Self-Replication Without Hydrogen-Bonds: An Exobiotic Design.

Life on Earth uses DNA as the central template for self-replication, genetic encoding, and information transfer. However, there are no physical laws precluding life's existence elsewhere in space, and alternative life forms may not need DNA. In the search for exobiology, knowing what to look for as a biosignature remains a challenge-especially if it is not from the obvious list of biologic building blocks. Clues from chemicals recently discovered on Mars and in the Taurus Molecular Cloud 1 (TMC-1), show that intriguing organic compounds exist beyond Earth, which could provide a starting point for unconventional exobiotic designs. Here we present a new self-replicating system with structural similarities to recently discovered compounds on Mars and TMC-1. Rather than using DNA's hydrogen-bonding motif for reliable base-paring, our design employs sulfur-nitrogen interactions to selectively template unique benzothiadiazole units in sequence. We synthesized and studied two versions of this system, one reversible and the other irreversible, and found experimental evidence of self-replication in d-chloroform solvent. These results are part of a larger pursuit in our lab for developing a basis for a potential exobiological system using starting blocks closely related to these cosmic compounds.

Chalcogen Bonding "2S-2N Squares" versus Competing Interactions: Exploring the Recognition Properties of Sulfur.

Chalcogen bonding (CB) is the focus of increased attention for its applications in medicinal chemistry, materials science, and crystal engineering. However, the origin of sulfur's recognition properties remains controversial, and experimental evidence for supporting theories is still emerging. Here, a comprehensive evaluation of sulfur CB interactions is presented by investigating 2,1,3-benzothiadiazole X-ray crystallographic structures gathered from the Cambridge Structure Database (CSD), Protein Data Bank (PDB), and own laboratory findings. Through the systematic analysis of substituent effects on a subset library of over thirty benzothiadiazole derivatives, the competing interactions have been categorized into four main classes, namely 2S-2N CB square, halogen bonding (XB), S⋅⋅⋅S, and hydrogen-bonding (HB). A geometric model is employed to characterize the 2S-2N CB square motifs and discuss the role of electrostatic, dipole, and orbital contributions toward the interaction.

Symmetry-Adapted Perturbation Theory Energy Analysis of Alkyl Fluorine-Aromatic Interactions in Torsion Balance Systems.

Symmetry-adapted perturbation theory (SAPT) calculations are carried out to elucidate the intermolecular interactions present between fluorinated and nonfluorinated alkyl chain groups and aromatic π systems in the folded and unfolded conformers of Wilcox torsion balance systems. The calculations predict the folded conformers to be 2.0-2.3 kcal/mol more stable than the unfolded conformers, with the preference for the folded conformer being greater in the fluorinated alkyl chain case. We also establish that a simple electrostatic analysis, based on atomic charges, is inadequate for understanding the conformational preferences of these systems. In the folded conformers, there are sizable charge penetration contributions that are not recovered by point charge models. Additionally, the SAPT analysis reveals that exchange-repulsion interactions make a significant contribution to the relative stability of the folded and unfolded conformer.

Unraveling the Role of Alkyl F on CH-π Interactions and Uncovering the Tipping Point for Fluorophobicity.

Although fluorine often plays an influential role in molecular recognition, little is known about the effect of aliphatic fluorine on the CH-π interaction in solution. A series of molecular balances were synthesized that contain fluorinated and nonfluorinated alkyl groups. Our findings indicate that fluorine's polarizing ability does enhance CH-π binding and depends on molecular orientation. Surprisingly, when the terminal end of the alkyl group is completely fluorinated, the balance tips toward fluorophobicity and assumes an unusual constrained conformation.

Effect of diazocine bridgehead modification on the folding of the Wilcox molecular torsion balance: a view from a different angle.

Replacing the methano (NCH(2)N) bridgehead with an ethano (NCH(2)CH(2)N) bridgehead affects the conformational equilibrium of the Wilcox molecular torsion balance. With a NCH(2)CH(2)N bridgehead, the phenyl and the cyclohexyl esters prefer the out conformation, whereas with the NCH(2)N bridgehead, they were found to prefer the folded conformation.

Supramolecular control of fluorescence through reversible encapsulation.

The trans to cis isomerization of 4,4'-dimethylazobenzene by the nonchemical stimuli light and heat alters its guest binding properties, allowing control over encapsulation of a second guest. We show here how this remote control for reversible encapsulation can be used as a supramolecular fluorescence on/off switch. If trans-4-ethyl-4'-methylstilbene is used as the second guest its fluorescence is altered depending on whether it is free in solution or encapsulated. We demonstrate that the change in fluorescence is indeed a consequence of the controlled encapsulation state of the stilbene by correlation of fluorescence and (1)H NMR data.

"Too small, too big, and just right"--optical sensing of molecular conformations in self-assembled capsules.

Irradiation of dimethylbenzil within a cylindrical capsule gives bright green phosphorescence, while irradiation of benzil and dimethoxybenzil in the same capsule results in high energy blue fluorescence. This difference is likely due to the geometric restrictions imposed by the capsule's space on its excited guests, forcing a trans-planar conformation in some cases and cis-skewed in others.

Control of stilbene conformation and fluorescence in self-assembled capsules.

The extensively studied trans-stilbene molecule is known to give only weak fluorescence in solution and inside loosely-fitting synthetic capsules. However, trans-stilbene has been recently studied in the context of antibody interiors, where binding results in strong blue fluorescence. The present research was undertaken to understand the spatial factors that influence stilbene fluorescence. trans-Stilbene was encapsulated in the snug, self-assembled complex 1.1 and exhibited fluorescence quenching due to the distortion of its ground-state geometry. When the complex is elongated by incorporating glycouril spacers, trans-stilbene is allowed to adapt a fully coplanar arrangement and fluorescence returns.

Benzil-tethered precipitons for controlling solubility: a round-trip energy-transfer mechanism in the isomerization of extended stilbene analogues.

We are investigating photoresponsive molecules called "precipitons" that undergo a solubility change co-incident with isomerization. Isomerization can be induced by light or by catalytic reagents. Previous work demonstrated that covalent attachment of a metal complex, Ru(II)(bpy)3, greatly accelerates photoisomerization and influences the photostationary state. In this paper, we describe precipitons (1,2-biphenylethenes; analogous to stilbenes) that are activated by a covalently attached organic sensitizer (benzil). We find that isomerization of these stilbene analogues is little effected by the presence of benzil in solution but that the intramolecular benzil effect is to increase the rate of isomerization and to significantly change the photostationary state. What is most interesting about these observations is that the precipiton is the primary chromophore in this bichromophoric system (precipiton absorbance is many times greater than benzil absorbance in the 300-400 nm range), yet the neighboring benzil has a significant effect on the rate and the photostationary state. The effect of unattached benzil on the rate was small, about a 24% increase in rate as compared with 4-6-fold changes for an attached benzil. We speculate that the isomerization process occurs by a "round-trip" energy-transfer mechanism. Initial excitation of the precipiton chromophore initiates a sequence that includes (1) formation of the precipiton singlet state, (2) singlet excitation transfer from the precipiton unit to the benzil, (3) benzil-centered intersystem crossing to the localized benzil triplet state, (4) triplet energy transfer from the benzil moiety back to the precipiton, and (5) isomerization.

Intramolecularly sensitized precipitons: a model system for application to metal sequestration.

We have investigated light-triggered or catalytically activated precipitation agents and have proposed the name "precipiton" for such molecules or molecular fragments. A phase separation is induced when the precipiton isomerizes to a low-solubility form. In this paper we describe the first intramolecularly activated precipitons. The isomerization process is induced by intramolecular triplet energy transfer from a covalently attached metal complex. As expected, intramolecular sensitization leads to a more rapid isomerization than can be achieved by intermolecular sensitization at accessible concentrations. Two isomeric bichromophoric precipiton species, each containing [Ru(bpy)(3)](2+) and 1,2-bis(biphenyl)ethene units covalently linked together by an ether tether, have been synthesized and characterized, and their photochemical properties have been investigated. The rates of photoisomerization of these complexes, [((Z)-1,2-bis(biphenyl)ethene-bpy)Ru(bpy)(2)](PF(6))(2) (2Z) and [((E)-1,2-bis(biphenyl)ethene-bpy)Ru(bpy)(2)](PF(6))(2) (2E), were compared to those of their untethered analogues, (Z)-1,2-bis(biphenyl)ethene-OTBS (1Z) and (E)-1,2-bis(biphenyl)ethene-OTBS (1E), where ruthenium sensitization occurred through an intermolecular pathway. Upon irradiation with visible light (lambda > or = 400 nm) in degassed solution, 2Z/E and 1Z/E obeyed reversible first-order rate kinetics. The intramolecularly sensitized precipiton 2Z isomerized 250 times faster (k(2Z-->2E) = 1.0 x 10(-3) s(-1) with a 51% neutral density filter) than the intermolecular case 1Z (k(1Z-->1E) = 0.80 x 10(-5) s(-1)). For 1E and 2E, the isomerization rates were k(1E-->1Z) = 11.0 x 10(-5) s(-1) and k(2E-->2Z) = 1.6 x 10(-3) s(-1), respectively. The average Z/E mole ratio at the photostationary state was 62/38 for 2Z/E and 93/7 for 1Z/E. The impetus for this study was our desire to evaluate the possibility of using metal-binding precipitons that would precipitate only upon metal-to-precipiton binding and would be inert to visible light in the absence of metals.