Facilitating Electron Transfer by Resizing Cyclocarbon Acceptor from C18 to C16

Recent advances in synthetic methods, combined with tip-induced on-surface chemistry, have enabled the formation of numerous cyclocarbon molecules. Here, we investigate computationally the experimentally studied C16 and C18 molecules as well as their van der Waals (vdW) complexes with several typical donor and acceptor molecules. Our results demonstrate a remarkable electron-withdrawing ability of cyclocarbon molecules. The vdW complexes of C16 and C18 exhibit a thermodynamically favorable photoinduced electron transfer (ET) from the donor partner to the cyclocarbons that occurs on a picosecond time scale. The lower reorganization energy of C16 compared to C18 leads to a significant acceleration of the ET reactions.

Photoinduced Electron Transfer in Inclusion Complexes of Carbon Nanohoops

ConspectusPhotoinduced electron transfer (PET) in carbon materials is a process of great importance in light energy conversion. Carbon materials, such as fullerenes, graphene flakes, carbon nanotubes, and cycloparaphenylenes (CPPs), have unusual electronic properties that make them interesting objects for PET research. These materials can be used as electron-hole transport layers, electrode materials, or passivation additives in photovoltaic devices. Moreover, their appropriate combination opens up new possibilities for constructing photoactive supramolecular systems with efficient charge transfer between the donor and acceptor parts. CPPs build a class of molecules consisting of para-linked phenylene rings. CPPs and their numerous derivatives are appealing building blocks in supramolecular chemistry, acting as suitable concave receptors with strong host-guest interactions for the convex surfaces of fullerenes. Efficient PET in donor-acceptor systems can be observed when charge separation occurs faster than charge recombination. This Account focuses on selected inclusion complexes of carbon nanohoops studied by our group. We modeled charge separation and charge recombination in both previously synthesized and computationally designed complexes to identify how various modifications of host and guest molecules affect the PET efficiency in these systems. A consistent computational protocol we used includes a time-dependent density-functional theory (TD-DFT) formalism with the Tamm-Dancoff approximation (TDA) and CAM-B3LYP functional to carry out excited state calculations and the nonadiabatic electron transfer theory to estimate electron-transfer rates. We show how the photophysical properties of carbon nanohoops can be modified by incorporating additional π-conjugated fragments and antiaromatic units, multiple fluorine substitutions, and extending the overall π-electron system. Incorporating π-conjugated groups or linkers is accompanied by the appearance of new charge transfer states. Perfluorination of the nanohoops radically changes their role in charge separation from an electron donor to an electron acceptor. Vacancy defects in π-extended nanohoops are shown to hinder PET between host and guest molecules, while large fully conjugated π-systems improve the electron-donor properties of nanohoops. We also highlight the role of antiaromatic structural units in tuning the electronic properties of nanohoops. Depending on the aromaticity degree of monomeric units in nanohoops, the direction of electron transfer in their complexes with C60 fullerene can be altered. Nanohoops with aromatic units usually act as electron donors, while those with antiaromatic monomers serve as electron acceptors. Finally, we discuss why charged fullerenes are better electron acceptors than neutral C60 and how the charge location allows for the design of more efficient donor-acceptor systems with an unusual hypsochromic shift of the charge transfer band in polar solvents.

Effect of external electric fields in the charge transfer rates of donor-acceptor dyads: A straightforward computational evaluation

We present a straightforward and low-cost computational protocol to estimate the variation of the charge transfer rate constant, kCT, in a molecular donor-acceptor caused by an external electric field. The proposed protocol also allows for determining the strength and direction of the field that maximize the kCT. The application of this external electric field results in up to a >4000-fold increase in the kCT for one of the systems studied. Our method allows the identification of field-induced charge-transfer processes that would not occur without the perturbation caused by an external electric field. In addition, the proposed protocol can be used to predict the effect on the kCT due to the presence of charged functional groups, which may allow for the rational design of more efficient donor-acceptor dyads.

Excited state processes in supramolecular complexes of cyclic dibenzopyrrolopyrroles isomers with C60 fullerene

An approach to modulating the properties of carbon nanorings by incorporating pyrrolo[3,2-b]pyrrole units is of particular interest due to the combined effect of heteroatom and antiaromatic character on electronic properties. The inclusion of units other than phenylene leads to the formation of stereoisomers. In this work, we computationally study how the spatial orientation of monomeric units in the ring affects the properties of cyclic dibenzopyrrolo[3,2-b]pyrroles and their complexes with C₆₀ fullerene. For [4]PP and [4]DHPP, the most symmetrical AAAA isomer is the most stable and forms stronger interactions with fullerene than the isomers where one or two monomeric units are flipped, mostly due to less Pauli repulsion. π-Electron delocalization in the monomeric unit is crucial for directing the electron transfer (from or to nanoring). The energy of excited states with charge transfer depends on the HOMO-LUMO gap, which varies from one stereoisomer to another only for [4]DHPP⊃C₆₀ with aromatic 1,4-dihydropyrrolo[3,2-b]pyrrole units. The rates of electron transfer and charge recombination reactions are relatively weakly dependent of the spatial isomerism of nanorings.

Aromaticity controls the excited-state properties of host-guest complexes of nanohoops

π-Conjugated organic molecules have exciting applications as materials for batteries, solar cells, light-emitting diodes, etc. Among these systems, antiaromatic compounds are of particular interest because of their smaller HOMO-LUMO energy gap compared to aromatic compounds. A small HOMO-LUMO gap is expected to facilitate charge transfer in the systems. Here we report the ground and excited-state properties of two model nanohoops that are nitrogen-doped analogs of recently synthesized [4]cyclodibenzopentalenes - tetramers of benzene-fused aromatic 1,4-dihydropyrrolo[3,2-b]pyrrole ([4]DHPP) and antiaromatic pyrrolo[3,2-b]pyrrole ([4]PP). Their complexes with C60 fullerene show different behavior upon photoexcitation, depending on the degree of aromaticity. [4]DHPP acts as an electron donor, whereas [4]PP is a stronger electron acceptor than C60. The ultrafast charge separation combined with the slow charge recombination that we found for [4]PP⊃C60 indicates a long lifetime of the charge transfer state.

The hunter falls prey: photoinduced oxidation of C60 in inclusion complex with perfluorocycloparaphenylene

Perfluorocycloparaphenylenes (PFCPPs) are cycloparaphenylenes (CPPs) in which all hydrogen atoms have been replaced by fluorine atoms. Like CPPs, PFCPPs are highly strained, hoop‐shaped π‐conjugated molecules. In this article, we report a computational modeling of photoinduced electron transfer processes in the inclusion complex of PF[10]CPP with C₆₀ fullerene. Its unique feature is the favorable electron transfer from C₆₀ to the host molecule. The photooxidation of C₆₀ is predicted to occur on a sub‐nanosecond timescale. The PF[10]CPP⊃C₆₀ dyad is the first nanoring‐fullerene complex in which C₆₀ acts as an electron donor in the photoinduced charge separation.

Nitrogen-doped molecular bowls as electron donors in photoinduced electron transfer reactions

In recent years, the chemistry of curved π-conjugated molecules has experienced a sharp rise. The inclusion of a heteroatom in the carbon network significantly affects its semiconducting properties. In this work, we computationally study the photoinduced electron transfer in a series of C₆₀ fullerene complexes with experimentally established nitrogen-doped molecular bowls. Our results demonstrate that introducing nitrogen into pentagonal rings of the bowl-shaped π-conjugated molecules and extending the π-conjugation can modulate their electron-transfer properties. Among the studied complexes, the hub-NCor⊃C₆₀ complex exhibits the most desirable combination of ultrafast charge separation and slow charge recombination, suggesting its potential use in photovoltaics.

Photoinduced electron transfer in non-covalent complexes of C60 and phosphangulene oxide derivatives

Investigation of photoinduced electron transfer (PET) in a series of experimentally reported complexes of fullerene with phosphangulene oxides shows that the replacement of O atoms in the bridge of phosphangulene with S atoms promotes efficient and ultrafast ET from phosphangulene oxide to fullerene in PGOOSS⊃C60 and PGOSSS⊃C60 complexes. The results obtained can be useful for the development of photovoltaic devices based on phosphangulenes.

Unexpected Disparity in Photoinduced Reactions of C60 and C70 in Water with the Generation of O2 •- or 1O2

Well-defined fullerene-PEG conjugates, C₆₀-PEG (1) and two C₇₀-PEG (2 and 3 with the addition sites on ab-[6,6] and cc-[6,6]-junctions), were prepared from their corresponding Prato monoadduct precursors. The resulting highly water-soluble fullerene-PEG conjugates 1-3 were evaluated for their DNA-cleaving activities and reactive oxygen species (ROS) generation under visible light irradiation. Unexpectedly, photoinduced cleavage of DNA by C₆₀-PEG 1 was much higher than that by C₇₀-PEG 2 and 3 with higher absorption intensity, especially in the presence of an electron donor (NADH). The preference of photoinduced ROS generation from fullerene-PEG conjugates 1-3 via the type II (energy transfer) or the type I (electron transfer) photoreaction was found to be dependent on the fullerene core (between C₆₀ and C₇₀) and functionalization pattern of C₇₀ (between 2 and 3). This was clearly supported by the electron transfer rate obtained from cyclic voltammetry data and computationally estimated relative rate of each step of the type II and the type I reactions, with the finding that type II energy transfer reactions occurred in the inverted Marcus regime while type I electron transfer reactions proceeded in the normal Marcus regime. This finding on the disparity in the pathways of photoinduced reactions (type I versus type II) provides insights into the behavior of photosensitizers in water and the design of photodynamic therapy drugs.

Solvation Free Energies for Aqueous and Nonaqueous Solutions Computed Using PM7 Atomic Charges

We describe a simple and accurate method, ESE-PM7, for calculating solvation free energies ΔG_solv^° in aqueous and nonaqueous solutions. The method is based on a noniterative COSMO algorithm. Molecular geometries and atomic charges calculated using the semiempirical method PM7 are used to calculate ΔG_solv^°. The method has been tested on 92 different solvents and 988 solutes. The mean absolute errors (MAEs) in ΔG_solv^° in aqueous solutions estimated by the ESE-PM7 approach are found to be 1.62 kcal/mol for 389 neutral solutes and 3.06 kcal/mol for 139 ions. The MAEs for neutral molecules in organic solvents are 0.97, 0.74, and 0.51 kcal/mol in polar protic, polar aprotic, and nonpolar solvents, respectively. The developed method can be employed to quickly screen ΔG_solv^° values of extended molecular systems including pharmaceutical and biological molecules.

Fast non-iterative calculation of solvation energies for water and non-aqueous solvents

We propose an efficient and accurate non-iterative method, dubbed uESE, for calculating solvation free energies. Apart from a COSMO-like electrostatic term, the model takes into account non-electrostatic contributions, which depend on atomic surfaces, induced surface charge densities, and the molecular volume. uESE is tested on 35 polar and 57 non-polar solvents. The calculated and experimental solvation free energies are compared for 2892 systems. The method exhibits an excellent performance, which is superior to major solvation methods. The mean absolute error of predicted solvation energies is found below 1 kcal/mol for neutral solutes and below 3 kcal/mol for ions. The calculated data are almost independent of the quantum-chemical method or/and basis sets employed.

How Do Defects in Carbon Nanostructures Regulate the Photoinduced Electron Transfer Processes? The Case of Phenine Nanotubes

Photoinduced electron transfer is studied in a series of inclusion complexes of structurally modified phenine nanotubes (pNT) with C70 using the TD-DFT method. Analysis of electronic properties of the complexes shows that the electron transfer is infeasible in pNT_4d⊃C70 built on the tetrameric array of [6]cyclo-meta-phenylene ([6]CMP) units. However, replacing one or more [6]CMP units with a coronene moiety enables electron transfer from pNT to C70 . The generation of the charge separated states from the lowest locally excited states occurs on a sub-nanosecond time scale. Depending on the number of the [6]CMP units, the charge recombination rate varies from 1.8 ⋅ 107 to 3.1 ⋅ 102  s-1 , i. e., five orders of magnitude.

[10]CPP-Based Inclusion Complexes of Charged Fulleropyrrolidines. Effect of the Charge Location on the Photoinduced Electron Transfer

A number of non-covalently bound donor-acceptor dyads, consisting of C₆₀ as the electron acceptor and cycloparaphenylene (CPP) as the electron donor, have been reported. A hypsochromic shift of the charge transfer (CT) band in polar medium has been found in [10]CPP⊃Li⁺ @C₆₀ . To explore this anomalous effect, we study inclusion complexes [10]CPP⊃Li⁺ @C₆₀ -MP, [10]CPP⊃C₆₀ -MPH⁺ , and [10]CPP⊃C₆₀ -PPyMe⁺ formed by fulleropyrrolidine derivatives and [10]CPP using the DFT/TDDFT approach. We show that the introduction of a positively charged fragment into fullerene stabilizes CT states that become the lowest-lying excited states. These charge-separated states can be generated by the decay of locally excited states on a nanosecond to picosecond time scale. The distance of the charged fragment to the center of the fullerenic cage and its accessibility to the solvent determine the strength of the hypsochromic shift.

Evaluation of charge-transfer rates in fullerene-based donor-acceptor dyads with different density functional approximations

The shift towards renewable energy is one of the main challenges of this generation. Dye-sensitized solar cells (DSSCs), based on donor-acceptor architectures, can help in this transition as they present excellent photovoltaic efficiencies yet cheap and simple manufacturing. For molecular heterojunction DSSCs, donor-acceptor pairs are linked in a covalent manner, which facilitates their tailoring and rational design. Nevertheless, reliable computational characterization of charge transfer rate constants (kCT) is needed to speed this development process up. In this context, the performance of time-dependent density functional theory for the calculation of kCT values in donor-acceptor fullerene-based dyads has not been benchmarked yet. Herein, we present a detailed analysis on the performance of seven well-known density functional approximations (DFAs) for this type of system, focusing on several parameters such as the reorganization energies (λ), electronic couplings (VDA), and Gibbs energies (ΔG0CT), as well as the final rate constants. The amount of exact exchange at short range (SR) and long range (LR) electron-electron distances (and the transition from the SR to LR) turned out to be key for the success of the prediction. The tuning of these parameters improves significantly the performance of current DFAs.

Photoinduced electron transfer in nano-Saturn complexes of fullerene

The photoinduced electron transfer is studied computationally in several Saturn-shaped inclusion complexes of carbo-aromatic rings and C60 fullerene - C72⊃C60, C96⊃C60, C120⊃C60, and C168⊃C60. Analysis of their structural and electronic properties shows that the charge separation process is efficient in C120⊃C60 and C168⊃C60 where the host molecule resembles the conjugated [24]circulene unit. In contrast, the electron transfer is not feasible in the complexes of the oligophenylene-based rings C72⊃C60 and C96⊃C60.

Photoinduced electron transfer in nanotube⊃C70 inclusion complexes: phenine vs. nanographene nanotubes

In this work, we computationally study the photoinduced electron transfer in fullerene inclusion complexes of two phenine nanotubes pre-pNT⊃C70 and pNT⊃C70 and their nanographene analog [4]CHBC⊃C70. Charge separation is shown to efficiently occur in [4]CHBC⊃C70. In contrast, the electron transfer process between the host and guest units in the pre-pNT⊃C70 and pNT⊃C70 complexes is blocked by the structural changes incorporated in the nanographene framework.

Electron Transfer in a Li+-Doped Zn-Porphyrin-[10]CPP⊃Fullerene Junction and Charge-Separated Bands with Opposite Response to Polar Environments

Recently synthesized porphyrin-cycloparaphenylene (ZnP-[10]CPP) junction is a powerful platform to develop useful organic photovoltaic devices. In this work, we computationally study photoinduced electron transfer processes in the supramolecular complex ZnP-[10]CPP⊃C₆₀ and its Li⁺-doped derivative. The most striking finding is charge-separated (CS) bands in ZnP-[10]CPP⊃Li⁺@C₆₀ with opposite response to solvent polarity. Besides CS bands that demonstrate a bathochromic shift, there exist CS transitions showing a rarely observed hypsochromic shift. The rates of energy transfer, charge separation, and charge recombination in the supramolecular complexes are computed by using the semiclassical approach. These estimates suggest that the both types of CS states can be efficiently populated in polar media by decay of locally excited states.

Covalent Functionalization of Single-Walled Carbon Nanotubes by the Bingel Reaction for Building Charge-Transfer Complexes

Functionalization of nanotubes with donor and acceptor partners by the Bingel reaction leads to the formation of charge-transfer dyads, which can operate in organic photovoltaic devices. In this work, we theoretically examine the mechanism of the Bingel reaction for the (6,5)-chiral, (5,5)-armchair, and (9,0)-zigzag single-walled carbon nanotubes (SWCNTs), and demonstrate that the reaction is regioselective and takes place at the perpendicular position of (6,5)- and (5,5)-SWCNTs, and the oblique position of (9,0)-SWCNT. Further, we design computationally the donor-acceptor complexes based on (6,5)-SWCNT coupled with partners of different electronic nature. Analysis of their excited states reveals that efficient photoinduced charge transfer can be achieved in the complexes with π-extended analogue of tetrathiafulvalene (exTTF), zinc tetraphenylporphyrin (ZnTPP), and tetracyanoanthraquinodimethane (TCAQ). The solvent can significantly affect the population of the charge-separated states. Our calculations show that electron transfer (ET) occurs in the normal Marcus regime on a sub-nanosecond time scale in the complexes with exTTF and ZnTPP, and in the inverted Marcus regime on a picosecond time scale in the case of the TCAQ derivative. The ET rate is found to be not very sensitive to the degree of functionalization of the nanotube.

Cyclo[18]carbon: the smallest all-carbon electron acceptor

The recently synthesized C₁₈ molecule demonstrates strong electron acceptor properties similar to C₆₀.

Correction: Cyclo[18]carbon: the smallest all-carbon electron acceptor

Correction for ‘Cyclo[18]carbon: the smallest all-carbon electron acceptor’ by Anton J. Stasyuk et al., Chem. Commun., 2020, 56, 352–355.

Fast and accurate calculation of hydration energies of molecules and ions

An accurate and efficient method for calculation of hydration free energy of ions and neutral molecules is presented.

Peculiar Photoinduced Electron Transfer in Porphyrin-Fullerene Akamptisomers

Porphyrin-fullerene dyads are promising candidates for organic photovoltaic devices. The electron-transfer (ET) properties of the molecular devices depend significantly on the mutual position of the donor and acceptor. Recently, a new type of molecular isomerism (akamptisomerism) has been discovered. In the present study, we explore how photoinduced ET can be modulated by passing from one akamptisomer to another. To this aim, four akamptisomers of the quinoxalinoporphyrin-[60]fullerene complex are selected for computational study. The most striking finding is that, depending on the isomer, the porphyrin unit in the dyad can act as either electron donor or electron acceptor. Thus, the stereoisomeric diversity allows one to change the direction of ET between the porphyrin and fullerene moieties. To understand the effect of akamptisomerism on the photoinduced ET processes, a detailed analysis of initial and final states involved in the ET is performed. The computed rate for charge separation is estimated to be in the region of 1-10 ns^-1 . The formation of a long-living quinoxalinoporphyrin anion radical species is predicted.

Iterative Atomic Charge Partitioning of Valence Electron Density

We propose an atomic charge partitioning scheme, iterative adjusted charge partitioning (I-ACP), belonging to the stockholder family and based on partitioning of the valence molecular electron density. The method uses a Slater-type weighting factor c_A r^2n-2 exp(-α_A r), where α_A is a fixed parameter and c_A is determined iteratively. The parameters α_A were fitted for 17 main-group elements. The I-ACP scheme is shown to produce consistent, chemically meaningful atomic charges. Several stockholder-type charge-partitioning are compared. Extensive numerical tests demonstrate that in most cases, I-ACP surpasses most other methods by reproducing more accurately molecular dipole moments. © 2018 Wiley Periodicals, Inc.

A simple COSMO-based method for calculation of hydration energies of neutral molecules

A simple yet accurate method to estimate hydration free energy of neutral molecules is developed.

Hypsochromic solvent shift of the charge separation band in ionic donor–acceptor Li+@C60⊂[10]CPP

Photoinduced electron transfer in CPP-based donor–acceptor complexes C₆₀⊂[10]CPP and Li⁺@C₆₀⊂[10]CPP was studied using DFT/TDDFT. Unusual blue shift of charge separated states for Li⁺@C₆₀⊂[10]CPP complexes in the polar medium is predicted.

A simple model for calculating atomic charges in molecules

We propose a new atomic-charge analysis, termed adjusted charge partitioning (ACP) scheme. To partition the molecular electronic density into atomic components, weighting factors cAr2n-2exp(-αAr) with atomic parameters cA and αA are used. Extensive numerical tests were performed for 540 molecules containing 17 main-group elements H, Li to F, Na to Cl, Br, and I. The estimated dipole moments and atomic charges are compared with the data provided by a large number of alternative atomic-charge schemes including the Mulliken, Löwdin, Hirshfeld, Hirshfeld Iterative, CM5, ESP, NPA, and QTAIM population analyses. These tests show that the resulting atomic charges are insensitive to basis sets used, chemically consistent and accurately reproduce experimental dipole moments.

Reliable charge assessment on encapsulated fragment for endohedral systems

A simple scheme to determine charge distribution in endohedral complexes is suggested. It is based on comparison of inner-shell atomic orbital energies of the encapsulated species to the corresponding energies in reference systems with unambiguously defined charges on X. This robust approach is applied to endohedral borospherenes X@B₃₉, for which the conventional schemes provide in some cases quite different results. Efficiency of proposed scheme also has been proven for typical fullerene based Sc₃N@C₈₀ endohedral complex.

Thermally induced hopping model for long-range triplet excitation energy transfer in DNA

Long-range triplet excitation energy transfer in DNA occurs through hops between T bases, providing it with a shallow distance dependence. Hops over two thymines on the same strand are preferred.

How abasic sites impact hole transfer dynamics in GC-rich DNA sequences

Hole transfer dynamics through GC-rich DNA duplexes containing abasic sites is strongly modulated by the nature of the unpaired nucleobase.

Direct estimation of the transfer integral for photoinduced electron transfer from TD DFT calculations

A simple approach to estimate the electronic coupling for photoinduced charge separation in materials and biomolecules is proposed.

The Driving Force of Photoinduced Charge Separation in Metal-Cluster-Encapsulated Triphenylamine-[80]fullerenes

Understanding photoinduced charge separation in fullerene-based dye-sensitized solar cells is crucial for the development of photovoltaic devices. We investigate here how the driving force of the charge separation process in conjugates of M@C₈₀ (M=Sc₃ N, Sc₃ CH, Sc₃ NC, Sc₄ O₂ , and Sc₄ O₃ ) with triphenylamine (TPA) depends on the nature of the metal cluster. Both singlet and triplet excited-state electron-transfer reactions are considered. These results based on TD-DFT calculations demonstrate that the driving force of charge separation in TPA-M@C₈₀ can be tuned well by varying the structure of the metal cluster encapsulated inside the fullerene cage.

Single photon triggered dianion formation in TCNQ and F4TCNQ crystals

Excited state dynamics in two strong organic electron acceptor systems, TCNQ and F₄TCNQ single crystals, was studied. After absorption of a single photon, dianions are formed in both crystals on ultrashort timescale: TCNQ τ < 50 fs, F₄TCNQ τ = 4 ps. By use of transient absorption spectroscopy, we demonstrate that the dianion formation in F₄TCNQ is mediated by the radical anion precursor which is described by a two-step model. Our measurements show the phenomenon that in this quinoid acceptor crystals in the absence of additional donor molecule, it is possible to resolve the two step formation of a doubly charged anion upon absorption of a single low energy photon (2.6 eV).

Theoretical estimation of the rate of photoinduced charge transfer reactions in triphenylamine C60 donor-acceptor conjugate

Fullerene-based molecular heterojunctions such as the [6,6]-pyrrolidine-C60 donor-acceptor conjugate containing triphenylamine (TPA) are potential materials for high-efficient dye-sensitized solar cells. In this work, we estimate the rate constants for the photoinduced charge separation and charge recombination processes in TPA-C60 using the unrestricted and time-dependent DFT methods. Different schemes are applied to evaluate excited state properties and electron transfer parameters (reorganization energies, electronic couplings, and Gibbs energies). The use of open-shell singlet or triplet states, several density functionals, and continuum solvation models is discussed. Strengths and limitations of the computational approaches are highlighted. The present benchmark study provides an overview of the expected performance of DFT-based methodologies in the description of photoinduced charge transfer reactions in fullerene heterojunctions. © 2016 Wiley Periodicals, Inc.

Multiple Decay Mechanisms and 2D-UV Spectroscopic Fingerprints of Singlet Excited Solvated Adenine-Uracil Monophosphate

The decay channels of singlet excited adenine uracil monophosphate (ApU) in water are studied with CASPT2//CASSCF:MM potential energy calculations and simulation of the 2D-UV spectroscopic fingerprints with the aim of elucidating the role of the different electronic states of the stacked conformer in the excited state dynamics. The adenine (1) La state can decay without a barrier to a conical intersection with the ground state. In contrast, the adenine (1) Lb and uracil S(U) states have minima that are separated from the intersections by sizeable barriers. Depending on the backbone conformation, the CT state can undergo inter-base hydrogen transfer and decay to the ground state through a conical intersection, or it can yield a long-lived minimum stabilized by a hydrogen bond between the two ribose rings. This suggests that the (1) Lb , S(U) and CT states of the stacked conformer may all contribute to the experimental lifetimes of 18 and 240 ps. We have also simulated the time evolution of the 2D-UV spectra and provide the specific fingerprint of each species in a recommended probe window between 25 000 and 38 000 cm(-1) in which decongested, clearly distinguishable spectra can be obtained. This is expected to allow the mechanistic scenarios to be discerned in the near future with the help of the corresponding experiments. Our results reveal the complexity of the photophysics of the relatively small ApU system, and the potential of 2D-UV spectroscopy to disentangle the photophysics of multichromophoric systems.

Single Amino Acid Mutation Controls Hole Transfer Dynamics in DNA-Methyltransferase HhaI Complexes

Different mutagenic effects are generated by DNA oxidation that implies the formation of radical cation states (so-called holes) on purine nucleobases. The interaction of DNA with proteins may protect DNA from oxidative damage owing to hole transfer (HT) from the stack to aromatic amino acids. However, how protein binding affects HT dynamics in DNA is still poorly understood. Here, we report a computational study of HT in DNA complexes with methyltransferase HhaI with the aim of elucidating the molecular factors that explain why long-range DNA HT is inhibited when the glutamine residue inserted in the double helix is mutated into a tryptophan. We combine molecular dynamics, quantum chemistry, and kinetic Monte Carlo simulations and find that protein binding stabilizes the energies of the guanine radical cation states and significantly impacts the corresponding electronic couplings, thus determining the observed behavior, whereas the formation of a tryptophan radical leads to less efficient HT.

Conformationally Gated Charge Transfer in DNA Three-Way Junctions

Molecular structures that direct charge transport in two or three dimensions possess some of the essential functionality of electrical switches and gates. We use theory, modeling, and simulation to explore the conformational dynamics of DNA three-way junctions (TWJs) that may control the flow of charge through these structures. Molecular dynamics simulations and quantum calculations indicate that DNA TWJs undergo dynamic interconversion among "well stacked" conformations on the time scale of nanoseconds, a feature that makes the junctions very different from linear DNA duplexes. The studies further indicate that this conformational gating would control charge flow through these TWJs, distinguishing them from conventional (larger size scale) gated devices. Simulations also find that structures with polyethylene glycol linking groups ("extenders") lock conformations that favor CT for 25 ns or more. The simulations explain the kinetics observed experimentally in TWJs and rationalize their transport properties compared with double-stranded DNA.

Fragment transition density method to calculate electronic coupling for excitation energy transfer

A general approach, the Fragment Transition Density (FTD) scheme, is introduced to estimate electronic coupling for excitation energy transfer in a molecular system. Within this method, the excitation energies and transition densities of the system are used to derive the coupling matrix element. The scheme allows one to treat systems where exciton donor and acceptor are close together and their exchange interaction and orbital overlap are significant. The FTD method can be applied in combination with any quantum mechanical approach to treat excited states of general nature including single-, double-, and higher excitations. Using FTD approach, we derive excitonic couplings for several systems computed with the CIS, TD DFT and MS-CASPT2 methods. In particular, it is shown that the estimated coupling values in DNA π-stacks are strongly affected by the short-range electronic interaction of adjacent nucleobases.

Influence of base stacking geometry on the nature of excited states in G-quadruplexes: a time-dependent DFT study

G-quadruplexes are four-stranded structures of nucleic acids that are formed from the association of guanine nucleobases into cyclical arrangements known as tetrads. G-quadruplexes are involved in a host of biological processes and are of interest in nanomaterial applications. However, not much is known about their electronic properties. In this paper, we analyze electronic excited states of G-quadruplexes using a combination of time-dependent DFT calculations and molecular dynamics simulations. We systematically consider experimentally observed arrangements of stacked guanine tetrads. The effects of structural features on exciton delocalization and photoinduced charge separation are explored using a quantitative analysis of the transition electron density. It is shown that collective coherent excitations shared between two guanine nucleobases dominate in the absorption spectrum of stacked G-tetrads. These excitations may also include a significant contribution of charge transfer states. Large variation in exciton localization is also observed between different structures with a general propensity toward localization between two bases. We reveal large differences in how charge separation occurs within different nucleobase arrangements, with some geometries favoring separation within a single tetrad and others favoring separation between tetrads. We also investigate the effects of the coordinating K(+) ion located in the central cavity of G-quadruplexes on the relative excited state properties of such systems. Our results demonstrate how the nature of excited states in G-quadruplexes depends on the nucleobase stacking geometry resulting from the mutual arrangement of guanine tetrads.