydrocarbons offers the potential for introducing enhanced molecular properties and advancing material development for electro-optical applications. Using density functional theory, we characterize the substitution of boron and nitrogen atoms into a 2,3,6,7,10,11-hexakis(hexathiol)triphenylene (TTP) core, a precursor for a material with a discotic liquid crystal phase, to determine the strength of exciton dissociation and the influence doping has on the formation of a heterojunction with graphene. The substitution of nitrogen and boron into the TTP motif enables tunability of both electron and hole coupling between hetero- and homodyads. The coupling is found to far exceed that of TTP and varied transport behavior with different combinations of doped cores of nitrogen-TTP and boron-TTP is reported. Heterodyads of nitrogen-TTP with boron-TTP appear to be ambipolar in electron/hole coupling, whereas heterodyads of boron- or nitrogen-TTP with TTP form strong electron coupling dyads and homodyads of nitrogen-TTP and boron-TTP form strong hole coupling. Finally, we describe the heterojunction of nitrogen- or boron-TTP with monolayer graphene and observe Ohmic contacts with large hole transport barriers. The presence of induced dipoles occurs at the interface in all heterojunctions, suggesting the possibility of tuning the junction with external potentials and improving exciton dissociation.

Controlling the charge-transfer dynamics of two-level systems around avoided crossings

Two-level quantum systems are fundamental physical models that continue to attract growing interest due to their crucial role as a building block of quantum technologies. The exact analytical solution of the dynamics of these systems is central to control theory and its applications, such as that to quantum computing. In this study, we reconsider the two-state charge transfer problem by extending and using a methodology developed to study (pseudo)spin systems in quantum electrodynamics contexts. This approach allows us to build a time evolution operator for the charge transfer system and to show new opportunities for the coherent control of the system dynamics, with a particular emphasis on the critical dynamic region around the transition state coordinate, where the avoided crossing of the energy levels occurs. We identify and propose possible experimental implementations of a class of rotations of the charge donor (or acceptor) that endow the electronic coupling matrix element with a time-dependent phase that can be employed to realize controllable coherent dynamics of the system across the avoided level crossing. The analogy of these rotations to reference frame rotations in generalized semiclassical Rabi models is discussed. We also show that the physical rotations in the charge-transfer systems can be performed so as to implement quantum gates relevant to quantum computing. From an exquisitely physical-mathematical viewpoint, our approach brings to light situations in which the time-dependent state of the system can be obtained without resorting to the special functions appearing in the Landau-Zener approach.

Towards the description of charge transfer states in solubilised LHCII using subsystem DFT

Light harvesting complex II (LHCII) in plants and green algae have been shown to adapt their absorption properties, depending on the concentration of sunlight, switching between a light harvesting and a non-harvesting or quenched state. In a recent work, combining classical molecular dynamics (MD) simulations with quantum chemical calculations (Liguori et al. in Sci Rep 5:15661, 2015) on LHCII, it was shown that the Chl611-Chl612 cluster of the terminal emitter domain can play an important role in modifying the spectral properties of the complex. In that work the importance of charge transfer (CT) effects was highlighted, in re-shaping the absorption intensity of the chlorophyll dimer. Here in this work, we investigate the combined effect of the local excited (LE) and CT states in shaping the energy landscape of the chlorophyll dimer. Using subsystem Density Functional Theory over the classical [Formula: see text]s MD trajectory we look explicitly into the excitation energies of the LE and the CT states of the dimer and their corresponding couplings. Upon doing so, we observe a drop in the excitation energies of the CT states, accompanied by an increase in the couplings between the LE/LE and the LE/CT states facilitated by a shorter interchromophoric distance upon equilibration. Both these changes in conjunction, effectively produces a red-shift of the low-lying mixed exciton/CT states of the supramolecular chromophore pair.

Multi-state formulation of the frozen-density embedding quasi-diabatization approach

We present a multi-state implementation of the recently developed frozen-density embedding diabatization (FDE-diab) methodology [D. G. Artiukhin and J. Neugebauer, J. Chem. Phys. 148, 214104 (2018)] in the Serenity program. The new framework extends the original approach such that any number of charge-localized quasi-diabatic states can be coupled, giving an access to calculations of ground and excited state spin-density distributions as well as to excitation energies. We show that it is possible to obtain results similar to those from correlated wave function approaches such as the complete active space self-consistent field method at much lower computational effort. Additionally, we present a series of approximate computational schemes, which further decrease the overall computational cost and systematically converge to the full FDE-diab solution. The proposed methodology enables computational studies on spin-density distributions and related properties for large molecular systems of biochemical interest.

Theoretical Assessment of Hinge-Type Models for Electron Donors in Reaction Centers of Photosystems I and II as well as of Purple Bacteria

Hinge-type molecular models for electron donors in reaction centers of Photosystems I and II and purple bacteria were investigated using a two-state computational approach based on frozen-density embedding (FDE). This methodology, dubbed FDE-diab, is known to avoid consequences of the self-interaction error as far as intermolecular phenomena are concerned, which allows a prediction of qualitatively correct spin densities for large biomolecular systems. The calculated spin density distributions are in a good agreement with available experimental results and demonstrated a very high sensitivity to changes in the relative orientation of cofactors and amino acid protonation states. This allows a validation of the previously proposed hinge-type models providing hints on possible protonation states of axial histidine molecules.

2'-Deoxy-2'-fluoro-arabinonucleic acid: a valid alternative to DNA for biotechnological applications using charge transport

The non-biological 2'-deoxy-2'-fluoro-arabinonucleic acid (2'F-ANA) may be used as a valid alternative to DNA in biomedical and electronic applications because of its higher resistance to hydrolysis and nuclease degradation. However, the advantage of using 2'F-ANA in such applications also depends on its charge-transfer properties compared to DNA. In this study, we compare the charge conduction properties of model 2'F-ANA and DNA double-strands, using structural snapshots from MD simulations to calculate the electronic couplings and reorganization energies associated with the hole transfer steps between adjacent nucleobase pairs. Inserting these charge-transfer parameters into a kinetic model for charge conduction, we find similar conductive properties for DNA and 2'F-ANA. Moreover, we find that 2'F-ANA's enhanced chemical stability does not correspond to a reduction in the nucleobase π-stack structural flexibility relevant to both electronic couplings and reorganization free energies. Our results promote the use of 2'F-ANA in applications that can be based on charge transport, such as biosensing and chip technology, where its chemical stability and conductivity can advantageously combine.

How To Extract Quantitative Information on Electronic Transitions from the Density Functional Theory "Black Box"

Electronic couplings and vertical excitation energies are crucial determinants of charge and excitation energy transfer rates in a broad variety of processes ranging from biological charge transfer to charge transport through inorganic materials, from molecular sensing to intracellular signaling. Density Functional Theory (DFT) is generally used to calculate these critical parameters, but the quality of the results is unpredictable because of the semiempirical nature of the available DFT approaches. This study identifies a small set of fundamental rules that enables accurate DFT computation of electronic couplings and vertical excitation energies in molecular complexes and materials. These rules are applied to predict efficient DFT approaches to coupling calculations. The result is an easy-to-use guide for reliable DFT descriptions of electronic transitions.

A single AT-GC exchange can modulate charge transfer-induced p53-DNA dissociation

Using molecular dynamics simulations and electronic structure theory, we shed light on the charge dynamics that causes the differential interaction of tumor suppressor protein p53 with the p21 and Gadd45 genes in response to oxidative stress. We show that the sequence dependence of this selectivity results from competing charge transfer to the protein and through the DNA, with implications on the use of genome editing tools to influence the p53 regulatory function.

Electron transfer characteristics of 2'-deoxy-2'-fluoro-arabinonucleic acid, a nucleic acid with enhanced chemical stability

The non-biological nucleic acid 2'-deoxy-2'-fluoro-arabinonucleic acid (2'F-ANA) may be of use because of its higher chemical stability than DNA in terms of resistance to hydrolysis and nuclease degradation. In order to investigate the charge transfer characteristics of 2'F-ANA, of relevance to applications in nucleic acid-based biosensors and chip technologies, we compare the electronic couplings for hole transfer between stacked nucleobase pairs in DNA and 2'F-ANA by carrying out density functional theory (DFT) calculations on geometries taken from molecular dynamics simulations. We find similar averages and distribution widths of the base-pair couplings in the two systems. On the basis of this result, 2'F-ANA is expected to have charge transfer properties similar to those of DNA, while offering the advantage of enhanced chemical stability. As such, 2'F-ANA may serve as a possible alternative to DNA for use in a broad range of nanobiotechnological applications. Furthermore, we show that the (experimentally observed) enhanced chemical stability resulting from the backbone modifications does not cause reduced fluctuations of the base-pair electronic couplings around the values found for "ideal" B-DNA (with standard step parameter values). Our study also supports the use of a DFT implementation, with the M11 functional, of the wave function overlap method to compute effective electronic couplings in nucleic acid systems.

Charge Transfer between [4Fe4S] Proteins and DNA Is Unidirectional: Implications for Biomolecular Signaling

Recent experiments suggest that DNA-mediated charge transport might enable signaling between the [4Fe4S] clusters in the C-terminal domains of human DNA primase and polymerase α, as well as the signaling between other replication and repair high-potential [4Fe4S] proteins. Our theoretical study demonstrates that the redox signaling cannot be accomplished exclusively by DNA-mediated charge transport because part of the charge transfer chain has an unfavorable free energy profile. We show that hole or excess electron transfer between a [4Fe4S] cluster and a nucleic acid duplex through a protein medium can occur within microseconds in one direction, while it is kinetically hindered in the opposite direction. We present a set of signaling mechanisms that may occur with the assistance of oxidants or reductants, using the allowed charge transfer processes. These mechanisms would enable the coordinated action of [4Fe4S] proteins on DNA, engaging the [4Fe4S] oxidation state dependence of the protein-DNA binding affinity.

Diabatic model for electrochemical hydrogen evolution based on constrained DFT configuration interaction

The accuracy of density functional theory (DFT) based kinetic models for electrocatalysis is diminished by spurious electron delocalization effects, which manifest as uncertainties in the predicted values of reaction and activation energies. In this work, we present a constrained DFT (CDFT) approach to alleviate overdelocalization effects in the Volmer-Heyrovsky mechanism of the hydrogen evolution reaction (HER). This method is applied a posteriori to configurations sampled along a reaction path to correct their relative stabilities. Concretely, the first step of this approach involves describing the reaction in terms of a set of diabatic states that are constructed by imposing suitable density constraints on the system. Refined reaction energy profiles are then recovered by performing a configuration interaction (CDFT-CI) calculation within the basis spanned by the diabatic states. After a careful validation of the proposed method, we examined HER catalysis on open-ended carbon nanotubes and discovered that CDFT-CI increased activation energies and decreased reaction energies relative to DFT predictions. We believe that a similar approach could also be adopted to treat overdelocalization effects in other electrocatalytic proton-coupled electron transfer reactions, e.g., in the oxygen reduction reaction.

Determinants of Photolyase's DNA Repair Mechanism in Mesophiles and Extremophiles

Light-driven DNA repair by extremophilic photolyases is of tremendous importance for understanding the early development of life on Earth. The mechanism for flavin adenine dinucleotide repair of DNA lesions is the subject of debate and has been studied mainly in mesophilic species. In particular, the role of adenine in the repair process is poorly understood. Using molecular docking, molecular dynamics simulations, electronic structure calculations, and electron tunneling pathways analysis, we examined adenine's role in DNA repair in four photolyases that thrive at different temperatures. Our results indicate that the contribution of adenine to the electronic coupling between the flavin and the cyclobutane pyrimidine dimer lesion to be repaired is significant in three (one mesophilic and two extremophilic) of the four enzymes studied. Our analysis suggests that thermophilic and hyperthermophilic photolyases have evolved structurally to preserve the functional position (and thus the catalytic function) of adenine at their high temperatures of operation. Water molecules can compete with adenine in establishing the strongest coupling pathway for the electron transfer repair process, but the adenine contribution remains substantial. The present study also reconciles prior seemingly contradictory conclusions on the role of adenine in mesophile electron transfer repair reactions, showing how adenine-mediated superexchange is conformationally gated.

Density Functional Physicality in Electronic Coupling Estimation: Benchmarks and Error Analysis

Electronic coupling estimates from constrained density functional theory configuration interaction (CDFT-CI) depend critically on choice of density functional. In this Letter, the orbital multielectron self-interaction error (OMSIE), vertical electron affinity (VEA), and vertical ionization potential (VIP) are shown to be the key indicators inherited from the density functional that determine the accuracy of electronic coupling estimates. An error metric η is derived to connect the three properties, based on the linear proportionality between electronic coupling and overlap integral, and the hypothesis that the slope of this line is a function of VEA/VIP, η = (1/N_testset)Σ_i^testset|-VE^Ref × OMSIE + ΔVE - ΔVE × OMSIE|_i. Based on η, BH&HLYP and LRC-ωPBEh are suggested as the best functionals for electron and hole transfer, respectively. Error metric η is therefore a useful predictor of errors in CDFT-CI electronic coupling, showing that the physical correctness of the density functional has a direct effect on the accuracy of the electronic coupling.

Efficient Constrained Density Functional Theory Implementation for Simulation of Condensed Phase Electron Transfer Reactions

Constrained density functional theory (CDFT) is a versatile tool for probing the kinetics of electron transfer (ET) reactions. In this work, we present a well-scaling parallel CDFT implementation relying on a mixed basis set of Gaussian functions and plane waves, which has been specifically tailored to investigate condensed phase ET reactions using an explicit, quantum chemical representation of the solvent. The accuracy of our implementation is validated against previous theoretical results for predicting electronic couplings and charge transfer energies. Subsequently, we demonstrate the efficiency of our method by studying the intramolecular ET reaction of an organic mixed-valence compound in water using a CDFT based molecular dynamics simulation.

Effects of G-Quadruplex Topology on Electronic Transfer Integrals

G-quadruplex is a quadruple helical form of nucleic acids that can appear in guanine-rich parts of the genome. The basic unit is the G-tetrad, a planar assembly of four guanines connected by eight hydrogen bonds. Its rich topology and its possible relevance as a drug target for a number of diseases have stimulated several structural studies. The superior stiffness and electronic π-π overlap between consecutive G-tetrads suggest exploitation for nanotechnologies. Here we inspect the intimate link between the structure and the electronic properties, with focus on charge transfer parameters. We show that the electronic couplings between stacked G-tetrads strongly depend on the three-dimensional atomic structure. Furthermore, we reveal a remarkable correlation with the topology: a topology characterized by the absence of syn-anti G-G sequences can better support electronic charge transfer. On the other hand, there is no obvious correlation of the electronic coupling with usual descriptors of the helix shape. We establish a procedure to maximize the correlation with a global helix shape descriptor.

Multistate Density Functional Theory for Effective Diabatic Electronic Coupling

Multistate density functional theory (MSDFT) is presented to estimate the effective transfer integral associated with electron and hole transfer reactions. In this approach, the charge-localized diabatic states are defined by block localization of Kohn-Sham orbitals, which constrain the electron density for each diabatic state in orbital space. This differs from the procedure used in constrained density functional theory that partitions the density within specific spatial regions. For a series of model systems, the computed transfer integrals are consistent with experimental data and show the expected exponential attenuation with the donor-acceptor separation. The present method can be used to model charge transfer reactions including processes involving coupled electron and proton transfer.

Constrained subsystem density functional theory

Constrained Subsystem Density Fucntional Theory (CSDFT) allows to compute diabatic states for charge transfer reactions using the machinery of the constrained DFT method, and at the same time is able to embed such diabatic states in a molecular environment via a subsystem DFT scheme.

Effect of metallation, substituents and inter/intra-molecular polarization on electronic couplings for hole transport in stacked porphyrin dyads

Hole transport properties for stacked porphyrins are analyzed with density functional theory.

A New Type of Electron Relay Station in Proteins: Three-Piece S:Π∴S↔S∴Π:S Resonance Structure

A type of relay station for electron transfer in proteins, three-piece five-electron bonding, is introduced in this paper, which is also first proposed here. The ab initio calculations predict the formation of S:Π∴S↔S∴Π:S resonance binding with an aromatic ring located in the middle of two sulfur-containing groups, which may participate in electron-hole transport in proteins. These special structures can lower the local ionization energies to capture electron holes efficiently and may be easily formed and broken because of their proper binding energies. In addition, the UV-vis spectra provide evidence of the formations of the three-piece five-electron binding. The cooperation of three adjacent pieces may be advantage to promote electron transfer a longer distance.

Topological analyses of time-dependent electronic structures: application to electron-transfers in methionine enkephalin

We have studied electron transfers (ET) between electron donors and acceptors, taking as illustrative example the case of ET in methionine enkephalin. Recent pulse and gamma radiolysis experiments suggested that an ultrafast ET takes place from the C-terminal tyrosine residue to the N-terminal, oxidized, methionine residue. According to standard theoretical frameworks like the Marcus theory, ET can be decomposed into two successive steps: i) the achievement through thermal fluctuations, of a set of nuclear coordinates associated with degeneracy of the two electronic states, ii) the electron tunneling from the donor molecular orbital to the acceptor molecular orbital. Here, we focus on the analysis of the time-dependent electronic dynamics during the tunneling event. This is done by extending the approaches based on the topological analyses of stationary electronic density and of the electron localization function (ELF) to the time-dependent domain. Furthermore, we analyzed isosurfaces of the divergence of the current density, showing the paths that are followed by the tunneling electron from the donor to the acceptor. We show how these functions can be calculated with constrained density functional theory. Beyond this work, the topological tools used here can open up new opportunities for the electronic description in the time-dependent domain.

Multistate treatments of the electronic coupling in donor-bridge-acceptor systems: insights and caveats from a simple model

We use a simple one-dimensional delta function electronic structure model (dfm) to investigate the results of a pair of multistate diabatization techniques (i.e., based on n states, with n ≥ 2) for linear DBA and DBBA (donor-bridge-acceptor) electron-transfer systems. In particular, we focus on the physical meaning of the couplings obtained from multistate methods and their relationship to two-state (n = 2) coupling elements. On the basis of the simple dfm approach, which allows exact as well as finite basis set treatment and has no many-electron effects, we conclude that for orthogonal diabatic states, it is difficult to assign clear physical significance to multistate matrix elements for coupling beyond nearest-neighbor contacts. The implications of these results for more complex multistate many-electron treatments are discussed. It is emphasized that physically meaningful coupling elements must involve states that are orthogonal, either explicitly or implicitly.

Dynamical treatment of charge transfer through duplex nucleic acids containing modified adenines

We address the issue of whether chemical alterations of nucleobases are an effective tool to modulate charge transfer through DNA molecules. Our investigation uses a multilevel computational approach based on classical molecular dynamics and quantum chemistry. We find yet another piece of evidence that structural fluctuations are a key factor to determine the electronic structure of double-stranded DNA. We argue that the electronic structure and charge transfer ability of flexible polymers is the result of a complex intertwining of various structural, dynamical and chemical factors. Chemical intuition may be used to design molecular wires, but this is not the sole component in the complex charge transfer mechanism through DNA.

On the Origins of the Linear Free Energy Relationships: Exploring the Nature of the Off-Diagonal Coupling Elements in S(N)2 Reactions

Understanding the relationship between the adiabatic free energy profiles of chemical reactions and the underlining diabatic states is central to the description of chemical reactivity. The diabatic states form the theoretical basis of Linear Free Energy Relationships (LFERs) and thus play a major role in physical organic chemistry and related fields. However, the theoretical justification for some of the implicit LFER assumptions has not been fully established by quantum mechanical studies. This study follows our earlier works(1,2) and uses the ab initio frozen density functional theory (FDFT) method(3) to evaluate both the diabatic and adiabatic free energy surfaces and to determine the corresponding off-diagonal coupling matrix elements for a series of S(N)2 reactions. It is found that the off-diagonal coupling matrix elements are almost the same regardless of the nucleophile and the leaving group but change upon changing the central group. Furthermore, it is also found that the off diagonal elements are basically the same in gas phase and in solution, even when the solvent is explicitly included in the ab initio calculations. Furthermore, our study establishes that the FDFT diabatic profiles are parabolic to a good approximation thus providing a first principle support to the origin of LFER. These findings further support the basic approximation of the EVB treatment.