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1. Valence-shell photoelectron circular dichroism of ruthenium( iii )-tris-(acetylacetonato) gas-phase enantiomers

   https://doi.org/10.1039/D1CP02921E  

   Darquié, Benoît ; Saleh, Nidal ; Tokunaga, Sean K. ; Srebro-Hooper, Monika ; Ponzi, Aurora ; Autschbach, Jochen ; Decleva, Piero ; Garcia, Gustavo A. ; Crassous, Jeanne ; Nahon, Laurent ( November 2021 , Physical Chemistry Chemical Physics)

   Chiral transition-metal complexes are of interest in many fields ranging from asymmetric catalysis and molecular materials science to optoelectronic applications or fundamental physics including parity violation effects. We present here a combined theoretical and experimental investigation of gas-phase valence-shell photoelectron circular dichroism (PECD) on the challenging open-shell ruthenium( iii )-tris-(acetylacetonato) complex, Ru(acac) 3 . Enantiomerically pure Δ- or Λ-Ru(acac) 3 , characterized by electronic circular dichroism (ECD), were vaporized and adiabatically expanded to produce a supersonic beam and photoionized by circularly-polarized VUV light from the DESIRS beamline at Synchrotron SOLEIL. Photoelectron spectroscopy (PES) and PECD experiments were conducted using a double imaging electron/ion coincidence spectrometer, and compared to density functional theory (DFT) and time-dependent DFT (TDDFT) calculations. The open-shell character of Ru(acac) 3 , which is not taken into account in our DFT approach, is expected to give rise to a wide multiplet structure, which is not resolved in our PES signals but whose presence might be inferred from the additional striking features observed in the PECD curves. Nevertheless, the DFT-based assignment of the electronic bands leads to the characterisation of the ionized orbitals. In line with other recent works, the results confirm that PECD persists independently on the localizationmore »and/or on the achiral or chiral nature of the initial orbital, but is rather a probe of the molecular potential as a whole. Overall, the measured PECD signals on Ru(acac) 3 , a system exhibiting D 3 propeller-type chirality, are of similar magnitude compared to those on asymmetric-carbon-based chiral organic molecules which constitute the vast majority of species investigated so far, thus suggesting that PECD is a universal mechanism, inherent to any type of chirality.« less
2. Understanding the Temperature Dependence and Finite Size Effects in Ab Initio MD Simulations of the Hydrated Electron

   https://doi.org/10.1021/acs.jctc.2c00335  

   Park, Sanghyun J. ; Schwartz, Benjamin J. ( July 2022 , Journal of Chemical Theory and Computation)

   The hydrated electron is of interest to both theorists and experimentalists as a paradigm solution-phase quantum system. Although the bulk of the theoretical work studying the hydrated electron is based on mixed quantum/classical (MQC) methods, recent advances in computer power have allowed several attempts to study this object using ab initio methods. The difficulty with employing ab initio methods for this system is that even with relatively inexpensive quantum chemistry methods such as density functional theory (DFT), such calculations are still limited to at most a few tens of water molecules and only a few picoseconds duration, leaving open the question as to whether the calculations are converged with respect to either system size or dynamical fluctuations. Moreover, the ab initio simulations of the hydrated electron that have been published to date have provided only limited analysis. Most works calculate the electron’s vertical detachment energy, which can be compared to experiment, and occasionally the electronic absorption spectrum is also computed. Structural features, such as pair distribution functions, are rare in the literature, with the majority of the structural analysis being simple statements that the electron resides in a cavity, which are often based only on a small number of simulationmore »snapshots. Importantly, there has been no ab initio work examining the temperature-dependent behavior of the hydrated electron, which has not been satisfactorily explained by MQC simulations. In this work, we attempt to remedy this situation by running DFT-based ab initio simulations of the hydrated electron as a function of both box size and temperature. We show that the calculated properties of the hydrated electron are not converged even with simulation sizes up to 128 water molecules and durations of several tens of picoseconds. The simulations show significant changes in the water coordination and solvation structure with box size. Our temperature-dependent simulations predict a red-shift of the absorption spectrum (computed using TD-DFT with an optimally tuned range-separated hybrid functional) with increasing temperature, but the magnitude of the predicted red-shift is larger than that observed experimentally, and the absolute position of the calculated spectra are off by over half an eV. The spectral red-shift at high temperatures is accompanied by both a partial loss of structure of the electron’s central cavity and an increased radius of gyration that pushes electron density onto and beyond the first solvation shell. Overall, although ab initio simulations can provide some insights into the temperature-dependent behavior of the hydrated electron, the simulation sizes and level of quantum chemistry theory that are currently accessible are inadequate for correctly describing the experimental properties of this fascinating object.« less
3. A vacuum ultraviolet ion source (VUV-IS) for iodide–chemical ionization mass spectrometry: a substitute for radioactive ion sources

   https://doi.org/10.5194/amt-13-3683-2020  

   Ji, Yi ; Huey, L. Gregory ; Tanner, David J. ; Lee, Young Ro ; Veres, Patrick R. ; Neuman, J. Andrew ; Wang, Yuhang ; Wang, Xinming ( January 2020 , Atmospheric Measurement Techniques)

   Abstract. A new ion source (IS) utilizing vacuum ultraviolet (VUV) light is developed and characterized for use with iodide–chemical ionization massspectrometers (I−-CIMS). The VUV-IS utilizes a compact krypton lamp that emits light at two wavelengths corresponding to energies of∼10.030 and 10.641 eV. The VUV light photoionizes either methyl iodide (ionization potential, IP = 9.54 ± 0.02 eV)or benzene (IP = 9.24378 ± 0.00007 eV) to form cations and photoelectrons. The electrons react with methyl iodide to formI−, which serves as the reagent ion for the CIMS. The VUV-IS is characterized by measuring the sensitivity of a quadrupole CIMS (Q-CIMS) toformic acid, molecular chlorine, and nitryl chloride under a variety of flow and pressure conditions. The sensitivity of the Q-CIMS, with theVUV-IS, reached up to ∼700 Hz pptv−1, with detection limits of less than 1 pptv for a 1 min integration period. Thereliability of the Q-CIMS with a VUV-IS is demonstrated with data from a month-long ground-based field campaign. The VUV-IS is further tested byoperation on a high-resolution time-of-flight CIMS (TOF-CIMS). Sensitivities greater than 25 Hz pptv−1 were obtained for formic acid andmolecular chlorine, which were similar to that obtained with a radioactive source. In addition, the mass spectra from sampling ambient air wascleaner with the VUV-IS on the TOF-CIMS compared to measurements using a radioactive source. These results demonstrate that the VUV lamp is a viablesubstitute for radioactivemore »ion sources on I−-CIMS systems for most applications. In addition, initial tests demonstrate that the VUV-IS canbe extended to other reagent ions by the use of VUV absorbers with low IPs to serve as a source of photoelectrons for high IP electron attachers,such as SF6-.« less
4. Assessment of software methods for estimating protein-protein relative binding affinities

   https://doi.org/10.1101/2020.09.30.320069  

   Gonzalez, Tawny ; Martin, Kyle P. ; Barnes, Jonathan E. ; Patel, Jagdish S. ; Ytreberg, F. Marty ( October 2020 , PloS one)

   A growing number of computational tools have been developed to accurately and rapidly predict the impact of amino acid mutations on protein-protein relative binding affinities. Such tools have many applications, for example, designing new drugs and studying evolutionary mechanisms. In the search for accuracy, many of these methods employ expensive yet rigorous molecular dynamics simulations. By contrast, non-rigorous methods use less exhaustive statistical mechanics, allowing for more efficient calculations. However, it is unclear if such methods retain enough accuracy to replace rigorous methods in binding affinity calculations. This trade-off between accuracy and computational expense makes it difficult to determine the best method for a particular system or study. Here, eight non-rigorous computational methods were assessed using eight antibody-antigen and eight non-antibody-antigen complexes for their ability to accurately predict relative binding affinities (ΔΔG) for 654 single mutations. In addition to assessing accuracy, we analyzed the CPU cost and performance for each method using a variety of physico-chemical structural features. This allowed us to posit scenarios in which each method may be best utilized. Most methods performed worse when applied to antibody-antigen complexes compared to non-antibody-antigen complexes. Rosetta-based JayZ and EasyE methods classified mutations as destabilizing (ΔΔG < -0.5 kcal/mol) with highmore »(83–98%) accuracy and a relatively low computational cost for non-antibody-antigen complexes. Some of the most accurate results for antibody-antigen systems came from combining molecular dynamics with FoldX with a correlation coefficient (r) of 0.46, but this was also the most computationally expensive method. Overall, our results suggest these methods can be used to quickly and accurately predict stabilizing versus destabilizing mutations but are less accurate at predicting actual binding affinities. This study highlights the need for continued development of reliable, accessible, and reproducible methods for predicting binding affinities in antibody-antigen proteins and provides a recipe for using current methods.« less
5. Simulating X-ray photoelectron spectra with strong electron correlation using multireference algebraic diagrammatic construction theory

   https://doi.org/10.1039/d1cp05476g  

   de Moura, Carlos E. ; Sokolov, Alexander Yu. ( February 2022 , Physical Chemistry Chemical Physics)

   We present a new theoretical approach for the simulations of X-ray photoelectron spectra of strongly correlated molecular systems that combines multireference algebraic diagrammatic construction theory (MR-ADC) [ J. Chem. Phys. , 2018, 149 , 204113] with a core–valence separation (CVS) technique. The resulting CVS-MR-ADC approach has a low computational cost while overcoming many challenges of the conventional multireference theories associated with the calculations of excitations from inner-shell and core molecular orbitals. Our results demonstrate that the CVS-MR-ADC methods are as accurate as single-reference ADC approximations for predicting core ionization energies of weakly-correlated molecules, but are more accurate and reliable for systems with a multireference character, such as a stretched nitrogen molecule, ozone, and isomers of the benzyne diradical. We also highlight the importance of multireference effects for the description of core–hole screening that determines the relative spacing and order of peaks in the XPS spectra of strongly correlated systems.