An interview with Sam C. Saunders

Sam C. Saunders, the son of Elizabeth Cundiff and Winston E. Saunders, was born in Richland, OR, on February 24, 1931. The family moved to La Grande, OR, in 1944, where Sam completed high school and two years at Eastern Oregon College. He then received the BSc degree in Mathematics from the University of Oregon, Eugene, OR, in 1952, and he attended the University of Washington, Seattle, WA, receiving a PhD degree under Z. W. Birnbaum. After graduating, he accepted employment at the Boeing Company in its Mathematical Services Unit and, in 1972, a position as a Full Professor at Washington State University, Pullman, WA, from which he retired in 1996.     

Lignin Biodegradation by a Cytochrome P450 Enzyme: A Computational Study into Syringol Activation by GcoA

A recently characterized cytochrome P450 isozyme GcoA activates lignin components through a selective O-demethylation or alternatively an acetal formation reaction. These are important reactions in biotechnology and, because lignin is readily available; it being the main component in plant cell walls. In this work we present a density functional theory study on a large active site model of GcoA to investigate syringol activation by an iron(IV)-oxo heme cation radical oxidant (Compound I) leading to hemiacetal and acetal products. Several substrate-binding positions were tested and full energy landscapes calculated. The study shows that substrate positioning determines the product distributions. Thus, with the phenol group pointing away from the heme, an O-demethylation is predicted, whereas an initial hydrogen-atom abstraction of the weak phenolic O-H group would trigger a pathway leading to ring-closure to form acetal products. Predictions on how to engineer P450 GcoA to get more selective product distributions are given.     

Theoretical Study on Photoisomerization Mechanisms of Diphenyl-Substituted N,C-Chelate Organoboron Compounds

N,C-chelate organoboron compounds are widely employed as photoresponsive and optoelectronic materials due to their efficient photochromic reactivity. It was found in experiments that two diphenyl-substituted organoboron compounds, namely B(ppy)Ph₂ (ppy=2-phenylpyridyl) and B(iba)Ph₂ (iba=N-isopropylbenzylideneamine), show distinct photochemical reactivity. B(ppy)Ph₂ is inert on irradiation, whereas B(iba)Ph₂ undergoes photoinduced transformations, yielding BN-cyclohepta-1,3,5-triene via a borirane intermediate. In this work, the complete active space self-consistent field and its second-order perturbation (CASPT2//CASSCF) methods were used to investigate the photoinduced reaction mechanisms of B(ppy)Ph₂ and B(iba)Ph₂. The calculations showed that the two compounds isomerize to borirane in the same way by passing a transition state in the S₁ state and a conical intersection between the S₁ and S₀ states. The energy barriers in the S₁ state of 0.54 and 0.26 eV for B(ppy)Ph₂ and B(iba)Ph₂, respectively, were explained by analyzing the charge distributions of minima in S₀ and S₁ states. The results provide helpful insights into the excited-state dynamics of organoboron compounds, which could assist in rational design of boron-based photoresponsive materials.     

Logging damage and injured tree mortality in tropical forest management

Using insights from the forest ecology literature, we analyze the effect of injured trees on stand composition and carbon stored in above‐ground biomass and the implications for forest management decisions. Results from a Faustmann model with data for a tropical forest on Kalimantan show that up to 50% of the basal area of the stand before harvest can consist of injured trees. Considering injured trees leads to an increase in the amount of carbon in above‐ground biomass of up to 165%. These effects are larger under reduced impact logging than under conventional logging. The effects on land expectation value and cutting cycle are relatively small. The results suggest that considering injured trees in models for tropical forest management is important for the correct assessment of the potential of financial programs to store carbon and conserve forest ecosystem services in managed tropical forests, such as reducing emissions from deforestation and forest degradation and payment for ecosystem services. Recommendations for Resource Managers

• Considering the role of injured trees is important for managing tropical forests
• These trees can cover up to 50% of basal area and contain more than 50% of the carbon stored in above‐ground biomass
• Reduced impact logging leads to a larger basal area of injured trees and more carbon stored in injured trees than conventional logging
• Injured trees play an important role when assessing the potential for carbon storage in the context of payment for forest ecosystem services.

     

In Situ Metal-Assisted Ligand Modification Induces Mn4 Cluster-to-Cluster Transformation: A Crystallography,Mass Spectrometry,and DFT Study

Dehydration of (S,S)-1,2-bis(1H-benzo[d]imidazol-2-yl)ethane-1,2-diol (H₄L) to (Z)-1,2-bis(1H-benzo[d]imidazol-2-yl)ethenol) (H₃L′) was found to be metal-assisted, occurs under solvothermal conditions (H₂O/CH₃OH), and leads to [Mn^II₄(H₃L)₄Cl₂]Cl₂ ⋅ 5 H₂O ⋅ 5 CH₃OH ( Mn₄L₄ ) and [Mn^II₄(H₂L′)₆(μ₃-OH)]Cl ⋅ 4 CH₃OH ⋅ H₂O ( Mn₄L′₆ ), respectively. Their structures were determined by single-crystal XRD. Extensive ESI-MS studies on solutions and solids of the reaction led to the proposal consisting of an initial stepwise assembly of Mn₄L₄ from the reactants via [MnL] and [Mn₂L₂] below 80 °C, and then disassembly to [MnL] and [MnL₂] followed by ligand modification before reassembly to Mn₄L′₆ via [MnL′], [MnL′₂], and [Mn₂L′₃] with increasing solvothermal temperature up to 140 °C. Identification of intermediates [Mn₄L_xL′_6−x] (x=5, 4, 3, 2, 1) in the process further suggested an assembly/disassembly/in situ reaction/reassembly transformation mechanism. These results not only reveal that multiple phase transformations are possible even though they were not realized in the crystalline state, but also help to better understand the complex transformation process between coordination clusters during “black-box” reactions.     

Can a Six‐Letter Alphabet Increase the Likelihood of Photochemical Assault to the Genetic Code?

In 2014, two unnatural nucleosides, d5SICS and dNaM, were shown to selectively base pair and replicate with high fidelity in a modified strain of E. coli, thus effectively expanding its genetic alphabet from four to six letters. More recently, a significant reduction in cell proliferation was reported in cells cultured with d5SICS, and putatively with dNaM, upon exposure to brief periods of near‐visible radiation. The photosensitizing properties of the lowest‐energy excited triplet state of both d5SICS and dNaM were implicated in their cytotoxicity. Importantly, however, the excited‐state mechanisms by which near‐visible excitation populates the triplet states of d5SICS and dNaM are currently unknown. In this study, steady‐state and time‐resolved spectroscopies are combined with quantum‐chemical calculations in order to reveal the excited‐state relaxation mechanisms leading to efficient population of the triplet states in these unnatural nucleosides in solution. It is shown that excitation of d5SICS or dNaM with near‐visible light leads overwhelmingly to ultrafast population of their triplet states on the femtosecond time scale. The results presented in this work lend strong support to the proposal that photoexcitation of these unnatural nucleosides can accelerate oxidatively generated damage to DNA and other biomolecules within the cellular environment.     

Exploring the Reactivity of α‐Lithiated Aryl Benzyl Ethers: Inhibition of the [1,2]‐Wittig Rearrangement and the Mechanistic Proposal Revisited

By carefully controlling the reaction temperature, treatment of aryl benzyl ethers with tBuLi selectively leads to α‐lithiation, generating stable organolithiums that can be directly trapped with a variety of selected electrophiles, before they can undergo the expected [1,2]‐Wittig rearrangement. This rearrangement has been deeply studied, both experimentally and computationally, with aryl α‐lithiated benzyl ethers bearing different substituents at the aryl ring. The obtained results support the competence of a concerted anionic intramolecular addition/elimination sequence and a radical dissociation/recombination sequence for explaining the tendency of migration for aryl groups. The more favored rearrangements are found for substrates with electron‐poor aryl groups that favor the anionic pathway.     

Synthesis of Aminopyridines and Aminopyridones by Cobalt‐Catalyzed [2+2+2] Cycloadditions Involving Yne‐Ynamides: Scope,Limitations, and Mechanistic Insights

An in‐depth study of the cobalt‐catalyzed [2+2+2] cycloaddition between yne‐ynamides and nitriles to afford aminopyridines has been carried out. About 30 nitriles exhibiting a broad range of steric demand and electronic properties have been evaluated, some of which open new perspectives in metal‐catalyzed arene formation. In particular, the use of [CpCo(CO)(dmfu)] (dmfu=dimethyl fumarate) as a precatalyst made possible the incorporation of electron‐deficient nitriles into the pyridine core. Modification of the substitution pattern at the yne‐ynamide allows the regioselectivity to be switched toward 3‐ or 4‐aminopyridines. Application of this synthetic methodology to the construction of the aminopyridone framework using a yne‐ynamide and an isocyanate was also briefly examined. DFT computations suggest that 3‐aminopyridines are formed by formal [4+2] cycloaddition between the nitrile and the intermediate cobaltacyclopentadiene, whereas 4‐aminopyridines arise from an insertion pathway.     

CPMD Simulation of a Bimolecular Chemical Reaction: Nucleophilic Attack of a Disulfide Bond under Mechanical Stress

Previous single‐molecule atomic force microscopy (AFM) experiments showed a change in the reactivity of a bimolecular substitution reaction with a definite force acting on a protein containing disulfide bonds. Using Car–Parrinello molecular dynamics (CPMD) simulations, we analyse the relevant reaction pathways for the breaking of a disulfide bond in the presence of nucleophiles.