VALIDATION OF SPECTRAL SIMULATION TOOLS FOR THE PREDICTION OF INDOOR ELECTRIC LIGHT EXPOSURE

As the interest in design applications related to responses to light beyond vision is growing, two simulation tools, ALFA and Lark, have been developed to incorporate spectral characteristics of light in the evaluation of indoor lighting conditions. The spectral characteristics of light are of particular relevance when studying ipRGC-influenced responses. This paper aims to assess the reliability of these tools in predicting indoor spectral irradiance specifically from electric lighting. Spectral irradiance was measured under three indoor electric lighting scenarios and compared against spectral irradiance simulated in ALFA and Lark. While the outcomes of the study tend to show that ALFA is both more accurate and faster, rather large errors were found for spectral irradiance (-28.6% to 33.4%). In comparison to a prior study focusing on daylighting, these results seem to indicate that spectral simulations of electrically lit scenes are generally less accurate than those of daylit scenes with these tools.

Distribution of H$$^\upbeta$$ Hyperfine Couplings in a Tyrosyl Radical Revealed by 263 GHz ENDOR Spectroscopy

Abstract$$^1$$ 1 H ENDOR spectra of tyrosyl radicals (Y$$^\bullet$$ ∙ ) have been the subject of numerous EPR spectroscopic studies due to their importance in biology. Nevertheless, assignment of all internal $$^1$$ 1 H hyperfine couplings has been challenging because of substantial spectral overlap. Recently, using 263 GHz ENDOR in conjunction with statistical analysis, we could identify the signature of the H$$^{\upbeta _2}$$ β 2 coupling in the essential Y$$_{122}$$ 122 radical of Escherichia coli ribonucleotide reductase, and modeled it with a distribution of radical conformations. Here, we demonstrate that this analysis can be extended to the full-width $$^1$$ 1 H ENDOR spectra that contain the larger H$$^{\upbeta _1}$$ β 1 coupling. The H$$^{\upbeta _2}$$ β 2 and H$$^{\upbeta _1}$$ β 1 couplings are related to each other through the ring dihedral and report on the amino acid conformation. The 263 GHz ENDOR data, acquired in batches instead of averaging, and data processing by a new “drift model” allow reconstructing the ENDOR spectra with statistically meaningful confidence intervals and separating them from baseline distortions. Spectral simulations using a distribution of ring dihedral angles confirm the presence of a conformational distribution, consistent with the previous analysis of the H$$^{\upbeta _2}$$ β 2 coupling. The analysis was corroborated by 94 GHz $$^2$$ 2 H ENDOR of deuterated Y$$_{122}^\bullet$$ 122 ∙ . These studies provide a starting point to investigate low populated states of tyrosyl radicals in greater detail.

Computational IR Spectroscopy of Insulin Dimer Structure and Conformational Heterogeneity

<div><div><div><p>We have investigated the structure and conformational dynamics of insulin dimer using a Markov state model (MSM) built from extensive unbiased atomistic MD simulations, and performed infrared spectral simulations of the insulin MSM to describe how structural variation within the dimer can be experimentally resolved. Our model reveals two significant conformations to the dimer: a dominant native state consistent with other experimental structures of the dimer, and a twisted state with a structure that appears to reflect a ~55° clockwise rotation of the native dimer interface. The twisted state primarily influences the contacts involving the C-terminus of insulin’s B chain, shifting the registry of its intermolecular hydrogen bonds and reorganizing its sidechain packing. The MSM kinetics predict that these configurations exchange on a 14 μs timescale, largely passing through two Markov states with a solvated dimer interface. Computational amide I spectroscopy of site-specifically 13C18O labeled amides indicates that the native and twisted conformation can be distinguished through a series of single and dual labels involving the B24F, B25F, and B26Y residues. Additional structural heterogeneity and disorder is observed within the native and twisted states, and amide I spectroscopy can also be used to gain insight into this variation. This study will provide important interpretive tools for IR spectroscopic investigations of insulin structure, and transient IR kinetics experiments studying the conformational dynamics of insulin dimer.</p></div></div></div>

Computational IR Spectroscopy of Insulin Dimer Structure and Conformational Heterogeneity

<div><div><div><p>We have investigated the structure and conformational dynamics of insulin dimer using a Markov state model (MSM) built from extensive unbiased atomistic MD simulations, and performed infrared spectral simulations of the insulin MSM to describe how structural variation within the dimer can be experimentally resolved. Our model reveals two significant conformations to the dimer: a dominant native state consistent with other experimental structures of the dimer, and a twisted state with a structure that appears to reflect a ~55° clockwise rotation of the native dimer interface. The twisted state primarily influences the contacts involving the C-terminus of insulin’s B chain, shifting the registry of its intermolecular hydrogen bonds and reorganizing its sidechain packing. The MSM kinetics predict that these configurations exchange on a 14 μs timescale, largely passing through two Markov states with a solvated dimer interface. Computational amide I spectroscopy of site-specifically 13C18O labeled amides indicates that the native and twisted conformation can be distinguished through a series of single and dual labels involving the B24F, B25F, and B26Y residues. Additional structural heterogeneity and disorder is observed within the native and twisted states, and amide I spectroscopy can also be used to gain insight into this variation. This study will provide important interpretive tools for IR spectroscopic investigations of insulin structure, and transient IR kinetics experiments studying the conformational dynamics of insulin dimer.</p></div></div></div>

Comment on ‘Open-boundary spectral and flux-balance Vlasov simulation by A. Klimas and A. Viñas’

An error in Klimas & Viñas (J. Plasma Phys., vol. 85 (6), 2019, 905850610) is noted and explained. It is shown that the results in Klimas and Viñas were unaffected by the error. Further ramifications for future non-periodic spectral simulations are discussed.

Characterization of Aqueous Lower Polarity Solvation Shells Around Amphiphilic TEMPO Radicals in Water

Solvation of the stable nitroxide radicals 2,2,6,6-Tetramethylpiperidine-1-oxyl (TEMPO) and 4-Oxo-TEMPO (TEMPONE) in water and THF is studied. With electron paramagnetic resonance (EPR) spectroscopy at X- and Q-band as well as spectral simulations, the existence of pure water shells enclosing TEMPO in aqueous solution that lead to significantly reduced local polarity at the nitroxide is shown. These aqueous lower polarity solvation shells (ALPSS) offer TEMPO a local polarity that is similar to that in organic solvents like THF. Furthermore, using double electron-electron resonance (DEER) spectroscopy, local enrichment and inhomogenous distribution without collisions of dissolved TEMPO in water is found that can be correlated with potentially attractive interactions mediated through ALPSS. However, no local enrichment of TEMPO is found in organic solvents such as THF. These results are substantiated by MD and metadynamics simulations and physical methods like DLS and MS.

Characterization of Aqueous Lower Polarity Solvation Shells Around Amphiphilic TEMPO Radicals in Water

Solvation of the stable nitroxide radicals 2,2,6,6-Tetramethylpiperidine-1-oxyl (TEMPO) and 4-Oxo-TEMPO (TEMPONE) in water and THF is studied. With electron paramagnetic resonance (EPR) spectroscopy at X- and Q-band as well as spectral simulations, the existence of pure water shells enclosing TEMPO in aqueous solution that lead to significantly reduced local polarity at the nitroxide is shown. These aqueous lower polarity solvation shells (ALPSS) offer TEMPO a local polarity that is similar to that in organic solvents like THF. Furthermore, using double electron-electron resonance (DEER) spectroscopy, local enrichment and inhomogenous distribution without collisions of dissolved TEMPO in water is found that can be correlated with potentially attractive interactions mediated through ALPSS. However, no local enrichment of TEMPO is found in organic solvents such as THF. These results are substantiated by MD and metadynamics simulations and physical methods like DLS and MS.

Simplified Ab Initio Molecular Dynamics-Based Raman Spectral Simulations

We describe a simplified approach to simulating Raman spectra from ab initio molecular dynamics (AIMD) calculations. The protocol relies on on-the-fly calculations of approximate molecular polarizabilities using the well-known sum over orbitals (as opposed to states) method. This approach bypasses the more accurate but computationally expensive approach to calculating molecular polarizabilities along AIMD trajectories, i.e., solving the coupled perturbed Hartree–Fock/Kohn–Sham equations. We demonstrate the advantages and limitations of our method through a few case studies targeting molecular systems of interest to surface- and/or tip-enhanced Raman spectroscopy practitioners.