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1. Evaluating Simple Ab Initio Models of the Hydrated Electron: The Role of Dynamical Fluctuations

   https://doi.org/10.1021/acs.jpcb.0c6356  

   Park, S. J. ; Schwartz, B. J. ( January 2020 , The journal of physical chemistry)

   Despite its importance in electron transfer reactions and radiation chemistry, there has been disagreement over the fundamental nature of the hydrated electron, such as whether or not it resides in a cavity. Mixed quantum/classical simulations of the hydrated electron give different structures depending on the pseudopotential employed, and ab initio models of computational necessity use small numbers of water molecules and/or provide insufficient statistics to compare to experimental observables. A few years ago, Kumar et al. (J. Phys. Chem. A 2015, 119, 9148) proposed a minimalist ab initio model of the hydrated electron with only a small number of explicitly treated water molecules plus a polarizable continuum model (PCM). They found that the optimized geometry had four waters arranged tetrahedrally around a central cavity, and that the calculated vertical detachment energy and radius of gyration agreed well with experiment, results that were largely independent of the level of theory employed. The model, however, is based on a fixed structure at 0 K and does not explicitly incorporate entropic contributions or the thermal fluctuations that should be associated with the room-temperature hydrated electron. Thus, in this paper, we extend the model of Kumar et al. by running Born−Oppenheimer molecular dynamics (BOMD)more »of a small number of water molecules with an excess electron plus PCM at room temperature. We find that when thermal fluctuations are introduced, the level of theory chosen becomes critical enough when only four waters are used that one of the waters dissociates from the cluster with certain density functionals. Moreover, even with an optimally tuned range-separated hybrid functional, at room temperature the tetrahedral orientation of the 0 K first-shell waters is entirely lost and the central cavity collapses, a process driven by the fact that the explicit water molecules prefer to make H-bonds with each other more than with the excess electron. The resulting average structure is quite similar to that produced by a noncavity mixed quantum/classical model, so that the minimalist 4-water BOMD models suffer from problems similar to those of noncavity models, such as predicting the wrong sign of the hydrated electron’s molar solvation volume. We also performed BOMD with 16 explicit water molecules plus an extra electron and PCM. We find that the inclusion of an entire second solvation shell of explicit water leads to little change in the outcome from when only four waters were used. In fact, the 16-water simulations behave much like those of water cluster anions, in which the electron localizes at the cluster surface, showing that PCM is not acceptable for use in minimalist models to describe the behavior of the bulk hydrated electron. For both the 4- and 16-water models, we investigate how the introduction of thermal motions alters the predicted absorption spectrum, vertical detachment energy, and resonance Raman spectrum of the simulated hydrated electron. We also present a set of structural criteria that can be used to numerically determine how cavity-like (or not) a particular hydrated electron model is. All of the results emphasize that the hydrated electron is a statistical object whose properties are inadequately captured using only a small number of explicit waters, and that a proper treatment of thermal fluctuations is critical to understanding the hydrated electron’s chemical and physical behavior.« less
2. ² H/ ¹ H variation in microbial lipids is controlled by NADPH metabolism

   https://doi.org/10.1073/pnas.1818372116  

   Wijker, Reto S. ; Sessions, Alex L. ; Fuhrer, Tobias ; Phan, Michelle ( June 2019 , Proceedings of the National Academy of Sciences)

   The hydrogen-isotopic compositions ( 2 H/ 1 H ratios) of lipids in microbial heterotrophs are known to vary enormously, by at least 40% (400‰) relative. This is particularly surprising, given that most C-bound H in their lipids appear to derive from the growth medium water, rather than from organic substrates, implying that the isotopic fractionation between lipids and water is itself highly variable. Changes in the lipid/water fractionation are also strongly correlated with the type of energy metabolism operating in the host. Because lipids are well preserved in the geologic record, there is thus significant potential for using lipid 2 H/ 1 H ratios to decipher the metabolism of uncultured microorganisms in both modern and ancient ecosystems. But despite over a decade of research, the precise mechanisms underlying this isotopic variability remain unclear. Differences in the kinetic isotope effects (KIEs) accompanying NADP + reduction by dehydrogenases and transhydrogenases have been hypothesized as a plausible mechanism. However, this relationship has been difficult to prove because multiple oxidoreductases affect the NADPH pool simultaneously. Here, we cultured five diverse aerobic heterotrophs, plus five Escherichia coli mutants, and used metabolic flux analysis to show that 2 H/ 1 H fractionations are highly correlated withmore »fluxes through NADP + -reducing and NADPH-balancing reactions. Mass-balance calculations indicate that the full range of 2 H/ 1 H variability in the investigated organisms can be quantitatively explained by varying fluxes, i.e., with constant KIEs for each involved oxidoreductase across all species. This proves that lipid 2 H/ 1 H ratios of heterotrophic microbes are quantitatively related to central metabolism and provides a foundation for interpreting 2 H/ 1 H ratios of environmental lipids and sedimentary hydrocarbons.« less
3. Quantum electronic control on chemical activation of methane by collision with spin–orbit state selected vanadium cation

   https://doi.org/10.1039/D0CP04333H  

   Ng, Cheuk-Yiu ; Xu, Yuntao ; Chang, Yih-Chung ; Wannenmacher, Anna ; Parziale, Matthew ; Armentrout, P. B. ( January 2021 , Physical Chemistry Chemical Physics)

   By coupling a newly developed quantum-electronic-state-selected supersonically cooled vanadium cation (V + ) beam source with a double quadrupole-double octopole (DQDO) ion–molecule reaction apparatus, we have investigated detailed absolute integral cross sections ( σ 's) for the reactions, V + [a 5 D J ( J = 0, 2), a 5 F J ( J = 1, 2), and a 3 F J ( J = 2, 3)] + CH 4 , covering the center-of-mass collision energy range of E cm = 0.1–10.0 eV. Three product channels, VH + + CH 3 , VCH 2 + + H 2 , and VCH 3 + + H, are unambiguously identified based on E cm -threshold measurements. No J -dependences for the σ curves ( σ versus E cm plots) of individual electronic states are discernible, which may indicate that the spin–orbit coupling is weak and has little effect on chemical reactivity. For all three product channels, the maximum σ values for the triplet a 3 F J state [ σ (a 3 F J )] are found to be more than ten times larger than those for the quintet σ (a 5 D J ) and σ (a 5 F Jmore ») states, showing that a reaction mechanism favoring the conservation of total electron spin. Without performing a detailed theoretical study, we have tentatively interpreted that a weak quintet-to-triplet spin crossing is operative for the activation reaction. The σ (a 5 D 0 , a 5 F 1 , and a 3 F 2) measurements for the VH + , VCH 2 + , and VCH 3 + product ion channels along with accounting of the kinetic energy distribution due to the thermal broadening effect for CH 4 have allowed the determination of the 0 K bond dissociation energies: D 0 (V + –H) = 2.02 (0.05) eV, D 0 (V + –CH 2 ) = 3.40 (0.07) eV, and D 0 (V + –CH 3 ) = 2.07 (0.09) eV. Detailed branching ratios of product ion channels for the titled reaction have also been reported. Excellent simulations of the σ curves obtained previously for V + generated by surface ionization at 1800–2200 K can be achieved by the linear combination of the σ (a 5 D J , a 5 F J , and a 3 F J ) curves weighted by the corresponding Boltzmann populations of the electronic states. In addition to serving as a strong validation of the thermal equilibrium assumption for the populations of the V + electronic states in the hot filament ionization source, the agreement between these results also confirmed that the V + (a 5 D J , a 5 F J , and a 3 F J ) states prepared in this experiment are in single spin–orbit states with 100% purity.« less
4. Enhancing understanding of the hydrological cycle via pairing of process‐oriented and isotope ratio tracers

   https://doi.org/10.5061/dryad.8w9ghx3mr  

   Fiorella, Richard ; Siler, Nicholas ; Nusbaumer, Jesse ; Noone, David ( January 2021 )

   Abstract

   This dataset contains monthly average output files from the iCAM6 simulations used in the manuscript "Enhancing understanding of the hydrological cycle via pairing of process-oriented and isotope ratio tracers," in review at the Journal of Advances in Modeling Earth Systems. A file corresponding to each of the tagged and isotopic variables used in this manuscript is included. Files are at 0.9° latitude x 1.25° longitude, and are in NetCDF format. Data from two simulations are included: 1) a simulation where the atmospheric model was "nudged" to ERA5 wind and surface pressure fields, by adding an additional tendency (see section 3.1 of associated manuscript), and 2) a simulation where the atmospheric state was allowed to freely evolve, using only boundary conditions imposed at the surface and top of atmosphere. Specific information about each of the variables provided is located in the "usage notes" section below. Associated article abstract: The hydrologic cycle couples the Earth's energy and carbon budgets through evaporation, moisture transport, and precipitation. Despite a wealth of observations and models, fundamental limitations remain in our capacity to deduce even the most basic properties of the hydrological cycle, including the spatial pattern of the residence time (RT) of water in the atmosphere and the mean distance traveled from evaporation sources to precipitation sinks. Meanwhile, geochemical tracers such as stable water isotope ratios provide a tool to probe hydrological processes, yet their interpretation remains equivocal despite several decades of use. As a result, there is a need for new mechanistic tools that link variations in water isotope ratios to underlying hydrological processes. Here we present a new suite of “process-oriented tags,” which we use to explicitly trace hydrological processes within the isotopically enabled Community Atmosphere Model, version 6 (iCAM6). Using these tags, we test the hypotheses that precipitation isotope ratios respond to parcel rainout, variations in atmospheric RT, and preserve information regarding meteorological conditions during evaporation. We present results for a historical simulation from 1980 to 2004, forced with winds from the ERA5 reanalysis. We find strong evidence that precipitation isotope ratios record information about atmospheric rainout and meteorological conditions during evaporation, but little evidence that precipitation isotope ratios vary with water vapor RT. These new tracer methods will enable more robust linkages between observations of isotope ratios in the modern hydrologic cycle or proxies of past terrestrial environments and the environmental processes underlying these observations.  
   

   Methods

   Details about the simulation setup can be found in section 3 of the associated open-source manuscript, "Enhancing understanding of the hydrological cycle via pairing of process‐oriented and isotope ratio tracers." In brief, we conducted two simulations of the atmosphere from 1980-2004 using the isotope-enabled version of the Community Atmosphere Model 6 (iCAM6) at 0.9x1.25° horizontal resolution, and with 30 vertical hybrid layers spanning from the surface to ~3 hPa. In the first simulation, wind and surface pressure fields were "nudged" toward the ERA5 reanalysis dataset by adding a nudging tendency, preventing the model from diverging from observed/reanalysis wind fields. In the second simulation, no additional nudging tendency was included, and the model was allowed to evolve 'freely' with only boundary conditions provided at the top (e.g., incoming solar radiation) and bottom (e.g., observed sea surface temperatures) of the model. In addition to the isotopic variables, our simulation included a suite of 'process-oriented tracers,' which we describe in section 2 of the manuscript. These variables are meant to track a property of water associated with evaporation, condensation, or atmospheric transport.
   

   Other

   Metadata are provided about each of the files below; moreover, since the attached files are NetCDF data - this information is also provided with the data files. NetCDF metadata can be accessed using standard tools (e.g., ncdump). Each file has 4 variables: the tagged quantity, and the associated coordinate variables (time, latitude, longitude). The latter three are identical across all files, only the tagged quantity changes. Twelve files are provided for the nudged simulation, and an additional three are provided for the free simulations: Nudged simulation files iCAM6_nudged_1980-2004_mon_RHevap: Mass-weighted mean evaporation source property: RH (%) with respect to surface temperature. iCAM6_nudged_1980-2004_mon_Tevap: Mass-weighted mean evaporation source property: surface temperature in Kelvin iCAM6_nudged_1980-2004_mon_Tcond: Mass-weighted mean condensation property: temperature (K) iCAM6_nudged_1980-2004_mon_columnQ: Total (vertically integrated) precipitable water (kg/m2).  Not a tagged quantity, but necessary to calculate depletion times in section 4.3 (e.g., Fig. 11 and 12). iCAM6_nudged_1980-2004_mon_d18O: Precipitation d18O (‰ VSMOW) iCAM6_nudged_1980-2004_mon_d18Oevap_0: Mass-weighted mean evaporation source property - d18O of the evaporative flux (e.g., the 'initial' isotope ratio prior to condensation), (‰ VSMOW) iCAM6_nudged_1980-2004_mon_dxs: Precipitation deuterium excess (‰ VSMOW) - note that precipitation d2H can be calculated from this file and the precipitation d18O as d2H = d-excess - 8*d18O. iCAM6_nudged_1980-2004_mon_dexevap_0: Mass-weighted mean evaporation source property - deuterium excess of the evaporative flux iCAM6_nudged_1980-2004_mon_lnf: Integrated property - ln(f) calculated from the constant-fractionation d18O tracer (see section 3.2). iCAM6_nudged_1980-2004_mon_precip: Total precipitation rate in m/s. Note there is an error in the metadata in this file - it is total precipitation, not just convective precipitation. iCAM6_nudged_1980-2004_mon_residencetime: Mean atmospheric water residence time (in days). iCAM6_nudged_1980-2004_mon_transportdistance: Mean atmospheric water transport distance (in km). Free simulation files iCAM6_free_1980-2004_mon_d18O: Precipitation d18O (‰ VSMOW) iCAM6_free_1980-2004_mon_dxs: Precipitation deuterium excess (‰ VSMOW) - note that precipitation d2H can be calculated from this file and the precipitation d18O as d2H = d-excess - 8*d18O. iCAM6_free_1980-2004_mon_precip: Total precipitation rate in m/s. Note there is an error in the metadata in this file - it is total precipitation, not just convective precipitation.
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5. A multiscale polymerization framework towards network structure and fracture of double-network hydrogels

   https://doi.org/10.1038/s41524-021-00509-5  

   Zhang, Mingzhen ; Zhang, Dong ; Chen, Hong ; Zhang, Yanxian ; Liu, Yonglan ; Ren, Baiping ; Zheng, Jie ( March 2021 , npj Computational Materials)

   Double-network (DN) hydrogels, consisting of two contrasting and interpenetrating polymer networks, are considered as perhaps the toughest soft-wet materials. Current knowledge of DN gels from synthesis methods to toughening mechanisms almost exclusively comes from chemically-linked DN hydrogels by experiments. Molecular modeling and simulations of inhomogeneous DN structure in hydrogels have proved to be extremely challenging. Herein, we developed a new multiscale simulation platform to computationally investigate the early fracture of physically-chemically linked agar/polyacrylamide (agar/PAM) DN hydrogels at a long timescale. A “random walk reactive polymerization” (RWRP) was developed to mimic a radical polymerization process, which enables to construct a physically-chemically linked agar/PAM DN hydrogel from monomers, while conventional and steered MD simulations were conducted to examine the structural-dependent energy dissipation and fracture behaviors at the relax and deformation states. Collective simulation results revealed that energy dissipation of agar/PAM hydrogels was attributed to a combination of the pulling out of agar chains from the DNs, the disruption of massive hydrogen bonds between and within DN structures, and the strong association of water molecules with both networks, thus explaining a different mechanical enhancement of agar/PAM hydrogels. This computational work provided atomic details of network structure, dynamics, solvation, and interactions of amore »hybrid DN hydrogel, and a different structural-dependent energy dissipation mode and fracture behavior of a hybrid DN hydrogel, which help to design tough hydrogels with new network structures and efficient energy dissipation modes. Additionally, the RWRP algorithm can be generally applied to construct the radical polymerization-produced hydrogels, elastomers, and polymers.

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