Excited-State Dynamics of Melamine and Its Lysine Derivative Investigated by Femtosecond Transient Absorption Spectroscopy

Vertical Excitation Energies and Lifetimes of the Two Lowest Singlet Excited States of Cytosine, 5-Aza-cytosine, and the Triazine Family: Quantum Mechanics-Molecular Mechanics Studies

A swarm of semi-classical quantum mechanics/molecular mechanics molecular-dynamics simulations where OM2/MNDO is combined with the Gromacs program for consideration of explicit water is performed, solving the time-dependent Schrödinger equation in each step of the trajectories together with the Tully's fewest switches algorithm. Within this stochastic treatment, time dependent probabilities of the three lowest electronic states are determined. The fact that nucleobases are quickly deactivated is confirmed in the cytosine case where our best lifetime estimation is τ₁=0.82 ps for the model with 100 water molecules with the SPCE force field and a time step of 0.1 fs. Lifetimes of the remaining molecules are visibly longer: 5-azacytosine, 2,4-diamino-1,3,5-triazine (DT), and 2,4,6-triamino-1,3,5-triazine (TT) molecules have an S₁ → S₀ de-excitation time of slightly above 10 ps. The lifetimes of the triazine family increases with the increasing number of exocyclic amino groups, that is, s-triazine < 2-amino-1,3,5-triazine < DT < TT. This can be explained by a higher mobility of the carbon-bonded hydrogen atoms in comparison with heavier amino groups since their movement is slowed down due to a substantially higher mass than hydrogen atoms, which can easier reach the out-of-plane positions required in the conical intersection structures. Moreover, bulkier NH₂ ligands suffer due to greater friction caused by the surrounding water environment. These mechanical aspects caused a change in the explored lifetime dependences in comparison with our previous gas-phase study.

Quantum mechanics/molecular mechanics studies on mechanistic photophysics of cytosine aza-analogues: 2,4-diamino-1,3,5-triazine and 2-amino-1,3,5-triazine in aqueous solution

The excited-state properties and photophysics of cytosine aza-analogues, i.e., 2,4-diamino-1,3,5-triazine (2,4-DT) and 2-amino-1,3,5-triazine (2-AT) in solution have been systematically explored using the QM(MS-CASPT2//CASSCF)/MM approach. The excited-state nonradiative relaxation mechanisms for the initially photoexcited S₁(ππ*) state decay back to the S₀ state are proposed in terms of the present computed minima, surface crossings (conical intersections and singlet-triplet crossings), and excited-state decay paths in the S₁, S₂, T₁, T₂, and S₀ states. Upon photoexcitation to the bright S₁(ππ*) state, 2,4-DT quickly relaxes to its S₁ minimum and then overcomes a small energy barrier of 5.1 kcal mol^-1 to approach a S₁/S₀ conical intersection, where the S₁ system hops to the S₀ state through S₁ → S₀ internal conversion (IC). In addition, at the S₁ minimum, the system could partially undergo intersystem crossing (ISC) to the T₁ state, followed by further ISC to the S₀ state via the T₁/S₀ crossing point. In the T₁ state, an energy barrier of 7.9 kcal mol^-1 will trap 2,4-DT for a while. In parallel, for 2-AT, the system first relaxes to the S₁ minimum and then S₁ → S₀ IC or S₁ → T₁ → S₀ ISCs take place to the S₀ state by surmounting a large barrier of 15.3 kcal mol^-1 or 11.9 kcal mol^-1, respectively, which heavily suppress electronic transition to the S₀ state. Different from 2,4-DT, upon photoexcitation in the Franck-Condon region, 2-AT can quickly evolve in an essentially barrierless manner to nearby S₂/S₁ conical intersection, where the S₂ and T₁ states can be populated. Once it hops to the S₂ state, the system will overcome a relatively small barrier (6.6 kcal mol^-1vs. 15.3 kcal mol^-1) through IC to the S₀ state. Similarly, an energy barrier of 11.9 kcal mol^-1 heavily suppresses the T₁ state transformation to the S₀ state. The present work manifests that the amination/deamination of the triazine rings can affect some degree of different vertical and adiabatic excitation energies and nonradiative decay pathways in solution. It not only rationalizes excited-state decay dynamics of 2,4-DT and 2-AT in aqueous solution but could also provide insights into the understanding of the photophysics of aza-nucleobases.

Water-Soluble Supramolecular Polymers of Paired and Stacked Heterocycles: Assembly, Structure, Properties, and a Possible Path to Pre-RNA

The hypothesis that RNA and DNA are products of chemical and biological evolution has motivated our search for alternative nucleic acids that may have come earlier in the emergence of life-polymers that possess a proclivity for covalent and non-covalent self-assembly not exhibited by RNA. Our investigations have revealed a small set of candidate ancestral nucleobases that self-assemble into hexameric rosettes that stack in water to form long, twisted, rigid supramolecular polymers. These structures exhibit properties that provide robust solutions to long-standing problems that have stymied the search for a prebiotic synthesis of nucleic acids. Moreover, their examination by experimental and computational methods provides insight into the chemical and physical principles that govern a particular class of water-soluble one-dimensional supramolecular polymers. In addition to efficient self-assembly, their lengths and polydispersity are modulated by a wide variety of positively charged, planar compounds; their assembly and disassembly are controlled over an exceedingly narrow pH range; they exhibit spontaneous breaking of symmetry; and homochirality emerges through non-covalent cross-linking during hydrogel formation. Some of these candidate ancestral nucleobases spontaneously form glycosidic bonds with ribose and other sugars, and, most significantly, functionalized forms of these heterocycles form supramolecular structures and covalent polymers under plausibly prebiotic conditions. This Perspective recounts a journey of discovery that continues to reveal attractive answers to questions concerning the origins of life and to uncover the principles that control the structure and properties of water-soluble supramolecular polymers.

Photoinduced phenomena in water solution of melamine explaining the photostability of the compound

Two tautomers of melamine (triamino and imino-diamino) were studied at the BLYP/aug-cc-pVDZ theoretical level. It was found that the two tautomers are bridged with the ¹πσ^* excited-state reaction path. The high photostability of melamine in water solution was explained with the mechanism of ring deformation which occurs along the ¹ππ^* excited-state reaction path. The two mechanisms are investigated at the TD BLYP level of theory using the linear interpolation in internal coordinates approach.

Excited-state dynamics of mononucleotides and DNA strands in a deep eutectic solvent

The photophysics of several mono- and oligonucleotides were investigated in a deep eutectic solvent for the first time. The solvent glyceline, prepared as a 1 : 2 mole ratio mixture of choline chloride and glycerol, was used to study excited-state deactivation in a non-aqueous solvent by the use of steady-state and time-resolved spectroscopy. DNA strands in glyceline retain the secondary structures that are present in aqueous solution to some degree, thus enabling a study of the effects of solvent properties on the excited states of stacked bases and stacked base pairs. The excited-state lifetime of the mononucleotide 5'-AMP in glyceline is 630 fs, or twice as long as in aqueous solution. Even slower relaxation is seen for 5'-TMP in glyceline, and a possible triplet state with a lifetime greater than 3 ns is observed. Circular dichroism spectra show that the single strand (dA)18 and the duplex d(AT)9·d(AT)9 adopt similar structures in glyceline and in aqueous solution. Despite having similar conformations in both solvents, femtosecond transient absorption experiments reveal striking changes in the dynamics. Excited-state decay and vibrational cooling generally take place more slowly in glyceline than in water. Additionally, the fraction of long-lived excited states in both oligonucleotide systems is lower in glyceline than in aqueous solution. For a DNA duplex, water is suggested to favor decay pathways involving intrastrand charge separation, while the deep eutectic solvent favors interstrand deactivation channels involving neutral species. Slower solvation dynamics in the viscous deep eutectic solvent may also play a role. These results demonstrate that the dynamics of excitations in stacked bases and stacked base pairs depend not only on conformation, but are also highly sensitive to the solvent.

Time-Resolved Spectroscopic and Density Functional Theory Investigation of the Photogeneration of a Bifunctional Quinone Methide in Neutral and Basic Aqueous Solutions

Binol quinone methides (BQMs) can be generated from 1,1'-(2,2'-dihydroxy-1,1'-binaphthyl-6,6'-diyl)bis(N,N,N-trimethylmethanamiuium) bromide (BQMP-b) in a 1:1 MeCN:H₂O mixed solution via a ground state intramolecular proton transfer (GSIPT), as mentioned in our previously reported studies. Here, the photoreaction of BQMP-b in neutral and basic aqueous solution (pH = 7, 10, 12) was investigated to explore the possible mechanisms and the key intermediates produced in the process of the photoreaction and to examine whether they are different from those in a neutral mild-mixed MeCN:H₂O solution. The studies were conducted using femtosecond transient absorption (fs-TA), nanosecond transient absorption (ns-TA), and nanosecond time-resolved resonance Raman spectroscopy (ns-TR³) in conjunction with results from density functional theory (DFT) computations. The results showed that BQMP-b was deprotonated initially and produced BQMs species more effectively through an E1bc elimination reaction in a strong basic aqueous condition (pH = 12), which differed from the reaction pathway that took place in the solution with pH = 7 or 10. A related single naphthol ring molecule 1-(6-hydroxynaphthalen-2-yl)-N,N,N-trimethylmethanaminium bromide (QMP-b) that did not contain a second naphthol ring was also investigated. The related reaction mechanisms are elucidated in this work, and it is briefly discussed how the mechanisms vary as a function of aqueous solution pH conditions.

Photophysics and Photocatalysis of Melem: A Spectroscopic Reinvestigation

Graphitic carbon nitride (g-CN) is one potential metal-free photocatalyst. The photocatalytic mechanism of g-CN is related to the heptazine ring building unit. Melem is the simplest heptazine-based compound and g-CN is its polymeric product. Thus, studies on the photophysical properties of melem will help to understand the photocatalytic mechanism of heptazine-based materials. Herein, the spectroscopic features of melem were systematically explored through measuring its absorption spectrum, fluorescence spectrum, and fluorescence decay. Both fluorescence spectroscopy and fluorescence decay measurements show that the condensation of melamine to melem causes stronger photoluminescence, whereas the condensation of melem to g-CN causes weaker photoluminescence. In addition, all observations reveal that a mixture of monomer melem and its higher condensates is more easily obtained during the preparation of melem, and that the higher condensates of melem affect the photophysical properties of melem dominantly. The photocatalytic hydrogen evolution of melem has also been measured and the monomer melem has negligible photoinduced water-splitting activity.

Mechanism of photocatalytic water splitting with triazine-based carbon nitrides: insights from ab initio calculations for the triazine–water complex

Valuable theoretical insights into the mechanism of photocatalytic water-splitting using triazine as a model system for carbon-nitride materials.

How nature covers its bases

The response of nucleobases to UV radiation depends on structure in subtle ways, as revealed by gas-phase experiments.

Photorelaxation and Photorepair Processes in Nucleic and Amino Acid Derivatives

Understanding the fundamental interaction between electromagnetic radiation and matter is essential for a large number of phenomena, with significance to civilization.[...].