We have measured the IR and UV spectra of cytosine in a low-temperature argon matrix. An attempt was made to determine the tautomeric ratios existing in the matrix, making use of the matrix-isolation IR spectrum and computed IR intensities of the tautomers in a least squares fitting procedure. The mole fractions are about 0.22 for oxo(-amino) form, 0.26 and 0.44 for the two rotamers, respectively, of the hydroxy(-amino) form and 0.08 for the (oxo-)imino tautomer. These ratios were then used to simulate the matrix-isolation UV spectrum as a composite of the individual spectra, the latter calculated ab initio at high levels of electron correlation theory. The agreement between simulated and experimental UV spectra seems satisfactory. This indicates that, in contrast to the solid state and solution spectra described up to now by the oxo(-amino) form alone, the reproduction of the matrix-isolation UV spectrum needs at least the hydroxy(-amino) and oxo(-amino) forms, and probably also the (oxo-)imino form.

Tautomers of Cytosine and Their Excited Electronic States: a Matrix Isolation Spectroscopic and Quantum Chemical Study

This Feature Article starts highlighting some recent experimental and theoretical advances in the field of IR and Raman spectroscopy, giving a taste of the breadth and dynamics of this striving field. The local mode theory is then reviewed, showing how local vibrational modes are derived from fundamental normal modes. New features are introduced that add to current theoretical efforts: (i) a unique measure of bond strength based on local mode force constants ranging from bonding in single molecules in different environments to bonding in periodic systems and crystals and (ii) a new way to interpret vibrational spectra by pinpointing and probing interactions between particular bond stretching contributions to the normal modes. All of this represents a means to work around the very nature of normal modes, namely that the vibrational motions in polyatomic molecules are delocalized. Three current focus points of the local mode analysis are reported, demonstrating how the local mode analysis extracts important information hidden in vibrational spectroscopy data supporting current experiments: (i) metal-ligand bonding in heme proteins, such as myoglobin and neuroglobin; (ii) disentanglement of DNA normal modes; and (iii) hydrogen bonding in water clusters and ice. Finally, the use of the local mode analysis by other research groups is summarized. Our vision is that in the future local mode analysis will be routinely applied by the community and that this Feature Article serves as an incubator for future collaborations between experiment and theory.

The Local Vibrational Mode Theory and Its Place in the Vibrational Spectroscopy Arena.

The acid-base properties of surfaces significantly influence catalytic and (photo)electrochemical processes. Estimation of acid dissociation constants (pKa values) for colloids is commonly performed through electroanalytical techniques or spectroscopic methods employing label molecules. Here, we show that polarimetric angle-resolved second harmonic scattering (AR-SHS) can be used as an all-optical, label-free probe of colloid surface pKa values. We apply AR-SHS to dispersions of 100 nm anatase TiO2 particles to extract surface potential and surface susceptibility, a measure of interfacial water orientation, as a function of pH. The surface potential follows changes in surface charge density, while the interfacial water orientation inverts at pH ∼4.8, ∼6, and ∼7.6. As the variation in bulk pH modifies the populations of Ti-OH2+, Ti-OH, and Ti-O- interfacial groups, a change in water orientation reports on the ratio of protonated/deprotonated species. Such observation allows for pKa evaluation from plots of surface susceptibility versus pH. A Nerstian trend in the surface potential is additionally demonstrated.

Water Orientation at the Anatase TiO2 Nanoparticle Interface: A Probe of Surface pKa Values.

Nonlinear electric response of the diffuse double layer to an abrupt charge displacement inside a biological membrane.

Influence of the Hydrogen-Bonding Environment on Vibrational Coupling in the Electrical Double Layer at the Silica/Aqueous Interface

The electric double layer governs the processes of all charged surfaces in aqueous solutions; however, elucidating the structure of the water molecules is challenging for even the most advanced spectroscopic techniques. Here, we present the individual Stern layer and diffuse layer OH stretching spectra at the silica/water interface in the presence of NaCl over a wide pH range using a combination of vibrational sum frequency generation spectroscopy, heterodyned second harmonic generation, and streaming potential measurements. We find that the Stern layer water molecules and diffuse layer water molecules respond differently to pH changes: unlike the diffuse layer, whose water molecules remain net-oriented in one direction, water molecules in the Stern layer flip their net orientation as the solution pH is reduced from basic to acidic. We obtain an experimental estimate of the non-Gouy-Chapman (Stern) potential contribution to the total potential drop across the insulator/electrolyte interface and discuss it in the context of dipolar, quadrupolar, and higher order potential contributions that vary with the observed changes in the net orientation of water in the Stern layer. Our findings show that a purely Gouy-Chapman (Stern) view is insufficient to accurately describe the electrical double layer of aqueous interfaces.

/pdf/water-structure-in-the-electrical-double-layer-and-the-dohknus9.pdf

Water Structure in the Electrical Double Layer and the Contributions to the Total Interfacial Potential at Different Surface Charge Densities.

The electric double layer governs the processes of all charged surfaces in aqueous solutions, however elucidating the structure of the water molecules is challenging for even the most advanced spectroscopic techniques. Here, we present the individual Stern layer and diffuse layer OH stretching spectra at the silica/water interface in the presence of NaCl over a wide pH range using a combination of vibrational sum frequency generation and heterodyned second harmonic generation techniques, streaming potential measurements, and the maximum entropy method. We find that the Stern layer water molecules and diffuse layer water molecules respond differently to pH changes: unlike the diffuse layer, whose water molecules remain net-oriented in one direction, water molecules in the Stern layer flip their net orientation as the solution pH is reduced from basic to acidic. We obtain an experimental estimate of the dipole potential contribution to the total potential drop across the insulator/electrolyte interface and find it to dominate over the Coulomb-only (Gouy-Chapman, Gouy-Chapman-Stern) contribution. We quantify how these contributions result in a considerable influence on the vibrational lineshapes. Our findings show that a purely Coulombic view is insufficient to accurately describe the electrical double layer over aqueous interfaces.

Water Dipole Populations in the Electrical Double Layer and Their Contributions to the Total Interfacial Potential at Different Surface Charge Densities

In this study, density functional theory (DFT) and time dependent density functional theory (TD-DFT) are used to investigate the stabilities and spectral properties [IR, UV–vis, and two-photon abso...

The thermochemical, structural, and spectroscopic analyses of the tautomers of sulfur and selenium modified emissive nucleobases

Self-replication of nucleic acids in the absence of enzymes represents an important and poorly understood step in the origin of life as such reported systems are strongly hindered by product inhibition. Studying one of the few successful examples of enzymatic DNA self-replication based on a simple ligation chain reaction, lesion-induced DNA amplification (LIDA), can shed light on how this fundamental process may have originally evolved. To identify the unknown factors that lead LIDA to overcome product inhibition we have employed isothermal titration calorimetry and global fitting of time-dependent ligation data to characterize the individual steps of the amplification process. We find that incorporating the abasic lesion into one of the four primers substantially decreases the stability difference between the product and intermediate complexes compared with complexes without the abasic group. In the presence of T4 DNA ligase this stability gap is further reduced by two orders of magnitude revealing that the ligase also helps overcome product inhibition. Kinetic simulations reveal that the intermediate complex stability and the magnitude of the ligation rate constant significantly impact the rate of self-replication, suggesting that catalysts that both facilitate ligation and stabilize the intermediate complex might be a route to efficient nonenzymatic replication.

https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/chem.202300080

Minimizing Product Inhibition in DNA Self-Replication: Insights for Prebiotic Replication from the Role of the Enzyme in Lesion-Induced DNA Amplification.

Shyam Parshotam

Papers

Water Structure in the Electrical Double Layer and the Contributions to the Total Interfacial Potential at Different Surface Charge Densities.

Influence of the Hydrogen-Bonding Environment on Vibrational Coupling in the Electrical Double Layer at the Silica/Aqueous Interface

Water Dipole Populations in the Electrical Double Layer and Their Contributions to the Total Interfacial Potential at Different Surface Charge Densities

The thermochemical, structural, and spectroscopic analyses of the tautomers of sulfur and selenium modified emissive nucleobases

Minimizing Product Inhibition in DNA Self-Replication: Insights for Prebiotic Replication from the Role of the Enzyme in Lesion-Induced DNA Amplification.