Genome-Wide Identification of Transcriptional Start Sites in the Plant Pathogen Pseudomonas syringae pv. tomato str. DC3000

RNA-Seq has provided valuable insights into global gene expression in a wide variety of organisms. Using a modified RNA-Seq approach and Illumina's high-throughput sequencing technology, we globally identified 5′-ends of transcripts for the plant pathogen Pseudomonas syringae pv. tomato str. DC3000. A substantial fraction of 5′-ends obtained by this method were consistent with results obtained using global RNA-Seq and 5′RACE. As expected, many 5′-ends were positioned a short distance upstream of annotated genes. We also captured 5′-ends within intergenic regions, providing evidence for the expression of un-annotated genes and non-coding RNAs, and detected numerous examples of antisense transcription, suggesting additional levels of complexity in gene regulation in DC3000. Importantly, targeted searches for sequence patterns in the vicinity of 5′-ends revealed over 1200 putative promoters and other regulatory motifs, establishing a broad foundation for future investigations of regulation at the genomic and single gene levels

Probing Intermolecular Electron Delocalization in Dimer Radical Anions by Vibrational Spectroscopy

Delocalization of charges is one of the factors controlling charge transport in conjugated molecules. It is considered to play an important role in the performance of a wide range of molecular technologies, including organic solar cells and organic electronics. Dimerization reactions are well-suited as a model to investigate intermolecular spatial delocalization of charges. While dimerization reactions of radical cations are well investigated, studies on radical anions are still scarce. Upon dimerization of radical anions with neutral counterparts, an electron is considered to delocalize over the two molecules. Here, by using time-resolved infrared (TRIR) detection coupled with pulse radiolysis, we show that radical anions of 4-<i>n</i>-hexyl-4′-cyanobiphenyl (<b>6CB</b>) undergo such dimerization reactions, with an electron equally delocalized over the two molecules. We have recently demonstrated that nitrile ν­(CN) vibrations respond to the degree of electron localization of nitrile-substituted anions: we can quantify the changes in the electronic charges from the neutral to the anion states in the nitriles by monitoring the ν­(CN) IR shifts. In the first part of this article, we show that the sensitivity of the ν­(CN) IR shifts does not depend on solvent polarity. In the second part, we describe how probing the shifts of the nitrile IR vibrational band unambiguously confirms the formation of dimer radical anions, with <i>K</i>_dim = 3 × 10⁴ M^–1. IR findings are corroborated by electronic absorption spectroscopy and electronic structure calculations. We find that the presence of a hexyl chain and the formation of π–π interactions are both crucial for dimerization of radical anions of <b>6CB</b> with neutral <b>6CB</b>. The present study provides clear evidence of spatial delocalization of electrons over two molecular fragments

Experimental Insight into the Thermodynamics of the Dissolution of Electrolytes in Room-Temperature Ionic Liquids: From the Mass Action Law to the Absolute Standard Chemical Potential of a Proton

Room-temperature ionic liquids (ILs) are a class of nonaqueous solvents that have expanded the realm of modern chemistry, drawing increasing interest over the last few decades, not only in terms of their own unique physical chemistry but also in many applications including organic synthesis, electrochemistry, and biological systems, wherein charged solutes (i.e., electrolytes) often play vital roles. However, our fundamental understanding of the dissolution of an electrolyte in an IL is still rather limited. For example, the activity of a charged species has frequently been assumed to be unity without a clear experimental basis. In this study, we have discussed a standard component-based scheme for the dissolution of an electrolyte in an IL, supported by our observation of ideal Nernstian responses for the reduction of silver and ferrocenium salts in a representative IL, 1-ethyl-3-methylimidazolium bis­(trifluoromethanesulfonyl)­imide ([emim⁺]­[NTf₂^–] or [emim⁺]­[TFSI^–]). Using this scheme, which was also supported by temperature-dependent measurements with ILs having longer alkyl chains in the imidazolium ring, and the solubility of the IL in water, we established the concept of Gibbs transfer energies of “pseudo-single ions” from the IL to conventional neutral molecular solvents (water, acetonitrile, and methanol). This concept, which bridges component- and constituent-based energetics, utilizes an extrathermodynamic assumption, which itself was justified by experimental observations. These energies enable us to eliminate inner potential differences between the IL and molecular solvents (solvent–solvent interactions), that is, on a practical level, conditional liquid junction potential differences, so that we can discuss ion–solvent interactions independently. Specifically, we have examined the standard electrode potential of the ferrocenium/ferrocene redox couple, Fc⁺/Fc, and the absolute intrinsic standard chemical potential of a proton in [emim⁺]­[NTf₂^–], finding that the proton is more acidic in the IL than in water by 6.5 ± 0.6 units on the unified pH scale. These results strengthen the progress on the physical chemistry of ions in IL solvent systems on the basis of their activities, providing a rigorous thermodynamic framework

Thermodynamic Aspects of Electrocatalytic CO₂ Reduction in Acetonitrile and with an Ionic Liquid as Solvent or Electrolyte

Thermodynamic Aspects of Electrocatalytic CO₂ Reduction in Acetonitrile and with an Ionic Liquid as Solvent or Electrolyt

Vibrational Stark Effects To Identify Ion Pairing and Determine Reduction Potentials in Electrolyte-Free Environments

A recently developed instrument for time-resolved infrared detection following pulse radiolysis has been used to measure the ν­(CN) IR band of the radical anion of a CN-substituted fluorene in tetrahydrofuran. Specific vibrational frequencies can exhibit distinct frequency shifts due to ion pairing, which can be explained in the framework of the vibrational Stark effect. Measurements of the ratio of free ions and ion pairs in different electrolyte concentrations allowed us to obtain an association constant and free energy change for ion pairing. This new method has the potential to probe the geometry of ion pairing and allows the reduction potentials of molecules to be determined in the absence of electrolyte in an environment of low dielectric constant

Identification of Ion-Pair Structures in Solution by Vibrational Stark Effects

Ion pairing is a fundamental consideration in many areas of chemistry and has implications in a wide range of sciences and technologies that include batteries and organic photovoltaics. Ions in solution are known to inhabit multiple possible states, including free ions (FI), contact ion pairs (CIP), and solvent-separated ion pairs (SSIP). However, in solutions of organic radicals and nonmetal electrolytes, it is often difficult to distinguish between these states. In the first part of this work, we report evidence for the formation of SSIPs in low-polarity solvents and distinct measurements of CIP, SSIP, and FI, by using the ν­(CN) infrared (IR) band of a nitrile-substituted fluorene radical anion. Use of time-resolved IR detection following pulse radiolysis allowed us to unambiguously assign the peak of the FI. In the presence of nonmetal electrolytes, two distinct red-shifted peaks were observed and assigned to the CIP and SSIP. The assignments are interpreted in the framework of the vibrational Stark effect (VSE) and are supported by (1) the solvent dependence of ion-pair populations, (2) the observation of a cryptand-separated sodium ion pair that mimics the formation of SSIPs, and (3) electronic structure calculations. In the second part of this work, we show that a blue-shift of the ν­(CN) IR band due to the VSE can be induced in a nitrile-substituted fluorene radical anion by covalently tethering it to a metal-chelating ligand that forms an intramolecular ion pair upon reduction and complexation with sodium ion. This adds support to the conclusion that the shift in IR absorptions by ion pairing originates from the VSE. These results combined show that we can identify ion-pair structures by using the VSE, including the existence of SSIPs in a low-polarity solvent