The Prebiotic Synthesis of Organic Molecules and Polymers

Miller, Stanley L.

doi:10.1002/9780470142790.ch7

Cited by 7 publications

(5 citation statements)

References 47 publications

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“…In contrast, both 5-methylcytosine and uracil undergo photohydration, which can ultimately lead to genome damage. If alternate xanthine bases were available in prebiotic times, − then the selection of today’s canonical purine bases over hypoxanthine as a genetic information carrier must have an explanation beyond UV hardiness.…”

Section: Discussionmentioning

confidence: 99%

Hydrogen Bond Donors Accelerate Vibrational Cooling of Hot Purine Derivatives in Heavy Water

2013

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Natural nucleobases and many of their derivatives have ultrashort excited state lifetimes that make them excellent model systems for studying intermolecular energy flow from a hot solute molecule to the solvent. UV-pump/broadband-mid-IR-probe transient absorption spectra of canonical purine nucleobases and several xanthine derivatives were acquired in D2O and acetonitrile in the probe frequency range of 1500-1750 cm(-1). The spectra reveal that vibrationally hot ground state molecules created by ultrafast internal conversion return to thermal equilibrium in several picoseconds by dissipating their excess energy to solvent molecules. In acetonitrile solution, where hydrogen bonding is minimal, vibrational cooling (VC) occurs with the same time constant of 10 ± 3 ps for paraxanthine, theophylline, and caffeine within experimental uncertainty. In D2O, VC by these molecules occurs more rapidly and at different rates that are correlated with the number of N-D bonds. Hypoxanthine has a VC time constant of 3 ± 1 ps, while similar lifetimes of 2.3 ± 0.8 ps and 3.1 ± 0.3 ps are seen for 5'-adenosine monophosphate and 5'-guanosine monophosphate, respectively. All three molecules have at least two N-D bonds. Slightly slower VC time constants are measured for paraxanthine (4 ± 1 ps) and theophylline (5.1 ± 0.8 ps), dimethylated xanthines that have only one N-D bond. Caffeine, a trimethylated xanthine with no N-D bonds, has a VC time constant of 7.7 ± 0.9 ps, the longest ever observed for any nucleobase in aqueous solution. Hydrogen bond donation by solute molecules is proposed to enable rapid energy disposal to water via direct coupling of high frequency solute-solvent modes.

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Section: Discussionmentioning

confidence: 99%

Hydrogen Bond Donors Accelerate Vibrational Cooling of Hot Purine Derivatives in Heavy Water

2013

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“…Without a fossil record of the prebiotic chemical world we are left to conjecture to understand the road map that led to RNA and DNA. [1][2][3] The key components of the reproductive machinery are unlikely to have been selected by a biological evolution that requires that very machinery to begin with. Instead it is conceivable that the choice of the molecular building blocks of life was mediated by a chemical selection that preceded biology.…”

Section: Introductionmentioning

confidence: 99%

How nature covers its bases

Boldissar

Vries

2018

Phys. Chem. Chem. Phys.

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The response of DNA and RNA bases to ultraviolet (UV) radiation has been receiving increasing attention for a number of important reasons: (i) the selection of the building blocks of life on an early earth may have been mediated by UV photochemistry, (ii) radiative damage of DNA depends critically on its photochemical properties, and (iii) the processes involved are quite general and play a role in more biomolecules as well as in other compounds. A growing number of groups worldwide have been studying the photochemistry of nucleobases and their derivatives. Here we focus on gas phase studies, which (i) reveal intrinsic properties distinct from effects from the molecular environment, (ii) allow for the most detailed comparison with the highest levels of computational theory, and (iii) provide isomeric selectivity. From the work so far a picture is emerging of rapid decay pathways following UV excitation. The main understanding, which is now well established, is that canonical nucleobases, when absorbing UV radiation, tend to eliminate the resulting electronic excitation by internal conversion (IC) to the electronic ground state in picoseconds or less. The availability of this rapid "safe" de-excitation pathway turns out to depend exquisitely on molecular structure. The canonical DNA and RNA bases are generally short-lived in the excited state, and thus UV protected. Many closely related compounds are longer lived, and thus more prone to other, potentially harmful, photochemical processes. It is this structure dependence that suggests a mechanism for the chemical selection of the building blocks of life on an early earth. However, the picture is far from complete and many new questions now arise.

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“…The appearance of ribonucleic acids (RNA) was the start of life due to its information storage capability and enzymatic functional properties. − Thus, revealing the origin of RNA is essential for understanding the origin of life in the RNA world theory. In the photophysical and photochemical aspects, it is generally assumed that the canonical nucleobases are favored to serve as chromophores in RNA due to their excellent photostability, which is reflected by their ultrafast excited state dynamics. − However, many studies have suggested that the canonical nucleobases which is common to today’s biology may have been preceded by alternative bases during the chemical evolution that took place before the RNA world. − Biological modification and total chemical synthesis − have provided large variety of minor nucleosides which could be possible ancestor nucleobases for prebiotic RNA. By studying the excited state dynamics of those nucleic base derivatives we hope to learn the impact of photostability which may have led to the selection of today’s canonical bases.…”

Section: Introductionmentioning

confidence: 99%

Ultrafast Excited-State Dynamics of Cytosine Aza-Derivative and Analogues

Zhou

Wang

et al. 2017

J. Phys. Chem. A

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Excited state dynamics of 5-azacytosine (5-AC), 2,4-diamino-1,3,5-triazine (2,4-DT), and 2-amino-1,3,5-triazine (2-AT) were comprehensively investigated by steady state absorption, fluorescence, and femtosecond transient absorption measurements. Time-dependent density functional theory (TDDFT) calculations were performed to help assign the absorption bands and understand the excited state decay mechanisms. The experimental results of excited singlet state dynamics for 5-AC, 2,4-DT, and 2-AT with femtosecond time resolution were reported for the first time. Two distinct decay pathways, with ∼1 ps and tens of picosecond lifetimes, were observed in 5-AC. Only one decay pathway with 17 ps lifetime was observed in 2,4-DT while an emissive state was found in 2-AT. TDDFT calculations suggest that 5-AC has a dark nπ* (S) state below the first allowed ππ* (S) state, which leads to the ultrafast decay of the ππ* state. In 2,4-DT, there is no dark nπ* state below the bright ππ* (S) state and the 17 ps lifetime is assigned to the relaxation from the ππ* (S) state to ground state. Two dark nπ* states (S and S) were found in 2-AT, which exhibits much more complex excited state dynamics compared with the other two. Photoluminescence in 2-AT has been confirmed to be fluorescence emission from its bright ππ* (S) state. Our results strongly suggest that electronic structures are very sensitive to the substitution on the triazine ring and that the photophysical properties of nucleic acid analogues depend highly on their molecular structures.

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The Prebiotic Synthesis of Organic Molecules and Polymers

Cited by 7 publications

References 47 publications

Hydrogen Bond Donors Accelerate Vibrational Cooling of Hot Purine Derivatives in Heavy Water

Hydrogen Bond Donors Accelerate Vibrational Cooling of Hot Purine Derivatives in Heavy Water

How nature covers its bases

Ultrafast Excited-State Dynamics of Cytosine Aza-Derivative and Analogues

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