A new method for in vivo assessment of corneal transparency using spectral-domain OCT.

Corneal transparency is essential to provide a clear view into and out of the eye, yet clinical means to assess such transparency are extremely limited and usually involve a subjective grading of visible opacities by means of slit-lamp biomicroscopy. Here, we describe an automated algorithm allowing extraction of quantitative corneal transparency parameters with standard clinical spectral-domain optical coherence tomography (SD-OCT). Our algorithm employs a novel pre-processing procedure to standardize SD-OCT image analysis and to numerically correct common instrumental artifacts before extracting mean intensity stromal-depth (z) profiles over a 6-mm-wide corneal area.

A Novel Pump-Pump-Probe Resonance Raman Approach Featuring Light-Induced Charge Accumulation on a Model Photosystem.

Light-induced charge accumulation is at the heart of biomimetic systems aiming at solar fuel production in the realm of artificial photosynthesis. Understanding the mechanisms upon which these processes operate is a necessary condition to drive down the rational catalyst design road. We have built a nanosecond pump-pump-probe resonance Raman setup to witness the sequential charge accumulation process while probing vibrational features of different charge-separated states.

DFT exchange: sharing perspectives on the workhorse of quantum chemistry and materials science.

In this paper, the history, present status, and future of density-functional theory (DFT) is informally reviewed and discussed by 70 workers in the field, including molecular scientists, materials scientists, method developers and practitioners. The format of the paper is that of a roundtable discussion, in which the participants express and exchange views on DFT in the form of 302 individual contributions, formulated as responses to a preset list of 26 questions. Supported by a bibliography of 777 entries, the paper represents a broad snapshot of DFT, anno 2022.

Prediction uncertainty validation for computational chemists.

Validation of prediction uncertainty (PU) is becoming an essential task for modern computational chemistry. Designed to quantify the reliability of predictions in meteorology, the calibration-sharpness (CS) framework is now widely used to optimize and validate uncertainty-aware machine learning (ML) methods. However, its application is not limited to ML and it can serve as a principled framework for any PU validation.

The long road to calibrated prediction uncertainty in computational chemistry.

Uncertainty quantification (UQ) in computational chemistry (CC) is still in its infancy. Very few CC methods are designed to provide a confidence level on their predictions, and most users still rely improperly on the mean absolute error as an accuracy metric. The development of reliable UQ methods is essential, notably for CC to be used confidently in industrial processes.

Modulation of the Directionality of Hole Transfer between the Base and the Sugar-Phosphate Backbone in DNA with the Number of Sulfur Atoms in the Phosphate Group.

This work shows that S atom substitution in phosphate controls the directionality of hole transfer processes between the base and sugar-phosphate backbone in DNA systems. The investigation combines synthesis, electron spin resonance (ESR) studies in supercooled homogeneous solution, pulse radiolysis in aqueous solution at ambient temperature, and density functional theory (DFT) calculations of in-house synthesized model compound dimethylphosphorothioate (DMTP(O)═S) and nucleotide (5'--methoxyphosphorothioyl-2'-deoxyguanosine (G-P(O)═S)). ESR investigations show that DMTP(O)═S reacts with Cl to form the σσ* adduct radical -P-S[Formula: see text]Cl, which subsequently reacts with DMTP(O)═S to produce [-P-S[Formula: see text]S-P-].

One Way Traffic: Base-to-Backbone Hole Transfer in Nucleoside Phosphorodithioate.

Invited for the cover of this issue are the groups of Roman Dembinski, Mehran Mostafavi, and Amitava Adhikary at the Polish Academy of Sciences, Université Paris-Saclay, and Oakland University. The image depicts a doughnut as a way of illustrating the hole transfer process. Read the full text of the article at 10.

Probabilistic performance estimators for computational chemistry methods: Systematic improvement probability and ranking probability matrix. II. Applications.

In Paper I [P. Pernot and A. Savin, J.

Probabilistic performance estimators for computational chemistry methods: Systematic improvement probability and ranking probability matrix. I. Theory.

The comparison of benchmark error sets is an essential tool for the evaluation of theories in computational chemistry. The standard ranking of methods by their mean unsigned error is unsatisfactory for several reasons linked to the non-normality of the error distributions and the presence of underlying trends. Complementary statistics have recently been proposed to palliate such deficiencies, such as quantiles of the absolute error distribution or the mean prediction uncertainty.

One Way Traffic: Base-to-Backbone Hole Transfer in Nucleoside Phosphorodithioate.

The directionality of the hole-transfer processes between DNA backbone and base was investigated by using phosphorodithioate [P(S )=S] components. ESR spectroscopy in homogeneous frozen aqueous solutions and pulse radiolysis in aqueous solution at ambient temperature confirmed initial formation of G -P(S )=S. The ionization potential of G-P(S )=S was calculated to be slightly lower than that of guanine in 5'-dGMP.

Quantitative measures of corneal transparency, derived from objective analysis of depth-resolved corneal images, demonstrated with full-field optical coherence tomographic microscopy.

Loss of corneal transparency, as occurs with various pathologies, infections, immune reactions, trauma, aging, and surgery, is a major cause of visual handicap worldwide. However, current means to assess corneal transparency are extremely limited and clinical and eye-bank practice usually involve a subjective and qualitative observation of opacities, sometimes with comparison against an arbitrary grading scale, by means of slit-lamp biomicroscopy. Here, we describe a novel objective optical data analysis-based method that enables quantifiable and standardized characterization of corneal transparency from depth-resolved corneal images, addressing the demand for such a means in both the laboratory and clinical ophthalmology setting.

Mechanism of (SCN) Formation and Decay in Neutral and Basic KSCN Solution under Irradiation from a Pico- to Microsecond Range.

The detailed mechanism of the reaction between SCN and the OH radical and the formation of the dimer radical (SCN) are studied by picosecond pulse radiolysis. First, concentrated SCN solutions are used to observe directly the formation and decay of SCNOH in neutral and basic solutions. Then, the spectro-kinetic data, constituting a large matrix of data of the absorbance at different times and different wavelengths, obtained by pulse radiolysis measurements with a streak camera, in neutral and basic SCN solutions, are analyzed simultaneously.

Ultrafast Electron Attachment and Hole Transfer Following Ionizing Radiation of Aqueous Uridine Monophosphate.

The primary localization process of radiation-induced charges (holes (cation radical sites) and excess electrons) remains poorly understood, even at the level of monomeric DNA/RNA models, in particular, in an aqueous environment. We report the first spectroscopic study of charge transfer occurring in radiolysis of aqueous uridine 5'-monophosphate (UMP) solutions and its components: uridine, uracil, ribose, and phosphate. Our results show that prehydrated electrons effectively attach to the base site of UMP; the holes in UMP formed by either direct ionization or reaction of UMP with the radiation-mediated water cation radical (HO) facilely localize on the ribose site, despite the fact that a part of them were initially created on either the phosphate or uracil.

Probabilistic performance estimators for computational chemistry methods: The empirical cumulative distribution function of absolute errors.

Benchmarking studies in computational chemistry use reference datasets to assess the accuracy of a method through error statistics. The commonly used error statistics, such as the mean signed and mean unsigned errors, do not inform end-users on the expected amplitude of prediction errors attached to these methods. We show that, the distributions of model errors being neither normal nor zero-centered, these error statistics cannot be used to infer prediction error probabilities.

Picosecond Pulse Radiolysis Study on the Radiation-Induced Reactions in Neat Tributyl Phosphate.

The ultrafast radiolytic behavior of tributyl phosphate, TBP, has been investigated using 7 ps electron pulses with 7 MeV kinetic energy, from which two key species have been observed and characterized: the TBP solvated electron (e) and the TBP triplet excited state TBP* (a) or its fragmentation products. The e exhibits a broad absorption band in the visible and near-infrared (NIR) spectrum, with a maximum beyond our 1500 nm detection limit. Nitromethane was used to scavenge e to confirm its absorption spectrum and to determine its associated rate coefficient, 1.

Direct observation of the oxidation of DNA bases by phosphate radicals formed under radiation: a model of the backbone-to-base hole transfer.

In irradiated DNA, by the base-to-base and backbone-to-base hole transfer processes, the hole (i.e., the unpaired spin) localizes on the most electropositive base, guanine.

Oxygen anion (O ) and hydroxide anion (HO ) reactivity with a series of old and new refrigerants.

The reactivity of a series of commonly used halogenated compounds (trihalomethanes, chlorofluorocarbon, hydrochlorofluorocarbon, fluorocarbons, and hydrofluoroolefin) with hydroxide and oxygen anion is studied in a compact Fourier transform ion cyclotron resonance. O is formed by dissociative electron attachment to N O and HO by a further ion-molecule reaction with ammonia. Kinetic experiments are performed by increasing duration of introduction of the studied molecule at a constant pressure.

The parameter uncertainty inflation fallacy.

Statistical estimation of the prediction uncertainty of physical models is typically hindered by the inadequacy of these models due to various approximations they are built upon. The prediction errors caused by model inadequacy can be handled either by correcting the model's results or by adapting the model's parameter uncertainty to generate prediction uncertainties representative, in a way to be defined, of model inadequacy errors. The main advantage of the latter approach (thereafter called PUI, for Parameter Uncertainty Inflation) is its transferability to the prediction of other quantities of interest based on the same parameters.

Effect of the solvation state of electron in dissociative electron attachment reaction in aqueous solutions.

It is generally considered that the pre-solvated electron and the solvated electron reacting with a solute yield the same product. Silver cyanide complex, Ag(CN), is used as a simple probe to demonstrate unambiguously the existence of a different reduction mechanism for pre-hydrated electrons. Using systematic multichannel transient absorption measurements at different solute concentrations from millimolar to decimolar, global data analysis and theoretical calculations, we present the dissociative electron attachment on Ag(CN).

Observation and Simulation of Transient Anion Oligomers (LiClO) (n = 1-4) in Diethyl Carbonate LiClO Solutions.

NMR measurements show that diethyl carbonate (DEC, a solvent with a low dielectric constant) solutions of LiClO contain (LiClO) oligomers. The reduction of these species by solvated and presolvated electrons is followed by picosecond pulse radiolysis measurements. The data analysis shows that several anions absorbing in the near-infrared (NIR) and visible range are formed after the 7 ps electron pulse.

When does a functional correctly describe both the structure and the energy of the transition state?

Requiring that several properties are well reproduced is a severe test on density functional approximations. This can be assessed through the estimation of joint and conditional success probabilities. An example is provided for a small set of molecules, for properties characterizing the transition states (geometries and energies).

Molecular Isomer Identification of Titan's Tholins Organic Aerosols by Photoelectron/Photoion Coincidence Spectroscopy Coupled to VUV Synchrotron Radiation.

The chemical composition of Titan organic haze is poorly known. To address this issue, laboratory analogues named tholins are synthesized and analyzed by methods often requiring an extraction process in a carrier solvent. These methods exclude the analysis of the insoluble tholins' fraction and assume a hypothetical chemical equivalence between soluble and insoluble fractions.

Energetics of Photoinduced Charge Migration within the Tryptophan Tetrad of an Animal (6-4) Photolyase.

Cryptochromes and photolyases are flavoproteins that undergo cascades of electron/hole transfers after excitation of the flavin cofactor. It was recently discovered that animal (6-4) photolyases, as well as animal cryptochromes, feature a chain of four tryptophan residues, while other members of the family contain merely a tryptophan triad. Transient absorption spectroscopy measurements on Xenopus laevis (6-4) photolyase have shown that the fourth residue is effectively involved in photoreduction but at the same time could not unequivocally ascertain the final redox state of this residue.