Theoretical insight into photodeactivation mechanisms of adenine-uracil and adenine-thymine nucleobase pairs.

In this work, several plausible intra- and intermolecular photoinduced processes of the Watson-Crick base pairs of adenine with uracil (A-U) or thymine (A-T) according to the results of spin component scaling variant of algebraic diagrammatic construction up to the second order [SCS-ADC(2)] calculations are discussed. Although widely explored, these systems lack complete characterization of possible intramolecular relaxation channels perturbed by intermolecular interactions. In particular, we address the still open debate on photodeactivation purine-ring puckering at the C2 or C6-atom position of adenine.

Photoinduced water-chromophore electron transfer causes formation of guanosine photodamage.

UV-induced photolysis of aqueous guanine nucleosides produces 8-oxo-guanine and Fapy-guanine, which can induce various types of cellular malfunction. The mechanistic rationale underlying photodestructive processes of guanine nucleosides is still largely obscure. Here, we employ accurate quantum chemical calculations and demonstrate that an excited-state non-bonding interaction of guanosine and a water molecule facilitates the electron-driven proton transfer process from water to the chromophore fragment.

Light-Induced Modulation of Chiral Functions in G-Quadruplex-Photochrome Systems.

The design of artificially engineered chiral structures has received much attention, but the implementation of dynamic functions to modulate the chiroptical response of the systems is less explored. Here, we present a light-responsive G-quadruplex (G4)-based assembly in which chirality enrichment is induced, tuned, and fueled by molecular switches. In particular, the mirror-image dependence on photoactivated azo molecules, undergoing -to- isomerization, shows chiral recognition effects on the inherent flexibility and conformational diversity of DNA G4s having distinct handedness (right- and left-handed).

Ribose Alters the Photochemical Properties of the Nucleobase in Thionated Nucleosides.

Substitution of exocyclic oxygen with sulfur was shown to substantially influence the properties of RNA/DNA bases, which are crucial for prebiotic chemistry and photodynamic therapies. Upon UV irradiation, thionucleobases were shown to efficiently populate triplet excited states and can be involved in characteristic photochemistry or generation of singlet oxygen. Here, we show that the photochemistry of a thionucleobase can be considerably modified in a nucleoside, that is, by the presence of ribose.

An effective potential for Frenkel excitons.

Excitation energy transfer (EET) is a ubiquitous process in life and materials sciences. Here, a new and computationally efficient method of evaluating the electronic EET couplings between interacting chromophores is introduced that is valid in a wide range of intermolecular distances. The proposed approach is based on the effective elimination of electron repulsion integrals from the excitonic Hamiltonian matrix elements via the density-fitting approach and distributed multipole approximation.

Ultrafast nonradiative deactivation of photoexcited 8-oxo-hypoxanthine: a nonadiabatic molecular dynamics study.

In the scientific endeavor to understand the chemical origins of life, the photochemistry of the smallest life building blocks, nucleobases, has been a constant object of focus and intense research. Here, we report the results of the first theoretical study on the photo-properties of an 8-oxo-hypoxanthine molecule, the chromophore of 8-oxo-inosine, which is relevant to the recently proposed, prebiotically plausible synthetic routes to the formation of purine- and pyrimidine-nucleotides. With ab initio and semi-empirical OM2/MRCI quantum-chemistry calculations, we predict a strong photostability of the 8-oxo-hypoxanthine system and see the origin of this effect in ultrafast nonradiative relaxation through puckering of the 6-membered heterocyclic ring.

Ab initio effective one-electron potential operators: Applications for charge-transfer energy in effective fragment potentials.

The concept of effective one-electron potentials (EOPs) has proven to be extremely useful in efficient description of electronic structure of chemical systems, especially extended molecular aggregates such as interacting molecules in condensed phases. Here, a general method for EOP-based elimination of electron repulsion integrals is presented, that is tuned toward the fragment-based calculation methodologies such as the second generation of the effective fragment potentials (EFP2) method. Two general types of the EOP operator matrix elements are distinguished and treated either via the distributed multipole expansion or the extended density fitting (DF) schemes developed in this work.

Selective prebiotic formation of RNA pyrimidine and DNA purine nucleosides.

The nature of the first genetic polymer is the subject of major debate. Although the 'RNA world' theory suggests that RNA was the first replicable information carrier of the prebiotic era-that is, prior to the dawn of life-other evidence implies that life may have started with a heterogeneous nucleic acid genetic system that included both RNA and DNA. Such a theory streamlines the eventual 'genetic takeover' of homogeneous DNA from RNA as the principal information-storage molecule, but requires a selective abiotic synthesis of both RNA and DNA building blocks in the same local primordial geochemical scenario.

Partitioning of interaction-induced nonlinear optical properties of molecular complexes. II. Halogen-bonded systems.

Following our study on hydrogen-bonded (HB) complexes [Phys. Chem. Chem.

UV-induced hydrogen transfer in DNA base pairs promoted by dark nπ* states.

Dark nπ* states were shown to have substantial contribution to the destructive photochemistry of pyrimidine nucleobases. Based on quantum-chemical calculations, we demonstrate that the characteristic hydrogen bonding pattern of the GC base pair could facilitate the formation of a wobble excited-state charge-transfer complex. This entails a barrierless electron-driven proton transfer (EDPT) process which enables damageless photodeactivation of the base pair.

Photostability of oxazoline RNA-precursors in UV-rich prebiotic environments.

Pentose aminooxazolines and oxazolidinone thiones are considered as the key precursors which could have enabled the formation of RNA nucleotides under the conditions of early Earth. UV-irradiation experiments and quantum-chemical calculations demonstrate that these compounds are remarkably photostable and could accumulate over long periods of time in UV-rich prebiotic environments to undergo stereoisomeric purification.

Electron-driven proton transfer enables nonradiative photodeactivation in microhydrated 2-aminoimidazole.

2-Aminoimidazole (2-AIM) was proposed as a plausible nucleotide activating group in a nonenzymatic copying and polymerization of short RNA sequences under prebiotically plausible conditions. One of the key selection factors controlling the lifespan and importance of organic molecules on early Earth was ultraviolet radiation from the young Sun. Therefore, to assess the suitability of 2-AIM for prebiotic chemistry, we performed non-adiabatic molecular dynamics simulations and static explorations of potential energy surfaces of the photoexcited 2-AIM-(H2O)5 model system by means of the algebraic diagrammatic construction method to the second order [ADC(2)].

Partitioning of interaction-induced nonlinear optical properties of molecular complexes. I. Hydrogen-bonded systems.

Understanding the effects of different fundamental intermolecular interactions on nonlinear optical properties is crucial for proposing efficient strategies to obtain new materials with tailored properties. In this study, we computed the electronic and vibrational (hyper)polarizabilities of ten hydrogen-bonded molecular complexes employing the MP2, CCSD and CCSD(T) methods combined with the aug-cc-pVTZ basis set. The vibrational contributions to hyperpolarizabilities included nuclear-relaxation anharmonic corrections.

Characterization of Klason lignin samples isolated from beech and aspen using microbore column size-exclusion chromatography.

The present study is focused on the separation and characterization of lignin samples isolated by Klason method from European beech (Fagus sylvatica) broadleaf hardwood and European aspen (Populus tremula) broadleaf softwood by size-exclusion chromatography. The separation was carried out using dimethylformamide as major component of the mobile phase and a 3 mm id microbore column packed with hydroxyethyl methacrylate gel, calibrated with polystyrene standards. The influence of mobile phase composition and sample solvent composition on the chromatographic behavior and molar mass distributions was investigated.

Development of a precolumn derivatization HPLC method with diode-array detection for the determination of amino sugars in peat and soil humic acids.

The work is focused on the development of a high-performance liquid chromatography method with diode-array detection for the separation and quantitation of the three most abundant amino sugars; d-glucosamine, d-galactosamine, and d-mannosamine. The high-performance liquid chromatography separation was carried out by reversed-phase chromatography on Chromolith Performance RP-18e monolithic column after acid hydrolysis (5 M HCl) and precolumn derivatization of samples using diethyl ethoxymethylenemalonate. Gradient elution and a mobile phase composed of ammonium formate buffer solution (10 mmol/L, pH 3.

Water-chromophore electron transfer determines the photochemistry of cytosine and cytidine.

Many of the UV-induced phenomena observed experimentally for aqueous cytidine were lacking the mechanistic interpretation for decades. These processes include the substantial population of the puzzling long-lived dark state, photohydration, cytidine to uridine conversion and oxazolidinone formation. Here, we present quantum-chemical simulations of excited-state spectra and potential energy surfaces of N1-methylcytosine clustered with two water molecules using the second-order approximate coupled cluster (CC2), complete active space with second-order perturbation theory (CASPT2), and multireference configuration interaction with single and double excitation (MR-CISD) methods.

A prebiotically plausible synthesis of pyrimidine β-ribonucleosides and their phosphate derivatives involving photoanomerization.

Previous research has identified ribose aminooxazoline as a potential intermediate in the prebiotic synthesis of the pyrimidine nucleotides with remarkable properties. It crystallizes spontaneously from reaction mixtures, with an enhanced enantiomeric excess if initially enantioenriched, which suggests that reservoirs of this compound might have accumulated on the early Earth in an optically pure form. Ribose aminooxazoline can be converted efficiently into α-ribocytidine by way of 2,2'-anhydroribocytidine, although anomerization to β-ribocytidine by ultraviolet irradiation is extremely inefficient.

Photorelaxation of imidazole and adenine via electron-driven proton transfer along HO wires.

Photochemically created πσ* states were classified among the most prominent factors determining the ultrafast radiationless deactivation and photostability of many biomolecular building blocks. In the past two decades, the gas phase photochemistry of πσ* excitations was extensively investigated and was attributed to N-H and O-H bond fission processes. However, complete understanding of the complex photorelaxation pathways of πσ* states in the aqueous environment was very challenging, owing to the direct participation of solvent molecules in the excited-state deactivation.

On the physical origins of interaction-induced vibrational (hyper)polarizabilities.

This paper presents the results of a pioneering exploration of the physical origins of vibrational contributions to the interaction-induced electric properties of molecular complexes. In order to analyze the excess nuclear relaxation (hyper)polarizabilities, a new scheme was proposed which relies on the computationally efficient Bishop-Hasan-Kirtman method for determining the nuclear relaxation contributions to electric properties. The extension presented herein is general and can be used with any interaction-energy partitioning method.

Ultrafast excited-state dynamics of isocytosine.

The alternative nucleobase isocytosine has long been considered as a plausible component of hypothetical primordial informational polymers. To examine this hypothesis we investigated the excited-state dynamics of the two most abundant forms of isocytosine in the gas phase (keto and enol). Our surface-hopping nonadiabatic molecular dynamics simulations employing the algebraic diagrammatic construction to the second order [ADC(2)] method for the electronic structure calculations suggest that both tautomers undergo efficient radiationless deactivation to the electronic ground state with time constants which amount to τketo = 182 fs and τenol = 533 fs.

Prebiotic synthesis of nucleic acids and their building blocks at the atomic level - merging models and mechanisms from advanced computations and experiments.

The origin of life on Earth is one of the most fascinating questions of contemporary science. Extensive research in the past decades furnished diverse experimental proposals for the emergence of first informational polymers that could form the basis of the early terrestrial life. Side by side with the experiments, the fast development of modern computational chemistry methods during the last 20 years facilitated the use of in silico modelling tools to complement the experiments.

Distributed Multipolar Expansion Approach to Calculation of Excitation Energy Transfer Couplings.

We propose a new approach for estimating the electrostatic part of the excitation energy transfer (EET) coupling between electronically excited chromophores based on the transition density-derived cumulative atomic multipole moments (TrCAMM). In this approach, the transition potential of a chromophore is expressed in terms of truncated distributed multipolar expansion and analytical formulas for the TrCAMMs are derived. The accuracy and computational feasibility of the proposed approach is tested against the exact Coulombic couplings, and various multipole expansion truncation schemes are analyzed.

Electron-Driven Proton Transfer Along H2O Wires Enables Photorelaxation of πσ* States in Chromophore-Water Clusters.

The fates of photochemically formed πσ* states are one of the central issues in photobiology due to their significant contribution to the photostability of biological matter, formation of hydrated electrons, and the phenomenon of photoacidity. Nevertheless, our understanding of the underlying molecular mechanisms in aqueous solution is still incomplete. In this paper, we report on the results of nonadiabatic photodynamics simulations of microhydrated 2-aminooxazole molecule employing algebraic diagrammatic construction to the second order.