Spectroscopic approaches for studies of site-specific DNA base and backbone 'breathing' using exciton-coupled dimer-labeled DNA

DNA regulation and repair processes require direct interactions between proteins and DNA at specific sites. Local fluctuations of the sugar-phosphate backbones and bases of DNA (a form of DNA 'breathing') play a central role in such processes. Here we review the development and application of novel spectroscopic methods and analyses - both at the ensemble and single-molecule levels - to study structural and dynamic properties of exciton-coupled cyanine and fluorescent nucleobase analogue dimer-labeled DNA constructs at key positions involved in protein-DNA complex assembly and function. The exciton-coupled dimer probes act as 'sensors' of the local conformations adopted by the sugar-phosphate backbones and bases immediately surrounding the dimer probes. These methods can be used to study the mechanisms of protein binding and function at these sites.

Using transition density models to interpret experimental optical spectra of exciton-coupled cyanine (iCy3)2 dimer probes of local DNA conformations at or near functional protein binding sites

Exciton-coupled chromophore dimers are an emerging class of optical probes for studies of site-specific biomolecular interactions. Applying accurate theoretical models for the electrostatic coupling of a molecular dimer probe is a key step for simulating its optical properties and analyzing spectroscopic data. In this work, we compare experimental absorbance and circular dichroism (CD) spectra of 'internally-labeled' (iCy3)2 dimer probes inserted site-specifically into DNA fork constructs to theoretical calculations of the structure and geometry of these exciton-coupled dimers. We compare transition density models of varying levels of approximation to determine conformational parameters of the (iCy3)2 dimer-labeled DNA fork constructs. By applying an atomistically detailed transition charge (TQ) model, we can distinguish between dimer conformations in which the stacking and tilt angles between planar iCy3 monomers are varied. A major strength of this approach is that the local conformations of the (iCy3)2 dimer probes that we determined can be used to infer information about the structures of the DNA framework immediately surrounding the probes at various positions within the constructs, both deep in the duplex DNA sequences and at sites at or near the DNA fork junctions where protein complexes bind to discharge their biological functions.

Excited state hydrogen or proton transfer pathways in microsolvated n-cyanoindole fluorescent probes

The sensitivity of the fluorescence properties of n-cyanoindole (n-CNI) fluorescent probes to the microenvironment makes them potential reporters of protein conformation and hydration. The fluorescence intensity of 5-CNI, 6-CNI, and 7-CNI is quenched when exposed to water solvent whereas substitution on position 4 of indoles dramatically increases it. A potential mechanism for this sensitivity to water may be similar to that found in indole. The fluorescence of indole is found to be quenched when interacting with water and ammonia solvent molecules via radiationless decay through an S1 (πσ*)/S0 conical intersection caused by excited state proton or hydrogen transfer to the solvent molecules. In this study we examine this fluorescence quenching mechanism along the N-H bond stretch of n-CNI probes using water cluster models and quantum mechanical calculations of the excited states. We find that n-CNI-(H2O)1-2 clusters form cyclic or non-cyclic structures via hydrogen bonds which lead to different photochemical reaction paths that can potentially quench the fluorescence by undergoing internal conversion from S1 to S0. However, the existence of a high energy barrier along the potential energy surface of the S1 state in most cases prevents this from occurring. We show that substitution on position 4 leads to the highest energy barrier that prevents the fluorophore from accessing these non-radiative channels, in agreement with its high intensity. We also find that the energy barrier in the S1 state of non-cyclic 5-CNI-(H2O)1-2 excited complexes decreases as the number of water molecules increases, which suggests great sensitivity of the fluorescence quenching on the aqueous environment.

Unravelling the Origin of the Vibronic Spectral Signatures in an Excitonically Coupled Indocarbocyanine Cy3 Dimer

The indocarbocyanine Cy3 dye is widely used to probe the dynamics of proteins and DNA. Excitonically coupled Cy3 dimers exhibit very unique spectral signatures that depend on the interchromophoric geometrical orientation induced by the environment, making them powerful tools to infer the dynamics of their surroundings. Understanding the origin of the dimeric spectral signatures is a necessity for an accurate interpretation of the experimental results. In this work, we simulate the vibronic spectrum of an experimentally well-studied Cy3 dimer, and we explain the origin of the experimental signatures present in its linear absorption spectrum. The Franck-Condon harmonic approximations, among other tests, are used to probe the factors contributing to the spectrum. It is found that the first peak in the absorption spectrum originates from the lower energy excitonic state, while the next two peaks are vibrational progressions of the higher energy excitonic state. The polar solvent plays a crucial role in the appearance of the spectrum, being responsible for the localized S1 minimum, which results in an increased intensity of the first peak.

Excited-state dynamics of o-nitrophenol studied with UV pump-VUV probe time-resolved photoelectron and photoion spectroscopy

Time-resolved photoionization measurements were performed on o-nitrophenol pumped with UV laser pulses at a central wavelength of 255 nm (4.9 eV) and probed with vacuum ultraviolet (VUV) pulses at 153 nm (8.1 eV). The photoelectron spectrum and time of flight mass spectrum for ions were recorded at each pump-probe delay. The measurements are interpreted with the aid of electronic structure calculations for both the neutral and ionic states. Evidence is found for the formation of a bicyclic intermediate followed by NO dissociation through a process of internal conversion and intersystem crossing. The combination of photoelectron and photoion spectroscopy, together with computational results, provides strong evidence of intersystem crossing that is difficult to establish with only a single technique.

Mechanistic Aspects of the Effect of Flanking Nucleotide Sequence on CPD Formation and CPD Self-Repair in DNA

A cyclobutane pyrimidine dimer (CPD) is a photolesion which is produced by a cycloaddition reaction between two stacked pyrimidine bases upon UV light absorption. Because of its harmful effect on important cellular processes involving DNA and especially its relevance to skin cancer, the mechanisms of how a CPD is formed or repaired have been studied extensively, and it has been demonstrated that flanking nucleotide sequences play a crucial role in CPD formation or self-repair. Understanding the mechanisms behind this sequence dependence of CPD formation or self-repair is of great importance because it can give us valuable information on which sequence will be vulnerable to this DNA photodamage. This Perspective focuses on the mechanisms of how flanking nucleotide sequences affect CPD formation or self-repair, especially highlighting the role of computational studies in this field.

Spectroscopy and Theoretical Modeling of Tetracene Anion Resonances

The positions and widths of the optically allowed electronic states of the tetracene radical anion located above the detachment threshold energy (i.e anion resonances) are mapped out using total photodetachment yield spectroscopy of cryogenically cooled ions. The presence of these states is detected via the sharp increase in the photodetachment yield compared to that of the monotonic nonresonant direct photodetachment background. The resolution of the resulting spectrum is limited by the ∼5 cm^-1 line width of the tunable laser and thus provides a stringent benchmark for computations of the energies and autodetachment lifetimes of these resonance states. The experimental results are compared to high-level electronic structure computations and line width modeling using the orbital stabilization method. These theoretical results are found to be in near quantitative agreement with the experimental data, highlighting their capability to accurately describe the energies and lifetimes of anion resonances for relatively large molecules.

Strong Field Double Ionization of Formaldehyde Investigated Using Momentum Resolved Covariance Imaging and Trajectory Surface Hopping

We use covariance velocity map imaging of fragment ions from the strong field double ionization of formaldehyde in conjunction with trajectory surface hopping calculations to determine the ionization yields to different singlet and triplet states of the dication. The calculated kinetic energy release for trajectories initiated on different electronic states is compared with the experimental values based on momentum resolved covariance measurements. We determine the state resolved double ionization yields as a function of laser intensity and pulse duration down to 6 fs (two optical cycles).

Nonadiabatic Excited State Dynamics of Organic Chromophores: Take-Home Messages

Nonadiabatic excited state dynamics are important in a variety of processes. Theoretical and experimental developments have allowed for a great progress in this area, while combining the two is often necessary and the best approach to obtain insight into the photophysical behavior of molecules. In this Feature Article we use examples of our recent work combining time-resolved photoelectron spectroscopy with theoretical nonadiabatic dynamics to highlight important lessons we learned. We compare the nonadiabatic excited state dynamics of three different organic molecules with the aim of elucidating connections between structure and dynamics. Calculations and measurements are compared for uracil, 1,3-cyclooctadiene, and 1,3-cyclohexadiene. The comparison highlights the role of rigidity in influencing the dynamics and the difficulty of capturing the dynamics accurately with calculations.

Stable excited dication: trapping on the S1 state of formaldehyde dication after strong field ionization

Combined theoretical and experimental work examines the dynamics of dication formaldehyde produced by strong field ionization. Trajectory surface hopping dynamics on the first several singlet electronic states of the formaldehyde dication are used to examine the relaxation pathways and dissociation channels, while kinetic energy distributions after strong field ionization of formaldehyde and deuterated formaldehyde are used to confirm the theoretical predictions. We find that the first excited state of the formaldehyde dication is stable, neither decays to the ground state nor dissociates, even though the ground state and higher lying states are directly dissociative. The stability of the first excited state is explained by its symmetry which does not allow for radiative or nonradiative transitions to the ground state and by large barriers to dissociate on the excited state surface.

Projected Complex Absorbing Potential Multireference Configuration Interaction Approach for Shape and Feshbach Resonances

Anion resonances are formed as metastable intermediates in low-energy electron-induced reactions. Due to the finite lifetimes of resonances, applying standard Hermitian formalism for their characterization presents a vexing problem for computational chemists. Numerous modifications to conventional quantum chemical methods have enabled satisfactory characterization of resonances, but specific issues remain, especially in describing two-particle one-hole (2p-1h) resonances. An accurate description of these resonances and their coupling with single-particle resonances requires a multireference approach. We propose a projected complex absorbing potential (CAP) implementation within the multireference configuration interaction (MRCI) framework to characterize single-particle and 2p-1h resonances. As a first application, we use the projected-CAP-MRCI approach to characterize and benchmark the ²Π_g shape resonance in N₂^-. We test its performance as a function of the size of the subspace and other parameters, and we compute the complex potential energy surface of the ²Π_g shape resonance to show that a smooth curve is obtained. One key benefit of MRCI is that it can describe Feshbach resonances (most common examples of 2p-1h resonances) at the same footing as shape resonances. Therefore, it is uniquely positioned to describe mixing between the different channels. To test these additional capabilities, we compute Feshbach resonances in H₂O^- and anions of dicyanoethylene isomers. We find that CAP-MRCI can efficiently capture the mixing between the Feshbach and shape resonances in dicyanoethylene isomers, which has significant consequences for their lifetimes.

Conformer-Specific Dissociation Dynamics in Dimethyl Methylphosphonate Radical Cation

The dynamics of the dimethyl methylphosphonate (DMMP) radical cation after production by strong field adiabatic ionization have been investigated. Pump-probe experiments using strong field 1300 nm pulses to adiabatically ionize DMMP and a 800 nm non-ionizing probe induce coherent oscillations of the parent ion yield with a period of about 45 fs. The yields of two fragments, PO2C2H7+ and PO2CH4+, oscillate approximately out of phase with the parent ion, but with a slight phase shift relative to each other. We use electronic structure theory and nonadiabatic surface hopping dynamics to understand the underlying dynamics. The results show that while the cation oscillates on the ground state along the P=O bond stretch coordinate, the probe excites population to higher electronic states that can lead to fragments PO2C2H7+ and PO2CH4+. The computational results combined with the experimental observations indicate that the two conformers of DMMP that are populated under experimental conditions exhibit different dynamics after being excited to the higher electronic states of the cation leading to different dissociation products. These results highlight the potential usefulness of these pump-probe measurements as a tool to study conformer-specific dynamics in molecules of biological interest.

Exact-Factorization-Based Surface Hopping for Multistate Dynamics

A surface-hopping algorithm recently derived from the exact factorization approach, SHXF [Ha et al. J. Phys. Chem. Lett. 2018, 9, 1097], introduces an additional term in the electronic equation of surface hopping that couples electronic states through the quantum momentum. This term not only provides a first-principles description of decoherence, but here we show it is crucial to accurately capture nonadiabatic dynamics when more than two states are occupied at any given time. Using a vibronic coupling model of the uracil cation, we show that the lack of this term in traditional surface-hopping methods, including those with decoherence corrections, leads to failure to predict the dynamics through a three-state intersection, while SHXF performs similarly to the multiconfiguration time-dependent Hartree quantum dynamics benchmark.

Developments in ultrafast spectroscopy

Guest editors, Chantal Daniel, Luis Banares, Spiridoula Matsika and Jin Zhao, introduce this Physical Chemistry Chemical Physics themed issue.

Accurate Modeling of Excitonic Coupling in Cyanine Dye Cy3

Accurate modeling of excitonic coupling in molecules is of great importance for inferring the structures and dynamics of coupled systems. Cy3 is a cyanine dye that is widely used in molecular spectroscopy. Its well-separated excitation bands, high sensitivity to the surroundings, and the high energy transfer efficiency make it a perfect choice for excitonic coupling experiments. Many methods have been used to model the excitonic coupling in molecules with varying degrees of accuracy. The atomic transition charge model offers a high-accuracy and cost-effective way to calculating the excitonic coupling. The main focus of this work is to generate high-quality atomic transition charges that can accurately model the Cy3 dye's transition density. The transition density of the excitation of the ground to first excited state is calculated using configuration-interaction singles and time-dependent density functional theory and is benchmarked against the algebraic diagrammatic construction method. Using the transition density we derived the atomic transition charges using two approaches: Mulliken population analysis and charges fitted to the transition electrostatic potential. The quality of the charges is examined, and their ability to accurately calculate the excitonic coupling is assessed via comparison to experimental data of an artificial biscyanine construct. Theoretical comparisons to the supermolecule ab initio couplings and the widely used point-dipole approximation are also made. Results show that using the transition electrostatic potential is a reliable approach for generating the transition atomic charges. A high-quality set of charges, that can be used to model the Cy3 dye dimer excitonic coupling with high-accuracy and a reasonable computational cost, is obtained.

Electronic Structure Methods for the Description of Nonadiabatic Effects and Conical Intersections

Nonadiabatic effects are ubiquitous in photophysics and photochemistry, and therefore, many theoretical developments have been made to properly describe them. Conical intersections are central in nonadiabatic processes, as they promote efficient and ultrafast nonadiabatic transitions between electronic states. A proper theoretical description requires developments in electronic structure and specifically in methods that describe conical intersections between states and nonadiabatic coupling terms. This review focuses on the electronic structure aspects of nonadiabatic processes. We discuss the requirements of electronic structure methods to describe conical intersections and nonadiabatic couplings, how the most common excited state methods perform in describing these effects, and what the recent developments are in expanding the methodology and implementing nonadiabatic couplings.

Modeling the Ultrafast Electron Attachment Dynamics of Solvated Uracil

Electron attachment to DNA by low energy electrons can lead to DNA damage, so a fundamental understanding of how electrons interact with the components of nucleic acids in solution is an open challenge. In solution, low energy electrons can generate presolvated electrons, e_pre^-, which are efficiently scavanged by pyrimidine nucleobases to form transient negative ions, able to relax to either stable valence bound anions or undergo dissociative electron detachment or transfer to other parts of DNA/RNA leading to strand breakages. In order to understand the initial electron attachment dynamics, this paper presents a joint molecular dynamics and high-level electronic structure study into the behavior of the electronic states of the solvated uracil anion. Both the valence π* and nonvalence e_pre^- states of the solvated uracil system are studied, and the effect of the solvent environment and the geometric structure of the uracil core are uncoupled to gain insight into the physical origin of the stabilization of the solvated uracil anion. Solvent reorganization is found to play a dominant role followed by relaxation of the uracil core.

Time Resolved Photoelectron Spectroscopy as a Test of Electronic Structure and Nonadiabatic Dynamics

We compare different levels of theory for simulating excited state molecular dynamics and use time-resolved photoelectron spectroscopy measurements to benchmark the theory. We perform trajectory surface hopping simulations for uracil excited to the first bright state (ππ*) using three different levels of theory (CASSCF, MRCIS, and XMS-CASPT2) in order to understand the role of dynamical correlation in determining the excited state dynamics, with a focus on the coupling between different electronic states and internal conversion back to the ground state. These dynamics calculations are used to simulate the time-resolved photoelectron spectra. The comparison of the calculated and measured spectra allows us to draw conclusions regarding the relative insights and quantitative accuracy of the calculations at the three different levels of theory, demonstrating that detailed quantitative comparisons of time-resolved photoelectron spectra can be used to benchmark methodology.

Modeling solvation effects on absorption and fluorescence spectra of indole in aqueous solution

Modeling the optical spectra of molecules in solution presents a challenge, so it is important to understand which of the solvation effects (i.e., electrostatics, mutual polarization, and hydrogen bonding interactions between solute and solvent molecules) are crucial in reproducing the various features of the absorption and fluorescence spectra and to identify a sufficient theoretical model that accurately captures these effects with minimal computational cost. In this study, we use various implicit and explicit solvation models, such as molecular dynamics coupled with non-polarizable and polarizable force fields, as well as Car-Parrinello molecular dynamics, to model the absorption and fluorescence spectra of indole in aqueous solution. The excited states are computed using the equation of motion coupled cluster with single and double excitations combined with the effective fragment potential to represent water molecules, which we found to be a computationally efficient approach for modeling large solute-solvent clusters at a high level of quantum theory. We find that modeling mutual polarization, compared to other solvation effects, is a dominating factor for accurately reproducing the position of the peaks and spectral line shape of the absorption spectrum of indole in solution. We present an in-depth analysis of the influence that different solvation models have on the electronic excited states responsible for the features of the absorption spectra. Modeling fluorescence is more challenging since it is hard to reproduce even the correct emitting state, and force field parameters need to be re-evaluated.

Effect of dynamic correlation on the ultrafast relaxation of uracil in the gas phase

High level multi-reference non-adiabatic dynamics simulations reveal that uracil’s photoexcited S₂ state decays very quickly without any significant trapping.

Benchmarking Quantum Mechanical Methods for the Description of Charge-Transfer States in π-Stacked Nucleobases

Charge-transfer (CT) states are of special interest in photochemical research because they can facilitate chemical reactions through the rearrangement of electrons and subsequently chemical bonds in a molecular system. Of particular importance to this research is the transfer of electrons between π-stacked nucleobases in DNA because they play an important role in its photophysics and photochemistry. Computational methods are paramount for the study of CT states because of the current inability of experimental methods to easily detect such states. However, many ab-initio wavefunction-based and density functional theory (DFT) methods fail to accurately describe these CT states. Here, we benchmark how 40 different quantum mechanical methods describe the excited states of a guanine-thymine π-stacked nucleobase dimer system, both in 5'-TG-3' and 5'-GT-3' conformations. We find that the distance between the nucleobases plays a major role in the energy of the CT state and in the difference of the dipole moments between the CT and ground state. There is a larger range of values (and errors) for the energies of CT states compared to those of states localized on one nucleobase. Wavefunction-based methods have similar errors for the CT and localized valence states, while DFT methods are very sensitive to the amount of Hartree-Fock exchange. Long-range-corrected functionals with a careful balance of the Hartree-Fock exchange included can predict very accurate CT states and a balanced description with the localized states.

Stabilization of the Triplet Biradical Intermediate of 5-Methylcytosine Enhances Cyclobutane Pyrimidine Dimer (CPD) Formation in DNA

Cyclobutane pyrimidine dimer (CPD) is a photoproduct formed by two stacked pyrimidine bases through a cycloaddition reaction upon irradiation. Owing to its close association with skin cancer, the mechanism of CPD formation has been studied thoroughly. Among many aspects of CPD, its formation involving 5-methylcytosine (5mC) has been of special interest because the CPD yield is known to increase with C5-methylation of cytosine. In this work, high-level quantum mechanics/molecular mechanics (QM/MM) calculations are used to examine a previously experimentally detected pathway for CPD formation in hetero (thymine-cytosine and thymine-5mC) dipyrimidines, which is facilitated through intersystem crossing in thymine and formation of a triplet biradical intermediate. A DNA duplex model system containing a core sequence TmCG or TCG is used. The stabilization of a radical center in the biradical intermediate by the methyl group of 5mC can lead to increased CPD yield in TmCG compared with its non-methylated counterpart, TCG, thereby suggesting the existence of a new pathway of CPD formation enhanced by 5mC.

Excited state dynamics of cis,cis-1,3-cyclooctadiene: UV pump VUV probe time-resolved photoelectron spectroscopy

We present UV pump, vacuum ultraviolet probe time-resolved photoelectron spectroscopy measurements of the excited state dynamics of cis,cis-1,3-cyclooctadiene. A 4.75 eV deep UV pump pulse launches a vibrational wave packet on the first electronically excited state, and the ensuing dynamics are probed via ionization using a 7.92 eV probe pulse. The experimental results indicate that the wave packet undergoes rapid internal conversion to the ground state in under 100 fs. Comparing the measurements with electronic structure and trajectory surface hopping calculations, we are able to interpret the features in the measured photoelectron spectra in terms of ionization to several states of the molecular cation.

Excited state dynamics of cis,cis-1,3-cyclooctadiene: Non-adiabatic trajectory surface hopping

We have performed trajectory surface hopping dynamics for cis,cis-1,3-cyclooctadiene to investigate the photochemical pathways involved after being excited to the S₁ state. Our calculations reveal ultrafast decay to the ground state, facilitated by conical intersections involving distortions around the double bonds. The main distortions are localized on one double bond, involving twisting and pyramidalization of one of the carbons of that double bond (similar to ethylene), while a limited number of trajectories decay via delocalized (non-local) twisting of both double bonds. The interplay between local and non-local distortions is important in our understanding of photoisomerization in conjugated systems. The calculations show that a broad range of the conical intersection seam space is accessed during the non-adiabatic events. Several products formed on the ground state have also been observed.

The generality of the GUGA MRCI approach in COLUMBUS for treating complex quantum chemistry

The core part of the program system COLUMBUS allows highly efficient calculations using variational multireference (MR) methods in the framework of configuration interaction with single and double excitations (MR-CISD) and averaged quadratic coupled-cluster calculations (MR-AQCC), based on uncontracted sets of configurations and the graphical unitary group approach (GUGA). The availability of analytic MR-CISD and MR-AQCC energy gradients and analytic nonadiabatic couplings for MR-CISD enables exciting applications including, e.g., investigations of π-conjugated biradicaloid compounds, calculations of multitudes of excited states, development of diabatization procedures, and furnishing the electronic structure information for on-the-fly surface nonadiabatic dynamics. With fully variational uncontracted spin-orbit MRCI, COLUMBUS provides a unique possibility of performing high-level calculations on compounds containing heavy atoms up to lanthanides and actinides. Crucial for carrying out all of these calculations effectively is the availability of an efficient parallel code for the CI step. Configuration spaces of several billion in size now can be treated quite routinely on standard parallel computer clusters. Emerging developments in COLUMBUS, including the all configuration mean energy multiconfiguration self-consistent field method and the graphically contracted function method, promise to allow practically unlimited configuration space dimensions. Spin density based on the GUGA approach, analytic spin-orbit energy gradients, possibilities for local electron correlation MR calculations, development of general interfaces for nonadiabatic dynamics, and MRCI linear vibronic coupling models conclude this overview.

Role of charge transfer states into the formation of cyclobutane pyrimidine dimers in DNA

Photoinduced charge transfer between neighboring bases plays an important role in DNA. One of its important effects is shown in its ability to affect the photochemical yields of the formation of cyclobutane pyrimidine dimer (CPD) products between adjacent pyrimidine bases. In this work we examine how the energies of charge transfer states depend on the sequences of oligonucleotides using a hybrid quantum and molecular mechanics (QM/MM) methodology combined with the algebraic diagrammatic construction through a second order electronic structure method for excited states. Specifically, we examine 10 sequences with guanine being on the 5' or 3' position of two pyrimidine bases. The results show that the energies of charge transfer states are affected by the nature of the donor acceptor pair, by the distance between them, and by other electrostatic effects created by the surrounding environment.

Photochemical Formation of Cyclobutane Pyrimidine Dimers in DNA through Electron Transfer from a Flanking Base

Electron transfer (ET) to a pyrimidine base from external moieties is a common step involved in the quenching or repair of the cyclobutane pyrimidine dimer (CPD). In contrast, we present a pathway that is initiated by an ET from a flanking guanine base to a pyrimidine base, leading to the formation of a CPD. We studied a T5mCG sequence with a methylated cytosine and our results demonstrate that the pathway involves the formation of an exciplex and intersystem crossings. This pathway also provides an explanation for why the mutational hot spots are correlated with the methylated CpG sequences, which has been a significant issue in cancer research.

Conformational and electronic effects on the formation of anti cyclobutane pyrimidine dimers in G-quadruplex structures

Cyclobutane pyrimidine dimers (CPDs) are the most commonly formed photochemical products when nucleic acids interact with UV radiation. In duplex DNA, the relative inflexible structure allows for only the cis, syn CPD isomer to be formed. G-quadruplex structures, however, have loops that are more flexible and allow for different orientations of the bases to interact. As a result, the highly unusual formation of an anti CPD has been observed in these structures. Due to the close proximity between two opposing loops containing the TTA sequence in two G-quadruplex structures (called "form-3" and "basket"), a high yield of anti CPD formation was expected in these structures. However, while significant yields of anti CPDs are observed in form-3, the anti CPD is hardly observed in the basket structure. To account for this inconsistency, we examine the process of anti CPD formation in form-3 and basket structures using simulations at the atomistic level. Here, we consider the conformational effect using MD simulations, which show whether the formation of the anti CPD is structurally feasible. Quantum mechanical/molecular mechanical (QM/MM) calculations of excited states are also used to consider the electronic effect by an adjacent guanine base which can quench the formation of the anti CPD through charge transfer (CT). Our results are in qualitative agreement with the experimental results, predicting a significant yield of the anti CPD in the form-3 structure and a negligible yield in the basket structure, while they also predict the formation of the cis, syn CPD between two opposing loops in form-3. Most importantly, our simulation results show that the yields of the anti CPD in the G-quadruplex are affected significantly by both conformational and electronic effects.

Photophysical properties of pyrrolocytosine, a cytosine fluorescent base analogue

The photophysical behavior of pyrrolocytosine (PC), a fluorescent base analogue of cytosine, has been investigated using theoretical approaches. The similarities between the PC and cytosine structures allow PC to maintain the pseudo-Watson-Crick base-pairing arrangement with guanine. Cytosine, similar to the other natural nucleobases, is practically non-fluorescent, because of ultrafast radiationless decay occurring through conical intersections. PC displays a much higher fluorescence quantum yield than cytosine, making it an effective fluorescent marker to study the structure, function, and dynamics of DNA/RNA complexes. Similar to 2-aminopurine, a constitutional isomer of adenine that base-pairs with thymine, PC's fluorescence is quenched when it is incorporated into a dinucleotide or a trinucleotide. In this work we examine the photophysical properties of isolated PC, microhydrated PC, as well as, complexes where PC is either base-stacked or hydrogen-bonded with guanine. Our results indicate that hydration affects the radiationless decay pathways in PC by destabilizing conical intersections. The calculations of dimers and trimers show that the radiative decay is affected by π stacking, while the presence of charge transfer states between PC and guanine may contribute to radiationless decay.

Core-excited and shape resonances of uracil

Attachment of an electron to nucleobases leads to metastable anion states called resonances. There are two types of electronic resonances present in the nucleobases. Shape resonances occur when the electron is attached to one of the previously unoccupied π* orbitals of the base. An electron can also be attached to an electronically excited state leading to core-excited or Feshbach resonances. In this work we present both types of resonances of uracil, a nucleobase present in RNA. Both the positions and widths of the resonances have been calculated using a stabilization method coupled with high level electronic structure methods. Core-excited resonances which are accessed with electrons of energy >4.6 eV are expected to play an important role in the dissociative electron attachment of uracil. Mixing between configurations corresponding to shape and core-excited resonances is also present which complicates the theoretical treatment of this system and necessitates multiconfigurational approaches for a proper description.

Electron-induced origins of prebiotic building blocks of sugars: mechanism of self-reactions of a methanol anion dimer

Reactions of methanol dimers in interstellar medium driven by low energy irradiation may lead to prebiotic precursors.

Mechanistic insights into photoinduced damage of DNA and RNA nucleobases in the gas phase and in bulk solution

The mechanistic details of well-known photohydrate lesions are explored using state-of-the-art computational methods.

Substituent Effects on the Absorption and Fluorescence Properties of Anthracene

Substitution can be used to efficiently tune the photophysical properties of chromophores. In this study, we examine the effect of substituents on the absorption and fluorescence properties of anthracene. The effects of mono-, di-, and tetrasubstitution of electron-donating and -withdrawing functional groups were explored. In addition, the influence of a donor-acceptor substituent pair and the position of substitution were investigated. Eleven functional groups were varied on positions 1, 2, and 9 of anthracene, and on position 6 of 2-methoxyanthracene and 2-carboxyanthracene. Moreover, the donor-acceptor pair NH₂/CO₂H was added on different positions of anthracene for additional studies of doubly substituted anthracenes. Finally, we looked into quadruple substitutions on positions 1,4,5,8 and 2,3,6,7. Vertical excitation energies and oscillator strengths were computed using density functional theory with the hybrid CAM-B3LYP functional and 6-311G(d) basis set. Correlations between the excitation energies or oscillator strengths of the low-lying bright L_a state and the Hammett sigma parameter, σ_p⁺, of the substituents were examined. The energy is red-shifted for all cases of substitution. Oscillator strengths increase when substituents are placed along the direction of the transition dipole moment of the bright L_a excited state. Substitution of long chain conjugated groups significantly increases the oscillator strength in comparison to the cases for other substituents. In addition, the results of quadruply substituted geometries reveal symmetric substitution at the 1,4,5,8 positions significantly increases the oscillator strength and can lower the band gap compared to that of the unsubstituted anthracene molecule by up to 0.5 eV.