On the propensity of formation of cyclobutane dimers in face-to-face and face-to-back uracil stacks in solution.

UV irradiation of RNA leads to the formation of intra- and inter-strand crosslinks of cyclobutane type. Despite the importance of this reaction, relatively little is known about how the mutual orientation of the two bases affects the outcome of the reaction. Here we report a comparative nonadiabatic molecular dynamics study of face-to-back (F2B) and face-to-face (F2F) stacked uracil-water clusters. The computations were performed using the second-order algebraic-diagrammatic-construction (ADC(2)) method. We found that F2B stacked uracil-water clusters either relax non-reactively to the ground state by an ethylenic twist around the CC bond or remain in the lowest nπ* state in which the two bases gradually move away from each other. This finding is consistent with the low propensity for the formation of intra-strand cyclobutane dimers between adjacent RNA bases. On the contrary, in F2F stacked uracil-water clusters, in addition to non-reactive deactivation, we found a pro-reactive deactivation pathway, which may lead to the formation of cyclobutane uracil dimers in the electronic ground state. On a qualitative level, the observed photodynamics of F2F stacked uracil-water clusters explains the greater propensity of RNA to form inter-strand cyclobutane-type crosslinks.

Proton leap: shuttling of protons onto benzonitrile.

The detailed description of chemical transformations in the interstellar medium allows deciphering the origin of a number of small and medium - sized organic molecules. We present density functional theory analysis of proton transfer from the trihydrogen cation and the ethenium cation to benzonitrile, a recently discovered species in the Taurus Molecular Cloud 1. Detailed energy transformations along the reaction paths were analyzed using the interacting quantum atoms methodology, which elucidated how the proton carrier influences the lightness to deliver the proton to benzonitrile's nitrogen atom. The proton carriers' deformation energy represents the largest destabilizing effect, whereas a proton's promotion energy, the benzonitrile-proton Coulomb attraction, as well as non-classical benzonitrile-proton and carrier-proton interaction are the dominant stabilizing energy components. As two ion-molecule reactions proceed without energy barriers, rate constants were estimated using the classical capture theory and were found to be an order of magnitude larger for the reaction with the trihydrogen cation compared to that with the ethenium cation (∼10-8 and 10-9 cm3 s-1, respectively). These results were obtained both with quantum chemical and ab initio molecular dynamics simulations (the latter performed at 10 K and 100 K), confirming that up to 100 K both systems choose energetically undemanding routes by tracking the corresponding minimum energy paths. A concept of a turning point is introduced, which is an equivalent to the transition state in barrierless reactions.

Self-assembly of rylene-decorated guanine ribbons on graphene surface for optoelectronic applications: a theoretical study.

We are witnessing a change of paradigm from the conventional top-down to the bottom-up fabrication of nanodevices and particularly optoelectronic devices. A promising example of the bottom-up approach is self-assembling of molecules into layers with predictable and reproducible structural, electronic and optical properties. Nucleobases possess extraordinary ability to self-assembly into one-, two-, and three-dimensional structures. Optical properties of nucleotides are not suitable for wider application to optoelectronics and photovoltaics due to their large optical band gap, which is in contrast to rylene-based dyes that have been intensively investigated in organic optoelectronics. However, these lack the self-assembly capability of nucleobases. Combinations of covalently decorated guanine molecules with rylene type chromophores present 'the best of the both worlds'. Due to the large size of such compounds and its flexible nature their self-assemblies have not been fully understood yet. Here, we use a theoretical approach to study the structural, energetic and optical properties of rylene-based dye decorated guanine (GPDI), as self-assembled on a graphene sheet. Particularly we utilize the density-functional based tight-binding method to study atomic structure of these systems including the potential energy surface of GPDI and stability and organization of single- and multilayered GPDIs on graphene sheet. Using density-functional theory (DFT) we employ the energy decomposition analysis to gain a deeper insight into the contributions of different moieties to stability of GPDI films. Using time dependent DFT we analyze optical properties of these systems. We find that atomically thin films consisting of only a few molecular layers with large surface areas are more favorable than isolated thick islands. Our study of excited states indicates existence of charge separated states similar to ones found in the well-studied hydrogen bonded organic frameworks. The self-assembly characterized with a large homogeneous coverage and long-living charge-separated states provide the great potential for optoelectronic applications.

The significance of the metal cation in guanine-quartet - metalloporphyrin complexes.

The planarity and the appropriate size of the porphyrin ring make porphyrin derivatives ideal ligands for stacking to guanine quartets and they could thus be used as anti-cancer drugs. In this contribution we analyzed complexes of a guanine quartet with a porphyrin molecule, magnesium porphyrin and calcium porphyrin. As magnesium and calcium ions are located in the center and above the porphyrin ring, respectively, the two metalloporphyrins are expected to have different impacts on the target. The optimized structures of the three systems revealed geometrical changes in the guanine quartet upon complexation: while stacking of porphyrin and magnesium porphyrin does not induce significant changes, calcium porphyrin considerably distorts the quartet's structure, which has significant implications for the binding properties among guanine molecules. Ab initio molecular dynamics simulations revealed that the systems perform small fluctuations around the equilibrium structures. The largest atom displacements are performed by the calcium ion. The interacting quantum atoms methodology enabled analysis of the binding properties in the studied complexes. Interestingly, although the proximity of the calcium ion is responsible for the quartet's pronounced deformation and weakening of guanine-guanine binding, it also enables stronger binding of the metal ion to the quartet, resulting in a more stable complex. These results imply that metalloporphyrin-like ligands with out-of-plane central ions might represent promising drug candidates in anti-tumor treatment.

Simulation of UV absorption spectra and relaxation dynamics of uracil and uracil-water clusters.

Despite many studies, the mechanisms of nonradiative relaxation of uracil in the gas phase and in aqueous solution are still not fully resolved. Here we combine theoretical UV absorption spectroscopy with nonadiabatic dynamics simulations to identify the photophysical mechanisms that can give rise to experimentally observed decay time constants. We first compute and theoretically assign the electronic spectra of uracil using the second-order algebraic-diagrammatic-construction (ADC(2)) method. The obtained electronic states, their energy differences and state-specific solvation effects are the prerequisites for understanding the photodynamics. We then use nonadiabatic trajectory-surface-hopping dynamics simulations to investigate the photoinduced dynamics of uracil and uracil-water clusters. In contrast to previous studies, we found that a single mechanism - the ethylenic twist around the C[double bond, length as m-dash]C bond - is responsible for the ultrafast component of the nonradiative decay, both in the gas phase and in solution. Very good agreement with the experimentally determined ultrashort decay time constants is obtained.

Unraveling the mechanism of biomimetic hydrogen fuel production - a first principles molecular dynamics study.

The Fe2(bdt)(CO)6 [bdt = benzenedithiolato] complex, a synthetic mimic of the [FeFe] hydrogenase enzyme can electrochemically convert protons into molecular hydrogen. Molecular understanding of the cascade of reaction steps is important for the design of more efficient catalysts. In this study, we investigate the reaction mechanism of the hydrogen production catalysis in explicit solution of acetonitrile using first principles molecular dynamics simulations. We have characterized all reduction and protonation intermediates taking part in the catalytic cycle. Free energy surfaces of the activated reaction steps are calculated using metadynamics. We find that the second protonation leading to molecular hydrogen formation is the rate limiting step. Direct protonation of the bridging hydride by a proton from the solution to form H2 is the most favorable reaction pathway. However, also a bdt sulfur atom can become protonated, leading to a possible proton trap state that reduces the catalytic efficiency. Our calculations validate the ECEC mechanism proposed using cyclic voltammetry.

Modulating Excited Charge-Transfer States of G-Quartet Self-Assemblies by Earth Alkaline Cations and Hydration.

Guanine self-assemblies are promising supramolecular platforms for optoelectronic applications. The study (Hua et al., J. Phys. Chem. C 2012, 116, 14,682-14,689) reported that alkaline cations cannot modulate the electronic absorption spectrum of G-quadruplexes, although a cation effect is observable during electronic relaxation due to different mobility of Na+ and K+ cations. In this work, we theoretically examined whether divalent Mg2+ and Ca2+ cations and hydration might shift excited charge-transfer states of a cation-templated stacked G-quartet to the absorption red tail. Our results showed that earth alkaline cations blue-shifted nπ* states and stabilized charge-transfer ππ* states relative to those of complexes with alkaline cations, although the number of charge-separation states was not significantly modified. Earth alkaline cations were not able to considerably increase the amount of charge-transfer states below the Lb excitonic states. Hydration shifted charge-transfer states of the Na+-coordinated G-octet to the absorption red tail, although this part of the spectrum was still dominated by monomer-like excitations. We found G-octet electron detachment states at low excitation energies in aqueous solution. These states were distributed over a broad range of excitation energies and could be responsible for oxidative damage observed upon UV irradiation of biological G-quadruplexes.

Elucidating Solvent Effects on Strong Intramolecular Hydrogen Bond: DFT-MD Study of Dibenzoylmethane in Methanol Solution.

The dynamic aspect of solvation plays a crucial role in determining properties of strong intramolecular hydrogen bonds since solvent fluctuations modify instantaneous hydrogen-bonded proton transfer barriers. Previous studies pointed out that solvent-solute interactions in the first solvation shell govern the position of the proton but the ability of the electric field due to other solvent molecules to localize the proton remains an important issue. In this work, we examine the structure of the O-H⋅⋅⋅O intramolecular hydrogen bond of dibenzoylmethane in methanol solution by employing density functional theory-based molecular dynamics and quantum chemical calculations. Our computations showed that homogeneous electric fields with intensities corresponding to those found in polar solvents are able to considerably alter the proton transfer barrier height in the gas phase. In methanol solution, the proton position is correlated with the difference in electrostatic potentials on the oxygen atoms of dibenzoylmethane even when dibenzoylmethane-methanol hydrogen bonding is lacking. On a timescale of our simulation, the hydrogen bonding and solvent electrostatics tend to localize the proton on different oxygen atoms. These findings provide an insight into the importance of the solvent electric field on the structure of a strong intramolecular hydrogen bond.

The UVA response of enolic dibenzoylmethane: beyond the static approach.

Enolic dibenzoylmethane is used in cosmetic sunscreens as a UVA filter because it strongly absorbs radiation around 340 nm. Assessing the absorption properties solely on the basis of the vertical excitation spectrum at the minimum of the potential energy surface leads to the conclusion that the nπ* state is not initially photoexcited. Since this molecule exhibits large changes in structure due to nuclear thermal and quantum fluctuations, it is not sufficient to consider one molecular configuration but an ensemble of configurations. In this work, we simulate its UVA response by employing the DFT/MRCI method in conjunction with configurations sampled from density functional theory-based classical and path integral molecular dynamics as well as by computing Franck-Condon factors. Our findings indicate that thermal and nuclear quantum fluctuations symmetrically broaden the excited states' absorption within the semi-classical approximation and thus it is necessary to include vibronic effects in order to correctly reproduce the experimental spectrum. The absorption is largely dominated by the ππ* state but there is a minor contribution from the nπ* state, contrary to the static result. The crossing between these two states occurs during the intramolecular proton transfer. This knowledge is of importance for studying photorelaxation mechanisms of dibenzoylmethane and other ß-diketone compounds.

Influence of the electron donor properties of hypericin on its sensitizing ability in DSSCs.

Rising demands for renewable energy sources have led to the development of dye sensitized solar cells. It is a challenge to find a good and low cost sensitizer, which has a low environmental impact. In this work, we conducted spectroscopic and electrochemical experiments, as well as quantum-chemical calculations of the natural pigment hypericin, in order to provide insight into its sensitizing efficiency. To this end, three identical cells were made and characterized. Although this pigment exhibited good adsorption onto a semiconductor surface, a high molar absorption coefficient (43 700 L mol-1 cm-1) and favorable alignment of energy levels and provided a long lifetime of electrons (17.8 ms) in the TiO2 photoanode, it was found that the efficiency of hypericin-sensitized solar cells was very low, only 0.0245%. We suggest that this inefficiency originated from a low injection of electrons into the conduction band of TiO2. This conclusion is supported by the density functional theory calculations which revealed a low electron density in the anchoring groups of electronically excited hypericin. The results of this work could be valuable not only in the photovoltaic aspect, but also for application of hypericin in medicine in photodynamic therapy.

When hydroquinone meets methoxy radical: Hydrogen abstraction reaction from the viewpoint of interacting quantum atoms.

Interacting Quantum Atoms methodology is used for a detailed analysis of hydrogen abstraction reaction from hydroquinone by methoxy radical. Two pathways are analyzed, which differ in the orientation of the reactants at the corresponding transition states. Although the discrepancy between the two barriers amounts to only 2 kJ/mol, which implies that the two pathways are of comparable probability, the extent of intra-atomic and inter-atomic energy changes differs considerably. We thus demonstrated that Interacting Quantum Atoms procedure can be applied to unravel distinct energy transfer routes in seemingly similar mechanisms. Identification of energy components with the greatest contribution to the variation of the overall energy (intra-atomic and inter-atomic terms that involve hydroquinone's oxygen and the carbon atom covalently bound to it, the transferring hydrogen and methoxy radical's oxygen), is performed using the Relative energy gradient method. Additionally, the Interacting Quantum Fragments approach shed light on the nature of dominant interactions among selected fragments: both Coulomb and exchange-correlation contributions are of comparable importance when considering interactions of the transferring hydrogen atom with all other atoms, whereas the exchange-correlation term dominates interaction between methoxy radical's methyl group and hydroquinone's aromatic ring. This study represents one of the first applications of Interacting Quantum Fragments approach on first order saddle points. © 2018 Wiley Periodicals, Inc.

Puzzle of the Intramolecular Hydrogen Bond of Dibenzoylmethane Resolved by Molecular Dynamics Simulations.

The enol form of dibenzoylmethane has been the subject of many experimental and theoretical studies, yet the symmetry and the spectral response of the OHO intramolecular hydrogen bond remains mysterious due to conflicting assignments. In order to qualitatively understand the complex proton dynamics, it is necessary to probe the neighborhood of stationary points on the potential energy landscape. Here, we employ density functional theory-based molecular dynamics (DFT-MD) simulations to sample the coupling between the intermolecular proton transfer and all other molecular modes. To account for the quantum nature of the proton motion, we employ the path integral formalism within the DFT-MD simulations. Our results reveal that the hydrogen-bonded proton is delocalized between two oxygen atoms with sightly higher probability to be observed in the asymmetric than the symmetric position. The simulated infrared spectrum is found to be in a reasonably good agreement with the experimental spectrum. The computed νOH band is remarkably broad and centered around 2640 cm-1. The origin of the discrepancy between the simulated and experimental intensities of the νOH band is discussed.

A theoretical study of low-lying singlet and triplet excited states of quinazoline, quinoxaline and phthalazine: insight into triplet formation.

Quinazoline, quinoxaline and phthalazine are nitrogen containing heterocyclic aromatic molecules which belong to the class diazanaphthalenes. These isomers have low-lying nπ* and naphthalene-like ππ* states that interact via spin-orbit coupling. In this contribution, we study their structure and electronic states by means of a coupled-cluster method. The computed properties are compared to those of cinnoline which were obtained in our previous study [Etinski et al., Phys. Chem. Chem. Phys., 2014, 16, 4740]. The excited state features of these isomers are dependent on the position of the nitrogen atoms. We find that quinazoline and quinoxaline exhibit similarities in the ordering and character of the excited states. In contrast, a marked difference in the electronic and geometric structures of the lowest excited triplet states of cinnoline and phthalazine is noticed, although both are orthodiazanaphthalenes. Our findings suggest that the S1 [radiolysis arrow - arrow with voltage kink] T1 channel is responsible for the rapid intersystem crossing in quinazoline and quinoxaline, whereas the S1 [radiolysis arrow - arrow with voltage kink] T2 pathway is active in phthalazine.

A new insight into the photochemistry of avobenzone in gas phase and acetonitrile from ab initio calculations.

Avobenzone (4-tert-butyl-4'-methoxydibenzoylmethane, AB) is one of the most widely used filters in sunscreens for skin photoprotection in the UVA band. The photochemistry of AB includes keto-enol tautomerization, cis-trans isomerization, rotation about the single bond and α bond cleavages of carbonyl groups. In this contribution we study chelated and non-chelated enol, rotamers Z and E, and keto tautomers of AB in the ground and excited states in gas phase and acetonitrile by means of a coupled cluster method. Our findings suggest that torsion around the double C2-C3 bond of photoexcited chelated enol leads to internal conversion to the ground state and formation of rotamer E. In addition, opening of the chelated hydrogen ring by torsion of the hydroxyl group creates non-chelated enol. The possible mechanisms of rotamer Z formation are discussed. The solvent dependent photolability is related to the relative order of the lowest triplet ππ* and nπ* states of the keto tautomer.

Stability and Anharmonic N-H Stretching Frequencies of 1-Methylthymine Dimers: Hydrogen Bonding versus π-Stacking.

Stability of three hydrogen-bonded and six stacked 1-methylthymine (1 mT) dimers was studied with the DFT-D3 method at various temperatures. It was demonstrated that the stacked dimers are slightly less stable than the hydrogen-bonded counterparts. Existence of T-shaped dimers is addressed. Anharmonic couplings that involve N-H stretching modes of the nine species are studied. Surprisingly, we find that N-H stretching modes of the two 1 mT molecules are significantly coupled in four stacked dimers. The presented results shed light on existence of strong mode couplings between the two N-H stretching modes in stacked aromatic species. Our calculations support the proposal ( J. Phys. Chem. A 2011 , 115 , 9429 - 9439 ) that presence of several dimers is responsible for appearance of wide and structured bands in 1 mT homodimers' jet-cooled spectra above 2900 cm(-1).

Using Density Functional Theory To Study Neutral and Ionized Stacked Thymine Dimers.

Stacking interactions in thymine dimers are studied with density functional theory. According to our calculations, six dimers of comparable stability can be prepared at low temperature, but dimerization is impossible at room temperature due to the large entropy contribution that accompanies it. Analysis of vibrational anharmonic coupling terms shows that each of the dimers exhibits distinct vibrational dynamics. Properties of electron density in the intermolecular region are used to analyze neutral stacked species and their ionized forms. Bond paths and critical points in the intermolecular region are identified, but a simple relationship between binding energy and total electron density in the intermolecular critical points could not be found due to an uneven electron distribution in the binding region. The reduced density gradient was confirmed to be a useful tool for analysis of weak stacking interactions. Those interactions also affect vertical and adiabatic ionization energies, which are computed to be slightly lower for the dimers compared to the monomer.

Intersystem crossing rates of S1 state keto-amino cytosine at low excess energy.

The amino-keto tautomer of supersonic jet-cooled cytosine undergoes intersystem crossing (ISC) from the v = 0 and low-lying vibronic levels of its S1((1)ππ(∗)) state. We investigate these ISC rates experimentally and theoretically as a function of S1 state vibrational excess energy Eexc. The S1 vibronic levels are pumped with a ∼5 ns UV laser, the S1 and triplet state ion signals are separated by prompt or delayed ionization with a second UV laser pulse. After correcting the raw ISC yields for the relative S1 and T1 ionization cross sections, we obtain energy dependent ISC quantum yields QISC (corr)=1%-5%. These are combined with previously measured vibronic state-specific decay rates, giving ISC rates kISC = 0.4-1.5 ⋅ 10(9) s(-1), the corresponding S1⇝S0 internal conversion (IC) rates are 30-100 times larger. Theoretical ISC rates are computed using SCS-CC2 methods, which predict rapid ISC from the S1; v = 0 state with kISC = 3 ⋅ 10(9) s(-1) to the T1((3)ππ(∗)) triplet state. The surprisingly high rate of this El Sayed-forbidden transition is caused by a substantial admixture of (1)nOπ(∗) character into the S1((1)ππ(∗)) wave function at its non-planar minimum geometry. The combination of experiment and theory implies that (1) below Eexc = 550 cm(-1) in the S1 state, S1⇝S0 internal conversion dominates the nonradiative decay with kIC ≥ 2 ⋅ 10(10) s(-1), (2) the calculated S1⇝T1 ((1)ππ(∗)⇝(3)ππ(∗)) ISC rate is in good agreement with experiment, (3) being El-Sayed forbidden, the S1⇝T1 ISC is moderately fast (kISC = 3 ⋅ 10(9) s(-1)), and not ultrafast, as claimed by other calculations, and (4) at Eexc ∼ 550 cm(-1) the IC rate increases by ∼50 times, probably by accessing the lowest conical intersection (the C5-twist CI) and thereby effectively switching off the ISC decay channels.

Thermal and solvent effects on the triplet formation in cinnoline.

Cinnoline (1,2-diazanaphthalene) is of particular interest among the diazanaphthalenes. Its triplet quantum yield upon photoexcitation depends strongly on the temperature and the solvent environment. At the beginning of this study, the properties of the lowest triplet electronic state were not understood either. To elucidate the photophysics of cinnoline, we implemented algorithms based on the time-dependent approach for calculating intersystem crossing rates and one-photon spectra of thermally equilibrated vibronic levels. Our quantum chemical investigations reveal that the triplet formation in hydrocarbon solutions at low temperatures is an El-Sayed forbidden process. At higher temperatures and in hydroxylic solutions an additional El-Sayed allowed channel opens up, increasing the intersystem crossing rate substantially. Furthermore, we have solved the old puzzle concerning the character of the lowest triplet state of cinnoline. In the gas phase the electronic structure has mainly nπ* character with additional contributions from ππ* configurations since the nuclear arrangement in the pyridazine ring is not planar. In hydroxylic solvents, the electronic structure of the T1 state is altered. The simulation of the triplet emission shows that the experimentally observed phosphorescence of cinnoline in ethanol most certainly stems from the (3)(ππ*) emission.

Reverse intersystem crossing in rhodamines by near-infrared laser excitation.

The population of the long-lived first excited triplet state (T1) of a fluorescence dye represents a major limitation in single-molecule spectroscopy. Reverse intersystem crossing (ReISC) is one of the processes that may prevent considerable loss of luminescence. In the present quantum chemical study we have analyzed rhodamine A in aqueous environment. The T2 ⇝ S1 and T3 ⇝ S2 ReISC channels are predicted to be viable. The rate constant computed for the former channel is ≈2 × 10(6) s(-1). Hence, an excitation with suitable wavelength to one of the triplets should help repopulate the optically bright singlet state S1.

Time-dependent approach to spin-vibronic coupling: implementation and assessment.

In this work, we present the generalization of a time-dependent method for the calculation of intersystem crossing (ISC) rates in the Condon approximation. When ISC takes place between electronic states with the same orbital type, i.e., when the transition is forbidden according to the El-Sayed rules, it is necessary to go beyond the Condon approximation. Similar to the Herzberg-Teller expansion of the vibronic interaction, the electronic spin-orbit matrix elements are assumed to depend linearly on the nuclear coordinates. The ISC rate is then a sum of three contributions: a direct, mixed direct-vibronic, and vibronic term. The method, presented in this work, is based on the generating function formalism and the multi-mode harmonic oscillator approximation. In addition to the zero-temperature case, we implemented formulae for finite-temperature conditions assuming a Boltzmann population of vibrational levels in the initial state. Tests have been carried out for a variety of molecules for which literature data were available. We computed vibronic one-photon spectra of free-base porphyrin and free-base chlorin and calculated ISC rates for xanthone, thioxanthone, thionine, as well as free-base porphyrin and found excellent agreement with previous results. Quantitative rates for triplet formation in rhodamine A have been determined theoretically for the first time. We find the S1↝ T2 channel to be the major source of triplet rhodamine formation in the gas phase.