Searching for Conical Intersections of Potential Energy Surfaces with the ONIOM Method: Application to Previtamin D

Galván I, Rivalta I, Aquilante F, Garavelli M, Lindh R, Segarra-Martí J. Characterizing Conical Intersections in DNA/RNA Nucleobases with Multiconfigurational Wave Functions of Varying Active Space Size

We characterize the photochemically relevant conical intersections between the lowest-lying accessible electronic excited states of the different DNA/RNA nucleobases using Cholesky decomposition-based complete active space self-consistent field (CASSCF) algorithms. We benchmark two different basis set contractions and several active spaces for each nucleobase and conical intersection type, measuring for the first time how active space size affects conical intersection topographies in these systems and the potential implications these may have toward their description of photoinduced phenomena. Our results show that conical intersection topographies are highly sensitive to the electron correlation included in the model: by changing the amount (and type) of correlated orbitals, conical intersection topographies vastly change, and the changes observed do not follow any converging pattern toward the topographies obtained with the largest and most correlated active spaces. Comparison across systems shows analogous topographies for almost all intersections mediating population transfer to the dark 1nO/Nπ* states, while no similarities are observed for the "ethylene-like" conical intersection ascribed to mediate the ultrafast decay component to the ground state in all DNA/RNA nucleobases. Basis set size seems to have a minor effect, appearing to be relevant only for purine-based derivatives. We rule out structural changes as a key factor in classifying the different conical intersections, which display almost identical geometries across active space and basis set change, and we highlight instead the importance of correctly describing the electronic states involved at these crossing points. Our work shows that careful active space selection is essential to accurately describe conical intersection topographies and therefore to adequately account for their active role in molecular photochemistry.

The carbonyl-lock mechanism underlying non-aromatic fluorescence in biological matter

Challenging the basis of our chemical intuition, recent experimental evidence reveals the presence of a new type of intrinsic fluorescence in biomolecules that exists even in the absence of aromatic or electronically conjugated chemical compounds. The origin of this phenomenon has remained elusive so far. In the present study, we identify a mechanism underlying this new type of fluorescence in different biological aggregates. By employing non-adiabatic ab initio molecular dynamics simulations combined with a data-driven approach, we characterize the typical ultrafast non-radiative relaxation pathways active in non-fluorescent peptides. We show that the key vibrational mode for the non-radiative decay towards the ground state is the carbonyl elongation. Non-aromatic fluorescence appears to emerge from blocking this mode with strong local interactions such as hydrogen bonds. While we cannot rule out the existence of alternative non-aromatic fluorescence mechanisms in other systems, we demonstrate that this carbonyl-lock mechanism for trapping the excited state leads to the fluorescence yield increase observed experimentally, and set the stage for design principles to realize novel non-invasive biocompatible probes with applications in bioimaging, sensing, and biophotonics.

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.

Photoinduced Forward and Backward Pedalo-Type Motion of a Molecular Switch

Photoresponsive molecular switches enable spatial and temporal control of molecular processes and are therefore crucial for the development of smart functional materials. Because the light-induced dynamics of these switching units are at the core of the resulting functionality, a detailed insight into their structural time evolution is fundamental for molecular embedding. Here, we performed a hybrid quantum mechanics (CASPT2 and TDDFT)/molecular mechanics (QM/MM) study to elucidate the photodynamics of an azodicarboxamide-based molecular switch, which is a promising candidate for implementation in highly dense environments such as polymers. In particular, we report a detailed picture of the molecular motion at the atomic level based on a relevant number of excited-state trajectories. We show that the azodicarboxamide-based molecular switch undergoes both a forward and backward pedalo-type motion upon excitation. Trans-cis photoisomerization on the other hand, which is well-known to occur for other azo-based chromophores, is shown to be a negligible pathway. By validating the volume-conserving pedalo-type motion, we provide a rational basis for the design of novel types of photoresponsive functional materials in which the active component must operate in a confined space.

Previtamin D: Z-E photoisomerization via a Hula-twist conical intersection

On photoisomerization of previtamin D - a steroid Z-triene - produced in situ by ring opening of 7-dehydrocholesterol in a cold matrix, it was found in A. M. Müller et al. [Angew. Chem., Int. Ed., 1998, 37, 505-507] that the product (tachysterol) had rotated not only its central double bond but also an adjacent single bond. This is called a Hula twist (HT) due to the alternative description, in which it is just one central CH group that rotates. It was pointed out that the results directly support the calculated molecular structure at a conical intersection, which mediates the Z-E isomerization of polyenes. With a more sophisticated technique, Saltiel et al. (J. Phys. Chem. Lett., 2013, 4, 716-721) confirmed this tachysterol rotamer as the main product but found two additional conformers. They believed to have seen also three previtamin D conformers, suggested to be a result of hot-ground-state reactions from the primary rotamer, and interpreted all tachysterol products to be a result of a double-bond twist (DBT), not a HT. On the basis of published circular dichroism data and consideration of other reactions, it is here shown that under these conditions hot-ground-state reactions are unimportant or even negligible and that there is practically only a single conformer of previtamin D after ring opening. All products can be easily understood on the basis of an HT-type conical intersection, which is thus further supported. Invoking a published pretwist model even rationalizes product ratios. The two twists in HT are concerted. Furthermore HT is fully consistent with the NEER principle (nonequilibration of excited rotamers) and even offers additional possibilities for conformer control.

Ultrafast non-adiabatic dynamics of excited diphenylmethyl bromide elucidated by quantum dynamics and semi-classical on-the-fly dynamics

Carbocations and carboradicals are key intermediates in organic chemistry. Typically UV laser excitation is used to induce homolytical or heterolytical bond cleavage in suitable precursor molecules. Of special interest hereby are diphenylmethyl compounds (Ph2CH-X) with X = Cl, Br as a leaving group as they form diphenylmethyl radicals (Ph2CH˙) and cations (Ph2CH+) within a femtosecond time scale in polar solvents. In this work, we build on our methodology developed for the chlorine case and investigate the photodissociation reaction of Ph2CH-Br by state-of-the-art theoretical methods. On the one hand, we employ specially adapted reactive coordinates for a grid-based wave packet dynamics in reduced dimensionality using the Wilson G-matrix ansatz for the kinetic part of the Hamiltonian. On the other hand, we use full-dimensional semiclassical on-the-fly dynamics with Tully's fewest switches surface hopping routine for comparison. We apply both methods to explain remarkable differences in experimental transient absorption measurements for Cl or Br as the leaving group. The wave packet motion, visible only for the bromine leaving group, can be related to the crucial role of the central carbon atom, which undergoes rehybridization from sp3 to sp2 during the photoinduced bond cleavage. Comparable features are the two consecutive conical intersections near the Franck-Condon region controlling the product splitting to Ph2CH˙/Br˙ and Ph2CH+/Br- as well as the difference in delay time for the respective product formation.

Point charge embedding for ONIOM excited states calculations

Hybrid quantum mechanical methods can assist in the interpretation and prediction of the electronic spectra of large molecular structures. In this work, we study the performance of the ONIOM (Our own N-layered Integrated molecular Orbital molecular Mechanics) hybrid method for the calculation of transition energies and oscillator strengths by embedding the core region in a field of fixed point charges. These charges introduce polarization effects from the substituent groups to the core region. We test various charge definitions, with particular attention to the issue of overpolarization near the boundary between layers. To minimize this issue, we fit the charges on the electrostatic potential of the entire structure in the presence of the link atoms used to cap dangling bonds. We propose two constrained fitting strategies: one that produces an average set of charges common to both model system calculations, EE(L1), and one that produces two separate sets of embedding charges, EE(L2). The results from our tests show that indeed electronic embedding with constrained-fitted charges tends to improve the performance of ONIOM compared to non-embedded calculations. However, the EE(L2) charges work best for transition energies, and the EE(L1) charges work best for oscillator strengths. This may be an indication that fixed point charges do not have enough flexibility to adapt to each system, and other effects (e.g., polarization of the embedding field) may be necessary.

Mechanism of ultrafast non-reactive deactivation of the retinal chromophore in non-polar solvents

Counterion sensitive photodynamics of the retinal chromophore in solution.

Molecular features in complex environment: Cooperative team players during excited state bond cleavage

Photoinduced bond cleavage is often employed for the generation of highly reactive carbocations in solution and to study their reactivity. Diphenylmethyl derivatives are prominent precursors in polar and moderately polar solvents like acetonitrile or dichloromethane. Depending on the leaving group, the photoinduced bond cleavage occurs on a femtosecond to picosecond time scale and typically leads to two distinguishable products, the desired diphenylmethyl cations (Ph2CH(+)) and as competing by-product the diphenylmethyl radicals ([Formula: see text]). Conical intersections are the chief suspects for such ultrafast branching processes. We show for two typical examples, the neutral diphenylmethylchloride (Ph2CH-Cl) and the charged diphenylmethyltriphenylphosphonium ions ([Formula: see text]) that the role of the conical intersections depends not only on the molecular features but also on the interplay with the environment. It turns out to differ significantly for both precursors. Our analysis is based on quantum chemical and quantum dynamical calculations. For comparison, we use ultrafast transient absorption measurements. In case of Ph2CH-Cl, we can directly connect the observed signals to two early three-state and two-state conical intersections, both close to the Franck-Condon region. In case of the [Formula: see text], dynamic solvent effects are needed to activate a two-state conical intersection at larger distances along the reaction coordinate.

Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases

The photophysics and photochemistry of DNA is of great importance due to the potential damage of the genetic code by UV light. Quantum mechanical studies have played a key role in interpretating the results of modern time-resolved pump-probe spectroscopy, and in elucidating the main photoactivated reactive paths. This review provides a concise, complete picture of the computational studies carried out, approximately, in the past decade. We start with an overview of the photophysics of the nucleobases in the gas phase and in solution. We discuss the proposed mechanisms for ultrafast decay to the ground state, that involve conical intersections, consider the role of triplet states, and analyze how the solvent modulates the photophysics. Then we move to larger systems, from dinucleotides to single- and double-stranded oligonucleotides. We focus on the possible role of charge transfer and delocalized or excitonic states in the photophysics of these systems and discuss the main photochemical paths. We finish with an outlook on the current challenges in the field and future directions of research.

Generalized trajectory surface-hopping method for internal conversion and intersystem crossing

Trajectory-based fewest-switches surface-hopping (FSSH) dynamics simulations have become a popular and reliable theoretical tool to simulate nonadiabatic photophysical and photochemical processes. Most available FSSH methods model internal conversion. We present a generalized trajectory surface-hopping (GTSH) method for simulating both internal conversion and intersystem crossing processes on an equal footing. We consider hops between adiabatic eigenstates of the non-relativistic electronic Hamiltonian (pure spin states), which is appropriate for sufficiently small spin-orbit coupling. This choice allows us to make maximum use of existing electronic structure programs and to minimize the changes to available implementations of the traditional FSSH method. The GTSH method is formulated within the quantum mechanics (QM)/molecular mechanics framework, but can of course also be applied at the pure QM level. The algorithm implemented in the GTSH code is specified step by step. As an initial GTSH application, we report simulations of the nonadiabatic processes in the lowest four electronic states (S0, S1, T1, and T2) of acrolein both in vacuo and in acetonitrile solution, in which the acrolein molecule is treated at the ab initio complete-active-space self-consistent-field level. These dynamics simulations provide detailed mechanistic insight by identifying and characterizing two nonadiabatic routes to the lowest triplet state, namely, direct S1 → T1 hopping as major pathway and sequential S1 → T2 → T1 hopping as minor pathway, with the T2 state acting as a relay state. They illustrate the potential of the GTSH approach to explore photoinduced processes in complex systems, in which intersystem crossing plays an important role.

A comprehensive spectroscopic investigation of α-(2-naphthyl)-N-methylnitrone: a computational study on photochemical nitrone–oxaziridine conversion and thermal E–Z isomerization processes

CASSCF and 2-layer hybrid ONIOM-based computational studies on α-(2-naphthyl)-N-methylnitrone have proposed its photochemical oxaziridine formation and thermal E–Z isomerization mechanisms.

QM/MM investigations of organic chemistry oriented questions

About 35 years after its first suggestion, QM/MM became the standard theoretical approach to investigate enzymatic structures and processes. The success is due to the ability of QM/MM to provide an accurate atomistic picture of enzymes and related processes. This picture can even be turned into a movie if nuclei-dynamics is taken into account to describe enzymatic processes. In the field of organic chemistry, QM/MM methods are used to a much lesser extent although almost all relevant processes happen in condensed matter or are influenced by complicated interactions between substrate and catalyst. There is less importance for theoretical organic chemistry since the influence of nonpolar solvents is rather weak and the effect of polar solvents can often be accurately described by continuum approaches. Catalytic processes (homogeneous and heterogeneous) can often be reduced to truncated model systems, which are so small that pure quantum-mechanical approaches can be employed. However, since QM/MM becomes more and more efficient due to the success in software and hardware developments, it is more and more used in theoretical organic chemistry to study effects which result from the molecular nature of the environment. It is shown by many examples discussed in this review that the influence can be tremendous, even for nonpolar reactions. The importance of environmental effects in theoretical spectroscopy was already known. Due to its benefits, QM/MM can be expected to experience ongoing growth for the next decade.In the present chapter we give an overview of QM/MM developments and their importance in theoretical organic chemistry, and review applications which give impressions of the possibilities and the importance of the relevant effects. Since there is already a bunch of excellent reviews dealing with QM/MM, we will discuss fundamental ingredients and developments of QM/MM very briefly with a focus on very recent progress. For the applications we follow a similar strategy.

ONIOM approach for non-adiabatic on-the-fly molecular dynamics demonstrated for the backbone controlled Dewar valence isomerization

Non-adiabatic on-the-fly molecular dynamics (NA-O-MD) simulations require the electronic wavefunction, energy gradients, and derivative coupling vectors in every timestep. Thus, they are commonly restricted to the excited state dynamics of molecules with up to ≈20 atoms. We discuss an approximation that combines the ONIOM(QM:QM) method with NA-O-MD simulations to allow calculations for larger molecules. As a proof of principle we present the excited state dynamics of a (6-4)-lesion containing dinucleotide (63 atoms), and especially the importance to include the confinement effects of the DNA backbone. The method is able to include electron correlation on a high level of theory and offers an attractive alternative to QM:MM approaches for moderate sized systems with unknown force fields.

Mechanism of UV-induced formation of Dewar lesions in DNA

The importance of a backbone: The mechanism of formation of Dewar lesions has been investigated by using femtosecond IR spectroscopy and ab initio calculations of the exited state. The 4π electrocyclization is rather slow, occurs with an unusual high quantum yield, and--surprisingly--is controlled by the phosphate backbone.

Unravelling the details of vitamin D photosynthesis by non-adiabatic molecular dynamics simulations

We investigate the photodynamics of vitamin D derivatives by a fully analytical implementation of the linear response time-dependent density functional theory surface hopping method (LR-TDDFT-SH). Our study elucidates the dynamics of the processes involved in vitamin D formation at the molecular level and with femtosecond resolution. We explain the major experimental findings and provide new insights that cannot directly be obtained from experiments: firstly, we investigate the dynamics of the photoinduced ring-opening of provitamin D (Pro) and cyclohexadiene (CHD) and the subsequent rotational isomerization. In agreement with recent experiments and CC2 calculations, only the bright S(1) state is involved in the ring-opening reaction. Our calculations confirm the experimentally reported 5 : 1 ratio between the excited state lifetimes of Pro and CHD. The longer lifetimes of Pro are attributed to steric constraints of the steroid skeleton and to temperature effects, both emerging directly from our simulations. For CHD and Pro, we present an explanation of the biexponential decay recently reported by Sension and coworkers [Tang et al., J. Phys. Chem., 2011, 134, 104503]: our calculations suggest that the fast and slow components arise from a reactive and an unreactive reaction pathway, respectively. Secondly, we assess the wavelength dependent photochemistry of previtamin D (Pre). Using replica exchange molecular dynamics we sample the Pre conformers present at thermal equilibrium. Based on this ensemble we explain the conformation dependent absorption and the essential features of Pre photochemistry. Consistent with the experiments, we find ring-closure to occur mostly after excitation of the cZc conformers and at lower energies, whereas Z/E isomerization of the central double bond preferably occurs after excitation at higher energies. For the isomerization we provide the first theoretical evidence of the proposed hula-twist mechanism. Our results show that LR-TDDFT-SH is a highly valuable tool for studying the photochemistry of moderately large systems, even though challenges remain in the vicinity of conical intersections.

Conical intersections in solution: formulation, algorithm, and implementation with combined quantum mechanics/molecular mechanics method

The significance of conical intersections in photophysics, photochemistry, and photodissociation of polyatomic molecules in gas phase has been demonstrated by numerous experimental and theoretical studies. Optimization of conical intersections of small- and medium-size molecules in gas phase has currently become a routine optimization process, as it has been implemented in many electronic structure packages. However, optimization of conical intersections of small- and medium-size molecules in solution or macromolecules remains inefficient, even poorly defined, due to large number of degrees of freedom and costly evaluations of gradient difference and nonadiabatic coupling vectors. In this work, based on the sequential quantum mechanics and molecular mechanics (QM/MM) and QM/MM-minimum free energy path methods, we have designed two conical intersection optimization methods for small- and medium-size molecules in solution or macromolecules. The first one is sequential QM conical intersection optimization and MM minimization for potential energy surfaces; the second one is sequential QM conical intersection optimization and MM sampling for potential of mean force surfaces, i.e., free energy surfaces. In such methods, the region where electronic structures change remarkably is placed into the QM subsystem, while the rest of the system is placed into the MM subsystem; thus, dimensionalities of gradient difference and nonadiabatic coupling vectors are decreased due to the relatively small QM subsystem. Furthermore, in comparison with the concurrent optimization scheme, sequential QM conical intersection optimization and MM minimization or sampling reduce the number of evaluations of gradient difference and nonadiabatic coupling vectors because these vectors need to be calculated only when the QM subsystem moves, independent of the MM minimization or sampling. Taken together, costly evaluations of gradient difference and nonadiabatic coupling vectors in solution or macromolecules can be reduced significantly. Test optimizations of conical intersections of cyclopropanone and acetaldehyde in aqueous solution have been carried out successfully.