Noncovalent interactions: a challenge for experiment and theory

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

Molecular Clusters of π-Systems: Theoretical Studies of Structures, Spectra, and Origin of Interaction Energies

We propose and discuss an efficient scheme for the in silico sampling for parts of the molecular chemical space by semiempirical tight-binding methods combined with a meta-dynamics driven search algorithm. The focus of this work is set on the generation of proper thermodynamic ensembles at a quantum chemical level for conformers, but similar procedures for protonation states, tautomerism and non-covalent complex geometries are also discussed. The conformational ensembles consisting of all significantly populated minimum energy structures normally form the basis of further, mostly DFT computational work, such as the calculation of spectra or macroscopic properties. By using basic quantum chemical methods, electronic effects or possible bond breaking/formation are accounted for and a very reasonable initial energetic ranking of the candidate structures is obtained. Due to the huge computational speedup gained by the fast low-cost quantum chemical methods, overall short computation times even for systems with hundreds of atoms (typically drug-sized molecules) are achieved. Furthermore, specialized applications, such as sampling with implicit solvation models or constrained conformational sampling for transition-states, metal-, surface-, or noncovalently bound complexes are discussed, opening many possible applications in modern computational chemistry and drug discovery. The procedures have been implemented in a freely available computer code called CREST, that makes use of the fast and reliable GFNn-xTB methods.

Automated exploration of the low-energy chemical space with fast quantum chemical methods

Infrared Spectroscopy of Size-Selected Water and Methanol Clusters

The vibronic spectrum of laser desorbed and jet cooled guanine consists of bands from three different tautomers of guanine as revealed by UV–UV and IR–UV double resonance spectroscopy. 1-methylguanine, in which the Keto–Enol tautomerism is blocked, shows hole burning spectra from the 9H-and 7H-Keto form. A comparison of the vibronic pattern of the different tautomers demonstrates that the vibronic spectrum built on the redmost guanine band at 32 870 cm−1 (electronic origin 0) can be traced back to the 9H-Enol tautomer, while the spectra built on the origins at 0+404 cm−1 and 0+1044 cm−1 stem from the two Keto tautomers. The IR–UV double resonance spectra of the OH-and NH-stretch vibrations of the different tautomers support this assignment. The UV and IR spectra can be partly assigned by comparison with ab initio calculated vibrational frequencies and with the help of deuteration experiments.

/pdf/guanine-tautomerism-revealed-by-uv-uv-and-ir-uv-hole-burning-3o78o5r4y2.pdf

Guanine tautomerism revealed by UV–UV and IR–UV hole burning spectroscopy

The vibronic spectra of jet cooled phenol(H2O)7,8 clusters were analyzed with mass selective resonance enhanced two photon ionization (R2PI) and ultraviolet-ultraviolet spectral hole burning (UV-UV SHB) A double resonance technique with an infrared (IR) laser as burn laser (IR-UV SHB) was used to measure the intramolecular OH stretching vibrations of the mass- and isomer-selected clusters Two isomers of phenol(H2O)7 and three isomers of phenol(H2O)8 could be distinguished via SHB and their IR spectra recorded The red- or blueshift of the electronic origin relative to the phenol monomer gives valuable hints on the hydrogen bonding between phenol and the water moiety All IR spectra contain four characteristic groups of OH stretching vibrations which give insight into the structure of the H bonded network The ab initio calculations show that the minimum energy structures for phenol(H2O)7,8 are very similar to the corresponding water clusters which are based on regular (H2O)8 cubes Comparison between experiment and calculation for phenol(H2O)8 shows that phenol can attach to and insert itself in the water network

Structure and vibrations of phenol(H2O)7,8 studied by infrared-ultraviolet and ultraviolet-ultraviolet double-resonance spectroscopy and ab initio theory

We present R2PI, IR–UV and UV–UV double resonance measurements of the guanine–cytosine (G–C) dimer formed in a supersonic jet. We show that there is only one isomer of G–C in the investigated wavelength range from 33200 to 34100 cm−1. We assigned the observed G–C isomer to a specific structure, based on comparisons of the IR spectra of the G and C monomers with the G–C dimer in the range of the OH and NH stretching vibrations and ab initio-calculated vibrational frequencies and dimer stabilities. The cluster exhibits an HNH⋯O/NH⋯N/CO⋯HNH bonding similar to the Watson–Crick G–C base pair bonding but with C as the enol tautomer. We did not observe any keto–keto or enol–enol G–C dimers in the investigated wavelength region.

/pdf/pairing-of-the-nucleobases-guanine-and-cytosine-in-the-gas-4jgyitedvi.pdf

Pairing of the nucleobases guanine and cytosine in the gas phase studied by IR–UV double-resonance spectroscopy and ab initio calculations

The intermolecular vibrations of jet-cooled phenol(H2O)2-5 and phenol(D2O)2-5-d1 were investigated in the S0 and S1 electronic states by using mass-selective UV spectral hole burning (SHB) and sing...

Intermolecular vibrations of phenol(h2o)2-5 and phenol(d2o)2-5-d1 studied by uv double-resonance spectroscopy and ab initio theory

The infrared spectra of (phenol)(H2O)n+ cluster ions (n = 1−4, 7, 8) have been recorded in the region from 2850 to 3800 cm-1. The method developed for this study (IR-PARI = infrared photodissociation after resonant ionization) allows sensitive IR spectroscopy of cluster ions from size-selected neutral precursors. The three-color laser scheme used for ion selection and dissociation consists of a two-color S0 → S1 → D0 ionization of a mass-selected cluster followed by IR photodissociation of the cluster ion. The IR spectra were taken by monitoring the photodissociation dip of the parent ion signal and by recording the rise of the −H2O fragment signal. The experimentally observed frequencies are compared to the results of ab initio calculations. No proton transfer is observed for the (phenol)(H2O)1,2+ clusters. In contrast to the S0 state, the structure of (phenol)(H2O)2+ turns out to be linear. In the case of the (phenol)(H2O)3,4+ clusters, linear and solvated structures are discussed. Within the solvated s...

Ch. Janzen

Papers

Guanine tautomerism revealed by UV–UV and IR–UV hole burning spectroscopy

Structure and vibrations of phenol(H2O)7,8 studied by infrared-ultraviolet and ultraviolet-ultraviolet double-resonance spectroscopy and ab initio theory

Pairing of the nucleobases guanine and cytosine in the gas phase studied by IR–UV double-resonance spectroscopy and ab initio calculations

Intermolecular vibrations of phenol(h2o)2-5 and phenol(d2o)2-5-d1 studied by uv double-resonance spectroscopy and ab initio theory

Infrared spectroscopy of resonantly ionized (phenol)(h2o)n