The scope of this review is the nature and dynamics of the singlet excited electronic states created in nucleic acids and their constituents by UV light. Interest in the UV photochemistry of nucleic acids has long been the motivation for photophysical studies of the excited states, because these states are at the beginning of the complex chain of events that culminates in photodamage. UV-induced damage to DNA has profound biological consequences, including photocarcinogenesis, a growing human health problem.1-3 Sunlight, which is essential for life on earth, contains significant amounts of harmful UV (λ < 400 nm) radiation. These solar UV photons constitute one of the most ubiquitous and potent environmental carcinogens. This extraterrestrial threat is impressive for its long history; photodamage is as old as life itself. The genomic information encoded by these biopolymers has been under photochemical attack for billions of years. It is not surprising then that the excited states of the nucleic acid bases (see Chart 1), the most important UV chromophores of nucleic acids, are highly stable to photochemical decay, perhaps as a result of selection pressure during a long period of molecular evolution. This photostability is due to remarkably rapid decay pathways for electronic energy, which are only now coming into focus through femtosecond laser spectroscopy. The recently completed map of the human genome and the ever-expanding crystallographic database of nucleic acid structures are two examples that illustrate the richly detailed information currently available about the static properties of nucleic acids. In contrast, much less is known about the dynamics of these macromolecules. This is particularly true of the dynamics of the excited states that play a critical role in DNA photodamage. Efforts to study nucleic acids by time-resolved spectroscopy have been stymied by the apparent lack of suitable fluorophores. In contrast, dynamical spectroscopy of proteins has flourished thanks to intrinsically fluorescent amino acids such as tryptophan, tyrosine, and phenylalanine.4 The primary UVabsorbing constituents of nucleic acids, the nucleic acid bases, have vanishingly small fluorescence quantum yields under physiological conditions of temperature and pH.5 In fact, the bases were frequently described as “nonfluorescent” in the early literature. * To whom correspondence should be addressed. E-mail: kohler@ chemistry.ohio-state.edu. Phone: (614) 688-3944. Fax: (614) 2921685. 1977 Chem. Rev. 2004, 104, 1977−2019

Ultrafast Excited-State Dynamics in Nucleic Acids

A benchmark set of 28 medium-sized organic molecules is assembled that covers the most important classes of chromophores including polyenes and other unsaturated aliphatic compounds, aromatic hydrocarbons, heterocycles, carbonyl compounds, and nucleobases. Vertical excitation energies and one-electron properties are computed for the valence excited states of these molecules using both multiconfigurational second-order perturbation theory, CASPT2, and a hierarchy of coupled cluster methods, CC2, CCSD, and CC3. The calculations are done at identical geometries (MP26-31G*) and with the same basis set (TZVP). In most cases, the CC3 results are very close to the CASPT2 results, whereas there are larger deviations with CC2 and CCSD, especially in singlet excited states that are not dominated by single excitations. Statistical evaluations of the calculated vertical excitation energies for 223 states are presented and discussed in order to assess the relative merits of the applied methods. CC2 reproduces the CC3 reference data for the singlets better than CCSD. On the basis of the current computational results and an extensive survey of the literature, we propose best estimates for the energies of 104 singlet and 63 triplet excited states.

https://www.chemie.hhu.de/fileadmin/redaktion/Fakultaeten/Mathematisch-Naturwissenschaftliche_Fakultaet/Chemie/SFB_663/Veroeffentlichungen/C4_043.pdf

Benchmarks for electronically excited states: CASPT2, CC2, CCSD, and CC3

We analyze the performance of a density functional model obtained by combining the Perdew–Burke–Erzenrhof (PBE) generalized gradient functional with a predetermined amount of exact exchange for predicting vertical electronic excitation energies within a time-dependent approach. Four molecules, namely, CO, H2CO, (CH3)2CO, and C2H4, have been chosen as benchmark cases. Our results show that this model (PBE0) provides accurate excitations both to valence and Rydberg states. Furthermore, the results are numerically close to those obtained using asymptotically correct exchange-correlation functionals. The performance of the PBE0 model for predicting excitation energies in larger molecules is assessed for benzene, pyridine, and naphthalene. Here, the PBE0 model provides results which are in fairly good agreement with experimental data and of similar quality to those obtained by more sophisticated (and time-consuming) post-Hartree–Fock methods.

Accurate excitation energies from time-dependent density functional theory: Assessing the PBE0 model

Multiconfiguration Self-Consistent Field and Multireference Configuration Interaction Methods and Applications

An implementation of transition moments and excited-state first-order properties is reported for the approximate coupled-cluster singles-and-doubles model (CC2) using the resolution of the identity (RI) approximation. In parallel to the previously reported code for the ground- and excited-state amplitude equations, we utilize a partitioned form of the CC2 equations and thus eliminate the need to store any N 4 intermediates. This opens the perspective for applications on molecules with 30 and more atoms. The accuracy of the RI approximation is tested for a set of 29 molecules for the aug-cc -p V X Z (X=D,T,Q) basis sets in connection with the recently optimized auxiliary basis sets. These auxiliary basis sets are found to be sufficient even for the description of diffuse states. The RI error is compared to the usual basis set error and is demonstrated to be insignificant.

Transition moments and excited-state first-order properties in the coupled-cluster model CC2 using the resolution-of-the-identity approximation

Theoretical Study of the Electronic Spectra of Uracil and Thymine

The valence excited states and the 3s, 3p, and 3d (united atom) Rydberg states of benzene and phenol have been obtained by the CASPT2 method, which computes a second-order perturbation correction to complete active space self-consistent field (CASSCF) energies. All non-zero dipole oscillator strengths are also computed, at the CASSCF level. For benzene, 16 singlet and 16 triplet states with excitation energies up to ca. 7.86 eV (63 400 cm–1) are obtained. Of these, 12 singlet and three triplet energies are experimentally known well enough to allow meaningful comparison. The average error is around 0.1 eV. The highest of these singlet states (21 E2g) is the highest valence ππ* state predicted by elementary π-electron theory. Its energy is then considerably lower than has been suggested from laser flash experiments, but in perfect agreement with a reinterpretation of that experiment. For phenol, 27 singlet states are obtained, in the range 4.53–7.84 eV (63 300 cm−1). Only the lowest has a well-known experimental energy, which agrees with the computed result within 0.03 eV. The ionization energy is in error by 0.05 eV.

A CASPT2 study of the valence and lowest Rydberg electronic states of benzene and phenol

Values or the inner-sphere reorganization energies (λ i ) for a number or small-molecule inorganic redox couples (NO + /NO, NO 2 + /NO 2 , NO 2 /NO 2 - , N 3 /N 3 - , O 2 /O 2 - , O 3 /O 3 - , SO 2 /SO 2 - , ClO/ClO - , ClO/ClO 2 - , and Cl 2 /Cl 2 - ) have been calculated by ab initio methods. The λ i values were calibrated by comparing calculated bond lengths/angles, electron affinities, and ionization potentials with experimental data and were round to be accurate to within ±2 kcal mol -1 or better

The ab initio calculation of inner sphere reorganization energies of inorganic redox couples

The electronic excitation spectra of pyridine and phosphabenzene have been studied using theoretical methods. The electronic states are described by wave functions derived from second-order perturbation theory based on multiconfigurational reference functions. The study includes singlet and triplet valences excited states as well as a number of Rydberg states. For both molecules the transition energies to the two lowest π → π* excited singlet states are known from experiment and reproduced with an accuracy of 0.15 eV or better, while then → π* transition energies are predicted with a somewhat uncertain error of about 0.2 eV. The calculations suggest the lowestn → π* transition detected experimentally in pyridine corresponds to an adiabatic transition. 43 electronic states have been determined in each of the molecules.

A theoretical study of the electronic spectra of pyridine and phosphabenzene

This study presents an approach for partitioned fluid-structure interaction (FSI) applied to large structural deformations, where an incompressible turbulent solver is combined with a structural solver. The implementation is based upon two different open-source libraries by using MPI as a parallel communication protocol, the packages and OpenFOAM. FSI is achieved through a strongly-coupled scheme. The solver has been validated against cases with a submerged cantilever in a channel flow to which experiments, numerical calculations and theoretical solutions are available. The verification of the procedure is performed by using a solid-solid interaction (SSI) study. The solver has proven to be robust and has the same parallel efficiency as the fluid and the solid solver stand-alone. (Less)

Johan Lorentzon

Papers

Theoretical Study of the Electronic Spectra of Uracil and Thymine

A CASPT2 study of the valence and lowest Rydberg electronic states of benzene and phenol

The ab initio calculation of inner sphere reorganization energies of inorganic redox couples

A theoretical study of the electronic spectra of pyridine and phosphabenzene

A numerical study of partitioned fluid-structure interaction applied to a cantilever in incompressible turbulent flow