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. The z-profiles are analyzed using our previously developed objective method that derives quantitative transparency parameters directly related to the physics of light propagation in tissues. Tissular heterogeneity is quantified by the Birge ratio Br and the photon mean-free path (ls) is determined for homogeneous tissues (i.e., Br~1). SD-OCT images of 83 normal corneas (ages 22-50 years) from a standard SD-OCT device (RTVue-XR Avanti, Optovue Inc.) were processed to establish a normative dataset of transparency values. After confirming stromal homogeneity (Br <10), we measured a median ls of 570 µm (interdecile range: 270-2400 µm). By also considering corneal thicknesses, this may be translated into a median fraction of transmitted (coherent) light Tcoh(stroma) of 51% (interdecile range: 22-83%). Excluding images with central saturation artifact raised our median Tcoh(stroma) to 73% (interdecile range: 34-84%). These transparency values are slightly lower than those previously reported, which we attribute to the detection configuration of SD-OCT with a relatively small and selective acceptance angle. No statistically significant correlation between transparency and age or thickness was found. In conclusion, our algorithm provides robust and quantitative measurements of corneal transparency from standard SD-OCT images with sufficient quality (such as 'Line' and 'CrossLine' B-scan modes without central saturation artifact) and addresses the demand for such an objective means in the clinical setting.

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. By employing a reversible model system featuring methyl viologen (MV) as a dual electron acceptor, we have been able to watch the photosensitized production of its neutral form, MV0, resulting from two sequential electron transfer reactions. We have found that, upon double excitation, a fingerprint vibrational mode corresponding to the doubly reduced species appears at 992 cm-1 and peaks at 30 µs after the second excitation. This has been further confirmed by simulated resonance Raman spectra which fully support our experimental findings in this unprecedented buildup of charge seen by a resonance Raman probe.

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 present article is intended as a step-by-step introduction to the concepts and techniques of PU validation in the CS framework, adapted to the specifics of computational chemistry. The presented methods range from elementary graphical checks to more sophisticated ones based on local calibration statistics. The concept of tightness, is introduced. The methods are illustrated on synthetic datasets and applied to uncertainty quantification data issued from the computational chemistry literature.

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. A review of the CC-UQ literature shows that there is no common standard procedure to report or validate prediction uncertainty. I consider here analysis tools using concepts (calibration and sharpness) developed in meteorology and machine learning for the validation of probabilistic forecasters. These tools are adapted to CC-UQ and applied to datasets of prediction uncertainties provided by composite methods, Bayesian ensembles methods, and machine learning and a posteriori statistical methods.

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'-O-methoxyphosphorothioyl-2'-deoxyguanosine (G-P(O-)═S)). ESR investigations show that DMTP(O-)═S reacts with Cl2•- to form the σ2σ*1 adduct radical -P-S[Formula: see text]Cl, which subsequently reacts with DMTP(O-)═S to produce [-P-S[Formula: see text]S-P-]-. -P-S[Formula: see text]Cl in G-P(O-)═S undergoes hole transfer to Gua, forming the cation radical (G•+) via thermally activated hopping. However, pulse radiolysis measurements show that DMTP(O-)═S forms the thiyl radical (-P-S•) by one-electron oxidation, which did not produce [-P-S[Formula: see text]S-P-]-. Gua in G-P(O-)═S is oxidized unimolecularly by the -P-S• intermediate in the sub-picosecond range. DFT thermochemical calculations explain the differences in ESR and pulse radiolysis results obtained at different temperatures.

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 10.1002/chem.202000247.

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. We introduce here a new score, the systematic improvement probability, based on the direct system-wise comparison of absolute errors. Independent of the chosen scoring rule, the uncertainty of the statistics due to the incompleteness of the benchmark datasets is also generally overlooked. However, this uncertainty is essential to appreciate the robustness of rankings. In the present article, we develop two indicators based on robust statistics to address this problem: Pinv, the inversion probability between two values of a statistic, and Pr, the ranking probability matrix. We demonstrate also the essential contribution of the correlations between error sets in these scores comparisons.

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. Chem. Phys. 152, 164108 (2020)], we introduced the systematic improvement probability as a tool to assess the level of improvement on absolute errors to be expected when switching between two computational chemistry methods. We also developed two indicators based on robust statistics to address the uncertainty of ranking in computational chemistry benchmarks: Pinv, the inversion probability between two values of a statistic, and Pr, the ranking probability matrix. In this second part, these indicators are applied to nine data sets extracted from the recent benchmarking literature. We also illustrate how the correlation between the error sets might contain useful information on the benchmark dataset quality, notably when experimental data are used as reference.

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. Subsequent thermally activated hole transfer from G.+ to P(S- )=S led to dithiyl radical (P-2S. ) formation on the µs timescale. In parallel, ESR spectroscopy, pulse radiolysis, and density functional theory (DFT) calculations confirmed P-2S. formation in an abasic phosphorodithioate model compound. ESR investigations at low temperatures and higher G-P(S- )=S concentrations showed a bimolecular conversion of P-2S. to the σ2 -σ*1 -bonded dimer anion radical [-P-2S - . 2S-P-]- [ΔG (150 K, DFT)=-7.2 kcal mol-1 ]. However, [-P-2S - . 2S-P-]- formation was not observed by pulse radiolysis [ΔG° (298 K, DFT)=-1.4 kcal mol-1 ]. Neither P-2S. nor [-P-2S - . 2S-P-]- oxidized guanine base; only base-to-backbone hole transfer occurs in phosphorodithioate.

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. Our approach is based on a mathematical analysis of the acquired optical data with respect to the light attenuation from scattering processes in the corneal stroma. Applicable to any depth-resolved corneal imaging modality, it has been validated by means of full-field optical coherence tomographic microscopy (FF-OCT or FF-OCM). Specifically, our results on ex-vivo corneal specimens illustrate that 1) in homogeneous tissues, characterized by an exponential light attenuation with stromal depth (z), the computation of the scattering mean-free path (ls) from the rate of exponential decay allows quantification of the degree of transparency; 2) in heterogeneous tissues, identified by significant deviations from the normal exponential z -profile, a measure of exponential-decay model inadequacy (e.g., by computation of the Birge ratio) allows the estimation of severity of stromal heterogeneity, and the associated depth-dependent variations around the average ls enables precise localization of the pathology.

Mechanism of (SCN)2·- 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)2·- 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. Data analysis allowed us to deduce the absorption spectra of different radicals with their extinction coefficient and also to determine the rate constants of different reactions involved in the formation and decay of (SCN)2·-. Molecular simulations of the absorption spectra of the different species were also performed. The absorption spectrum of the radical SCN· is determined and is found to be different than that reported previously. It does not present a Gaussian shape centered at 330 nm; the absorption around 310 and 380 nm is not negligible. In addition, in a solution at pH 13, it is found that the (SCN)2·- radical is paired with an alkaline cation, inducing a blueshift of the absorption band compared to the free (SCN)2·-. Finally, the presence of K+ cations catalyzes the disproportionation reaction of (SCN)2·- and affects the kinetics.

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 (H2O•+) facilely localize on the ribose site, despite the fact that a part of them were initially created on either the phosphate or uracil. The nature of phosphate-to-sugar hole transfer is characterized as a barrierless intramolecular electron transfer with a time constant of 2.5 ns, while the base-to-sugar hole transfer occurs much faster, within a 5 ps electron pulse.

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. To overcome this limitation, we advocate for the use of more informative statistics, based on the empirical cumulative distribution function of unsigned errors, namely, (1) the probability for a new calculation to have an absolute error below a chosen threshold and (2) the maximal amplitude of errors one can expect with a chosen high confidence level. Those statistics are also shown to be well suited for benchmarking and ranking studies. Moreover, the standard error on all benchmarking statistics depends on the size of the reference dataset. Systematic publication of these standard errors would be very helpful to assess the statistical reliability of benchmarking conclusions.

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 (eTBP-) and the TBP triplet excited state TBP* (3a) or its fragmentation products. The eTBP- 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 eTBP- to confirm its absorption spectrum and to determine its associated rate coefficient, 1.0 × 1010 M-1 s-1. The electron's molar extinction coefficients were found by an isosbestic method using biphenyl as a solvated electron scavenger. The time-dependent radiolytic yield of eTBP- was also determined directly from 7 ps to 7 ns and compared with those in water, tetrahydrofuran, and diethyl carbonate. In less than 10 ns, the decay is not due to the reaction with other solvent molecules and is instead predominantly due to the reactions with cations issued from the proton transfer by the TBP radical cation (TBP•+). In addition to eTBP-, another absorption band, stable up to 7 ns, was identified in the visible range. This has been attributed mainly to the TBP triplet excited state, TBP*(3a), by a combination of molecular modeling methodologies. Interestingly, we did not observe any absorption band in the visible nor in the NIR range arising from TBP•+. Calculations suggest that TBP•+ undergoes rapid proton transfer to yield a UV-absorbing species, TBP(-H+). Experimental results and supporting molecular simulations provide detailed identification of the earliest species yielded from the radiolysis of neat TBP.

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. Phosphate radicals formed via ionization events in the DNA-backbone must play an important role in the backbone-to-base hole transfer process. However, earlier studies on irradiated hydrated DNA, on irradiated DNA-models in frozen aqueous solution and in neat dimethyl phosphate showed the formation of carbon-centered radicals and not phosphate radicals. Therefore, to model the backbone-to-base hole transfer process, we report picosecond pulse radiolysis studies of the reactions between H2PO4˙ with the DNA bases - G, A, T, and C in 6 M H3PO4 at 22 °C. The time-resolved observations show that in 6 M H3PO4, H2PO4˙ causes the one-electron oxidation of adenine, guanine and thymine, by forming the cation radicals via a single electron transfer (SET) process; however, the rate constant of the reaction of H2PO4˙ with cytosine is too low (<107 L mol-1 s-1) to be measured. The rates of these reactions are influenced by the protonation states and the reorganization energies of the base radicals and of the phosphate radical in 6 M H3PO4.

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 N2 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. Hydroxide anion reactions mainly proceed by proton transfer for all the acidic compounds. However, nucleophilic substitution is observed for chlorinated and brominated compounds. For fluorinated compounds, a specific elimination of a neutral fluorinated alkene is observed in our results in parallel with the proton transfer reaction. Oxygen anion reacts rapidly and extensively with all compounds. Main reaction channels result from nucleophilic substitution, proton transfer, and formal H2+ transfer. We highlight the importance of transfer processes (atom or ion) in the intermediate ion-neutral complex, explaining part of the observed reactivity and formed ions. In this paper, we present the first reactivity study of anions with HFO 1234yf. Finally, the potential of O- and HO- as chemical ionization reagents for trace analysis is discussed.

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. A critical review of implementations of PUI in several areas of computational chemistry shows that it is biased, in the sense that it does not produce prediction uncertainty bands conforming to model inadequacy errors.

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)2-, 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)2-. The short-lived silver complex, Ag0(CN)22-, formed by hydrated electron with nanosecond pulse radiolysis, can be observed at room temperature. However, at higher temperatures only the free silver atom, Ag0, is detected, suggesting that Ag0(CN)22- dissociation is fast. Surprisingly, pulse radiolysis measurements on Ag(CN)2- reduction, performed by a 7 ps electron pulse at room temperature, show clearly that a new reduced form of silver complex, AgCN-, is produced within the pulse. This species, absorbing at 560 nm, is not formed by the hydrated electron but exclusively by its precursor. DFT calculations show that the different reactivity of the hydrated and pre-hydrated electrons can be due to the formation of different electronic states of Ag0(CN)22-: the prehydrated electron can form an excited state of this complex, which mainly dissociates into Ag0CN- + CN-.